From td5u19 at soton.ac.uk Sun Jul 5 01:41:10 2020 From: td5u19 at soton.ac.uk (du t. (td5u19)) Date: Sat, 4 Jul 2020 23:41:10 +0000 Subject: [Simnibs-discuss] (no subject) Message-ID: Hi, I am a junior learner of simNIBS, and I used the command line tool simnibs ernie_simu.mat to do the simulation and I get three simulation results. My question is how to modify the mat file to do more simulation automatically, and what's the meaning of the three output file TDCS_1_scalar, TDCS_2_dir and TDCS_3_vn? Best regards Tianyu Du -------------- next part -------------- An HTML attachment was scrubbed... URL: From guilhermebs at drcmr.dk Mon Jul 6 08:47:57 2020 From: guilhermebs at drcmr.dk (Guilherme B Saturnino) Date: Mon, 6 Jul 2020 08:47:57 +0200 Subject: [Simnibs-discuss] (no subject) In-Reply-To: References: Message-ID: <341bbb6f-d4df-cb57-f604-4267934ea3b6@drcmr.dk> Hello, You can script SimNIBS simulations in matlab or python (https://simnibs.github.io/simnibs/build/html/tutorial/scripting.html). Or you can open the ".mat" files in matlab, octave, or python and modify them. The "scalar", "vn", "dir" and "mc" refers to different conductivity models? (see *anisotropy_type* in https://simnibs.github.io/simnibs/build/html/documentation/sim_struct/tdcslist.html). Unless you have a strong need to account for tissue conductivity anisotropy effects, we recommend you use the "scalar" conductivity model (that is isotropic conductivity, no DTI data required). If you want to incorporate tissue conductivity anisotropy (requires DTI data), we recommend you use the "vn" model. The other two are there in a more experimental capacity. Best Regards, Guilherme On 05/07/2020 01.41, du t. (td5u19) wrote: > > Hi, > > I am a junior learner of simNIBS, and I used the command line tool > simnibs ernie_simu.mat to do the simulation and I get three simulation > results. My question is how to modify the mat file to do more > simulation automatically, and what?s the meaning of the three output > file TDCS_1_scalar, TDCS_2_dir and TDCS_3_vn? > > Best regards > > Tianyu Du > > > _______________________________________________ > Simnibs-discuss mailing list > Simnibs-discuss at drcmr.dk > https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -------------- next part -------------- An HTML attachment was scrubbed... URL: From anantbshinde at gmail.com Tue Jul 7 19:29:27 2020 From: anantbshinde at gmail.com (Anant Shinde) Date: Tue, 7 Jul 2020 13:29:27 -0400 Subject: [Simnibs-discuss] How to save group analysis mesh file Message-ID: I am trying to save my simnibs group analysis results average to a mesh file in MATLAB. Here are details of my group analysis file thresholded_m_test = struct with fields: node_data: {[1?1 struct]} element_data: {} nodes: [327684?3 double] triangles: [655360?3 int32] triangle_regions: [655360?1 int32] tetrahedra: [] tetrahedron_regions: [] When I tried to save this file I got the following error message. How do I solve this issue? >> mesh_save_gmsh4(thresholded_m_test, 'All_Comb_Stim.msh') Error using mesh_save_gmsh4 (line 149) node data has to contain one data point per node Also, I am not able to sign up to the mailing list. I was not able to open the archive/signing up link. Is that a firewall problem at my end? -------------- next part -------------- An HTML attachment was scrubbed... URL: From guilhermebs at drcmr.dk Wed Jul 8 08:19:57 2020 From: guilhermebs at drcmr.dk (Guilherme B Saturnino) Date: Wed, 8 Jul 2020 08:19:57 +0200 Subject: [Simnibs-discuss] How to save group analysis mesh file In-Reply-To: References: Message-ID: Hello, Probably the error is likely before, in the script generating "thresholded_m_test". Please check if the length of mesh.node_data{1}.data is different from the length of mesh.nodes. About the mailing list, can you access this link ? the problem could be a spam filter or firewall in your end. On 07/07/2020 19.29, Anant Shinde wrote: > I am trying to save my simnibs group analysis results average to a > mesh file in MATLAB. > Here are details of my group analysis file > thresholded_m_test = > > ? struct with fields: > > ? ? ? ? ? ? ? node_data: {[1?1 struct]} > ? ? ? ? ? ?element_data: {} > ? ? ? ? ? ? ? ? ? nodes: [327684?3 double] > ? ? ? ? ? ? ? triangles: [655360?3 int32] > ? ? ? ?triangle_regions: [655360?1 int32] > ? ? ? ? ? ? ?tetrahedra: [] > ? ? tetrahedron_regions: [] > When I tried to save this file I got the following error message. How > do I solve this issue? > >> mesh_save_gmsh4(thresholded_m_test, 'All_Comb_Stim.msh') > Error using mesh_save_gmsh4 (line 149) node data has to contain one > data point per node > > Also, I am not able to sign up to the mailing list. I was not able to > open the archive/signing up link. Is that a firewall problem at my end? > > _______________________________________________ > Simnibs-discuss mailing list > Simnibs-discuss at drcmr.dk > https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -------------- next part -------------- An HTML attachment was scrubbed... URL: From mccalled at musc.edu Thu Jul 9 19:48:54 2020 From: mccalled at musc.edu (Mccalley, Daniel) Date: Thu, 9 Jul 2020 17:48:54 +0000 Subject: [Simnibs-discuss] Targeting subject specific locations on the scalp Message-ID: Hi all, Our lab targets the FP1 with TMS. We use a simple measurement system (http://clinicalresearcher.org/F3/) to locate exactly where we want to place the coil for each subject. Typically, we measure the subject's head, and then, starting from nasion, we'll move up Y mm and left X mm (where X and Y are determined from each subject's given head size). Ideally, we'd like to create an electric field model for each subject that accounts for the TMS parameters as well as the exact location used. To implement this in SIMNIBS, I've tried the following: 1) Open a subjects m2m file and find the coordinates for nasion (say, for example, that these coordinates are X= -2.78, Y= 117.59, Z= -20.63). 2) Determine Y and X used to locate FP1 for the given subject (say, for example, that starting from nasion, we moved 37 mm in the Y direction, and over 32 mm in the X direction). 3) Subtract the displacements in the Y and X directions from the original nasion coordinates, resulting in X= -34.78 and Y=80.69 4) Add a new position wherein the reference coordinates match the original nasion coordinates (and the Define Reference Coordinates box is checked) and the coordinates calculated in step 3 are input in the position fields (Z is left blank for SIMNIBs to calculate) 5) Adjust for coil orientation and TMS parameters This seems to have worked well for 90-95% of our subjects, however there are a few subjects in which the resulting coil placement appears to be over the eye (Note: Ordinarily I'd attach examples of the working and not-working subjects, but I'm not sure if the skin reconstruction of our participants falls under PHI). Am I going about this the wrong way? Could this reflect a problem with segmentation/meshing? Or maybe a problem with the experimenter measurements of the subjects head? Any advice would be greatly appreciated. Thank you all so much! Best, Dan McCalley Medical University of South Carolina College of Graduate Studies, Neuroscience -------------- next part -------------- An HTML attachment was scrubbed... URL: From guilhermebs at drcmr.dk Fri Jul 10 09:31:07 2020 From: guilhermebs at drcmr.dk (Guilherme B Saturnino) Date: Fri, 10 Jul 2020 09:31:07 +0200 Subject: [Simnibs-discuss] Targeting subject specific locations on the scalp In-Reply-To: References: Message-ID: <1943989e-b733-515a-21dd-5b2287e5548c@drcmr.dk> Hello, SimNIBS 3 offers two ways of getting 10/10 EEG positions out of the box. 1) Use the eeg positions calculated using MNI transformations, which are stored in m2m_{SubID}/eeg_positions/EEG10-10_UI_Jurak_2007.csv. Those can also be accessed in the GUI , which loads it automatically, or in? scripts (MATLAB example ) 2) Using the eeg_positions command line tool with the Nz, LPA, RPA and Iz as an input Those two were compared and validated here . I'm not sure why it is not working in your case though, might be due to head size, as you are moving by constant amounts? Best Regards, Guilherme On 09/07/2020 19.48, Mccalley, Daniel wrote: > Hi all, > > Our lab targets the FP1 with TMS. We use a simple measurement system > (http://clinicalresearcher.org/F3/) to locate exactly where we want to > place the coil for each subject. Typically, we measure the subject's > head, and then, starting from nasion, we'll move up Y mm and left X mm > (where X and Y are determined from each subject's given head size). > > Ideally, we'd like to create an electric field model for each subject > that accounts for the TMS parameters as well as the exact location > used. To implement this in SIMNIBS, I've tried the following: > > 1) Open a subjects m2m file and find the coordinates for nasion (say, > for example, that these coordinates are X= -2.78, Y= 117.59, Z= -20.63). > > 2) Determine Y and X used to locate FP1 for the given subject (say, > for example, that starting from nasion, we moved 37 mm in the Y > direction, and over 32 mm in the X direction). > > 3) Subtract the displacements in the Y and X directions from the > original nasion coordinates, resulting in X= -34.78 and Y=80.69 > > 4) Add a new position wherein the reference coordinates match the > original nasion coordinates (and the Define Reference Coordinates box > is checked) and the coordinates calculated in step 3 are input in the > position fields (Z is left blank for SIMNIBs to calculate) > > 5) Adjust for coil orientation and TMS parameters > > This seems to have worked well for 90-95% of our subjects, however > there are a few subjects in which the resulting coil placement appears > to be over the eye (Note: Ordinarily I'd attach examples of the > working and not-working subjects, but I'm not sure if the skin > reconstruction of our participants falls under PHI). > > Am I going about this the wrong way? Could this reflect a problem with > segmentation/meshing? Or maybe a problem with the experimenter > measurements of the subjects head? Any advice would be greatly > appreciated. Thank you all so much! > > Best, > > Dan McCalley > Medical University of South Carolina > College of Graduate Studies, Neuroscience > > > _______________________________________________ > Simnibs-discuss mailing list > Simnibs-discuss at drcmr.dk > https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -------------- next part -------------- An HTML attachment was scrubbed... URL: From guilhermebs at drcmr.dk Mon Jul 13 10:40:03 2020 From: guilhermebs at drcmr.dk (Guilherme B Saturnino) Date: Mon, 13 Jul 2020 10:40:03 +0200 Subject: [Simnibs-discuss] Targeting subject specific locations on the scalp In-Reply-To: <6c2d5d4ae0cb4dbe923df0f188f1a641@dtu.dk> References: <1943989e-b733-515a-21dd-5b2287e5548c@drcmr.dk> <87678107fcb141e68989a781e131aa94@dtu.dk> <6c2d5d4ae0cb4dbe923df0f188f1a641@dtu.dk> Message-ID: Also adding to Oula's response: The SimNIBS eeg positions are also adapted to each patient, using either non-linear MNI transformations (the positions in m2m_{SubID}/eeg_positions/EEG10-10_UI_Jurak_2007.csv) or by measuring distances (in %) with respect to the fiducials (eeg_positions) script. Best, Guilherme On 13/07/2020 08.44, Oula Puonti wrote: > > Hi Daniel, > > > Thanks for the clarification. > > > I could see two problems: > > > 1) The Nz coordinate from SimNIBS is not correctly placed. This can > happen due to segmentation/registration errors. You should open the > MRI scan in a viewer, for example freeview, and check that the Nz > coordinate that SimNIBS outputs matches the nasion location on the scan. > > > 2) The header, i.e., voxel-to-world transformation, of the MRIs is > different between subjects. If you always substract the X and Y > distances you might end up moving in a different direction than intended. > > > Best, > > Oula > > ------------------------------------------------------------------------ > *From:* Mccalley, Daniel > *Sent:* Friday, July 10, 2020 6:43:03 PM > *To:* Oula Puonti; Guilherme B Saturnino; discuss at simnibs.org > *Subject:* Re: [Simnibs-discuss] Targeting subject specific locations > on the scalp > Hi all, > > Thank you so much for the fast replies! > > Let me clear up a few things about our experiment -- > > When our participants come in, the experimenter measures the > individual's head (nasion to inion, tragus to tragus, circumference). > Each person's measurements are of course different and there is some > amount of error/rounding made by the experimenter in each measurement. > *Our participants are never fitted with an EEG cap* to locate our > cortical target (FP1). > > Instead, starting at Nz, we take 10% of the distance for Nz to Inion > (generally ranges from 2-4 cm, I referred to this as Y in my initial > example) and move up and we take 5% of the total head circumference > and move that distance left (towards FP1, I referred to this as X in > my initial example). The experimenter makes a mark on the persons head > with sharpie, but *unfortunately we did not use a fiducial for this > study*. > > Given that the FP1 location is determined in a patient-tailored manner > and we expect some degree of experimenter error in making these > measurements, I'd like to as closely as possible recreate an e-field > at the site of stimulation for each person using these measurements. > Thus far, I have used the coordinates for Nz that SIMNIBs produces and > made adjustments from there based on X and Y displacement for each > subject. This almost always produces a result close to FP1, but in > some instances it seems the result remains near the eye or in entirely > unexpected head locations > > Does that information help? > > Thank you all again for your help! > > Best, > > > Dan McCalley > Medical University of South Carolina > College of Graduate Studies, Neuroscience > > ------------------------------------------------------------------------ > *From:* Oula Puonti > *Sent:* Friday, July 10, 2020 3:35 AM > *To:* Guilherme B Saturnino ; Mccalley, Daniel > ; discuss at simnibs.org > *Subject:* Re: [Simnibs-discuss] Targeting subject specific locations > on the scalp > * > > CAUTION: External > > * > > Hi, > > > Just to add to what Guilherme said: Are you locating the nasion > manually or using coordinates that SimNIBS outputs automatically? If > the latter, please check that the fiducial placements look correct. > > > Best, > > Oula > > > > ------------------------------------------------------------------------ > *From:* Simnibs-discuss on behalf > of Guilherme B Saturnino > *Sent:* Friday, July 10, 2020 9:31:07 AM > *To:* Mccalley, Daniel; discuss at simnibs.org > *Subject:* Re: [Simnibs-discuss] Targeting subject specific locations > on the scalp > > Hello, > > > SimNIBS 3 offers two ways of getting 10/10 EEG positions out of the box. > > > 1) Use the eeg positions calculated using MNI transformations, which > are stored in m2m_{SubID}/eeg_positions/EEG10-10_UI_Jurak_2007.csv. > Those can also be accessed in the GUI > , > which loads it automatically, or in? scripts (MATLAB example > ) > > > 2) Using the eeg_positions > > command line tool with the Nz, LPA, RPA and Iz as an input > > > Those two were compared and validated here > . > > > I'm not sure why it is not working in your case though, might be due > to head size, as you are moving by constant amounts? > > > Best Regards, > > Guilherme > > > > On 09/07/2020 19.48, Mccalley, Daniel wrote: >> Hi all, >> >> Our lab targets the FP1 with TMS. We use a simple measurement system >> (http://clinicalresearcher.org/F3/ >> ) >> to locate exactly where we want to place the coil for each subject. >> Typically, we measure the subject's head, and then, starting from >> nasion, we'll move up Y mm and left X mm (where X and Y are >> determined from each subject's given head size). >> >> Ideally, we'd like to create an electric field model for each subject >> that accounts for the TMS parameters as well as the exact location >> used. To implement this in SIMNIBS, I've tried the following: >> >> 1) Open a subjects m2m file and find the coordinates for nasion (say, >> for example, that these coordinates are X= -2.78, Y= 117.59, Z= -20.63). >> >> 2) Determine Y and X used to locate FP1 for the given subject (say, >> for example, that starting from nasion, we moved 37 mm in the Y >> direction, and over 32 mm in the X direction). >> >> 3) Subtract the displacements in the Y and X directions from the >> original nasion coordinates, resulting in X= -34.78 and Y=80.69 >> >> 4) Add a new position wherein the reference coordinates match the >> original nasion coordinates (and the Define Reference Coordinates box >> is checked) and the coordinates calculated in step 3 are input in the >> position fields (Z is left blank for SIMNIBs to calculate) >> >> 5) Adjust for coil orientation and TMS parameters >> >> This seems to have worked well for 90-95% of our subjects, however >> there are a few subjects in which the resulting coil placement >> appears to be over the eye (Note: Ordinarily I'd attach examples of >> the working and not-working subjects, but I'm not sure if the skin >> reconstruction of our participants falls under PHI). >> >> Am I going about this the wrong way? Could this reflect a problem >> with segmentation/meshing? Or maybe a problem with the experimenter >> measurements of the subjects head? Any advice would be greatly >> appreciated. Thank you all so much! >> >> Best, >> >> Dan McCalley >> Medical University of South Carolina >> College of Graduate Studies, Neuroscience >> >> >> _______________________________________________ >> Simnibs-discuss mailing list >> Simnibs-discuss at drcmr.dk >> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -------------- next part -------------- An HTML attachment was scrubbed... URL: From guilhermebs at drcmr.dk Wed Jul 15 07:57:26 2020 From: guilhermebs at drcmr.dk (Guilherme B Saturnino) Date: Wed, 15 Jul 2020 07:57:26 +0200 Subject: [Simnibs-discuss] Targeting subject specific locations on the scalp In-Reply-To: References: <1943989e-b733-515a-21dd-5b2287e5548c@drcmr.dk> <87678107fcb141e68989a781e131aa94@dtu.dk> <6c2d5d4ae0cb4dbe923df0f188f1a641@dtu.dk> Message-ID: Hi Dan, This transformation is embedded inside the NifTi files. It's often called the "affine". Normally the X axis corresponds to left/right, Y to posterior/anterior and Z to bottom/top, but it can vary depending on how the image was acquired and how the subject was positioned inside the scanner, so it is not so reliable. However, the co-register images, located in the m2m_{subID}/toMNI folder, are sure to follow this convention, if the co-registration worked (it generally does). We also use the co-registrations to calculate the 10-10 EEG positions, including FP1, which are stored in m2m_{SubID}/eeg_positions/EEG10-10_UI_Jurak_2007.csv. Best Regards, Guilherme On 14/07/2020 23.12, Mccalley, Daniel wrote: > Hi all, > > Thanks again for the help! > > Oula, would you be able to point me toward the header file that may > have information on the voxel-to-world transformation? It would be > useful to know which direction is up/down, left/right, > forward/backward if X Y and Z aren't always accurate > > Best, > > Dan McCalley > Medical University of South Carolina > College of Graduate Studies, Neuroscience > > ------------------------------------------------------------------------ > *From:* Oula Puonti > *Sent:* Monday, July 13, 2020 2:44 AM > *To:* Mccalley, Daniel ; Guilherme B Saturnino > ; discuss at simnibs.org > *Subject:* Re: [Simnibs-discuss] Targeting subject specific locations > on the scalp > * > > CAUTION: External > > * > > Hi Daniel, > > > Thanks for the clarification. > > > I could see two problems: > > > 1) The Nz coordinate from SimNIBS is not correctly placed. This can > happen due to segmentation/registration errors. You should open the > MRI scan in a viewer, for example freeview, and check that the Nz > coordinate that SimNIBS outputs matches the nasion location on the scan. > > > 2) The header, i.e., voxel-to-world transformation, of the MRIs is > different between subjects. If you always substract the X and Y > distances you might end up moving in a different direction than intended. > > > Best, > > Oula > > ------------------------------------------------------------------------ > *From:* Mccalley, Daniel > *Sent:* Friday, July 10, 2020 6:43:03 PM > *To:* Oula Puonti; Guilherme B Saturnino; discuss at simnibs.org > *Subject:* Re: [Simnibs-discuss] Targeting subject specific locations > on the scalp > Hi all, > > Thank you so much for the fast replies! > > Let me clear up a few things about our experiment -- > > When our participants come in, the experimenter measures the > individual's head (nasion to inion, tragus to tragus, circumference). > Each person's measurements are of course different and there is some > amount of error/rounding made by the experimenter in each measurement. > *Our participants are never fitted with an EEG cap* to locate our > cortical target (FP1). > > Instead, starting at Nz, we take 10% of the distance for Nz to Inion > (generally ranges from 2-4 cm, I referred to this as Y in my initial > example) and move up and we take 5% of the total head circumference > and move that distance left (towards FP1, I referred to this as X in > my initial example). The experimenter makes a mark on the persons head > with sharpie, but *unfortunately we did not use a fiducial for this > study*. > > Given that the FP1 location is determined in a patient-tailored manner > and we expect some degree of experimenter error in making these > measurements, I'd like to as closely as possible recreate an e-field > at the site of stimulation for each person using these measurements. > Thus far, I have used the coordinates for Nz that SIMNIBs produces and > made adjustments from there based on X and Y displacement for each > subject. This almost always produces a result close to FP1, but in > some instances it seems the result remains near the eye or in entirely > unexpected head locations > > Does that information help? > > Thank you all again for your help! > > Best, > > > Dan McCalley > Medical University of South Carolina > College of Graduate Studies, Neuroscience > > ------------------------------------------------------------------------ > *From:* Oula Puonti > *Sent:* Friday, July 10, 2020 3:35 AM > *To:* Guilherme B Saturnino ; Mccalley, Daniel > ; discuss at simnibs.org > *Subject:* Re: [Simnibs-discuss] Targeting subject specific locations > on the scalp > * > > CAUTION: External > > * > > Hi, > > > Just to add to what Guilherme said: Are you locating the nasion > manually or using coordinates that SimNIBS outputs automatically? If > the latter, please check that the fiducial placements look correct. > > > Best, > > Oula > > > > ------------------------------------------------------------------------ > *From:* Simnibs-discuss on behalf > of Guilherme B Saturnino > *Sent:* Friday, July 10, 2020 9:31:07 AM > *To:* Mccalley, Daniel; discuss at simnibs.org > *Subject:* Re: [Simnibs-discuss] Targeting subject specific locations > on the scalp > > Hello, > > > SimNIBS 3 offers two ways of getting 10/10 EEG positions out of the box. > > > 1) Use the eeg positions calculated using MNI transformations, which > are stored in m2m_{SubID}/eeg_positions/EEG10-10_UI_Jurak_2007.csv. > Those can also be accessed in the GUI > , > which loads it automatically, or in scripts (MATLAB example > ) > > > 2) Using the eeg_positions > > command line tool with the Nz, LPA, RPA and Iz as an input > > > Those two were compared and validated here > . > > > I'm not sure why it is not working in your case though, might be due > to head size, as you are moving by constant amounts? > > > Best Regards, > > Guilherme > > > > On 09/07/2020 19.48, Mccalley, Daniel wrote: >> Hi all, >> >> Our lab targets the FP1 with TMS. We use a simple measurement system >> (http://clinicalresearcher.org/F3/ >> ) >> to locate exactly where we want to place the coil for each subject. >> Typically, we measure the subject's head, and then, starting from >> nasion, we'll move up Y mm and left X mm (where X and Y are >> determined from each subject's given head size). >> >> Ideally, we'd like to create an electric field model for each subject >> that accounts for the TMS parameters as well as the exact location >> used. To implement this in SIMNIBS, I've tried the following: >> >> 1) Open a subjects m2m file and find the coordinates for nasion (say, >> for example, that these coordinates are X= -2.78, Y= 117.59, Z= -20.63). >> >> 2) Determine Y and X used to locate FP1 for the given subject (say, >> for example, that starting from nasion, we moved 37 mm in the Y >> direction, and over 32 mm in the X direction). >> >> 3) Subtract the displacements in the Y and X directions from the >> original nasion coordinates, resulting in X= -34.78 and Y=80.69 >> >> 4) Add a new position wherein the reference coordinates match the >> original nasion coordinates (and the Define Reference Coordinates box >> is checked) and the coordinates calculated in step 3 are input in the >> position fields (Z is left blank for SIMNIBs to calculate) >> >> 5) Adjust for coil orientation and TMS parameters >> >> This seems to have worked well for 90-95% of our subjects, however >> there are a few subjects in which the resulting coil placement >> appears to be over the eye (Note: Ordinarily I'd attach examples of >> the working and not-working subjects, but I'm not sure if the skin >> reconstruction of our participants falls under PHI). >> >> Am I going about this the wrong way? Could this reflect a problem >> with segmentation/meshing? Or maybe a problem with the experimenter >> measurements of the subjects head? Any advice would be greatly >> appreciated. Thank you all so much! >> >> Best, >> >> Dan McCalley >> Medical University of South Carolina >> College of Graduate Studies, Neuroscience >> >> >> _______________________________________________ >> Simnibs-discuss mailing list >> Simnibs-discuss at drcmr.dk >> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -------------- next part -------------- An HTML attachment was scrubbed... URL: From oupu at dtu.dk Fri Jul 10 09:35:45 2020 From: oupu at dtu.dk (Oula Puonti) Date: Fri, 10 Jul 2020 07:35:45 +0000 Subject: [Simnibs-discuss] Targeting subject specific locations on the scalp In-Reply-To: <1943989e-b733-515a-21dd-5b2287e5548c@drcmr.dk> References: , <1943989e-b733-515a-21dd-5b2287e5548c@drcmr.dk> Message-ID: <87678107fcb141e68989a781e131aa94@dtu.dk> Hi, Just to add to what Guilherme said: Are you locating the nasion manually or using coordinates that SimNIBS outputs automatically? If the latter, please check that the fiducial placements look correct. Best, Oula ________________________________ From: Simnibs-discuss on behalf of Guilherme B Saturnino Sent: Friday, July 10, 2020 9:31:07 AM To: Mccalley, Daniel; discuss at simnibs.org Subject: Re: [Simnibs-discuss] Targeting subject specific locations on the scalp Hello, SimNIBS 3 offers two ways of getting 10/10 EEG positions out of the box. 1) Use the eeg positions calculated using MNI transformations, which are stored in m2m_{SubID}/eeg_positions/EEG10-10_UI_Jurak_2007.csv. Those can also be accessed in the GUI, which loads it automatically, or in scripts (MATLAB example) 2) Using the eeg_positions command line tool with the Nz, LPA, RPA and Iz as an input Those two were compared and validated here. I'm not sure why it is not working in your case though, might be due to head size, as you are moving by constant amounts? Best Regards, Guilherme On 09/07/2020 19.48, Mccalley, Daniel wrote: Hi all, Our lab targets the FP1 with TMS. We use a simple measurement system (http://clinicalresearcher.org/F3/) to locate exactly where we want to place the coil for each subject. Typically, we measure the subject's head, and then, starting from nasion, we'll move up Y mm and left X mm (where X and Y are determined from each subject's given head size). Ideally, we'd like to create an electric field model for each subject that accounts for the TMS parameters as well as the exact location used. To implement this in SIMNIBS, I've tried the following: 1) Open a subjects m2m file and find the coordinates for nasion (say, for example, that these coordinates are X= -2.78, Y= 117.59, Z= -20.63). 2) Determine Y and X used to locate FP1 for the given subject (say, for example, that starting from nasion, we moved 37 mm in the Y direction, and over 32 mm in the X direction). 3) Subtract the displacements in the Y and X directions from the original nasion coordinates, resulting in X= -34.78 and Y=80.69 4) Add a new position wherein the reference coordinates match the original nasion coordinates (and the Define Reference Coordinates box is checked) and the coordinates calculated in step 3 are input in the position fields (Z is left blank for SIMNIBs to calculate) 5) Adjust for coil orientation and TMS parameters This seems to have worked well for 90-95% of our subjects, however there are a few subjects in which the resulting coil placement appears to be over the eye (Note: Ordinarily I'd attach examples of the working and not-working subjects, but I'm not sure if the skin reconstruction of our participants falls under PHI). Am I going about this the wrong way? Could this reflect a problem with segmentation/meshing? Or maybe a problem with the experimenter measurements of the subjects head? Any advice would be greatly appreciated. Thank you all so much! Best, Dan McCalley Medical University of South Carolina College of Graduate Studies, Neuroscience _______________________________________________ Simnibs-discuss mailing list Simnibs-discuss at drcmr.dk https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -------------- next part -------------- An HTML attachment was scrubbed... URL: From mccalled at musc.edu Fri Jul 10 18:43:03 2020 From: mccalled at musc.edu (Mccalley, Daniel) Date: Fri, 10 Jul 2020 16:43:03 +0000 Subject: [Simnibs-discuss] Targeting subject specific locations on the scalp In-Reply-To: <87678107fcb141e68989a781e131aa94@dtu.dk> References: , <1943989e-b733-515a-21dd-5b2287e5548c@drcmr.dk>, <87678107fcb141e68989a781e131aa94@dtu.dk> Message-ID: Hi all, Thank you so much for the fast replies! Let me clear up a few things about our experiment -- When our participants come in, the experimenter measures the individual's head (nasion to inion, tragus to tragus, circumference). Each person's measurements are of course different and there is some amount of error/rounding made by the experimenter in each measurement. Our participants are never fitted with an EEG cap to locate our cortical target (FP1). Instead, starting at Nz, we take 10% of the distance for Nz to Inion (generally ranges from 2-4 cm, I referred to this as Y in my initial example) and move up and we take 5% of the total head circumference and move that distance left (towards FP1, I referred to this as X in my initial example). The experimenter makes a mark on the persons head with sharpie, but unfortunately we did not use a fiducial for this study. Given that the FP1 location is determined in a patient-tailored manner and we expect some degree of experimenter error in making these measurements, I'd like to as closely as possible recreate an e-field at the site of stimulation for each person using these measurements. Thus far, I have used the coordinates for Nz that SIMNIBs produces and made adjustments from there based on X and Y displacement for each subject. This almost always produces a result close to FP1, but in some instances it seems the result remains near the eye or in entirely unexpected head locations Does that information help? Thank you all again for your help! Best, Dan McCalley Medical University of South Carolina College of Graduate Studies, Neuroscience ________________________________ From: Oula Puonti Sent: Friday, July 10, 2020 3:35 AM To: Guilherme B Saturnino ; Mccalley, Daniel ; discuss at simnibs.org Subject: Re: [Simnibs-discuss] Targeting subject specific locations on the scalp CAUTION: External Hi, Just to add to what Guilherme said: Are you locating the nasion manually or using coordinates that SimNIBS outputs automatically? If the latter, please check that the fiducial placements look correct. Best, Oula ________________________________ From: Simnibs-discuss on behalf of Guilherme B Saturnino Sent: Friday, July 10, 2020 9:31:07 AM To: Mccalley, Daniel; discuss at simnibs.org Subject: Re: [Simnibs-discuss] Targeting subject specific locations on the scalp Hello, SimNIBS 3 offers two ways of getting 10/10 EEG positions out of the box. 1) Use the eeg positions calculated using MNI transformations, which are stored in m2m_{SubID}/eeg_positions/EEG10-10_UI_Jurak_2007.csv. Those can also be accessed in the GUI, which loads it automatically, or in scripts (MATLAB example) 2) Using the eeg_positions command line tool with the Nz, LPA, RPA and Iz as an input Those two were compared and validated here. I'm not sure why it is not working in your case though, might be due to head size, as you are moving by constant amounts? Best Regards, Guilherme On 09/07/2020 19.48, Mccalley, Daniel wrote: Hi all, Our lab targets the FP1 with TMS. We use a simple measurement system (http://clinicalresearcher.org/F3/) to locate exactly where we want to place the coil for each subject. Typically, we measure the subject's head, and then, starting from nasion, we'll move up Y mm and left X mm (where X and Y are determined from each subject's given head size). Ideally, we'd like to create an electric field model for each subject that accounts for the TMS parameters as well as the exact location used. To implement this in SIMNIBS, I've tried the following: 1) Open a subjects m2m file and find the coordinates for nasion (say, for example, that these coordinates are X= -2.78, Y= 117.59, Z= -20.63). 2) Determine Y and X used to locate FP1 for the given subject (say, for example, that starting from nasion, we moved 37 mm in the Y direction, and over 32 mm in the X direction). 3) Subtract the displacements in the Y and X directions from the original nasion coordinates, resulting in X= -34.78 and Y=80.69 4) Add a new position wherein the reference coordinates match the original nasion coordinates (and the Define Reference Coordinates box is checked) and the coordinates calculated in step 3 are input in the position fields (Z is left blank for SIMNIBs to calculate) 5) Adjust for coil orientation and TMS parameters This seems to have worked well for 90-95% of our subjects, however there are a few subjects in which the resulting coil placement appears to be over the eye (Note: Ordinarily I'd attach examples of the working and not-working subjects, but I'm not sure if the skin reconstruction of our participants falls under PHI). Am I going about this the wrong way? Could this reflect a problem with segmentation/meshing? Or maybe a problem with the experimenter measurements of the subjects head? Any advice would be greatly appreciated. Thank you all so much! Best, Dan McCalley Medical University of South Carolina College of Graduate Studies, Neuroscience _______________________________________________ Simnibs-discuss mailing list Simnibs-discuss at drcmr.dk https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -------------- next part -------------- An HTML attachment was scrubbed... URL: From oupu at dtu.dk Mon Jul 13 08:44:15 2020 From: oupu at dtu.dk (Oula Puonti) Date: Mon, 13 Jul 2020 06:44:15 +0000 Subject: [Simnibs-discuss] Targeting subject specific locations on the scalp In-Reply-To: References: , <1943989e-b733-515a-21dd-5b2287e5548c@drcmr.dk>, <87678107fcb141e68989a781e131aa94@dtu.dk>, Message-ID: <6c2d5d4ae0cb4dbe923df0f188f1a641@dtu.dk> Hi Daniel, Thanks for the clarification. I could see two problems: 1) The Nz coordinate from SimNIBS is not correctly placed. This can happen due to segmentation/registration errors. You should open the MRI scan in a viewer, for example freeview, and check that the Nz coordinate that SimNIBS outputs matches the nasion location on the scan. 2) The header, i.e., voxel-to-world transformation, of the MRIs is different between subjects. If you always substract the X and Y distances you might end up moving in a different direction than intended. Best, Oula ________________________________ From: Mccalley, Daniel Sent: Friday, July 10, 2020 6:43:03 PM To: Oula Puonti; Guilherme B Saturnino; discuss at simnibs.org Subject: Re: [Simnibs-discuss] Targeting subject specific locations on the scalp Hi all, Thank you so much for the fast replies! Let me clear up a few things about our experiment -- When our participants come in, the experimenter measures the individual's head (nasion to inion, tragus to tragus, circumference). Each person's measurements are of course different and there is some amount of error/rounding made by the experimenter in each measurement. Our participants are never fitted with an EEG cap to locate our cortical target (FP1). Instead, starting at Nz, we take 10% of the distance for Nz to Inion (generally ranges from 2-4 cm, I referred to this as Y in my initial example) and move up and we take 5% of the total head circumference and move that distance left (towards FP1, I referred to this as X in my initial example). The experimenter makes a mark on the persons head with sharpie, but unfortunately we did not use a fiducial for this study. Given that the FP1 location is determined in a patient-tailored manner and we expect some degree of experimenter error in making these measurements, I'd like to as closely as possible recreate an e-field at the site of stimulation for each person using these measurements. Thus far, I have used the coordinates for Nz that SIMNIBs produces and made adjustments from there based on X and Y displacement for each subject. This almost always produces a result close to FP1, but in some instances it seems the result remains near the eye or in entirely unexpected head locations Does that information help? Thank you all again for your help! Best, Dan McCalley Medical University of South Carolina College of Graduate Studies, Neuroscience ________________________________ From: Oula Puonti Sent: Friday, July 10, 2020 3:35 AM To: Guilherme B Saturnino ; Mccalley, Daniel ; discuss at simnibs.org Subject: Re: [Simnibs-discuss] Targeting subject specific locations on the scalp CAUTION: External Hi, Just to add to what Guilherme said: Are you locating the nasion manually or using coordinates that SimNIBS outputs automatically? If the latter, please check that the fiducial placements look correct. Best, Oula ________________________________ From: Simnibs-discuss on behalf of Guilherme B Saturnino Sent: Friday, July 10, 2020 9:31:07 AM To: Mccalley, Daniel; discuss at simnibs.org Subject: Re: [Simnibs-discuss] Targeting subject specific locations on the scalp Hello, SimNIBS 3 offers two ways of getting 10/10 EEG positions out of the box. 1) Use the eeg positions calculated using MNI transformations, which are stored in m2m_{SubID}/eeg_positions/EEG10-10_UI_Jurak_2007.csv. Those can also be accessed in the GUI, which loads it automatically, or in scripts (MATLAB example) 2) Using the eeg_positions command line tool with the Nz, LPA, RPA and Iz as an input Those two were compared and validated here. I'm not sure why it is not working in your case though, might be due to head size, as you are moving by constant amounts? Best Regards, Guilherme On 09/07/2020 19.48, Mccalley, Daniel wrote: Hi all, Our lab targets the FP1 with TMS. We use a simple measurement system (http://clinicalresearcher.org/F3/) to locate exactly where we want to place the coil for each subject. Typically, we measure the subject's head, and then, starting from nasion, we'll move up Y mm and left X mm (where X and Y are determined from each subject's given head size). Ideally, we'd like to create an electric field model for each subject that accounts for the TMS parameters as well as the exact location used. To implement this in SIMNIBS, I've tried the following: 1) Open a subjects m2m file and find the coordinates for nasion (say, for example, that these coordinates are X= -2.78, Y= 117.59, Z= -20.63). 2) Determine Y and X used to locate FP1 for the given subject (say, for example, that starting from nasion, we moved 37 mm in the Y direction, and over 32 mm in the X direction). 3) Subtract the displacements in the Y and X directions from the original nasion coordinates, resulting in X= -34.78 and Y=80.69 4) Add a new position wherein the reference coordinates match the original nasion coordinates (and the Define Reference Coordinates box is checked) and the coordinates calculated in step 3 are input in the position fields (Z is left blank for SIMNIBs to calculate) 5) Adjust for coil orientation and TMS parameters This seems to have worked well for 90-95% of our subjects, however there are a few subjects in which the resulting coil placement appears to be over the eye (Note: Ordinarily I'd attach examples of the working and not-working subjects, but I'm not sure if the skin reconstruction of our participants falls under PHI). Am I going about this the wrong way? Could this reflect a problem with segmentation/meshing? Or maybe a problem with the experimenter measurements of the subjects head? Any advice would be greatly appreciated. Thank you all so much! Best, Dan McCalley Medical University of South Carolina College of Graduate Studies, Neuroscience _______________________________________________ Simnibs-discuss mailing list Simnibs-discuss at drcmr.dk https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -------------- next part -------------- An HTML attachment was scrubbed... URL: From mccalled at musc.edu Tue Jul 14 23:12:38 2020 From: mccalled at musc.edu (Mccalley, Daniel) Date: Tue, 14 Jul 2020 21:12:38 +0000 Subject: [Simnibs-discuss] Targeting subject specific locations on the scalp In-Reply-To: <6c2d5d4ae0cb4dbe923df0f188f1a641@dtu.dk> References: , <1943989e-b733-515a-21dd-5b2287e5548c@drcmr.dk>, <87678107fcb141e68989a781e131aa94@dtu.dk>, , <6c2d5d4ae0cb4dbe923df0f188f1a641@dtu.dk> Message-ID: Hi all, Thanks again for the help! Oula, would you be able to point me toward the header file that may have information on the voxel-to-world transformation? It would be useful to know which direction is up/down, left/right, forward/backward if X Y and Z aren't always accurate Best, Dan McCalley Medical University of South Carolina College of Graduate Studies, Neuroscience ________________________________ From: Oula Puonti Sent: Monday, July 13, 2020 2:44 AM To: Mccalley, Daniel ; Guilherme B Saturnino ; discuss at simnibs.org Subject: Re: [Simnibs-discuss] Targeting subject specific locations on the scalp CAUTION: External Hi Daniel, Thanks for the clarification. I could see two problems: 1) The Nz coordinate from SimNIBS is not correctly placed. This can happen due to segmentation/registration errors. You should open the MRI scan in a viewer, for example freeview, and check that the Nz coordinate that SimNIBS outputs matches the nasion location on the scan. 2) The header, i.e., voxel-to-world transformation, of the MRIs is different between subjects. If you always substract the X and Y distances you might end up moving in a different direction than intended. Best, Oula ________________________________ From: Mccalley, Daniel Sent: Friday, July 10, 2020 6:43:03 PM To: Oula Puonti; Guilherme B Saturnino; discuss at simnibs.org Subject: Re: [Simnibs-discuss] Targeting subject specific locations on the scalp Hi all, Thank you so much for the fast replies! Let me clear up a few things about our experiment -- When our participants come in, the experimenter measures the individual's head (nasion to inion, tragus to tragus, circumference). Each person's measurements are of course different and there is some amount of error/rounding made by the experimenter in each measurement. Our participants are never fitted with an EEG cap to locate our cortical target (FP1). Instead, starting at Nz, we take 10% of the distance for Nz to Inion (generally ranges from 2-4 cm, I referred to this as Y in my initial example) and move up and we take 5% of the total head circumference and move that distance left (towards FP1, I referred to this as X in my initial example). The experimenter makes a mark on the persons head with sharpie, but unfortunately we did not use a fiducial for this study. Given that the FP1 location is determined in a patient-tailored manner and we expect some degree of experimenter error in making these measurements, I'd like to as closely as possible recreate an e-field at the site of stimulation for each person using these measurements. Thus far, I have used the coordinates for Nz that SIMNIBs produces and made adjustments from there based on X and Y displacement for each subject. This almost always produces a result close to FP1, but in some instances it seems the result remains near the eye or in entirely unexpected head locations Does that information help? Thank you all again for your help! Best, Dan McCalley Medical University of South Carolina College of Graduate Studies, Neuroscience ________________________________ From: Oula Puonti Sent: Friday, July 10, 2020 3:35 AM To: Guilherme B Saturnino ; Mccalley, Daniel ; discuss at simnibs.org Subject: Re: [Simnibs-discuss] Targeting subject specific locations on the scalp CAUTION: External Hi, Just to add to what Guilherme said: Are you locating the nasion manually or using coordinates that SimNIBS outputs automatically? If the latter, please check that the fiducial placements look correct. Best, Oula ________________________________ From: Simnibs-discuss on behalf of Guilherme B Saturnino Sent: Friday, July 10, 2020 9:31:07 AM To: Mccalley, Daniel; discuss at simnibs.org Subject: Re: [Simnibs-discuss] Targeting subject specific locations on the scalp Hello, SimNIBS 3 offers two ways of getting 10/10 EEG positions out of the box. 1) Use the eeg positions calculated using MNI transformations, which are stored in m2m_{SubID}/eeg_positions/EEG10-10_UI_Jurak_2007.csv. Those can also be accessed in the GUI, which loads it automatically, or in scripts (MATLAB example) 2) Using the eeg_positions command line tool with the Nz, LPA, RPA and Iz as an input Those two were compared and validated here. I'm not sure why it is not working in your case though, might be due to head size, as you are moving by constant amounts? Best Regards, Guilherme On 09/07/2020 19.48, Mccalley, Daniel wrote: Hi all, Our lab targets the FP1 with TMS. We use a simple measurement system (http://clinicalresearcher.org/F3/) to locate exactly where we want to place the coil for each subject. Typically, we measure the subject's head, and then, starting from nasion, we'll move up Y mm and left X mm (where X and Y are determined from each subject's given head size). Ideally, we'd like to create an electric field model for each subject that accounts for the TMS parameters as well as the exact location used. To implement this in SIMNIBS, I've tried the following: 1) Open a subjects m2m file and find the coordinates for nasion (say, for example, that these coordinates are X= -2.78, Y= 117.59, Z= -20.63). 2) Determine Y and X used to locate FP1 for the given subject (say, for example, that starting from nasion, we moved 37 mm in the Y direction, and over 32 mm in the X direction). 3) Subtract the displacements in the Y and X directions from the original nasion coordinates, resulting in X= -34.78 and Y=80.69 4) Add a new position wherein the reference coordinates match the original nasion coordinates (and the Define Reference Coordinates box is checked) and the coordinates calculated in step 3 are input in the position fields (Z is left blank for SIMNIBs to calculate) 5) Adjust for coil orientation and TMS parameters This seems to have worked well for 90-95% of our subjects, however there are a few subjects in which the resulting coil placement appears to be over the eye (Note: Ordinarily I'd attach examples of the working and not-working subjects, but I'm not sure if the skin reconstruction of our participants falls under PHI). Am I going about this the wrong way? Could this reflect a problem with segmentation/meshing? Or maybe a problem with the experimenter measurements of the subjects head? Any advice would be greatly appreciated. Thank you all so much! Best, Dan McCalley Medical University of South Carolina College of Graduate Studies, Neuroscience _______________________________________________ Simnibs-discuss mailing list Simnibs-discuss at drcmr.dk https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -------------- next part -------------- An HTML attachment was scrubbed... URL: From mccalled at musc.edu Wed Jul 15 18:39:21 2020 From: mccalled at musc.edu (Mccalley, Daniel) Date: Wed, 15 Jul 2020 16:39:21 +0000 Subject: [Simnibs-discuss] Targeting subject specific locations on the scalp In-Reply-To: References: <1943989e-b733-515a-21dd-5b2287e5548c@drcmr.dk> <87678107fcb141e68989a781e131aa94@dtu.dk> <6c2d5d4ae0cb4dbe923df0f188f1a641@dtu.dk> , Message-ID: Great, thank you all so much for the help! Best, Dan McCalley Medical University of South Carolina College of Graduate Studies, Neuroscience ________________________________ From: Guilherme B Saturnino Sent: Wednesday, July 15, 2020 1:57 AM To: Mccalley, Daniel ; Oula Puonti ; discuss at simnibs.org Subject: Re: [Simnibs-discuss] Targeting subject specific locations on the scalp CAUTION: External Hi Dan, This transformation is embedded inside the NifTi files. It's often called the "affine". Normally the X axis corresponds to left/right, Y to posterior/anterior and Z to bottom/top, but it can vary depending on how the image was acquired and how the subject was positioned inside the scanner, so it is not so reliable. However, the co-register images, located in the m2m_{subID}/toMNI folder, are sure to follow this convention, if the co-registration worked (it generally does). We also use the co-registrations to calculate the 10-10 EEG positions, including FP1, which are stored in m2m_{SubID}/eeg_positions/EEG10-10_UI_Jurak_2007.csv. Best Regards, Guilherme On 14/07/2020 23.12, Mccalley, Daniel wrote: Hi all, Thanks again for the help! Oula, would you be able to point me toward the header file that may have information on the voxel-to-world transformation? It would be useful to know which direction is up/down, left/right, forward/backward if X Y and Z aren't always accurate Best, Dan McCalley Medical University of South Carolina College of Graduate Studies, Neuroscience ________________________________ From: Oula Puonti Sent: Monday, July 13, 2020 2:44 AM To: Mccalley, Daniel ; Guilherme B Saturnino ; discuss at simnibs.org Subject: Re: [Simnibs-discuss] Targeting subject specific locations on the scalp CAUTION: External Hi Daniel, Thanks for the clarification. I could see two problems: 1) The Nz coordinate from SimNIBS is not correctly placed. This can happen due to segmentation/registration errors. You should open the MRI scan in a viewer, for example freeview, and check that the Nz coordinate that SimNIBS outputs matches the nasion location on the scan. 2) The header, i.e., voxel-to-world transformation, of the MRIs is different between subjects. If you always substract the X and Y distances you might end up moving in a different direction than intended. Best, Oula ________________________________ From: Mccalley, Daniel Sent: Friday, July 10, 2020 6:43:03 PM To: Oula Puonti; Guilherme B Saturnino; discuss at simnibs.org Subject: Re: [Simnibs-discuss] Targeting subject specific locations on the scalp Hi all, Thank you so much for the fast replies! Let me clear up a few things about our experiment -- When our participants come in, the experimenter measures the individual's head (nasion to inion, tragus to tragus, circumference). Each person's measurements are of course different and there is some amount of error/rounding made by the experimenter in each measurement. Our participants are never fitted with an EEG cap to locate our cortical target (FP1). Instead, starting at Nz, we take 10% of the distance for Nz to Inion (generally ranges from 2-4 cm, I referred to this as Y in my initial example) and move up and we take 5% of the total head circumference and move that distance left (towards FP1, I referred to this as X in my initial example). The experimenter makes a mark on the persons head with sharpie, but unfortunately we did not use a fiducial for this study. Given that the FP1 location is determined in a patient-tailored manner and we expect some degree of experimenter error in making these measurements, I'd like to as closely as possible recreate an e-field at the site of stimulation for each person using these measurements. Thus far, I have used the coordinates for Nz that SIMNIBs produces and made adjustments from there based on X and Y displacement for each subject. This almost always produces a result close to FP1, but in some instances it seems the result remains near the eye or in entirely unexpected head locations Does that information help? Thank you all again for your help! Best, Dan McCalley Medical University of South Carolina College of Graduate Studies, Neuroscience ________________________________ From: Oula Puonti Sent: Friday, July 10, 2020 3:35 AM To: Guilherme B Saturnino ; Mccalley, Daniel ; discuss at simnibs.org Subject: Re: [Simnibs-discuss] Targeting subject specific locations on the scalp CAUTION: External Hi, Just to add to what Guilherme said: Are you locating the nasion manually or using coordinates that SimNIBS outputs automatically? If the latter, please check that the fiducial placements look correct. Best, Oula ________________________________ From: Simnibs-discuss on behalf of Guilherme B Saturnino Sent: Friday, July 10, 2020 9:31:07 AM To: Mccalley, Daniel; discuss at simnibs.org Subject: Re: [Simnibs-discuss] Targeting subject specific locations on the scalp Hello, SimNIBS 3 offers two ways of getting 10/10 EEG positions out of the box. 1) Use the eeg positions calculated using MNI transformations, which are stored in m2m_{SubID}/eeg_positions/EEG10-10_UI_Jurak_2007.csv. Those can also be accessed in the GUI, which loads it automatically, or in scripts (MATLAB example) 2) Using the eeg_positions command line tool with the Nz, LPA, RPA and Iz as an input Those two were compared and validated here. I'm not sure why it is not working in your case though, might be due to head size, as you are moving by constant amounts? Best Regards, Guilherme On 09/07/2020 19.48, Mccalley, Daniel wrote: Hi all, Our lab targets the FP1 with TMS. We use a simple measurement system (http://clinicalresearcher.org/F3/) to locate exactly where we want to place the coil for each subject. Typically, we measure the subject's head, and then, starting from nasion, we'll move up Y mm and left X mm (where X and Y are determined from each subject's given head size). Ideally, we'd like to create an electric field model for each subject that accounts for the TMS parameters as well as the exact location used. To implement this in SIMNIBS, I've tried the following: 1) Open a subjects m2m file and find the coordinates for nasion (say, for example, that these coordinates are X= -2.78, Y= 117.59, Z= -20.63). 2) Determine Y and X used to locate FP1 for the given subject (say, for example, that starting from nasion, we moved 37 mm in the Y direction, and over 32 mm in the X direction). 3) Subtract the displacements in the Y and X directions from the original nasion coordinates, resulting in X= -34.78 and Y=80.69 4) Add a new position wherein the reference coordinates match the original nasion coordinates (and the Define Reference Coordinates box is checked) and the coordinates calculated in step 3 are input in the position fields (Z is left blank for SIMNIBs to calculate) 5) Adjust for coil orientation and TMS parameters This seems to have worked well for 90-95% of our subjects, however there are a few subjects in which the resulting coil placement appears to be over the eye (Note: Ordinarily I'd attach examples of the working and not-working subjects, but I'm not sure if the skin reconstruction of our participants falls under PHI). Am I going about this the wrong way? Could this reflect a problem with segmentation/meshing? Or maybe a problem with the experimenter measurements of the subjects head? Any advice would be greatly appreciated. Thank you all so much! Best, Dan McCalley Medical University of South Carolina College of Graduate Studies, Neuroscience _______________________________________________ Simnibs-discuss mailing list Simnibs-discuss at drcmr.dk https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -------------- next part -------------- An HTML attachment was scrubbed... URL: From mccalled at musc.edu Fri Jul 24 18:50:43 2020 From: mccalled at musc.edu (Mccalley, Daniel) Date: Fri, 24 Jul 2020 16:50:43 +0000 Subject: [Simnibs-discuss] Scalp to cortex distance and eField thresholding Message-ID: Hi all, I have two questions about some eField models that I've created: 1) Is there a simple way to extract the measured scalp-to-cortex distance between the defined TMS position and the cortex? I imagine SIMNIBs must calculate this in creating the eField. I would be very interested in extracting that information for other analyses. 2) In interpolating my electric field models to .nii files, I'm attempting to discern how best to threshold the eFields such that I might create a Region of Interest of mask based on the precise site of stimulation. I know that there is much debate surrounding 1 V/m as a critical value in tDCS modeling. In TMS, I've noticed that even in my modeling of stimulation intensities that are particularly low (40% MSO, 58.4 dI/dT on Magventure), the resulting eField has a rough value of about 45 V/m at the site of stimulation (crosshairs at the first image), but even areas near the occipital cortex have a rough value of 3-4 V/m (crosshairs at second image). While proportionally this V/m is much smaller than the actual site of stimulation, I could imagine one might argue that a value of 3-4V/m may influence cortical neurons. Is this a typical result or is it possible I've made some critical mistake in my modeling? Thank you so much for your help! Best, Dan McCalley Medical University of South Carolina College of Graduate Studies, Neuroscience -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Messages Image(918841510).png Type: image/png Size: 58370 bytes Desc: Messages Image(918841510).png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Messages Image(3770568445).png Type: image/png Size: 52671 bytes Desc: Messages Image(3770568445).png URL: From guilhermebs at drcmr.dk Mon Jul 27 10:33:04 2020 From: guilhermebs at drcmr.dk (Guilherme B Saturnino) Date: Mon, 27 Jul 2020 10:33:04 +0200 Subject: [Simnibs-discuss] Scalp to cortex distance and eField thresholding In-Reply-To: References: Message-ID: Hello, 1) As of now you would need to write a small python or matlab script which loads the mesh file and calculates the distances from your coil to the cortex. But I've implemented this calculation as a part of the standard pipeline for the next version. Beginning in version 3.2 this value will be written out in the log. 2) I'm by no means an electrophysiology specialist (my background is physics and computer science) but the time dynamics of tDCS and TMS are very different. While tDCS uses a direct current applied over a long time (typically minutes), TMS happens at a quite short time scale (typically microseconds) and have strong variations in time, even monophasic pulses. So I guess that, while it is valid to speculate if small fields can have an effect in TMS, direct comparison with tDCS using only field strength is not very appropriate. Best Regards, Guilherme On 24/07/2020 18.50, Mccalley, Daniel wrote: > Hi all, > > I have two questions about some eField models that I've created: > > 1) Is there a simple way to extract the measured scalp-to-cortex > distance between the defined TMS position and the cortex? I imagine > SIMNIBs must calculate this in creating the eField. I would be very > interested in extracting that information for other analyses. > > 2) In interpolating my electric field models to .nii files, I'm > attempting to discern how best to threshold the eFields such that I > might create a Region of Interest of mask based on the precise site of > stimulation. I know that there is much debate surrounding 1 V/m as a > critical value in tDCS modeling. In TMS, I've noticed that even in my > modeling of stimulation intensities that are particularly low (40% > MSO, 58.4 dI/dT on Magventure), the resulting eField has a rough value > of about 45 V/m at the site of stimulation (crosshairs at the first > image), but even areas near the occipital cortex have a rough value of > 3-4 V/m (crosshairs at second image). While proportionally this V/m is > much smaller than the actual site of stimulation, I could imagine one > might argue that a value of 3-4V/m may influence cortical neurons. > > Is this a typical result or is it possible I've made some critical > mistake in my modeling? > > Thank you so much for your help! > > Best, > > Dan McCalley > Medical University of South Carolina > College of Graduate Studies, Neuroscience > > > _______________________________________________ > Simnibs-discuss mailing list > Simnibs-discuss at drcmr.dk > https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -------------- next part -------------- An HTML attachment was scrubbed... URL: