From axelt at drcmr.dk Wed Nov 2 17:21:31 2022 From: axelt at drcmr.dk (Axel Thielscher) Date: Wed, 2 Nov 2022 17:21:31 +0100 Subject: [Simnibs-discuss] Differences in Efield depending on Processing In-Reply-To: References: Message-ID: <562e6304-1269-fbc3-1941-5c7a83302ea5@drcmr.dk> Hi Joel, a question for better understanding: When you set up the 2nd pathway, do you then model ALL electrodes of the EEG10-20 system, or only those which you actually need for the montage? I am asking because adding many well-conducting electrodes to the model will slightly increase the amount of current shunted through the scalp(+electrodes). Think of it as covering many parts of the scalp with well-conductive paste. We never quantified the size of this effect, but it will cause the leadfield e-fields in the brain to be consistently lower. Best regards, Axel On 19-10-2022 21:07, Joel Upston wrote: > Hi there, > > I have noticed a systematic difference between the two different lines > of simulating the same currents, electrodes and underlying dataset. > One is through processing through the leadfield and using only the > electrodes and currents as given and the other is through only > modeling those electrodes and currents without the leadfield. Now the > 2^nd ?pathway (no leadfield) is giving higher E_mag than the leadfield > version (~7-12%), the spatial maps look similar but just the intensity > differences. I think it has to do with the scaling that is done after > the solve by scaling the estimated current calibration error, which if > I understand?correctly isn't done in the leadfield processing.? If > this is the case I am trying to establish which would be more accurate > to use in your view if I need a specific target value of (0.3 V/m for > example). I have attached an image of a case where this is shown with > the leadfield processed is on the left and the non-leadfield is on the > right. I have tried this on about 5 different datasets and the pattern > is consistent. > > Thanks, > > Joel > > _______________________________________________ > Simnibs-discuss mailing list > Simnibs-discuss at drcmr.dk > https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -- Dr. Axel Thielscher Professor of Neurophysics and Neuroimaging Danish Research Center for Magnetic Resonance Copenhagen University Hospital Hvidovre DK-2650 Hvidovre, Denmark www.drcmr.dk & Department of Health Technology Technical University of Denmark DK-2800 Kgs. Lyngby http://www.healthtech.dtu.dk/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From axelt at drcmr.dk Wed Nov 2 17:44:06 2022 From: axelt at drcmr.dk (Axel Thielscher) Date: Wed, 2 Nov 2022 17:44:06 +0100 Subject: [Simnibs-discuss] Downsample surface In-Reply-To: References: Message-ID: <504ad054-55e1-4c50-f9c6-1f1de14312fc@drcmr.dk> Hi, the way to do this is to first run the simnibs simulation with the full resolution headmesh and afterwards interpolate the results onto the nodes of the 16k surface. This is done using the method "interpolate_to_surface" that is part of simnibs.msh.mesh_io There is currently no example code which we can share, but you can look at line 1480 in https://github.com/simnibs/simnibs/blob/master/simnibs/msh/transformations.py where we use that method to interpolate the e-field results to the central GM surfaces created by CAT12. Best regards, Axel On 18-10-2022 07:45, Huertas Penen, Silvana (UT-EEMCS) wrote: > Hi, > > I need to have a headmesh in Simnibs with 16k vertices in the surface. > This to be able to use the output of simnibs in TVB. What I did was to > import the headmesh I did in Simnibs to Brainstorm and then downsample > to 16k. Now I have the surface downsampled but I do not know how to > input/merge this with the headmesh I made in SimNibs. Do you know how > to do this? > > Or if there is a method in simnibs to downsample the surface in the > headmesh? > > Get Outlook for Android > > _______________________________________________ > Simnibs-discuss mailing list > Simnibs-discuss at drcmr.dk > https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -- Dr. Axel Thielscher Professor of Neurophysics and Neuroimaging Danish Research Center for Magnetic Resonance Copenhagen University Hospital Hvidovre DK-2650 Hvidovre, Denmark www.drcmr.dk & Department of Health Technology Technical University of Denmark DK-2800 Kgs. Lyngby http://www.healthtech.dtu.dk/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From rebecca.anne.roth at emory.edu Tue Nov 1 15:41:41 2022 From: rebecca.anne.roth at emory.edu (Roth, Rebecca) Date: Tue, 1 Nov 2022 14:41:41 +0000 Subject: [Simnibs-discuss] Adapting SimNibs for tACS Message-ID: Hello, I am hoping to use SimNibs to model tACS. I see one FAQ about this topic, but I was wondering if you have any more information or directions, specifically related to in and out of phase cycles. Thank you in advance. Rebecca Wilkes Roth, BA Research Specialist Department of Neurology Emory University Research Scholar Department of Neurology Medical University of South Carolina (864)-634-0526 raroth at emory.edu [Text Description automatically generated] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 26496 bytes Desc: image001.png URL: From stephen.ball-4 at postgrad.manchester.ac.uk Tue Nov 1 16:33:26 2022 From: stephen.ball-4 at postgrad.manchester.ac.uk (Stephen Ball) Date: Tue, 1 Nov 2022 15:33:26 +0000 Subject: [Simnibs-discuss] tDCS optimization for 4x1 set-up Message-ID: Hi There, I'm running a study with a similar set-up to this post: [Simnibs-discuss] 4x1 Optamization (drcmr.dk) using a 4x1 hd-tDCS arrangement, with 2mA on the anode and 4 cathodes at -0.5mA. I'm hoping to optimize the location of these electrodes. Is there still no optimization setting specific to this arrangement? If not, can I clarify your response in the link above - are you saying tune the target intensity parameter and check the output for the arrangement where the current at each electrode looks closest to what we're hoping to achieve? Best, Steve -------------------------------------------- Stephen Ball -------------------------------------------- PhD Student in Cognitive Neuroscience University of Manchester MRC DTP Division of Neuroscience and Experimental Psychology (DNEP) Zochonis Building stephen.ball-4 at postgrad.manchester.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From G.Lale at campus.lmu.de Thu Nov 3 11:16:08 2022 From: G.Lale at campus.lmu.de (=?utf-8?Q?G=C3=BClce_Lale?=) Date: Thu, 3 Nov 2022 11:16:08 +0100 Subject: [Simnibs-discuss] Question about the scripting electrodes and the connector with Python Message-ID: <80FF338F-22B4-48D5-8F19-798FCAF8C8B2@campus.lmu.de> I have a question about scripting simulation with python which can also be beneficial for others. Could you share it in the mailing list? Thank you. I am currently working on a project where I have to simulate our tDCS with python in SimNIBS. I am trying to write a script, where I give the electrode coordinates, dimensions, and other parameters within the script. In addition to the electrode, I have to model the connector (the plug). The anode is 5x5 and its connector has a height of 2.3 and width of 1.3. Whereas, the cathode is 4x4 and the connector has the same height and width. I calculated the plug dimensions and the distance from the centre of the electrode, however, when I try to model it in SimNIBS I have 2 problems: 1. Since I have both a cathode and an anode, I have to simulate 2 plugs. However, when I try to simulate them I got this following error for the second electrode?s plug: NotImplementedError in the function put_electrode_on_mesh. Which tells me that the length of the plug shouldn?t be greater than 1 (len(elec.plug)<1). 2. I tried to simulate only one electrode with a plug, and simulated the other electrode without a plug. Then, I noticed that the plug isn?t being simulated at all. Or, I can not see it on the SimNIBS pop up screen which opens after running my simulation script. I wanted to ask if anyone simulated the connector(plug) of the electrode before, and by any chance has a solution to my problem. Thank you for your answers in advance. Best, G?lce -------------- next part -------------- An HTML attachment was scrubbed... URL: From oulap at drcmr.dk Wed Nov 9 08:22:27 2022 From: oulap at drcmr.dk (Oula) Date: Wed, 9 Nov 2022 08:22:27 +0100 Subject: [Simnibs-discuss] Question about the scripting electrodes and the connector with Python In-Reply-To: <80FF338F-22B4-48D5-8F19-798FCAF8C8B2@campus.lmu.de> References: <80FF338F-22B4-48D5-8F19-798FCAF8C8B2@campus.lmu.de> Message-ID: <4a1fc366-802d-e78f-3370-d2a43aed4552@drcmr.dk> Hi G?lce, Could you share your script so we can have a look? The len(elec.plug) probably refers to the number of plugs on an electrode, so maybe you're trying to put multiple plugs on the same electrode. Best, Oula On 11/3/22 11:16, G?lce Lale wrote: > I have a question about scripting simulation with python which can > also be beneficial for others. Could you share it in the mailing list? > Thank you. > > I am currently working on a project where I have to simulate our tDCS > with python in SimNIBS. I am trying to write a script, where I give > the electrode coordinates, dimensions, and other parameters within the > script. In addition to the electrode, I have to model the connector > (the plug). > The anode is 5x5 and its connector has a height of 2.3 and width of > 1.3. Whereas, the cathode is 4x4 and the connector has the same height > and width. I calculated the plug dimensions and the distance from the > centre of the electrode, however, when I try to model it in SimNIBS I > have 2 problems: > > 1. Since I have both a cathode and an anode, I have to simulate 2 > plugs. However, when I try to simulate them I got this following error > for the second electrode?s plug:?NotImplementedError in the function > put_electrode_on_mesh. Which tells me that the length of the plug > shouldn?t be greater than 1 (len(elec.plug)<1). > 2. I tried to simulate only one electrode with a plug, and simulated > the other electrode without a plug. Then, I noticed that the plug > isn?t being simulated at all. Or, I can not see it on the SimNIBS pop > up screen which opens after running my simulation script. > > I wanted to ask if anyone simulated the connector(plug) of the > electrode before, and by any chance has a solution to my problem. > > Thank you for your answers in advance. > Best, > G?lce > > > > _______________________________________________ > 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 oulap at drcmr.dk Wed Nov 9 08:33:06 2022 From: oulap at drcmr.dk (Oula) Date: Wed, 9 Nov 2022 08:33:06 +0100 Subject: [Simnibs-discuss] tDCS optimization for 4x1 set-up In-Reply-To: References: Message-ID: Hi Steve, We don't have an optimization procedure for the 4x1 yet. You can simulate different configurations with the currents you have specified and read the e-field at the target (and outside the target if you're interested in focality). Then pick the one that matches your optimization criteria best. For hitting a target the best configuration will most likely have the center electrode directly above the target. The radius of the montage (how far the surrounding electrodes are) will depend on how deep the target is. The other option is to run the optimization as Axel pointed out in the previous answer and change the target intensity parameter so that the optimized currents match the ones you're after as you say. Best, Oula On 11/1/22 16:33, Stephen Ball wrote: > > Hi There, > > I?m running a study with a similar set-up to this post: > [Simnibs-discuss] 4x1 Optamization (drcmr.dk) > > using a 4x1 hd-tDCS arrangement, with 2mA on the anode and 4 cathodes > at -0.5mA. I?m hoping to optimize the location of these electrodes. Is > there still no optimization setting specific to this arrangement? > > If not, can I clarify your response in the link above ? are you saying > tune the target intensity parameter and check the output for the > arrangement where the current at each electrode looks closest to what > we?re hoping to achieve? > > Best, > > Steve > > -------------------------------------------- > > Stephen Ball > > -------------------------------------------- > > PhD Student in Cognitive Neuroscience > > University of Manchester MRC DTP > > Division of Neuroscience and Experimental Psychology (DNEP) > > Zochonis Building > > stephen.ball-4 at postgrad.manchester.ac.uk > > > _______________________________________________ > 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 laurent.torlay at univ-grenoble-alpes.fr Tue Nov 15 10:49:25 2022 From: laurent.torlay at univ-grenoble-alpes.fr (LAURENT TORLAY) Date: Tue, 15 Nov 2022 10:49:25 +0100 (CET) Subject: [Simnibs-discuss] Focality with a specific threshold Message-ID: <747242290.8128668.1668505765449.JavaMail.zimbra@univ-grenoble-alpes.fr> Hello, First, I use Simnibs for several years and thank you for developping such a software ! My question : in the file fields_summary.txt, focality is measured by 'area with a field >= X% of the 99.9th percentile', how can we get a similar measurement with a specific threshold in V/m ? (moreover, why the result is a volume ? The area is multiplied by a mean cortical thickness (of the area, the whole brain ?) ) Thanks in advance, Best, L. Torlay -------------- next part -------------- An HTML attachment was scrubbed... URL: From axelt at drcmr.dk Wed Nov 16 08:17:00 2022 From: axelt at drcmr.dk (Axel Thielscher) Date: Wed, 16 Nov 2022 08:17:00 +0100 Subject: [Simnibs-discuss] Differences in Efield depending on Processing In-Reply-To: References: <562e6304-1269-fbc3-1941-5c7a83302ea5@drcmr.dk> Message-ID: <176b4f89-90c6-1469-ec01-cdd35f3cce54@drcmr.dk> Joel, when you have small electrodes as is usually the case for multi-electrode montages, a simple solution is to lower the conductivity of the modelled electrode materials. This will not affect the field distribution in the brain, but reduce the amount of shunting when you place many electrodes on the head. This solution will be fine for small electrodes, where it is not important that the modelled electrode properties correspond well to the ones used in the real experiment. Best regards, Axel On 15-11-2022 20:33, Joel Upston wrote: > Axel, > > Thanks for the clarification. In the inital post I modeled the second > pathway with only the electrodes that were used in the pipeline, but > your reasoning makes sense about the conductive paste being used > essentially covers a majority of the head. > > I reran using all modeled electrodes, and the electrodes not used are > modeled with 0 mA current. I have attached the images where the right > is the non-leadfield model and the left is the leadfield model. Where > now the fields look very similar between the two different pipelines. > It looks like it does lower the field by about ~10% (max given with > all electrodes 0.47 V/m and only used electrodes 0.521 V/m). This > would be consistent with what I have found with other stimulations. > The benefit is that although it does seem to change the magnitude of > the electric field, the spatial distribution does not seem to change. > > So, if we were to target a specific value efield magnitude for a ROI, > any optimization problem using the leadfield might be incorrect due to > the lower magnitude of the leadfield processing. I wonder how to > correct for this during any optimization, or maybe not necessary since > it could be that the scale is similar no matter what stimulation is > modeled. So maybe you could just correct in post optimal solution > found. Do you think it is worth looking at the spherical model with a > possible additional tissue representing the conductive paste compared > to the one without the additional conductive paste tissue, to get a > sense of the scale estimate? > > Thanks, > > Joel > ------------------------------------------------------------------------ > *From:* Axel Thielscher > *Sent:* Wednesday, November 2, 2022 10:21 AM > *To:* Joel Upston ; discuss at simnibs.org > > *Subject:* Re: [Simnibs-discuss] Differences in Efield depending on > Processing > > > You don't often get email from axelt at drcmr.dk. Learn why this is > important > > > *? [EXTERNAL]* > > ** > > Hi Joel, > > > a question for better understanding: When you set up the 2nd pathway, > do you then model ALL electrodes of the EEG10-20 system, or only those > which you actually need for the montage? > > > I am asking because adding many well-conducting electrodes to the > model will slightly increase the amount of current shunted through the > scalp(+electrodes). Think of it as covering many parts of the scalp > with well-conductive paste. We never quantified the size of this > effect, but it will cause the leadfield e-fields in the brain to be > consistently lower. > > > Best regards, > > Axel > > > On 19-10-2022 21:07, Joel Upston wrote: >> Hi there, >> >> I have noticed a systematic difference between the two different >> lines of simulating the same currents, electrodes and underlying >> dataset. One is through processing through the leadfield and using >> only the electrodes and currents as given and the other is through >> only modeling those electrodes and currents without the leadfield. >> Now the 2^nd ?pathway (no leadfield) is giving higher E_mag than the >> leadfield version (~7-12%), the spatial maps look similar but just >> the intensity differences. I think it has to do with the scaling that >> is done after the solve by scaling the estimated current calibration >> error, which if I understand?correctly isn't done in the leadfield >> processing.? If this is the case I am trying to establish which would >> be more accurate to use in your view if I need a specific target >> value of (0.3 V/m for example). I have attached an image of a case >> where this is shown with the leadfield processed is on the left and >> the non-leadfield is on the right. I have tried this on about 5 >> different datasets and the pattern is consistent. >> >> Thanks, >> >> Joel >> >> _______________________________________________ >> Simnibs-discuss mailing list >> Simnibs-discuss at drcmr.dk >> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss > -- > Dr. Axel Thielscher > Professor of Neurophysics and Neuroimaging > Danish Research Center for Magnetic Resonance > Copenhagen University Hospital Hvidovre > DK-2650 Hvidovre, Denmark > www.drcmr.dk > & > Department of Health Technology > Technical University of Denmark > DK-2800 Kgs. Lyngby > http://www.healthtech.dtu.dk/ -- Dr. Axel Thielscher Professor of Neurophysics and Neuroimaging Danish Research Center for Magnetic Resonance Copenhagen University Hospital Hvidovre DK-2650 Hvidovre, Denmark www.drcmr.dk & Department of Health Technology Technical University of Denmark DK-2800 Kgs. Lyngby http://www.healthtech.dtu.dk/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From jupston at unm.edu Tue Nov 15 20:33:40 2022 From: jupston at unm.edu (Joel Upston) Date: Tue, 15 Nov 2022 19:33:40 +0000 Subject: [Simnibs-discuss] Differences in Efield depending on Processing In-Reply-To: <562e6304-1269-fbc3-1941-5c7a83302ea5@drcmr.dk> References: <562e6304-1269-fbc3-1941-5c7a83302ea5@drcmr.dk> Message-ID: Axel, Thanks for the clarification. In the inital post I modeled the second pathway with only the electrodes that were used in the pipeline, but your reasoning makes sense about the conductive paste being used essentially covers a majority of the head. I reran using all modeled electrodes, and the electrodes not used are modeled with 0 mA current. I have attached the images where the right is the non-leadfield model and the left is the leadfield model. Where now the fields look very similar between the two different pipelines. It looks like it does lower the field by about ~10% (max given with all electrodes 0.47 V/m and only used electrodes 0.521 V/m). This would be consistent with what I have found with other stimulations. The benefit is that although it does seem to change the magnitude of the electric field, the spatial distribution does not seem to change. So, if we were to target a specific value efield magnitude for a ROI, any optimization problem using the leadfield might be incorrect due to the lower magnitude of the leadfield processing. I wonder how to correct for this during any optimization, or maybe not necessary since it could be that the scale is similar no matter what stimulation is modeled. So maybe you could just correct in post optimal solution found. Do you think it is worth looking at the spherical model with a possible additional tissue representing the conductive paste compared to the one without the additional conductive paste tissue, to get a sense of the scale estimate? Thanks, Joel ________________________________ From: Axel Thielscher Sent: Wednesday, November 2, 2022 10:21 AM To: Joel Upston ; discuss at simnibs.org Subject: Re: [Simnibs-discuss] Differences in Efield depending on Processing You don't often get email from axelt at drcmr.dk. Learn why this is important [EXTERNAL] Hi Joel, a question for better understanding: When you set up the 2nd pathway, do you then model ALL electrodes of the EEG10-20 system, or only those which you actually need for the montage? I am asking because adding many well-conducting electrodes to the model will slightly increase the amount of current shunted through the scalp(+electrodes). Think of it as covering many parts of the scalp with well-conductive paste. We never quantified the size of this effect, but it will cause the leadfield e-fields in the brain to be consistently lower. Best regards, Axel On 19-10-2022 21:07, Joel Upston wrote: Hi there, I have noticed a systematic difference between the two different lines of simulating the same currents, electrodes and underlying dataset. One is through processing through the leadfield and using only the electrodes and currents as given and the other is through only modeling those electrodes and currents without the leadfield. Now the 2nd pathway (no leadfield) is giving higher E_mag than the leadfield version (~7-12%), the spatial maps look similar but just the intensity differences. I think it has to do with the scaling that is done after the solve by scaling the estimated current calibration error, which if I understand correctly isn't done in the leadfield processing. If this is the case I am trying to establish which would be more accurate to use in your view if I need a specific target value of (0.3 V/m for example). I have attached an image of a case where this is shown with the leadfield processed is on the left and the non-leadfield is on the right. I have tried this on about 5 different datasets and the pattern is consistent. Thanks, Joel _______________________________________________ Simnibs-discuss mailing list Simnibs-discuss at drcmr.dk https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -- Dr. Axel Thielscher Professor of Neurophysics and Neuroimaging Danish Research Center for Magnetic Resonance Copenhagen University Hospital Hvidovre DK-2650 Hvidovre, Denmark www.drcmr.dk & Department of Health Technology Technical University of Denmark DK-2800 Kgs. Lyngby http://www.healthtech.dtu.dk/ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot from 2022-11-15 11-55-21.png Type: image/png Size: 846900 bytes Desc: Screenshot from 2022-11-15 11-55-21.png URL: From oulap at drcmr.dk Wed Nov 16 11:49:40 2022 From: oulap at drcmr.dk (Oula Puonti) Date: Wed, 16 Nov 2022 11:49:40 +0100 Subject: [Simnibs-discuss] Focality with a specific threshold In-Reply-To: <747242290.8128668.1668505765449.JavaMail.zimbra@univ-grenoble-alpes.fr> References: <747242290.8128668.1668505765449.JavaMail.zimbra@univ-grenoble-alpes.fr> Message-ID: Hi Laurent, Please see here for the function that calculates the field_summary: https://github.com/simnibs/simnibs/blob/master/simnibs/msh/mesh_io.py#L2231 If you want to calculate a different percentile you can do this (in python): from simnibs.msh import mesh_io m = mesh_io.read_msh('ernie_TDCS_1_scalar.msh') #This produces volumes with 50%tile m.fields_summary(roi=2, percentiles=[50]) #This produces areas m.fields_summary(roi=1002, percentiles=[50]) Note that the output units differ between the two calls, for volumes it will be mm^3 and for areas it will be mm^2. This will depend on the roi you pass. roi=2 means that you calculate the volume of the tetrahedra where the field is higher than the %tile you define, whereas for roi=1002 calculates the area of the triangles the same way. Best, Oula On 11/15/22 10:49, LAURENT TORLAY wrote: > > Hello, > > First, I use Simnibs for several years and thank you for developping > such a software ! > My question : in the file fields_summary.txt, focality is measured by > 'area with a field >= X% of the 99.9th percentile', how can we get a > similar measurement with a specific threshold in V/m ? (moreover, why > the result is a volume ? The area is multiplied by a mean cortical > thickness (of the area, the whole brain ?) ) > Thanks in advance, > Best, > > L. Torlay > > > _______________________________________________ > 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 laurent.torlay at univ-grenoble-alpes.fr Mon Nov 21 09:58:57 2022 From: laurent.torlay at univ-grenoble-alpes.fr (LAURENT TORLAY) Date: Mon, 21 Nov 2022 09:58:57 +0100 (CET) Subject: [Simnibs-discuss] Focality with a specific threshold In-Reply-To: <747242290.8128668.1668505765449.JavaMail.zimbra@univ-grenoble-alpes.fr> References: <747242290.8128668.1668505765449.JavaMail.zimbra@univ-grenoble-alpes.fr> Message-ID: <771653242.16206316.1669021137166.JavaMail.zimbra@univ-grenoble-alpes.fr> I answer to myself if anyone search about the same question : You have to modify mesh_io.py in this way : line 2673 focality[i] = np.sum(weights[norm > c * peak_value]) -> replace by focality[i] = np.sum(weights[norm > c * your_threshold]) additionnaly, replace cuttofs by [100,100] in 'def get_focality' (line ) and 'def summary' (line 2677) L.T. [ https://www.univ-grenoble-alpes.fr/ | ] Laurent Torlay Ing?nieur - CNRS Bureau E 110 33 (0)4 76 74 81 38 [ http://www.univ-grenoble-alpes.fr/ | www.univ-grenoble-alpes.fr ] Rejoignez-nous sur [ https://www.facebook.com/UGrenobleAlpes/ | Facebook ] - Suivez-nous sur [ https://twitter.com/UGrenobleAlpes | Twitter ] [ https://zimbra.univ-grenoble-alpes.fr/zimbra/VARIABLE-URL | VARIABLE-URL ] De: "LAURENT TORLAY" ?: "discuss" Envoy?: Mardi 15 Novembre 2022 10:49:25 Objet: Focality with a specific threshold Hello, First, I use Simnibs for several years and thank you for developping such a software ! My question : in the file fields_summary.txt, focality is measured by 'area with a field >= X% of the 99.9th percentile', how can we get a similar measurement with a specific threshold in V/m ? (moreover, why the result is a volume ? The area is multiplied by a mean cortical thickness (of the area, the whole brain ?) ) Thanks in advance, Best, L. 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