[Simnibs-discuss] coil positioning in simnibs 3.2.6
Grace Hallenbeck
geh261 at nyu.edu
Tue Apr 26 17:21:39 CEST 2022
Hi Axel,
Wonderful!! Thank you so very much for confirming this. We are working on
setting up a protocol and instructions for younger lab members on how to
use simnibs and I can now include a note about this. We thank you immensely
for not only answering the above q, but for all of the work you and the
team have put in to bring simnibs to the world.
Cheers!
Grace
On Tue, Apr 26, 2022 at 4:11 AM Axel Thielscher <axelt at drcmr.dk> wrote:
> Hi Grace,
>
> the two files are indeed identical, unless you specify something else
> using the -d option.
>
> The qform and sform of the T1fs_conform just are set to the same, which
> then likely causes AFNI to select TLRC.
>
> Best regards,
>
> Axel
>
>
> On 25-04-2022 21:37, Grace Hallenbeck wrote:
>
> Hi Annalisa,
>
> Thanks for your reply. We have made progress on the translation matrix
> cited above, but currently we have a more pressing question.
>
> The file output from a successful headreco, T1fs_conform.nii, appears to
> be identical to our input T1, though from the simnibs website, "The head
> meshing procedures create a NifTI file called m2m_*subID*
> /T1fs_conform.nii.gz. This file contains a transformed T1 image of the
> subject, with the world coordinates used by SimNIBS."
>
> However, the voxel orientations and resolutions are identical (per 3dinfo
> from afni), with one exception: the template space of the conform file is
> TLRC while that of the original T1 is ORIG. So, my questions are the
> following:
>
> 1. Should these files be identical?
> 2. Why is the template space of the conform file TLRC?
>
> copy/pasting header info here for clarity:
>
> INPUT T1
>
> (base) darkphoenix:/home/grace/simnibs_simulation_GH5/subject_volumes
> grace> 3dinfo T1.nii
>
> ++ 3dinfo: AFNI version=AFNI_16.2.09 (Aug 6 2016) [64-bit]
>
>
> Dataset File: T1.nii
>
> Identifier Code: NII_Hd_qtnnMonBYdt6jsb2XWw Creation Date: Fri Aug 31
> 11:14:18 2018
>
> Template Space: ORIG
>
> Dataset Type: Anat Bucket (-abuc)
>
> Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
>
> Storage Mode: NIFTI
>
> Storage Space: 32,768,000 (33 million [mega]) bytes
>
> Geometry String:
> "MATRIX(0.8,0,0,-128.1,0,0,-0.8,128.1,0,-0.8,0,128.1):320,320,320"
>
> Data Axes Tilt: Plumb
>
> Data Axes Orientation:
>
> first (x) = Right-to-Left
>
> second (y) = Superior-to-Inferior
>
> third (z) = Posterior-to-Anterior [-orient RSP]
>
> R-to-L extent: -128.100 [R] -to- 127.100 [L] -step- 0.800 mm [320
> voxels]
>
> A-to-P extent: -127.100 [A] -to- 128.100 [P] -step- 0.800 mm [320
> voxels]
>
> I-to-S extent: -127.100 [I] -to- 128.100 [S] -step- 0.800 mm [320
> voxels]
>
> Number of values stored at each pixel = 1
>
> -- At sub-brick #0 '?' datum type is byte: 0 to 255
>
> T1fs_conform
>
> (base) darkphoenix:/home/grace/simnibs_simulation_GH5/subject_volumes
> grace> 3dinfo T1fs_conform.nii
>
> ++ 3dinfo: AFNI version=AFNI_16.2.09 (Aug 6 2016) [64-bit]
>
> ** AFNI converts NIFTI_datatype=512 (UINT16) in file T1fs_conform.nii to
> FLOAT32
>
> Warnings of this type will be muted for this session.
>
> Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
>
>
> Dataset File: T1fs_conform.nii
>
> Identifier Code: NII_BDbiP8aLlBK7bpodSIpPwA Creation Date: Mon Apr 25
> 15:30:40 2022
>
> Template Space: TLRC
>
> Dataset Type: Anat Bucket (-abuc)
>
> Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
>
> Storage Mode: NIFTI
>
> Storage Space: 131,072,000 (131 million [mega]) bytes
>
> Geometry String:
> "MATRIX(0.8,0,0,-128.1,0,0,-0.8,128.1,0,-0.8,0,128.1):320,320,320"
>
> Data Axes Tilt: Plumb
>
> Data Axes Orientation:
>
> first (x) = Right-to-Left
>
> second (y) = Superior-to-Inferior
>
> third (z) = Posterior-to-Anterior [-orient RSP]
>
> R-to-L extent: -128.100 [R] -to- 127.100 [L] -step- 0.800 mm [320
> voxels]
>
> A-to-P extent: -127.100 [A] -to- 128.100 [P] -step- 0.800 mm [320
> voxels]
>
> I-to-S extent: -127.100 [I] -to- 128.100 [S] -step- 0.800 mm [320
> voxels]
>
> Number of values stored at each pixel = 1
>
> -- At sub-brick #0 '?' datum type is float
>
> Thanks very much for your help!
>
> Sincerely,
>
> Grace
>
> On Tue, Apr 19, 2022 at 6:16 AM Annalisa Schuler <
> annalisa.schuler at hsancamillo.it> wrote:
>
>> Dear all,
>>
>> are you using neuronavigation for your project, if yes you should get a
>> matrix including coil position, translation and orientation from your
>> stimulation session, which allows you to calculate exact positions using
>> matsimnibs (
>> https://simnibs.github.io/simnibs/build/html/documentation/sim_struct/position.html
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__simnibs.github.io_simnibs_build_html_documentation_sim-5Fstruct_position.html&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=hlYoGF-M-jRATsmPq_apB2jsYCrtnhaxmOo1DPoxuno&e=>
>> ).
>>
>> All the best,
>>
>> AL
>>
>> *Annalisa Schuler*
>> Ricercatrice Psicologa
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>>
>> ------------------------------
>> *Da: *"Clayton E Curtis" <clayton.curtis at nyu.edu>
>> *A: *"Grace Hallenbeck" <geh261 at nyu.edu>
>> *Cc: *"discuss at simnibs.org" <discuss at simnibs.org>
>> *Inviato: *Venerdì, 15 aprile 2022 19:12:59
>> *Oggetto: *Re: [Simnibs-discuss] coil positioning in simnibs 3.2.6
>>
>> Hi,
>> I just wanted to add a couple of details here. We are using Brainsight
>> to acquire the Coil Position, and that looks spot on. But we are interested
>> in correctly orienting the coil before running the model. The documentation
>> was rather sparse here.
>>
>> Also, Grace is alluding the fact that when we make changes to the
>> Reference Coordinates, it makes changes to the Coil Position. Not sure
>> what this is about?
>>
>> Thanks for your help!
>>
>> /cc
>>
>> On Fri, Apr 15, 2022 at 12:48 PM Grace Hallenbeck <geh261 at nyu.edu> wrote:
>>
>>> Dear simnibs crew,
>>> Hello! My name is Grace Hallenbeck and I'm a post-doc working with Clay
>>> Curtis (cc'ed here) at NYU. We're interested in using simnibs to model the
>>> effects of TMS and today we've been trying to correctly position the coil
>>> orientation in the simnibs gui but are having some difficulty.
>>>
>>> We have a coordinate of interest that we're plugging in for the x,y,z
>>> 'Position' fields. But we're unclear on the best way to work with the
>>> 'Direction Reference' coordinates, which is what we think controls the coil
>>> orientation. In the screenshot below, I've plugged in the same x,y,z coords
>>> as in 'Position', but this has the coil handle (as I understand, 180 deg
>>> opposite the green line) pointing slightly off the coil orientation we
>>> actually applied TMS at with this subject (what we are attempting to
>>> model).
>>>
>>> So our question is: how can we finely modulate the coil orientation,
>>> keeping the 'Position' x,y,z coords constant? We would greatly appreciate
>>> any help on this as we're getting a publication ready and hope to include
>>> some modeling results.
>>> [image: Screen Shot 2022-04-15 at 12.32.29 PM.png]
>>>
>>> All the best & thanks for your work,
>>> Grace Hallenbeck
>>>
>>
>> _______________________________________________
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>> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss
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>>
>
> _______________________________________________
> Simnibs-discuss mailing listSimnibs-discuss at drcmr.dkhttps://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss <https://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.drcmr.dk_mailman_listinfo_simnibs-2Ddiscuss&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=TilFEc3dmbkVu85iQtGYtRln6F-wp_0E42GGp3pyMAsoDDJV8Iki3W6sDdqGiQZk&s=KAH5UaWKhHK6O-_kvXWhmw6pE88SJ4H7rAMP2A_EwbE&e=>
>
> --
> Dr. Axel Thielscher
> Professor of Neurophysics and Neuroimaging
> Danish Research Center for Magnetic Resonance
> Copenhagen University Hospital Hvidovre
> DK-2650 Hvidovre, Denmarkwww.drcmr.dk <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.drcmr.dk&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=TilFEc3dmbkVu85iQtGYtRln6F-wp_0E42GGp3pyMAsoDDJV8Iki3W6sDdqGiQZk&s=y-8OqGfp5QNYyd4Z-vICXp4-YKY5U5G0nPHvB2FWBdc&e=>
> &
> Department of Health Technology
> Technical University of Denmark
> DK-2800 Kgs. Lyngbyhttp://www.healthtech.dtu.dk/ <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.healthtech.dtu.dk_&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=TilFEc3dmbkVu85iQtGYtRln6F-wp_0E42GGp3pyMAsoDDJV8Iki3W6sDdqGiQZk&s=0__DQITmG8VYJwqHpTIbjBxmsjxxXgoPyEWPfVlWG6s&e=>
>
>
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