[Simnibs-discuss] coil positioning in simnibs 3.2.6
Axel Thielscher
axelt at drcmr.dk
Tue Apr 26 10:11:40 CEST 2022
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 (Aug6 2016) [64-bit]
>
>
> Dataset File:T1.nii
>
> Identifier Code: NII_Hd_qtnnMonBYdt6jsb2XWwCreation 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 (Aug6 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_BDbiP8aLlBK7bpodSIpPwACreation 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.
> Screen Shot 2022-04-15 at 12.32.29 PM.png
>
> All the best & thanks for your work,
> Grace Hallenbeck
>
>
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--
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/
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