[Simnibs-discuss] coil positioning in simnibs 3.2.6
Grace Hallenbeck
geh261 at nyu.edu
Mon Apr 25 21:37:12 CEST 2022
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
> _______________________________________________
> *SAN CAMILLO IRCCS S.R.L. società unipersonale*
> soggetta a direzione e coordinamento da parte della
> Fondazione Villa Salus
> Via Alberoni, 70 - 30126 Venezia - Lido
> P.IVA e C.F. 04554270274 - Codice SDI: T04ZHR3
>
>
> *Certificazione UNI EN ISO 9001:2015* Certificato SGQ 5010016444 emesso
> da TUV SUD Italia
>
> *Laboratorio di Imaging Clinico e Stimolazione*
>
> Sito web
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__hsancamillo.it_&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=n7WrKbPtiB6T0x_y37Fmp6LflxWHPketwsV8lhgBvnc&e=>
> | Facebook
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.facebook.com_SanCamilloIRCCS&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=8yayA4Zr6-zDVlz5EXiQU6dbWv8kwh2opI5qhf6nQ4A&e=>
> | Linkedin
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.linkedin.com_company_san-2Dcamillo-2Dirccs&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=MZSfKGfVvtq97KLPP2EEhBcCTZI3HlBavqLi2mkM0Zw&e=>
> | Twitter
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_SanCamilloIRCCS&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=81zmg2aVNdMorLXTwO7exfqWC_MIwZiGlqWOBdx40c0&e=> |
> Instagram
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.instagram.com_irccssancamillo_&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=MZqznf8r5k9Gxtz2IU0Cc0DEBhVgeKeGiE6B4SO2p_0&e=>
> [image: San Camillo IRCCS]
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__hsancamillo.it&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=CIYDpmlDD17OMI-6_fbAAXJJrT1lO7mpXWEoum-BN8I&e=>
>
> [image: 5x1000 al San Camillo Onlus]
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__hsancamillo.it_5x1000&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=wBw6kgoykSkkYXdHiOIBs_hvP1kQL0rnA1sqinrb5oQ&e=>
>
> ------------------------------
> *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
>>
>
> _______________________________________________
> 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: <https://mailman.drcmr.dk/pipermail/simnibs-discuss/attachments/20220425/d3c13da3/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screen Shot 2022-04-15 at 12.32.29 PM.png
Type: image/png
Size: 964741 bytes
Desc: not available
URL: <https://mailman.drcmr.dk/pipermail/simnibs-discuss/attachments/20220425/d3c13da3/attachment-0001.png>
More information about the Simnibs-discuss
mailing list