Try using 1024 (precentral) and 1022 (postcentral) with the aparc
On 10/3/2019 3:11 AM, sang ho shin wrote:
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Dear Freesurfer Developers,
I have analyzed connectivity between striatum and different brain cortex with diffusion weighted MRI. I completed recon-all on all participants. SHINui-iMac:~ shinsangho$ recon-all -s NOR86_AHJ -i ~/sangho/NOR86_AHJ/NOR86_AHJ_T1/coT1.nii –all
And I processed to get seed mask of DLPFC as follows and got the mask. SHINui-iMac:nor86_ahj shinsangho$ mri_binarize --i nor86_ahj_fs/mri/aparc+aseg.mgz --match 1027 --o nor86_ahj_dlpfc/nor86_ahj_rostalmiddlefrontal.nii.gz
However, I can't get the mask of both premotor and motor cortex. According to FreeSurferColorLUT, matching numbers are as follows,
Premotor - 9002 ctx_lh_premotor, 9502 ctx_rh_premotor Primotor - 9001 ctx_lh_primary motor, 9501 ctx_rh_primary motor
While I put any other mgz files(ex, aparc.a2009s+aseg.mgz, aparc.DKTatlas+aseg.mgz..) in mri folder instead of aparc+aseg.mgz, I was not able to get the mask.
The command lines and results are as follows,
SHINui-iMac:dti_analysis_kings shinsangho$ mri_binarize --i nor82_pji/nor82_pji_fs/mri/aparc.a2009s+aseg.mgz --match 9002 --o nor82_pji/nor82_pji_dlpfc/NOR82_PJI_LH_PREMOTOR.nii.gz
$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /Users/shinsangho/sangho/DTI_analysis_kings
cmdline mri_binarize.bin --i nor82_pji/nor82_pji_fs/mri/aparc.a2009s+aseg.mgz --match 9002 --o nor82_pji/nor82_pji_dlpfc/NOR82_PJI_LH_PREMOTOR.nii.gz
sysname Darwin
hostname SHINui-iMac.local
machine x86_64
user shinsangho
input nor82_pji/nor82_pji_fs/mri/aparc.a2009s+aseg.mgz
frame 0
nErode3d 0
nErode2d 0
output nor82_pji/nor82_pji_dlpfc/NOR82_PJI_LH_PREMOTOR.nii.gz
Binarizing based on matching values
nMatch 1
0 9002
binval 1
binvalnot 0
fstart = 0, fend = 0, nframes = 1
Found 0 values in range
Counting number of voxels in first frame
Found 0 voxels in final mask
Count: 0 0.000000 16777216 0.000000
mri_binarize done
Can you tell me how to get the mask of premotor cortex and primary motor cortex?
I am looking forward to your help.
Best wishes,
Sangho
[https://mailfoogae.appspot.com/t?sender=aaGFwcHlzYXJhbTIwQGdtYWlsLmNvbQ%3D%3...
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