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