External Email - Use Caution        

Dear Douglas,

Thank you for your reply.😊

I already ran the full recon-all and I got the results(label, mri, scripts, stats, surf, tmp, touch, trash).

But though I tried to get the mask of both brodmann area 4 and 6, I couldn't get the masks.

(404BA4a, 405BA4p, 406BA6)

The command lines are follows.

SHINui-iMac:dti_analysis_kings shinsangho$ mri_binarize --i nor82_pji/nor82_pji_fs/mri/aparc.a2009s+aseg.mgz --match 404 --o nor82_pji/nor82_pji_dlpfc/NOR82_PJI_LH_PREMOTOR.nii.gz

Even though I replaced aparc.a2009s+aseg.mgzn with any other atlases(aparc.DKTatlas+aseg.mgz, aparc+aseg.mgz...), I couldn't get the mask. Could you help me how to get the Brodmann area 4 & 6?

Best regards,

Sangho

=============

$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 404 --o nor82_pji/nor82_pji_dlpfc/NOR82_PJI_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_PREMOTOR.nii.gz

Binarizing based on matching values

nMatch 1

 0   404

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

========================

ᐧ

2019년 10월 7일 (월) 오후 4:20, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>님이 작성:

You can to run the full recon-all on a given subject's data, and it will create the broadmann areas

On 10/5/2019 1:31 AM, sang ho shin wrote:

        External Email - Use Caution        

Dear Freesurfer Developers,

I am trying to get the seed mask of premotor and motor cortex. Because I can't get it through 'recon-all -all', I tried to find brodmann area ('recon-all -s subjid -ba-labels')

But I received ERROR message. Can you tell me how to get Brodmann area through recon-all or freesurfer parcellation? And I appreciate if you can help me to solve this error message as follows,

=================================================================

sinsanghoui-MBP:~ shinsangho$ export SUBJECTS_DIR=~/freesurfer_subjects

sinsanghoui-MBP:~ shinsangho$ echo $SUBJECTS_DIR

sinsanghoui-MBP:~ shinsangho$ recon-all -s NOR82_PJI -i ~/DTI_analysis/nor82_pji_t1/coT1.nii -ba-labels

Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

INFO: SUBJECTS_DIR is /Users/shinsangho/freesurfer_subjects

Actual FREESURFER_HOME /Applications/freesurfer

Darwin sinsanghoui-MBP 15.6.0 Darwin Kernel Version 15.6.0: Thu Jun 23 18:25:34 PDT 2016; root:xnu-3248.60.10~1/RELEASE_X86_64 x86_64

/Users/shinsangho/freesurfer_subjects/NOR82_PJI

\n mri_convert /Users/shinsangho/DTI_analysis/nor82_pji_t1/coT1.nii /Users/shinsangho/freesurfer_subjects/NOR82_PJI/mri/orig/001.mgz \n

mri_convert.bin /Users/shinsangho/DTI_analysis/nor82_pji_t1/coT1.nii /Users/shinsangho/freesurfer_subjects/NOR82_PJI/mri/orig/001.mgz 

$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $

reading from /Users/shinsangho/DTI_analysis/nor82_pji_t1/coT1.nii...

TR=1670.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (0.000121244, -1, 0)

j_ras = (-0.0235518, -2.85817e-06, 0.999723)

k_ras = (0.999723, 0.000121211, 0.0235518)

writing to /Users/shinsangho/freesurfer_subjects/NOR82_PJI/mri/orig/001.mgz...

/Users/shinsangho/freesurfer_subjects/NOR82_PJI/label

#--------------------------------------------

#@# BA_exvivo Labels lh Fri Oct  4 17:43:23 BST 2019

\n mri_label2label --srcsubject fsaverage --srclabel /Users/shinsangho/freesurfer_subjects/fsaverage/label/lh.BA1_exvivo.label --trgsubject NOR82_PJI --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface \n

 

srclabel = /Users/shinsangho/freesurfer_subjects/fsaverage/label/lh.BA1_exvivo.label

srcsubject = fsaverage

trgsubject = NOR82_PJI

trglabel = ./lh.BA1_exvivo.label

regmethod = surface

 

srchemi = lh

trghemi = lh

trgsurface = white

srcsurfreg = sphere.reg

trgsurfreg = sphere.reg

usehash = 1

Use ProjAbs  = 0, 0

Use ProjFrac = 0, 0

DoPaint 0

 

SUBJECTS_DIR    /Users/shinsangho/freesurfer_subjects

FREESURFER_HOME /Applications/freesurfer

Loading source label.

Found 4129 points in source label.

MRISread(/Users/shinsangho/freesurfer_subjects/NOR82_PJI/surf/lh.white): could not open file

Starting surface-based mapping

Reading source registration 

 /Users/shinsangho/freesurfer_subjects/fsaverage/surf/lh.sphere.reg

Rescaling ...  original radius = 100

Reading target surface 

 /Users/shinsangho/freesurfer_subjects/NOR82_PJI/surf/lh.white

No such file or directory

ERROR: could not read /Users/shinsangho/freesurfer_subjects/NOR82_PJI/surf/lh.white

Darwin sinsanghoui-MBP 15.6.0 Darwin Kernel Version 15.6.0: Thu Jun 23 18:25:34 PDT 2016; root:xnu-3248.60.10~1/RELEASE_X86_64 x86_64

 

recon-all -s NOR82_PJI exited with ERRORS at Fri Oct  4 17:43:25 BST 2019

 

For more details, see the log file /Users/shinsangho/freesurfer_subjects/NOR82_PJI/scripts/recon-all.log

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

==================================================

Best wishes,

Sangho

 

ᐧ

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