when you look in the label file, do you see lh.BA1_exvivo.label lh.BA2_exvivo.label lh.BA3a_exvivo.label lh.BA3b_exvivo.label lh.BA44_exvivo.label lh.BA45_exvivo.label lh.BA4a_exvivo.label lh.BA4p_exvivo.label lh.BA6_exvivo.label
On 10/7/2019 11:50 AM, sang ho shin wrote:
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Dear Douglas,
Thank you for your reply.đ 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
========================
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2019ë 10ě 7ěź (ě) ě¤í 4:20, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu>ëě´ ěěą: 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
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