meaning you have to give recon-all the -all switch so it can create
things like the lh.white surface
cheers
Bruce
On Mon, 7 Oct 2019, Greve, Douglas N.,Ph.D.
wrote:
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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211-186d-4ed5-bb8d-ba24e6e1b044] ᐧ
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