7 Oct
2019
7 Oct
'19
11:37 a.m.
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[t?sender=aaGFwcHlzYXJhbTIwQGdtYWlsLmNvbQ%3D%3D&type=zerocontent&guid=f5c48 211-186d-4ed5-bb8d-ba24e6e1b044] ᐧ
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