first, run it with -subject sbj1_rec (ie, don't give it the full path). There is something wrong with the dash before the "i". It looks like a dash, but it is really something else. Did you cut and paste it from somewhere? At the command line, Try deleting it and typing a dash.
On 08/14/2017 12:30 PM, Yeseul Kim wrote:
Hi
I'm beginner of freesurfer and have an error while using recon-all. I'm Mac (Sierra) user.
My subject's data is under:
/Applications/freesurfer/subjects/yeseul_dataAfter open terminal, I put commands like:
export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh export SUBJECTS_DIR=/Applications/freesurfer/subjects/yeseul_data/sbj1 recon-all –i $SUBJECTS_DIR/20170720_LHS.MR <http://20170720_LHS.MR>.HEAD_CNIR_IBS.0017.0001.2017.07.20.16.26.07.667681.198987303.IMA –subject $SUBJECTS_DIR/sbj1_rec -all(My subjects' data is *.IMA format. Filenames are like "20170720_LHS.MR_HEAR_CNIR_IBS.0017.0001......198987303.IMA". I don't think I need to convert IMA format to another, right? Each subject has 192 IMA files and I want to apply recon-all to all of these files.)
When I run these commands, I get a messages like:
-------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
Yeseului-MacBook-Pro:~ yeseulkim$
Yeseului-MacBook-Pro:~ yeseulkim$ export SUBJECTS_DIR=/Applications/freesurfer/subjects/yeseul_data/sbj1
Yeseului-MacBook-Pro:~ yeseulkim$
Yeseului-MacBook-Pro:~ yeseulkim$ recon-all –i $SUBJECTS_DIR/20170720_LHS.MR http://20170720_LHS.MR.HEAD_CNIR_IBS.0017.0001.2017.07.20.16.26.07.667681.198987303 –subject $SUBJECTS_DIR/sbj1_rec -all
ERROR: Flag i unrecognized.
i /Applications/freesurfer/subjects/yeseul_data/sbj1/20170720_LHS.MR.HEAD_CNIR_IBS.0017.0001.2017.07.20.16.26.07.667681.198987303 subject /Applications/freesurfer/subjects/yeseul_data/sbj1/sbj1_rec -all
Darwin Yeseului-MacBook-Pro.local 16.7.0 Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64
recon-all -s exited with ERRORS at Tue Aug 15 01:08:53 KST 2017
For more details, see the log file
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Does it matter with the format of my data files? Or did I set variables incorrectly? Thank you in advance!
Best wishes, Yeseul -- Yeseul Kim Visual Cognitive Neuroscience Lab Department of Psychology Korea University Seoul, Korea
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