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_data > <http://20170720_LHS.MR>.HEAD_
>
>
> After 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
CNIR_IBS.0017.0001.2017.07.20. 16.26.07.667681.198987303.IMA
> –subject $SUBJECTS_DIR/sbj1_rec -all
>
>
> (My subjects' data is *.IMA format. Filenames are like
> "20170720_LHS.MR_HEAR_CNIR_IBS.0017.0001......198987303. > <http://20170720_LHS.MR>.HEAD_IMA". I don't
> think I need to convert IMA format to another, right? Each subject has
> 192 IMA files and I want to apply recon-all to all of these files.)
>
> When I run these commands, I get a messages like:
>
> -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c --------
>
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>
> FREESURFER_HOME /Applications/freesurfer
>
> FSFAST_HOME /Applications/freesurfer/fsfast
>
> FSF_OUTPUT_FORMAT nii.gz
>
> SUBJECTS_DIR /Applications/freesurfer/subjects
>
> MNI_DIR /Applications/freesurfer/mni
>
> Yeseului-MacBook-Pro:~ yeseulkim$
>
> 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
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
>
>
_________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/ freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/ greve/
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