It works now! Thank you :)
On 15 August 2017 at 03:30, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > 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 > > > > > > 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 > > <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 > > > > > > _______________________________________________ > > 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 > gr...@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/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > -- Yeseul Kim Visual Cognitive Neuroscience Lab Department of Psychology Korea University Seoul, Korea
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