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.
