It works now! Thank you :)

On 15 August 2017 at 03:30, Douglas N Greve greve@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

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-- 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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