Subject directory is defined. Try running export SUBJECTS_DIR=$PWD and then run tkmedit command. That might work.

Kind regards,

Sam

On Mon, Apr 17, 2017 at 8:12 PM, David Semanek SemanekD@nyspi.columbia.edu wrote:

In my experience, OSX has weird issues with things in system and Application directories. My guess would be your files have inherited some permission flags from the Linux environment and OSX is having trouble making them properly available.

The first thing I would try would be to copy them to a location in your User directory. I use a folder conveniently called ~/MRI/FS_Subject_Folders/[study_name] for all my freesurfer work and then just edit the SetUpFreeSurfer.sh file to change my SUBJECTS_DIR for my current project.

If Freesurfer (and Finder) still can’t see them there, you could try copying them again from your Linux box using the cp --no-preserve=mode to copy just the files without any inherited permissions and see if that works. I’ve personally never needed to do that bringing files over from Linux so I’m not totally sure what the outcome would be but that’s my first thought.

Best,

David P. Semanek, HCISPP

Research Technician, Posner Lab

Division of Child and Adolescent Psychiatry

Columbia University Medical Center

New York State Psychiatric Institute

1051 Riverside Drive, Pardes Bldg. Rm. 2424

New York, NY 10032

PH: (646) 774-5885

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*From: *Damien MARIE damien.marie@unige.ch *Date: *Saturday, April 15, 2017 at 9:21 AM *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] ERROR

Hi,

I ran recon-all on a server where Ubuntu is running.

Recently I installed separately freesurfer on a macbook, it is working (e.g. tkmedit bert), I moved my processed subjects to freesurfer/subjects on the macbook but I can not work with them. I have the below error. I changed the permission to 777, it is still not working. Now what is really strange is that, using the finder I do not see the files in freesurfer/subjects but by doing ls -l in a terminal, I can see them…

Please note that SUBJECT_DIR is defined.

Any idea is welcome.

Thank you and best,

Damiens-MacBook-Pro-2:subjects dmarie2$ tkmedit hires_ct_pp1_N4_bet_MP2RAGEcorr/ brainmask.mgz -aux T1.mgz

ERROR: cannot find subject hires_ct_pp1_N4_bet_MP2RAGEcorr/ in /Applications/freesurfer/subjects or it is not readable by you

*Damien *

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