Re: [Freesurfer] Freesurfer Digest, Vol 199, Issue 42 - Problem running infant FreeSurfer - failure to create symbolic link

External Email - Use Caution

Hi Tim,

You're right, that was the issue - local computer running Ubuntu and a Windows server.

Thanks very much! --

Fleur Warton

Postdoctoral Research Fellow Division of Biomedical Engineering Faculty of Health Sciences University of Cape Town

On Mon, Sep 21, 2020 at 6:00 PM freesurfer-request@nmr.mgh.harvard.edu wrote:

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Today's Topics:

1. Problem running infant FreeSurfer - failure to create symbolic link (Fleur Warton)
2. Re: Problem running infant FreeSurfer - failure to create symbolic link (Tim Sch?fer)
3. Re: Viewing labels in freeview (Wang, Ruopeng)
4. Re: Masking surface overlays and spatial correlations (Douglas N. Greve)
5. Re: Functional connectivity preprocessing and seed analysis (Douglas N. Greve)
6. Re: recon-all 7.1.1 (James Hartzell)
7. Re: Functional connectivity preprocessing and seed analysis (Wenzhen Zhao)
8. Re: Functional connectivity preprocessing and seed analysis (Douglas N. Greve)

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Message: 1 Date: Mon, 21 Sep 2020 11:51:53 +0200 From: Fleur Warton fleur.warton@gmail.com Subject: [Freesurfer] Problem running infant FreeSurfer - failure to create symbolic link To: freesurfer@nmr.mgh.harvard.edu Message-ID: <CANGE1NGZK2QiKjwFBzVP4-wyyB6GoD= HkzKdGwc_8_+KWNf1Xw@mail.gmail.com> Content-Type: text/plain; charset="utf-8"

    External Email - Use Caution

Hi FreeSurfer team,

I'm trying to run the infant freesurfer (version: freesurfer-infant-20200205 ) and get the following error:

ln: failed to create symbolic link 'brain.nii.gz': Operation not supported

The command I used was:

infant_recon_all --s 002B --age 0

I think this may have to do with the fact that my subjects_dir is located on a server (not the computer I'm running FreeSurfer on), since when I ran the command with the subjects_dir located on my local computer it ran fine and completed without errors. Unfortunately for space reasons it isn't possible for me to do that for my entire dataset.

Thanks,

Fleur

Fleur Warton