Re: [Freesurfer] niiWrite(): error opening file tmp.nii

Hi Konstantina, you have to set SUBJECTS_DIR equal to an actual directory path in your filesystem, the “<path to subject directory>” is just a placeholder. Best, Andrew

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Konstantina Skolariki konstantinaskol@outlook.com Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Monday, July 9, 2018 at 10:30 AM To: FS Help freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] niiWrite(): error opening file tmp.nii

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Hi Bruce,

I managed to overcome said error but now during example 2 another error pops up.

Skol-MacBook-Pro:~ kskol$ export SUBJECTS_DIR=<path to subject directory>

-bash: syntax error near unexpected token `newline'

Thanks,

Konstantina

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: 09 July 2018 17:17 To: Freesurfer support list Subject: Re: [Freesurfer] niiWrite(): error opening file tmp.nii

Hi Konstantina

do you have write access to the partition you are putting the subjects_dir on? And can you please send us the full command line, screen output and recon-all.log?

cheers Bruce

On Mon, 9 Jul 2018, Konstantina Skolariki wrote:

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Hi FreeSurfer Developers, I have downloaded freesurfer on my mac and after "setup & configuration” I tried to perform example 1 from "test your FreeSurfer Installation”. However when I type the command, this error message shows up:

$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from sample-001.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to tmp.nii... niiWrite(): error opening file tmp.nii ERROR: failure writing tmp.nii

Thanks, Konstantina