Dear Bruce,

thank you very much for replying promptly. Here are the commands they I use and the error messages that I get.

export SUBJECTS_DIR=/storage/shared/research/cinn/2017/SEMLRN/Data/Participant10/fMRIData/StructuralSegment

export FREESURFER_HOME='/usr/share/freesurfer'

source $FREESURFER_HOME/FreeSurferEnv.sh

recon-all -i /storage/shared/research/cinn/2017/SEMLRN/Data/Participant10/fMRIData/StructuralSegment/1.3.12.2.1107.5.2.43.167013.2017120817330360897940188.0.0.0_0001_000001_1512762943b783.dcm -autorecon1 -subjid 10

if: Expression Syntax.

$FREESURFER_HOME/bin/mri_convert /storage/shared/research/cinn/2017/SEMLRN/Data/Participant10/fMRIData/StructuralSegment/sSEMLRN10-0001-00001-000128-01.nii

bash: /usr/share/freesurfer/bin/mri_convert: Permission denied

I guess the second is more to be solved with IT, but I cannot understand the reason for the first error, so I would really appreciate if you could suggest a solution please.

Thank you very much for the help in advance

Isil

On Sat, Jan 19, 2019 at 8:04 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Isil

can you send us the full command line and screen output of the commands
you ran?

cheers
Bruce
On Sat, 19 Jan 2019, Isil Bilgin wrote:

>
> External Email - Use Caution
>
> Dear All,
>
> I want to convert my .nii structural file to .mgz file. I tried using mri_convert however I got a permission denied
> message. Since I am not the administrator in the system, hence I cannot change the permissions at the moment, so I
> guess I will have to wait for IT to help me soon.
>
> Instead, I wanted to try recon-all -i STRUCT_FOLDER1/xxx.dcm -i STRUCT_FOLDER2/xxx.dcm -autorecon1 -subjid 10
> [/bash] command. However, I am getting an "if: Expression Syntax" error. So I am not sure why might be the cause
> for that, though. So I might really appreciate your helps please.
>
>
> I am using 4.4.0-139-generic #165-Ubuntu SMP Wed Oct 24 10:58:50 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux and bash.
>
> I found a similar discussion from the archive
> (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-September/025691.html) but there was no agreed solution
> I guess. So I wonder if there is any other way of converting the structural nii file to .mgz until these problems
> are solved?
>
> Thank you very much for the help in advance
>
> Kind regards
>
> Isil
>
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