Hi Isil
I'll leave it to someone else to answer the first quesion, but if mri_convert is not executable I can't understand how recon-all can run at all, so you should probably get someone with root access to fix that first
cheers Bruce
On Sat, 19 Jan 2019, Isil Bilgin wrote:
External Email - Use Caution
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/1.3.12.2.1107.5.2.43.16701 3.2017120817330360897940188.0.0.0_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/sSEMLRN10-0001-00001-00012 8-01.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 > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer