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/1.3.12.2.1107.5.2.43.167013.2017120817330360897940188.0.0.0_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 CautionDear 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...) 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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