Hi Isil, this issue might resolve itself once the executable permissions are
taken care of, but if not, it's possible it's related to the dicom input. If
you're still getting the error, can you run recon-all with the -debug flag and
send us the output?
best,
Andrew
On 1/22/19, 11:23 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Bruce Fischl" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
fis...@nmr.mgh.harvard.edu> wrote:
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 <fis...@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
>
>
>
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