Hi Rosalia
-i must point to a file that you want to import, usually a single dicom
file in the correct (e.g. mprage) series.
cheers
Bruce
On Thu, 18 Oct 2018, Rosalia
Dacosta Aguayo wrote:
External Email - Use Caution
Hi Bruce,
There is not recon-all.log.
The full command line is:
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $ recon-all -sd
~/Desktop/MS_STUDY/subjects -s 001 -i
/home/rosalia/Desktop/MS_STUDY/subjects/MS001/mri -autorecon1
ERROR: You cannot give recon-all a folder as input. It must be an image file.
If you have multiple files, you need multiple -i flags.
Linux rosalia-Lenovo-Y520-15IKBN 4.10.0-40-generic #44~16.04.1-Ubuntu SMP Thu
Nov 9 15:37:44 UTC
2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 001 exited with ERRORS at Thu 18 Oct 19:13:35 CEST 2018
For more details, see the log file
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $
On Thu, Oct 18, 2018 at 7:11 PM Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
Hi Rosalia
can you send us the full command line, screen output and recon-all.log?
In the arrangement you show below it would be:
recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -i <path to dicom file>
-all
cheers
Bruce
On Thu, 18 Oct 2018, Rosalia
Dacosta Aguayo wrote:
>
> External Email - Use Caution
>
> Hi Bruce,
>
> Thank you very much for answering my questions.
> This is how I have organized my subject_dir for one subject so you can
see better. It
is still not
> working.
> rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $ ls
> FOLDERS S_011.nii.gz S_020.nii.gz S_028.nii.gz S_041.nii.gz
> MS001 S_012.nii.gz S_021.nii.gz S_029.nii.gz S_042.nii.gz
> S_004.nii.gz S_013.nii.gz S_022.nii.gz S_030.nii.gz S_043.nii.gz
> S_005.nii.gz S_014.nii.gz S_023.nii.gz S_031.nii.gz S_044.nii.gz
> S_006.nii.gz S_015.nii.gz S_024.nii.gz S_032.nii.gz S_045.nii.gz
> S_008.nii.gz S_016.nii.gz S_025.nii.gz S_033.nii.gz S_046.nii.gz
> S_009.nii.gz S_017.nii.gz S_026.nii.gz S_034.nii.gz S_047.nii.gz
> S_010.nii.gz S_018.nii.gz S_027.nii.gz S_040.nii.gz SCRIPTS
> rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $ cd
MS001/
> rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001 $
ls
> mri orig
> rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001 $
cd mri/
> rosalia@rosalia-Lenovo-Y520-15IKBN
~/Desktop/MS_STUDY/subjects/MS001/mri $ ls
> 001.nii.gz
> rosalia@rosalia-Lenovo-Y520-15IKBN
~/Desktop/MS_STUDY/subjects/MS001/mri $ cd
> ..rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001
$ cd orig
> rosalia@rosalia-Lenovo-Y520-15IKBN
~/Desktop/MS_STUDY/subjects/MS001/orig $ ls
> 001.nii.gz
> rosalia@rosalia-Lenovo-Y520-15IKBN
~/Desktop/MS_STUDY/subjects/MS001/orig $
>
> Regards,
> Rosalia
>
> On Thu, Oct 18, 2018 at 6:55 PM Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
> Hi Rosalia
>
> you either need to give recon-all an input file (or more than
one) with the
> -i switch, or create the subject directory tree under
SUBJECTS_DIR for that
> subject, and put a file named 001.mgz in the mri/orig subdir.
Note you can
> also specify SUBJECTS_DIR explicitly on the recon-all command
line with -sd
<dir>
> if you don't want to put it in the environment.
>
> That is, try this:
>
> recon-all -s 001 -autorecon1 -sd ~/Desktop/subjects
>
> cheers
> Bruce
>
> On Thu, 18 Oct 2018, Rosalia Dacosta Aguayo wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear Free Surfer team,
> >
> > Surely this is a basic question but I am having a trouble
setting the
subjects_dir in
> my terminal
> > and, as a result, any of the commands work.
> >
> > This is how I have my Free Surfer configurated in my computer:
> >
> > --------
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
> > Setting up environment for FreeSurfer/FS-FAST (and FSL)
> > FREESURFER_HOME /usr/local/freesurfer
> > FSFAST_HOME /usr/local/freesurfer/fsfast
> > FSF_OUTPUT_FORMAT nii.gz
> > SUBJECTS_DIR /usr/local/freesurfer/subjects
> > MNI_DIR /usr/local/freesurfer/mni
> > FSL_DIR /usr/share/fsl/5.0
>
>-------------------------------------------------------------------------------------------------
--
>
> > -----
> >
> > As it is, I cannot work in the SUBJECTS_DIR, as it is protected.
> > I tried to set a new subjects_dir:
> > export SUBJECTS_DIR=/home/rosalia/Desktop
> >
> > Then I try to run the first step (autorecon1) with one subject,
and it appears
the
> following error:
> > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/subjects $
recon-all -s 001
-autorecon1
> > ERROR: cannot find /usr/local/freesurfer/subjects/001
> > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/subjects $
> >
> > I have even changed my .bashrc file...but it seems I am doing
something wrong
as my
> terminal keeps
> > pointing to the same subject_dir.
> > I have tried to use sudo so in order to move my folder and
subfolders to the
> subjects_dir set by
> > default, and I am experiencing problems as well.
> >
> > I would much appreciate any help with this basic question.
> > Kind regards,
> > Rosalia
> >
> >
> >
> >
> >
> >_______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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