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 <fischl@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
>
>
>
>
>
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