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
