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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