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:
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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 > > > > > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer