On Thu, Oct 18, 2018 at 7:47 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

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 <fischl@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 <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
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> >
> >
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