On Thu, Oct 18, 2018 at 7:56 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

yes, you can do that. If you run recon-all through the skill stripping,
then replace the brainmask.mgz with yours generated by bet, we should
detect that and retain it for further processing

cheers
Bruce
On Thu, 18 Oct 2018,
Rosalia Dacosta Aguayo wrote:

>
>         External Email - Use Caution
>
> Yes, you are right. I saw the error.
> I have been running one of the participants and here it is the report.log.
> Also, because these kind of participants are special, I used some bet parameters to run the
> skull-stripping. This is the main reason why I did not run recon all -all. I would like to replace
> the skull stripped image by my betted one. Is this right?
> Thanks,
> Rosalia
>
> 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
> > > >
> > > >
> > > >
> > > >
> > > >
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