Hi Rosalia
that you would do outside of FreeSurfer, probably with a shell script. I
typically make a scripts dir under SUBJECTS_DIR and put a file names
subjects.csh that creates an env variable listing the subjects and setting
the SUBJECTS_DIR, then write scripts that source it and run things like
recons, etc....
cheers
Bruce
On Thu, 18 Oct 2018, Rosalia Dacosta Aguayo wrote:
External Email - Use Caution
Thank you a lot Bruce.
Just one more question. If I would like to run all the participants. where
should I include the
subject.list?
Regards,
Rosalia
On Thu, Oct 18, 2018 at 7:56 PM Bruce Fischl <fis...@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
<fis...@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
<fis...@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
<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
> > >
> > >
> > >_______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> >
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> >
> >
> >_______________________________________________
> Freesurfer mailing list
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>
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