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 CautionHi 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 andrecon-all.log?
In the arrangement you show below it would be: recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -i <path to dicomfile> -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 soyou 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.gzS_041.nii.gz
> MS001 S_012.nii.gz S_021.nii.gz S_029.nii.gzS_042.nii.gz
> S_004.nii.gz S_013.nii.gz S_022.nii.gz S_030.nii.gzS_043.nii.gz
> S_005.nii.gz S_014.nii.gz S_023.nii.gz S_031.nii.gzS_044.nii.gz
> S_006.nii.gz S_015.nii.gz S_024.nii.gz S_032.nii.gzS_045.nii.gz
> S_008.nii.gz S_016.nii.gz S_025.nii.gz S_033.nii.gzS_046.nii.gz
> S_009.nii.gz S_017.nii.gz S_026.nii.gz S_034.nii.gzS_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 morethan one) with the
> -i switch, or create the subject directory tree underSUBJECTS_DIR for that
> subject, and put a file named 001.mgz in the mri/origsubdir. Note you can
> also specify SUBJECTS_DIR explicitly on the recon-allcommand 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 atrouble 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 mycomputer:
> > > > --------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 isprotected.
> > I tried to set a new subjects_dir: > > export SUBJECTS_DIR=/home/rosalia/Desktop > > > > Then I try to run the first step (autorecon1) with onesubject, 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 amdoing something wrong
as my > terminal keeps > > pointing to the same subject_dir. > > I have tried to use sudo so in order to move my folderand subfolders to the
> subjects_dir set by > > default, and I am experiencing problems as well. > > > > I would much appreciate any help with this basicquestion.
> > 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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