18 Oct
2018
18 Oct
'18
1:46 p.m.
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 > 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