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 > > > > 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 > > > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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