I'm guessing that there's some confusion about the instructions in the tracula tutorial and that you are settin the trainfile variable in your configuration file to look for a file in that directory. If so, just delete that line from your configuration file.
On Tue, 5 Feb 2013, std...@virgilio.it wrote:
Yes directory exist but no there is lh.cst_AS.flt.trkin /Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion_tutorial/Diff0 01/ > dlabel/mni/ Stefano ----Messaggio originale---- Da: ayend...@nmr.mgh.harvard.edu Data: 5-feb-2013 22.23 A: <std...@virgilio.it> Cc: <freesurfer@nmr.mgh.harvard.edu> Ogg: Re: R: Re: [Freesurfer] R: Re: R: Re: tracula and recon-all It's looking for files in /Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion Does this directory actually exist? On Tue, 5 Feb 2013, std...@virgilio.it wrote: > Thank you very much Shantanu and Anastasia.Now I'm running trac-all but I > have an error: > > niiRead(): error openingfile/Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion_tutorial/Diff 001/ > dlabel/mni/lh.cst_AS_roi2.flt.nii.gz > WARN: Could notopen/Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion_tutorial/Diff 001/ > dlabel/mni/lh.cst_AS.flt.trk for reading > WARN: Error was: Can not open file > WARN: Skipping to next subject > > dmri_train(5801) malloc: *** mmap(size=159744) failed (error code=12) > *** error: can't allocate region > *** set a breakpoint in malloc_error_break to debug > MRIalloc(218, 182, 182): could not allocate 158704 bytes for 13th slice > > Cannot allocate memory > Darwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 > 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 > > What's meaning? > > > Stefano > > > > ----Messaggio originale---- > Da: shant...@nmr.mgh.harvard.edu > Data: 5-feb-2013 21.53 > A: <std...@virgilio.it> > Cc: <freesurfer@nmr.mgh.harvard.edu>, <ayend...@nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] R: Re: R: Re: tracula and recon-all > > Hi Stefano, > > Just use the cp command to move your recon-all directories to the Diff01 > directory and source it from there. > > HTH, > Shantanu > > > On Tue, February 5, 2013 3:38 pm, std...@virgilio.it wrote: > > Because initially I have run recon-all and trac-all in two separate > > folder.Now I'd like rerun them in a unique folder.I have put MPRAGE and > > data.nii.gz in Diff01 > > When I run:recon-all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -sd > > $SUBJECTS_DIR/Diff01 -all I have:ERROR: must specify a subject id > > I do not understand as I should placed the my file in the folder. > > > > Stefano > > > > > > > > ----Messaggio originale---- > > Da: ayend...@nmr.mgh.harvard.edu > > Data: 5-feb-2013 21.08 > > A: <std...@virgilio.it> > > Cc: <freesurfer@nmr.mgh.harvard.edu> > > Ogg: Re: [Freesurfer] R: Re: tracula and recon-all > > > > > > Why do you want to rerun recon-all after trac-all? You just need to run it > > before trac-all. > > > > On Tue, 5 Feb 2013, std...@virgilio.it wrote: > > > >> No, I 'm sorry. I try to reformulate my question. > >> I have a folder called Diff01 in > >> my $SUBJECTS_DIR (/Applications/freesurfer/subjects/subject_prova) > >> This folder (Diff01) contains four files: data.nii.gz (DWI), bvecs.txt, > >> bvals.txt and MPRAGE.nii.gz. > >> > >> Which is the exact command line (and the exact files name in the folder) > >> that you advise me for running recon-all and after trac-all? > >> > >> > >> > >> Stefano > >> > >> > >> > >> You mean the exact command line to delete a folder? It's rm -rf. > >> > >> On Tue, 5 Feb 2013, std...@virgilio.it wrote: > >> > >> > Thanks. I have a folder called Diff01 in my $SUBJECTS_DIR > >> > (/Applications/freesurfer/subjects/subject_prova)In Diff01 folder I > >> have > >> > data.nii.gz bvecs bvals MPRAGE.nii.gz > >> > > >> > If I write on terminal > >> > > >> > recon-all -all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -subject > >> > $SUBJECTS_DIR/Diff01 > >> > > >> > with this ERROR: You are trying to re-run an existing subject with > >> > (possibly) > >> > new input data (-i). If this is truly new input data, you should > >> delete > >> > the subject folder and re-run, or specify a different subject name. > >> > If you are just continuing an analysis of an existing subject, then > >> > > >> > How is the exact command line, please? > >> > > >> > Thanks, > >> > > >> > > >> > Stefano > >> > > >> > omit all -i flags.The subject name needs to be the same for recon-all > >> and > >> t > >> > rac-all. There is > >> > no way for trac-all to guess that hpth_subj01 and Diff01 are the same > >> > subject. > >> > > >> > > Hi Anastasia, > >> > > my original folder Diff01 in > >> > > /Applications/freesurfer/subjects/subject_prova/Diff01 now > >> > > contains:data.nii.gz (DWI), MPRAGE.nii.gz, bvecs, bvals.I have > >> runned > >> > > recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject > >> > > $SUBJECTS_DIR/hpth_subj01 without error and after trac-all -prep -c > >> > > $FREESURFER_HOME/dmrirc_single_subject but I still have this error: > >> > > /Applications/freesurfer/bin/dmri_train --outdir > >> > > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mni > >> --out > >> > > lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt > >> lh.ilf_AS_avg33_mni_flt > >> > > rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt > >> rh.unc_AS_avg33_mni_flt > >> > > fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt > >> lh.atr_PP_avg33_mni_flt > >> > > rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt > >> rh.cab_PP_avg33_mni_flt > >> > > lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt > >> lh.slfp_PP_avg33_mni_flt > >> > > rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt > >> rh.slft_PP_avg33_mni_flt > >> > > --slist /tmp/subj33.Diff01.21529.txt --trk > >> dlabel/mni/lh.cst_AS.flt.trk > >> > > dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk > >> > > dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk > >> > > dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk > >> > > dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk > >> > > dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk > >> > > dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk > >> > > dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk > >> > > dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk > >> > > dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz > >> --cmask > >> > > dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 > >> 0 0 > >> 0 > >> > > 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz > >> > > dlabel/mni/lh.cst_AS_roi2.flt.nii.gz > >> dlabel/mni/rh.cst_AS_roi1.flt.nii.gz > >> > > dlabel/mni/rh.cst_AS_roi2.flt.nii.gz > >> dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz > >> > > dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz > >> dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz > >> > > dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz > >> dlabel/mni/lh.unc_AS_roi1.flt.nii.gz > >> > > dlabel/mni/lh.unc_AS_roi2.flt.nii.gz > >> dlabel/mni/rh.unc_AS_roi1.flt.nii.gz > >> > > dlabel/mni/rh.unc_AS_roi2.flt.nii.gz > >> dlabel/mni/fmajor_PP_roi1.flt.nii.gz > >> > > dlabel/mni/fmajor_PP_roi2.flt.nii.gz > >> dlabel/mni/fminor_PP_roi1.flt.nii.gz > >> > > dlabel/mni/fminor_PP_roi2.flt.nii.gz > >> dlabel/mni/lh.atr_PP_roi1.flt.nii.gz > >> > > dlabel/mni/lh.atr_PP_roi2.flt.nii.gz > >> dlabel/mni/rh.atr_PP_roi1.flt.nii.gz > >> > > dlabel/mni/rh.atr_PP_roi2.flt.nii.gz > >> dlabel/mni/lh.cab_PP_roi1.flt.nii.gz > >> > > dlabel/mni/lh.cab_PP_roi2.flt.nii.gz > >> dlabel/mni/rh.cab_PP_roi1.flt.nii.gz > >> > > dlabel/mni/rh.cab_PP_roi2.flt.nii.gz > >> dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz > >> > > dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz > >> dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz > >> > > dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz > >> dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz > >> > > dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz > >> > > dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz > >> > > dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz > >> > > dlabel/mni/lh.slft_PP_roi1.flt.nii.gz > >> > > dlabel/mni/lh.slft_PP_roi2.flt.nii.gz > >> > > dlabel/mni/rh.slft_PP_roi1.flt.nii.gz > >> > > dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask > >> > > > >> > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mni/lowb_bra > >> > in_mask.flt.nii.gz > >> > > --fa > >> > > > >> > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/mni/dtifit_FA. > >> > flt.nii.gz > >> > > --ncpts 5 --debugERROR: fio_pushd: > >> > > > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mniERROR: > >> > > must specify brain mask volume for output subjectDarwin > >> > > iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct > >> 18 > >> > > 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 > >> > > trac-preproc exited with ERRORS at Tue Feb 5 07:54:09 CET 2013 > >> > > Why? Can it depends from the files in the original folder Diff01? > >> Please, > >> > > if yes, may you explain which is the better arrangement of the > >> MPRAGE > >> and > >> > > DWI in the folders. > >> > > Thank you very much, > >> > > > >> > > Stefano > >> > > > >> > > > >> > > > >> > > > >> > > ----Messaggio originale---- > >> > > Da: ayend...@nmr.mgh.harvard.edu > >> > > Data: 4-feb-2013 4.48 > >> > > A: <std...@virgilio.it> > >> > > Cc: <freesurfer@nmr.mgh.harvard.edu> > >> > > Ogg: Re: [Freesurfer] R: Re: tracula bvecs error > >> > > > >> > > > >> > > No, putting your T1 in a folder is not the same as running > >> freesurfer on > >> > > it. You need to run recon-all on your T1. This is a piece of > >> software > >> that > >> > > will segment your T1 (among other things). Tracula will need that > >> > > segmentation to reconstruct your tracts. > >> > > > >> > > On Sun, 3 Feb 2013, std...@virgilio.it wrote: > >> > > > >> > >> Hi Anastasia, > >> > >> I have put T1 in > >> /Applications/freesurfer/subjects/subject_prova/Diff01/ > >> > >> together data.nii.gz, bvals and bvecs. > >> > >> My $SUBJECTS_DIR=$FREESURFER_HOME/subjects/subject_prova > >> > >> T1 was called as T1_01.nii.gz. > >> > >> This is well done? > >> > >> > >> > >> Thanks, > >> > >> > >> > >> Stefano > >> > >> > >> > >> ----Messaggio originale---- > >> > >> Da: ayend...@nmr.mgh.harvard.edu > >> > >> Data: 3-feb-2013 20.50 > >> > >> A: <std...@virgilio.it> > >> > >> Cc: <freesurfer@nmr.mgh.harvard.edu> > >> > >> Ogg: Re: [Freesurfer] tracula bvecs error > >> > >> > >> > >> > >> > >> Do you have a freesurfer recon of your subject's T1 in the > >> > >> $SUBJECTS_DIR? > >> > >> > >> > >> On Sun, 3 Feb 2013, std...@virgilio.it wrote: > >> > >> > >> > >> > I think that I have resolved the bvecs error by using sudo nano > >> option > >> > >> but > >> > >> > now in the next step I visualize this error: > >> > >> > ERROR: fio_pushd: > >> > >> > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mni > >> > >> > ERROR: must specify brain mask volume for output subject > >> > >> > > >> > >> > Thanks, > >> > >> > > >> > >> > Stefano > >> > >> > > >> > >> > > >> > >> _______________________________________________ > >> > >> Freesurfer mailing list > >> > >> Freesurfer@nmr.mgh.harvard.edu > >> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> > >> > >> > >> The information in this e-mail is intended only for the person to > >> whom > >> > >> it is > >> > >> addressed. If you believe this e-mail was sent to you in error and > >> the > >> > >> e-mail > >> > >> contains patient information, please contact the Partners > >> Compliance > >> > >> HelpLine at > >> > >> http://www.partners.org/complianceline . If the e-mail was sent to > >> you > >> > >> in > >> > >> error > >> > >> but does not contain patient information, please contact the sender > >> and > >> > >> properly > >> > >> dispose of the e-mail. > >> > >> > >> > >> > >> > >> > >> > >> > >> > >>_______________________________________________ > >> > > Freesurfer mailing list > >> > > Freesurfer@nmr.mgh.harvard.edu > >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > > >> > > > >> > > The information in this e-mail is intended only for the person to > >> whom > >> it > >> > > is > >> > > addressed. If you believe this e-mail was sent to you in error and > >> the > >> > > e-mail > >> > > contains patient information, please contact the Partners Compliance > >> > > HelpLine at > >> > > http://www.partners.org/complianceline . If the e-mail was sent to > >> you > >> in > >> > > error > >> > > but does not contain patient information, please contact the sender > >> and > >> > > properly > >> > > dispose of the e-mail. > >> > > > >> > > > >> > > > >> > > > >> > > >> > _______________________________________________ > >> > > >> > > >> >_______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> The information in this e-mail is intended only for the person to whom > >> it is > >> addressed. If you believe this e-mail was sent to you in error and the > >> e-mail > >> contains patient information, please contact the Partners Compliance > >> HelpLine at > >> http://www.partners.org/complianceline . If the e-mail was sent to you > >> in > >> error > >> but does not contain patient information, please contact the sender and > >> properly > >> dispose of the e-mail. > >> > >> > >> > >>_______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the person to whom it > > is > > addressed. If you believe this e-mail was sent to you in error and the > > e-mail > > contains patient information, please contact the Partners Compliance > > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to you in > > error > > but does not contain patient information, please contact the sender and > > properly > > dispose of the e-mail. > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Shantanu Ghosh, Ph.D. > Harvard Medical School & Massachusetts General Hospital > Martinos Center for Biomedical Imaging > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >
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