Freesurfer February 2013

freesurfer@nmr.mgh.harvard.edu

136 participants
236 discussions

Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: tracula and recon-all
by Anastasia Yendiki 06 Feb '13

06 Feb '13

Hi Stefano - You need to download the file dmri_5.1_snow_leopard.tar.gz from the wiki page, unzip it, and copy ALL the files that come out into the same directory where you copied the trac-all update. The trac-all update doesn't solve the memory issue, for that you need the executables in dmri_5.1_snow_leopard.tar.gz. I will be going on a short vacation for the rest of the week and will not be able to answer questions during this time unfortunately. If you don't manage to get through the tutorial independently by Monday, please send in your questions then. Best of luck, a.y On Wed, 6 Feb 2013, stdp82(a)virgilio.it wrote: > Hi Anastasia, > which is the forder where I should put leopard uploade? > > I try to put it in folder where trac-all lives, but when I re-run trac-all I > obtain the same error: > > dmri_train(11214) 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 15th slice > Cannot allocate memory > > Thanks, > > > Stefano > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 6-feb-2013 0.11 > A: <stdp82(a)virgilio.it> > Ogg: Re: R: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: > tracula and recon-all > > > Type "which trac-all" to find out where trac-all lives on your computer, > then copy the update files there. > > On Wed, 6 Feb 2013, stdp82(a)virgilio.it wrote: > > > Anastasia, thank you for your patience and kindness. I apologie but how > can > > I use them, particularly trac-all updates. > > ----Messaggio originale---- > > Da: ayendiki(a)nmr.mgh.harvard.edu > > Data: 5-feb-2013 23.58 > > A: <stdp82(a)virgilio.it> > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: tracula > and > > recon-all > > > > > > See "updates": > > http://www.freesurfer.net/fswiki/Tracula > > > > On Tue, 5 Feb 2013, stdp82(a)virgilio.it wrote: > > > > > I delete it and I attached my last configuration file. > > > This is the error after rerunning: > > > dmri_train(11214) 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 15th 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 > > > > > > trac-preproc exited with ERRORS at Tue Feb 5 23:46:51 CET 2013 > > > ----Messaggio originale---- > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > Data: 5-feb-2013 22.53 > > > A: <stdp82(a)virgilio.it> > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: tracula and > > > recon-all > > > > > > > > > Is there a line that says "set trainfile = ..." in your configuration > > > file? If so please delete it. > > > > > > On Tue, 5 Feb 2013, stdp82(a)virgilio.it wrote: > > > > > > > I set $TUTORIAL_DATA as setenv TUTORIAL_DATA > > > > /Applications/freesurfer/subjects/TUTORIAL_DATA > > > > > > > > In $TUTORIAL_DATA/diffusion_tutorial I do not found > > > > subj,train,difftutorial23.txtsubjI find > > subj,train,difftutorial32.txtsubj > > > in > > > > > $TUTORIAL_DATA/diffusion_tutorial/scripts/subj,train,difftutorial32.txt > > > > > > > > Stefano > > > > > > > > ----Messaggio originale---- > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > Data: 5-feb-2013 22.33 > > > > A: <stdp82(a)virgilio.it> > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: tracula and > recon-all > > > > > > > > > > > > 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, stdp82(a)virgilio.it wrote: > > > > > > > > > Yes directory existbutnothereis lh.cst_AS.flt.trkin /Applications/freesurfer/subjects/TUTORIAL > _DA > > TA > > > /diff > > > > usion_tutorial/Diff0 > > > > > 01/ > > > > > > dlabel/mni/ > > > > > Stefano > > > > > > > > > > ----Messaggio originale---- > > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > > Data: 5-feb-2013 22.23 > > > > > A: <stdp82(a)virgilio.it> > > > > > Cc: <freesurfer(a)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, stdp82(a)virgilio.it wrote: > > > > > > > > > > > Thank you very much Shantanu and Anastasia.Now I'm running > trac-all > > > but > > > > I > > > > > > have an error: > > > > > > > > > > >>niiRead():erroropeningfile/Applications/freesurfer/subjects/TUTORIAL_DATA/ > d > > iffusion_t > > > utori > > > > al/Diff > > > > > 001/ > > > > > > dlabel/mni/lh.cst_AS_roi2.flt.nii.gz > > > > >>WARN:Couldnotopen/Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion > _ > > tutor > > > ial/D > > > > iff > > > > > 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: shantanu(a)nmr.mgh.harvard.edu > > > > > > Data: 5-feb-2013 21.53 > > > > > > A: <stdp82(a)virgilio.it> > > > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu>, > <ayendiki(a)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, stdp82(a)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: ayendiki(a)nmr.mgh.harvard.edu > > > > > > > Data: 5-feb-2013 21.08 > > > > > > > A: <stdp82(a)virgilio.it> > > > > > > > Cc: <freesurfer(a)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, stdp82(a)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, stdp82(a)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...(a)nmr.mgh.harvard.edu > > > > > > >> > > Data: 4-feb-2013 4.48 > > > > > > >> > > A: <std...(a)virgilio.it> > > > > > > >> > > Cc: <freesurfer(a)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...(a)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...(a)nmr.mgh.harvard.edu > > > > > > >> > >> Data: 3-feb-2013 20.50 > > > > > > >> > >> A: <std...(a)virgilio.it> > > > > > > >> > >> Cc: <freesurfer(a)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...(a)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(a)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(a)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(a)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(a)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(a)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(a)nmr.mgh.harvard.edu > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >_______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)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(a)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(a)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. > > > > > > > > > > >

1 0

intracranial volume
by Linn Mittlestein 05 Feb '13

05 Feb '13

Hi, Is there a command that can be used just to extract just the intracranial volume of all participants? Many kind regards

3 4

when aseg fails
by Joshua Lee 05 Feb '13

05 Feb '13

Hi All, I'm just wondering what kind of protocol people are using to address the situation when Freesurfer has a catastrophic failure in accurately segmenting the sub-cortical structures. While manual editing is an option, are there upstream changes that might improve the subcortical segmentation is re-run (e.g. wm control points?). Drop them? If conducting an analysis of Freesurfer subcortical segmentation in some population, how have people handled these cases? Thanks, Josh

2 1

R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: tracula and recon-all
by stdp82＠virgilio.it 05 Feb '13

05 Feb '13

I delete it and I attached my last configuration file.This is the error after rerunning:dmri_train(11214) malloc: *** mmap(size=159744) failed (error code=12)*** error: can't allocate region*** set a breakpoint in malloc_error_break to debugMRIalloc(218, 182, 182): could not allocate 158704 bytes for 15th slice Cannot allocate memoryDarwin 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 23:46:51 CET 2013 ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 5-feb-2013 22.53 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: tracula and recon-all Is there a line that says "set trainfile = ..." in your configuration file? If so please delete it. On Tue, 5 Feb 2013, stdp82(a)virgilio.it wrote: > I set $TUTORIAL_DATA as setenv TUTORIAL_DATA > /Applications/freesurfer/subjects/TUTORIAL_DATA > > In $TUTORIAL_DATA/diffusion_tutorial I do not found > subj,train,difftutorial23.txtsubjI find subj,train,difftutorial32.txtsubj in > $TUTORIAL_DATA/diffusion_tutorial/scripts/subj,train,difftutorial32.txt > > Stefano > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 5-feb-2013 22.33 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: tracula and recon-all > > > 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, stdp82(a)virgilio.it wrote: > > > Yes directory exist but no thereis lh.cst_AS.flt.trkin /Applications/freesurfer/subjects/TUTORIAL_DATA/diff > usion_tutorial/Diff0 > > 01/ > > > dlabel/mni/ > > Stefano > > > > ----Messaggio originale---- > > Da: ayendiki(a)nmr.mgh.harvard.edu > > Data: 5-feb-2013 22.23 > > A: <stdp82(a)virgilio.it> > > Cc: <freesurfer(a)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, stdp82(a)virgilio.it wrote: > > > > > Thank you very much Shantanu and Anastasia.Now I'm running trac-all but > I > > > have an error: > > > > > > niiRead(): erroropeningfile/Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion_tutori > al/Diff > > 001/ > > > dlabel/mni/lh.cst_AS_roi2.flt.nii.gz > > > WARN: Couldnotopen/Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion_tutorial/D > iff > > 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: shantanu(a)nmr.mgh.harvard.edu > > > Data: 5-feb-2013 21.53 > > > A: <stdp82(a)virgilio.it> > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu>, <ayendiki(a)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, stdp82(a)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: ayendiki(a)nmr.mgh.harvard.edu > > > > Data: 5-feb-2013 21.08 > > > > A: <stdp82(a)virgilio.it> > > > > Cc: <freesurfer(a)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, stdp82(a)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, stdp82(a)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...(a)nmr.mgh.harvard.edu > > > >> > > Data: 4-feb-2013 4.48 > > > >> > > A: <std...(a)virgilio.it> > > > >> > > Cc: <freesurfer(a)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...(a)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...(a)nmr.mgh.harvard.edu > > > >> > >> Data: 3-feb-2013 20.50 > > > >> > >> A: <std...(a)virgilio.it> > > > >> > >> Cc: <freesurfer(a)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...(a)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(a)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(a)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(a)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(a)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(a)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(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer(a)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(a)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.

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R: Re: R: Re: R: Re: R: Re: R: Re: tracula and recon-all
by stdp82＠virgilio.it 05 Feb '13

05 Feb '13

I set $TUTORIAL_DATA as setenv TUTORIAL_DATA /Applications/freesurfer/subjects/TUTORIAL_DATA In $TUTORIAL_DATA/diffusion_tutorial I do not found subj,train,difftutorial23.txtsubjI find subj,train,difftutorial32.txtsubj in $TUTORIAL_DATA/diffusion_tutorial/scripts/subj,train,difftutorial32.txt Stefano ----Messaggio originale----Da: ayendiki(a)nmr.mgh.harvard.edu Data: 5-feb-2013 22.33 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: tracula and recon-all 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, stdp82(a)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: ayendiki(a)nmr.mgh.harvard.edu > Data: 5-feb-2013 22.23 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)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, stdp82(a)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: shantanu(a)nmr.mgh.harvard.edu > > Data: 5-feb-2013 21.53 > > A: <stdp82(a)virgilio.it> > > Cc: <freesurfer(a)nmr.mgh.harvard.edu>, <ayendiki(a)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, stdp82(a)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: ayendiki(a)nmr.mgh.harvard.edu > > > Data: 5-feb-2013 21.08 > > > A: <stdp82(a)virgilio.it> > > > Cc: <freesurfer(a)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, stdp82(a)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, stdp82(a)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...(a)nmr.mgh.harvard.edu > > >> > > Data: 4-feb-2013 4.48 > > >> > > A: <std...(a)virgilio.it> > > >> > > Cc: <freesurfer(a)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...(a)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...(a)nmr.mgh.harvard.edu > > >> > >> Data: 3-feb-2013 20.50 > > >> > >> A: <std...(a)virgilio.it> > > >> > >> Cc: <freesurfer(a)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...(a)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(a)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(a)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(a)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(a)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(a)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(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > >_______________________________________________ Freesurfer mailing list Freesurfer(a)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.

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R: Re: R: Re: R: Re: R: Re: tracula and recon-all
by stdp82＠virgilio.it 05 Feb '13

05 Feb '13

Yes directory exist but no there is lh.cst_AS.flt.trk in /Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion_tutorial/Diff001/ > dlabel/mni/ Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 5-feb-2013 22.23 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)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, stdp82(a)virgilio.it wrote: > Thank you very much Shantanu and Anastasia.Now I'm running trac-all but I > have an error: > > niiRead(): error opening file/Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion_tutorial/Diff001/ > dlabel/mni/lh.cst_AS_roi2.flt.nii.gz > WARN: Could not open/Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion_tutorial/Diff001/ > 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: shantanu(a)nmr.mgh.harvard.edu > Data: 5-feb-2013 21.53 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu>, <ayendiki(a)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, stdp82(a)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: ayendiki(a)nmr.mgh.harvard.edu > > Data: 5-feb-2013 21.08 > > A: <stdp82(a)virgilio.it> > > Cc: <freesurfer(a)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, stdp82(a)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, stdp82(a)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...(a)nmr.mgh.harvard.edu > >> > > Data: 4-feb-2013 4.48 > >> > > A: <std...(a)virgilio.it> > >> > > Cc: <freesurfer(a)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...(a)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...(a)nmr.mgh.harvard.edu > >> > >> Data: 3-feb-2013 20.50 > >> > >> A: <std...(a)virgilio.it> > >> > >> Cc: <freesurfer(a)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...(a)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(a)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(a)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(a)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(a)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(a)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(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >

3 2

R: Re: R: Re: R: Re: tracula and recon-all
by stdp82＠virgilio.it 05 Feb '13

05 Feb '13

Thank you very much Shantanu and Anastasia.Now I'm running trac-all but I have an error: niiRead(): error opening file /Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi2.flt.nii.gzWARN: Could not open /Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS.flt.trk for readingWARN: Error was: Can not open fileWARN: 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 debugMRIalloc(218, 182, 182): could not allocate 158704 bytes for 13th slice Cannot allocate memoryDarwin 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: shantanu(a)nmr.mgh.harvard.edu Data: 5-feb-2013 21.53 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu>, <ayendiki(a)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, stdp82(a)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: ayendiki(a)nmr.mgh.harvard.edu > Data: 5-feb-2013 21.08 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)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, stdp82(a)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, stdp82(a)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...(a)nmr.mgh.harvard.edu >> > > Data: 4-feb-2013 4.48 >> > > A: <std...(a)virgilio.it> >> > > Cc: <freesurfer(a)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...(a)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...(a)nmr.mgh.harvard.edu >> > >> Data: 3-feb-2013 20.50 >> > >> A: <std...(a)virgilio.it> >> > >> Cc: <freesurfer(a)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...(a)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(a)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(a)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(a)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(a)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(a)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(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

R: Re: R: Re: tracula and recon-all
by stdp82＠virgilio.it 05 Feb '13

05 Feb '13

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: ayendiki(a)nmr.mgh.harvard.edu Data: 5-feb-2013 21.08 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)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, stdp82(a)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, stdp82(a)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...(a)nmr.mgh.harvard.edu > > > Data: 4-feb-2013 4.48 > > > A: <std...(a)virgilio.it> > > > Cc: <freesurfer(a)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...(a)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...(a)nmr.mgh.harvard.edu > > >> Data: 3-feb-2013 20.50 > > >> A: <std...(a)virgilio.it> > > >> Cc: <freesurfer(a)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...(a)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(a)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(a)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(a)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(a)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.

3 2

R: Re: tracula and recon-all
by stdp82＠virgilio.it 05 Feb '13

05 Feb '13

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, stdp82(a)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...(a)nmr.mgh.harvard.edu > > Data: 4-feb-2013 4.48 > > A: <std...(a)virgilio.it> > > Cc: <freesurfer(a)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...(a)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...(a)nmr.mgh.harvard.edu > >> Data: 3-feb-2013 20.50 > >> A: <std...(a)virgilio.it> > >> Cc: <freesurfer(a)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...(a)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(a)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(a)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(a)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.

3 2

tracula and recon-all
by stdp82＠virgilio.it 05 Feb '13

05 Feb '13

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 trac-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_brain_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...(a)nmr.mgh.harvard.edu > Data: 4-feb-2013 4.48 > A: <std...(a)virgilio.it> > Cc: <freesurfer(a)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...(a)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...(a)nmr.mgh.harvard.edu >> Data: 3-feb-2013 20.50 >> A: <std...(a)virgilio.it> >> Cc: <freesurfer(a)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...(a)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(a)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(a)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. > > > > _______________________________________________

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Freesurfer February 2013