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@nmr.mgh.harvard.edu
Data: 5-feb-2013 22.53
A: <stdp82@virgilio.it>
Cc: <freesurfer@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@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@nmr.mgh.harvard.edu
> Data: 5-feb-2013 22.33
> A: <stdp82@virgilio.it>
> Cc: <freesurfer@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@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@nmr.mgh.harvard.edu
> > Data: 5-feb-2013 22.23
> > A: <stdp82@virgilio.it>
> > Cc: <freesurfer@nmr.mgh.harvard.edu>
> > Ogg: Re: R: Re: [Freesurfer] R: Re: R: Re: tracula and recon-all
> >
> >
> > It's looking for files in
> > /Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion
> >
> > Does this directory actually exist?
> >
> > On Tue, 5 Feb 2013, stdp82@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@nmr.mgh.harvard.edu
> > > Data: 5-feb-2013 21.53
> > > A: <stdp82@virgilio.it>
> > > Cc: <freesurfer@nmr.mgh.harvard.edu>, <ayendiki@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@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@nmr.mgh.harvard.edu
> > > > Data: 5-feb-2013 21.08
> > > > A: <stdp82@virgilio.it>
> > > > Cc: <freesurfer@nmr.mgh.harvard.edu>
> > > > Ogg: Re: [Freesurfer] R: Re: tracula and recon-all
> > > >
> > > >
> > > > Why do you want to rerun recon-all after trac-all? You just need to
> run
> > it
> > > > before trac-all.
> > > >
> > > > On Tue, 5 Feb 2013, stdp82@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@virgilio.it wrote:
> > > >>
> > > >> > Thanks. I have a folder called Diff01 in my $SUBJECTS_DIR
> > > >> > (/Applications/freesurfer/subjects/subject_prova)In Diff01 folder I
> > > >> have
> > > >> > data.nii.gz bvecs bvals MPRAGE.nii.gz
> > > >> >
> > > >> > If I write on terminal
> > > >> >
> > > >> > recon-all -all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -subject
> > > >> > $SUBJECTS_DIR/Diff01
> > > >> >
> > > >> > with this ERROR: You are trying to re-run an existing subject with
> > > >> > (possibly)
> > > >> > new input data (-i). If this is truly new input data, you should
> > > >> delete
> > > >> > the subject folder and re-run, or specify a different subject
> name.
> > > >> > If you are just continuing an analysis of an existing subject,
> then
> > > >> >
> > > >> > How is the exact command line, please?
> > > >> >
> > > >> > Thanks,
> > > >> >
> > > >> >
> > > >> > Stefano
> > > >> >
> > > >> > omit all -i flags.The subject name needs to be the same for
> > recon-all
> > > >> and
> > > >> t
> > > >> > rac-all. There is
> > > >> > no way for trac-all to guess that hpth_subj01 and Diff01 are the
> same
> > > >> > subject.
> > > >> >
> > > >> > > Hi Anastasia,
> > > >> > > my original folder Diff01 in
> > > >> > > /Applications/freesurfer/subjects/subject_prova/Diff01 now
> > > >> > > contains:data.nii.gz (DWI), MPRAGE.nii.gz, bvecs, bvals.I have
> > > >> runned
> > > >> > > recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject
> > > >> > > $SUBJECTS_DIR/hpth_subj01 without error and after trac-all -prep
> -c
> > > >> > > $FREESURFER_HOME/dmrirc_single_subject but I still have this
> error:
> > > >> > > /Applications/freesurfer/bin/dmri_train --outdir
> > > >> > > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mni
> > > >> --out
> > > >> > > lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt
> > > >> lh.ilf_AS_avg33_mni_flt
> > > >> > > rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt
> > > >> rh.unc_AS_avg33_mni_flt
> > > >> > > fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt
> > > >> lh.atr_PP_avg33_mni_flt
> > > >> > > rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt
> > > >> rh.cab_PP_avg33_mni_flt
> > > >> > > lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt
> > > >> lh.slfp_PP_avg33_mni_flt
> > > >> > > rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt
> > > >> rh.slft_PP_avg33_mni_flt
> > > >> > > --slist /tmp/subj33.Diff01.21529.txt --trk
> > > >> dlabel/mni/lh.cst_AS.flt.trk
> > > >> > > dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk
> > > >> > > dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk
> > > >> > > dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk
> > > >> > > dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk
> > > >> > > dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk
> > > >> > > dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk
> > > >> > > dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk
> > > >> > > dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk
> > > >> > > dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz
> > > >> --cmask
> > > >> > > dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0
> 0
> > 0
> > > >> 0 0
> > > >> 0
> > > >> > > 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz
> > > >> > > dlabel/mni/lh.cst_AS_roi2.flt.nii.gz
> > > >> dlabel/mni/rh.cst_AS_roi1.flt.nii.gz
> > > >> > > dlabel/mni/rh.cst_AS_roi2.flt.nii.gz
> > > >> dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz
> > > >> > > dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz
> > > >> dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz
> > > >> > > dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz
> > > >> dlabel/mni/lh.unc_AS_roi1.flt.nii.gz
> > > >> > > dlabel/mni/lh.unc_AS_roi2.flt.nii.gz
> > > >> dlabel/mni/rh.unc_AS_roi1.flt.nii.gz
> > > >> > > dlabel/mni/rh.unc_AS_roi2.flt.nii.gz
> > > >> dlabel/mni/fmajor_PP_roi1.flt.nii.gz
> > > >> > > dlabel/mni/fmajor_PP_roi2.flt.nii.gz
> > > >> dlabel/mni/fminor_PP_roi1.flt.nii.gz
> > > >> > > dlabel/mni/fminor_PP_roi2.flt.nii.gz
> > > >> dlabel/mni/lh.atr_PP_roi1.flt.nii.gz
> > > >> > > dlabel/mni/lh.atr_PP_roi2.flt.nii.gz
> > > >> dlabel/mni/rh.atr_PP_roi1.flt.nii.gz
> > > >> > > dlabel/mni/rh.atr_PP_roi2.flt.nii.gz
> > > >> dlabel/mni/lh.cab_PP_roi1.flt.nii.gz
> > > >> > > dlabel/mni/lh.cab_PP_roi2.flt.nii.gz
> > > >> dlabel/mni/rh.cab_PP_roi1.flt.nii.gz
> > > >> > > dlabel/mni/rh.cab_PP_roi2.flt.nii.gz
> > > >> dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz
> > > >> > > dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz
> > > >> dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz
> > > >> > > dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz
> > > >> dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz
> > > >> > > dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz
> > > >> > > dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz
> > > >> > > dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz
> > > >> > > dlabel/mni/lh.slft_PP_roi1.flt.nii.gz
> > > >> > > dlabel/mni/lh.slft_PP_roi2.flt.nii.gz
> > > >> > > dlabel/mni/rh.slft_PP_roi1.flt.nii.gz
> > > >> > > dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask
> > > >> > >
> > > >>
> > >
> /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mni/lowb_bra
> > > >> > in_mask.flt.nii.gz
> > > >> > > --fa
> > > >> > >
> > > >>
> > >
> /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/mni/dtifit_FA.
> > > >> > flt.nii.gz
> > > >> > > --ncpts 5 --debugERROR: fio_pushd:
> > > >> > >
> > > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mniERROR:
> > > >> > > must specify brain mask volume for output subjectDarwin
> > > >> > > iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu
> Oct
> > > >> 18
> > > >> > > 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64
> > > >> > > trac-preproc exited with ERRORS at Tue Feb 5 07:54:09 CET 2013
> > > >> > > Why? Can it depends from the files in the original folder Diff01?
> > > >> Please,
> > > >> > > if yes, may you explain which is the better arrangement of the
> > > >> MPRAGE
> > > >> and
> > > >> > > DWI in the folders.
> > > >> > > Thank you very much,
> > > >> > >
> > > >> > > Stefano
> > > >> > >
> > > >> > >
> > > >> > >
> > > >> > >
> > > >> > > ----Messaggio originale----
> > > >> > > Da: ayend...@nmr.mgh.harvard.edu
> > > >> > > Data: 4-feb-2013 4.48
> > > >> > > A: <std...@virgilio.it>
> > > >> > > Cc: <freesurfer@nmr.mgh.harvard.edu>
> > > >> > > Ogg: Re: [Freesurfer] R: Re: tracula bvecs error
> > > >> > >
> > > >> > >
> > > >> > > No, putting your T1 in a folder is not the same as running
> > > >> freesurfer on
> > > >> > > it. You need to run recon-all on your T1. This is a piece of
> > > >> software
> > > >> that
> > > >> > > will segment your T1 (among other things). Tracula will need that
> > > >> > > segmentation to reconstruct your tracts.
> > > >> > >
> > > >> > > On Sun, 3 Feb 2013, std...@virgilio.it wrote:
> > > >> > >
> > > >> > >> Hi Anastasia,
> > > >> > >> I have put T1 in
> > > >> /Applications/freesurfer/subjects/subject_prova/Diff01/
> > > >> > >> together data.nii.gz, bvals and bvecs.
> > > >> > >> My $SUBJECTS_DIR=$FREESURFER_HOME/subjects/subject_prova
> > > >> > >> T1 was called as T1_01.nii.gz.
> > > >> > >> This is well done?
> > > >> > >>
> > > >> > >> Thanks,
> > > >> > >>
> > > >> > >> Stefano
> > > >> > >>
> > > >> > >> ----Messaggio originale----
> > > >> > >> Da: ayend...@nmr.mgh.harvard.edu
> > > >> > >> Data: 3-feb-2013 20.50
> > > >> > >> A: <std...@virgilio.it>
> > > >> > >> Cc: <freesurfer@nmr.mgh.harvard.edu>
> > > >> > >> Ogg: Re: [Freesurfer] tracula bvecs error
> > > >> > >>
> > > >> > >>
> > > >> > >> Do you have a freesurfer recon of your subject's T1 in the
> > > >> > >> $SUBJECTS_DIR?
> > > >> > >>
> > > >> > >> On Sun, 3 Feb 2013, std...@virgilio.it wrote:
> > > >> > >>
> > > >> > >> > I think that I have resolved the bvecs error by using sudo
> nano
> > > >> option
> > > >> > >> but
> > > >> > >> > now in the next step I visualize this error:
> > > >> > >> > ERROR: fio_pushd:
> > > >> > >> >
> > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mni
> > > >> > >> > ERROR: must specify brain mask volume for output subject
> > > >> > >> >
> > > >> > >> > Thanks,
> > > >> > >> >
> > > >> > >> > Stefano
> > > >> > >> >
> > > >> > >> >
> > > >> > >> _______________________________________________
> > > >> > >> Freesurfer mailing list
> > > >> > >> Freesurfer@nmr.mgh.harvard.edu
> > > >> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > >> > >>
> > > >> > >>
> > > >> > >> The information in this e-mail is intended only for the person
> to
> > > >> whom
> > > >> > >> it is
> > > >> > >> addressed. If you believe this e-mail was sent to you in error
> and
> > > >> the
> > > >> > >> e-mail
> > > >> > >> contains patient information, please contact the Partners
> > > >> Compliance
> > > >> > >> HelpLine at
> > > >> > >> http://www.partners.org/complianceline . If the e-mail was sent
> to
> > > >> you
> > > >> > >> in
> > > >> > >> error
> > > >> > >> but does not contain patient information, please contact the
> > sender
> > > >> and
> > > >> > >> properly
> > > >> > >> dispose of the e-mail.
> > > >> > >>
> > > >> > >>
> > > >> > >>
> > > >> > >>
> > > >> > >>_______________________________________________
> > > >> > > Freesurfer mailing list
> > > >> > > Freesurfer@nmr.mgh.harvard.edu
> > > >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > >> > >
> > > >> > >
> > > >> > > The information in this e-mail is intended only for the person to
> > > >> whom
> > > >> it
> > > >> > > is
> > > >> > > addressed. If you believe this e-mail was sent to you in error
> and
> > > >> the
> > > >> > > e-mail
> > > >> > > contains patient information, please contact the Partners
> > Compliance
> > > >> > > HelpLine at
> > > >> > > http://www.partners.org/complianceline . If the e-mail was sent
> to
> > > >> you
> > > >> in
> > > >> > > error
> > > >> > > but does not contain patient information, please contact the
> sender
> > > >> and
> > > >> > > properly
> > > >> > > dispose of the e-mail.
> > > >> > >
> > > >> > >
> > > >> > >
> > > >> > >
> > > >> >
> > > >> > _______________________________________________
> > > >> >
> > > >> >
> > > >> >_______________________________________________
> > > >> Freesurfer mailing list
> > > >> Freesurfer@nmr.mgh.harvard.edu
> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > >>
> > > >>
> > > >> The information in this e-mail is intended only for the person to
> whom
> > > >> it is
> > > >> addressed. If you believe this e-mail was sent to you in error and
> the
> > > >> e-mail
> > > >> contains patient information, please contact the Partners Compliance
> > > >> HelpLine at
> > > >> http://www.partners.org/complianceline . If the e-mail was sent to
> you
> > > >> in
> > > >> error
> > > >> but does not contain patient information, please contact the sender
> and
> > > >> properly
> > > >> dispose of the e-mail.
> > > >>
> > > >>
> > > >>
> > > >>_______________________________________________
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > >
> > > >
> > > > The information in this e-mail is intended only for the person to whom
> > it
> > > > is
> > > > addressed. If you believe this e-mail was sent to you in error and the
> > > > e-mail
> > > > contains patient information, please contact the Partners Compliance
> > > > HelpLine at
> > > > http://www.partners.org/complianceline . If the e-mail was sent to you
> > in
> > > > error
> > > > but does not contain patient information, please contact the sender
> and
> > > > properly
> > > > dispose of the e-mail.
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > >
> > > --
> > > Shantanu Ghosh, Ph.D.
> > > Harvard Medical School & Massachusetts General Hospital
> > > Martinos Center for Biomedical Imaging
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > >
> > >
> > >
> >
> >
> >_______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
>
>_______________________________________________
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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.