Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: tracula and recon-all
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@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@nmr.mgh.harvard.edu Data: 6-feb-2013 0.11 A: stdp82@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@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@nmr.mgh.harvard.edu Data: 5-feb-2013 23.58 A: stdp82@virgilio.it Cc: freesurfer@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@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@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 existbutnothereis lh.cst_AS.flt.trkin /Applications/freesurfer/subjects/TUTORIAL
_DA
TA
/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/
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@nmr.mgh.harvard.edu Data: 5-feb-2013 21.53 A: stdp82@virgilio.it Cc: freesurfer@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.
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@nmr.mgh.harvard.edu
-
Anastasia Yendiki