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@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.
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.
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 exist but nothereis 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_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, 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
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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
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the > > e-mail > > contains patient information, please contact the Partners
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> > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent
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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
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the
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HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to
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in error but does not contain patient information, please contact the sender
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The information in this e-mail is intended only for the person to
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-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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The information in this e-mail is intended only for the person to whom it
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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.
freesurfer@nmr.mgh.harvard.edu
-
Anastasia Yendiki -
stdp82＠virgilio.it