Re: [Freesurfer] intracranial volume

[Douglas Greve]

Not only this value, but you can run asegstats2table and specify only 
one segmentation. It will give you that segmentation as well as various 
other whole brain measures. You run this on multiple subjects to give 
you a table of values.
doug

On 2/5/13 7:51 PM, Bruce Fischl wrote:
> Hi Linn
>
> I think the answer is "yes", but Doug or Nick can hopefully give you
> details
> Bruce
> On Tue, 5 Feb 2013, Linn Mittlestein wrote:
>
>> Dear Bruce,
>> Thank you for your kind reply. I was however wondering whether there is a
>> specific command used to extract this value from all stats files from
>> multiple subjects
>>
>> Kind regards
>>
>>
>> On Tue, Feb 5, 2013 at 3:06 PM, Bruce Fischl 
>> wrote:
>>Hi Linn
>>
>>the ICV is estimated as part of the recon-all process and ends
>>up in one of the stats files. Is that good enough?
>>Bruce
>>On Tue, 5 Feb 2013, Linn Mittlestein wrote:
>>
>>  Hi,
>>
>>  Is there a command that can be used just to extract
>>  just the intracranial volume of all participants?
>>
>>  Many kind regards
>>
>>
>>
>>
>> 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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>
>

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Re: [Freesurfer] when aseg fails

[Bruce Fischl]

Hi Josh

catastrophic subcortical failures are pretty rare. What kind do you mean? 
You will need to diagnose the cause before figuring out how to fix it. I'm 
happy to take a look if you upload it

cheers
Bruce

On Tue, 5 Feb 2013, Joshua Lee wrote:

> 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
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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>
>
>
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[Freesurfer] when aseg fails

[Joshua Lee]

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
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] intracranial volume

[Bruce Fischl]

Hi Linn

I think the answer is "yes", but Doug or Nick can hopefully give you 
details
Bruce
On Tue, 5 Feb 2013, Linn Mittlestein wrote:

> Dear Bruce,
> Thank you for your kind reply. I was however wondering whether there is a
> specific command used to extract this value from all stats files from
> multiple subjects
> 
> Kind regards
> 
> 
> On Tue, Feb 5, 2013 at 3:06 PM, Bruce Fischl 
> wrote:
>   Hi Linn
>
>   the ICV is estimated as part of the recon-all process and ends
>   up in one of the stats files. Is that good enough?
>   Bruce
>   On Tue, 5 Feb 2013, Linn Mittlestein wrote:
>
> Hi,
>
> Is there a command that can be used just to extract
> just the intracranial volume of all participants?
>
> Many kind regards
> 
> 
> 
> 
> 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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Re: [Freesurfer] intracranial volume

[Linn Mittlestein]

Dear Bruce,

Thank you for your kind reply. I was however wondering whether there is a
specific command used to extract this value from all stats files from
multiple subjects

Kind regards


On Tue, Feb 5, 2013 at 3:06 PM, Bruce Fischl wrote:

> Hi Linn
>
> the ICV is estimated as part of the recon-all process and ends up in one
> of the stats files. Is that good enough?
> Bruce
>
> On Tue, 5 Feb 2013, Linn Mittlestein wrote:
>
>  Hi,
>>
>> Is there a command that can be used just to extract just the intracranial
>> volume of all participants?
>>
>> Many kind regards
>>
>>
>>
>
> 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
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: tracula and recon-all

[Anastasia Yendiki]

See "updates":
http://www.freesurfer.net/fswiki/Tracula

On Tue, 5 Feb 2013, std...@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: ayend...@nmr.mgh.harvard.edu
Data: 5-feb-2013 22.53
A: 
Cc: 
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, std...@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: ayend...@nmr.mgh.harvard.edu
> Data: 5-feb-2013 22.33
> A: 
> Cc: 
> 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, std...@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: ayend...@nmr.mgh.harvard.edu
> > Data: 5-feb-2013 22.23
> > A: 
> > Cc: 
> > Ogg: Re: R: Re: [Freesurfer] R: Re:  R: Re:  tracula and recon-all
> >
> >
> > It's looking for files in
> > /Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion
> >
> > Does this directory actually exist?
> >
> > On Tue, 5 Feb 2013, std...@virgilio.it wrote:
> >
> > > Thank you very much Shantanu and Anastasia.Now I'm running trac-all
but
> I
> > > have an error:
> > >
> > > 
niiRead():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: shant...@nmr.mgh.harvard.edu
> > > Data: 5-feb-2013 21.53
> > > A: 
> > > Cc: , 
> > > Ogg: Re: [Freesurfer] R: Re:  R: Re:  tracula and recon-all
> > >
> > > Hi Stefano,
> > >
> > > Just use the cp command to move your recon-all directories to the
Diff01
> > > directory and source it from there.
> > >
> > > HTH,
> > > Shantanu
> > >
> > >
> > > On Tue, February 5, 2013 3:38 pm, std...@virgilio.it wrote:
> > > > Because initially I have run recon-all and trac-all in two separate
> > > > folder.Now I'd like rerun them in a unique folder.I have put MPRAGE
> and
> > > > data.nii.gz in Diff01
> > > > When I run:recon-all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -sd
> > > > $SUBJECTS_DIR/Diff01 -all I have:ERROR: must specify a subject id
> > > > I do not understand as I should placed the my file in the folder.
> > > >
> > > > Stefano
> > > >
> > > >
> > > >
> > > > Messaggio originale
> > > > Da: ayend...@nmr.mgh.harvard.edu
> > > > Data: 5-feb-2013 21.08
> > > > A: 
> > > > Cc: 
> > > > Ogg: Re: [Freesurfer] R: Re:  tracula and recon-all
> > > >
> > > >
> > > > Why do you want to rerun recon-all after trac-all? You just need to
> run
> > it
> > > > before trac-all.
> > > >
> > > > On Tue, 5 Feb 2013, std...@virgilio.it wrote:
> > > >
> > > >> No, I 'm sorry. I try to reformulate my question.
> > > >> I have a folder called Diff01 in
> > > >> my $SUBJECTS_DIR (/Applications/freesurfer/subjects/subject_prova)
> > > >> This folder (Diff01) contains four files: data.nii.gz (DWI),
> bvecs.txt,
> > > >> bvals.txt and MPRAGE.nii.gz.
> > > >>
> > > >> 

[Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: tracula and recon-all

[stdp82]

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: ayend...@nmr.mgh.harvard.edu
Data: 5-feb-2013 22.53
A: 
Cc: 
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, std...@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: ayend...@nmr.mgh.harvard.edu
> Data: 5-feb-2013 22.33
> A: 
> Cc: 
> 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, std...@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: ayend...@nmr.mgh.harvard.edu
> > Data: 5-feb-2013 22.23
> > A: 
> > Cc: 
> > Ogg: Re: R: Re: [Freesurfer] R: Re:  R: Re:  tracula and recon-all
> >
> >
> > It's looking for files in
> > /Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion
> >
> > Does this directory actually exist?
> >
> > On Tue, 5 Feb 2013, std...@virgilio.it wrote:
> >
> > > Thank you very much Shantanu and Anastasia.Now I'm running trac-all but
> I
> > > have an error:
> > >
> > > niiRead(): 
> > > 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: shant...@nmr.mgh.harvard.edu
> > > Data: 5-feb-2013 21.53
> > > A: 
> > > Cc: , 
> > > Ogg: Re: [Freesurfer] R: Re:  R: Re:  tracula and recon-all
> > >
> > > Hi Stefano,
> > >
> > > Just use the cp command to move your recon-all directories to the Diff01
> > > directory and source it from there.
> > >
> > > HTH,
> > > Shantanu
> > >
> > >
> > > On Tue, February 5, 2013 3:38 pm, std...@virgilio.it wrote:
> > > > Because initially I have run recon-all and trac-all in two separate
> > > > folder.Now I'd like rerun them in a unique folder.I have put MPRAGE
> and
> > > > data.nii.gz in Diff01
> > > > When I run:recon-all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -sd
> > > > $SUBJECTS_DIR/Diff01 -all I have:ERROR: must specify a subject id
> > > > I do not understand as I should placed the my file in the folder.
> > > >
> > > > Stefano
> > > >
> > > >
> > > >
> > > > Messaggio originale
> > > > Da: ayend...@nmr.mgh.harvard.edu
> > > > Data: 5-feb-2013 21.08
> > > > A: 
> > > > Cc: 
> > > > Ogg: Re: [Freesurfer] R: Re:  tracula and recon-all
> > > >
> > > >
> > > > Why do you want to rerun recon-all after trac-all? You just need to
> run
> > it
> > > > before trac-all.
> > > >
> > > > On Tue, 5 Feb 2013, std...@virgilio.it wrote:
> > > >
> > > >> No, I 'm sorry. I try to reformulate my question.
> > > >> I have a folder called Diff01 in
> > > >> my $SUBJECTS_DIR (/Applications/freesurfer/subjects/subject_prova)
> > > >> This folder (Diff01) contains four files: data.nii.gz (DWI),
> bvecs.txt,
> > > >> bvals.txt and MPRAGE.nii.gz.
> > > >>
> > > >> Which is the exact command line (and the exact files name in the
> > folder)
> > > >>

Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: tracula and recon-all

[Anastasia Yendiki]

Is there a line that says "set trainfile = ..." in your configuration 
file? If so please delete it.


On Tue, 5 Feb 2013, std...@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: ayend...@nmr.mgh.harvard.edu
Data: 5-feb-2013 22.33
A: 
Cc: 
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, std...@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: ayend...@nmr.mgh.harvard.edu
> Data: 5-feb-2013 22.23
> A: 
> Cc: 
> Ogg: Re: R: Re: [Freesurfer] R: Re:  R: Re:  tracula and recon-all
>
>
> It's looking for files in
> /Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion
>
> Does this directory actually exist?
>
> On Tue, 5 Feb 2013, std...@virgilio.it wrote:
>
> > Thank you very much Shantanu and Anastasia.Now I'm running trac-all but
I
> > have an error:
> >
> > niiRead(): 
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: shant...@nmr.mgh.harvard.edu
> > Data: 5-feb-2013 21.53
> > A: 
> > Cc: , 
> > Ogg: Re: [Freesurfer] R: Re:  R: Re:  tracula and recon-all
> >
> > Hi Stefano,
> >
> > Just use the cp command to move your recon-all directories to the Diff01
> > directory and source it from there.
> >
> > HTH,
> > Shantanu
> >
> >
> > On Tue, February 5, 2013 3:38 pm, std...@virgilio.it wrote:
> > > Because initially I have run recon-all and trac-all in two separate
> > > folder.Now I'd like rerun them in a unique folder.I have put MPRAGE
and
> > > data.nii.gz in Diff01
> > > When I run:recon-all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -sd
> > > $SUBJECTS_DIR/Diff01 -all I have:ERROR: must specify a subject id
> > > I do not understand as I should placed the my file in the folder.
> > >
> > > Stefano
> > >
> > >
> > >
> > > Messaggio originale
> > > Da: ayend...@nmr.mgh.harvard.edu
> > > Data: 5-feb-2013 21.08
> > > A: 
> > > Cc: 
> > > Ogg: Re: [Freesurfer] R: Re:  tracula and recon-all
> > >
> > >
> > > Why do you want to rerun recon-all after trac-all? You just need to
run
> it
> > > before trac-all.
> > >
> > > On Tue, 5 Feb 2013, std...@virgilio.it wrote:
> > >
> > >> No, I 'm sorry. I try to reformulate my question.
> > >> I have a folder called Diff01 in
> > >> my $SUBJECTS_DIR (/Applications/freesurfer/subjects/subject_prova)
> > >> This folder (Diff01) contains four files: data.nii.gz (DWI),
bvecs.txt,
> > >> bvals.txt and MPRAGE.nii.gz.
> > >>
> > >> Which is the exact command line (and the exact files name in the
> folder)
> > >> that you advise me for running recon-all and after trac-all?
> > >>
> > >>
> > >>
> > >> Stefano
> > >>
> > >>
> > >>
> > >> You mean the exact command line to delete a folder? It's rm -rf.
> > >>
> > >> On Tue, 5 Feb 2013, std...@virgilio.it wrote:
> > >>
> > >> > Thanks. I have a folder called Diff01 in my $SUBJECTS_DIR
> > >> > (/Applications/freesurfer/subjects/subject_prova)In Diff01 folder I
> > >> have
> > >> > data.nii.gz bvecs bvals MPRAGE.nii.gz
> > >> >
> > >> > If I write on terminal
> > >> >
> > >> > recon-all -all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -subject
> > >> > $SUBJECTS_DIR/Diff01
> > >> >
> > >> > with this ERROR: You are trying to re-run an existing subject with
> > >> > (possibly)
> > >> >  new input data (-i). If this is truly new input data, you should
> > >> delete
> > >> >  the subject folder and re-run, or specify a different subject
name.
> > >> >  If you are just continuing an analysis of an existing subject,
then
> > >> >
> > >> > How is the ex

[Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: tracula and recon-all

[stdp82]

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 originaleDa: ayend...@nmr.mgh.harvard.edu
Data: 5-feb-2013 22.33
A: 
Cc: 
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, std...@virgilio.it wrote:

> Yes directory exist but no there is lh.cst_AS.flt.trkin 
> /Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion_tutorial/Diff0
> 01/
> > dlabel/mni/
> Stefano
> 
> Messaggio originale
> Da: ayend...@nmr.mgh.harvard.edu
> Data: 5-feb-2013 22.23
> A: 
> Cc: 
> Ogg: Re: R: Re: [Freesurfer] R: Re:  R: Re:  tracula and recon-all
> 
> 
> It's looking for files in
> /Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion
> 
> Does this directory actually exist?
> 
> On Tue, 5 Feb 2013, std...@virgilio.it wrote:
> 
> > Thank you very much Shantanu and Anastasia.Now I'm running trac-all but I
> > have an error:
> >
> > niiRead(): error 
> > openingfile/Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion_tutorial/Diff
> 001/
> > dlabel/mni/lh.cst_AS_roi2.flt.nii.gz
> > WARN: Could 
> > notopen/Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion_tutorial/Diff
> 001/
> > dlabel/mni/lh.cst_AS.flt.trk for reading
> > WARN: Error was: Can not open file
> > WARN: Skipping to next subject
> >
> > dmri_train(5801) malloc: *** mmap(size=159744) failed (error code=12)
> > *** error: can't allocate region
> > *** set a breakpoint in malloc_error_break to debug
> > MRIalloc(218, 182, 182): could not allocate 158704 bytes for 13th slice
> >
> > Cannot allocate memory
> > Darwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct
> 18
> > 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64
> >
> > What's meaning?
> >
> >
> > Stefano
> >
> >
> >
> > Messaggio originale
> > Da: shant...@nmr.mgh.harvard.edu
> > Data: 5-feb-2013 21.53
> > A: 
> > Cc: , 
> > Ogg: Re: [Freesurfer] R: Re:  R: Re:  tracula and recon-all
> >
> > Hi Stefano,
> >
> > Just use the cp command to move your recon-all directories to the Diff01
> > directory and source it from there.
> >
> > HTH,
> > Shantanu
> >
> >
> > On Tue, February 5, 2013 3:38 pm, std...@virgilio.it wrote:
> > > Because initially I have run recon-all and trac-all in two separate
> > > folder.Now I'd like rerun them in a unique folder.I have put MPRAGE and
> > > data.nii.gz in Diff01
> > > When I run:recon-all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -sd
> > > $SUBJECTS_DIR/Diff01 -all I have:ERROR: must specify a subject id
> > > I do not understand as I should placed the my file in the folder.
> > >
> > > Stefano
> > >
> > >
> > >
> > > Messaggio originale
> > > Da: ayend...@nmr.mgh.harvard.edu
> > > Data: 5-feb-2013 21.08
> > > A: 
> > > Cc: 
> > > Ogg: Re: [Freesurfer] R: Re:  tracula and recon-all
> > >
> > >
> > > Why do you want to rerun recon-all after trac-all? You just need to run
> it
> > > before trac-all.
> > >
> > > On Tue, 5 Feb 2013, std...@virgilio.it wrote:
> > >
> > >> No, I 'm sorry. I try to reformulate my question.
> > >> I have a folder called Diff01 in
> > >> my $SUBJECTS_DIR (/Applications/freesurfer/subjects/subject_prova)
> > >> This folder (Diff01) contains four files: data.nii.gz (DWI), bvecs.txt,
> > >> bvals.txt and MPRAGE.nii.gz.
> > >>
> > >> Which is the exact command line (and the exact files name in the
> folder)
> > >> that you advise me for running recon-all and after trac-all?
> > >>
> > >>
> > >>
> > >> Stefano
> > >>
> > >>
> > >>
> > >> You mean the exact command line to delete a folder? It's rm -rf.
> > >>
> > >> On Tue, 5 Feb 2013, std...@virgilio.it wrote:
> > >>
> > >> > Thanks. I have a folder called Diff01 in my $SUBJECTS_DIR
> > >> > (/Applications/freesurfer/subjects/subject_prova)In Diff01 folder I
> > >> have
> > >> > data.nii.gz bvecs bvals MPRAGE.nii.gz
> > >> >
> > >> > If I write on terminal
> > >> >
> > >> > recon-all -all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -subject
> > >> > $SUBJECTS_DIR/Diff01
> > >> >
> > >> > with this ERROR: You are trying to re-run an existing subject with
> > >> > (possibly)
> > >> >  new input data (-i). If this is truly new input data, you should
> > >> delete
> > >> >  the subject folder and re-run, or specify a different subject name.
> > >> >  If you are just continuing an analysis of an existing subject, then
> > >> >
> > >> > How is the exact command line, please?
> > >> >
> > >> > Thanks,
> > >> >
> > >> >
> > >> > Stefano
> > >> >
> > >> >  omit all -i flags.The subjec

Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: tracula and recon-all

[Anastasia Yendiki]

I'm guessing that there's some confusion about the instructions in the 
tracula tutorial and that you are settin the trainfile variable in your 
configuration file to look for a file in that directory. If so, just 
delete that line from your configuration file.


On Tue, 5 Feb 2013, std...@virgilio.it wrote:


Yes directory exist but no there is lh.cst_AS.flt.trkin 
/Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion_tutorial/Diff0
01/
> dlabel/mni/
Stefano

Messaggio originale
Da: ayend...@nmr.mgh.harvard.edu
Data: 5-feb-2013 22.23
A: 
Cc: 
Ogg: Re: R: Re: [Freesurfer] R: Re:  R: Re:  tracula and recon-all


It's looking for files in
/Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion

Does this directory actually exist?

On Tue, 5 Feb 2013, std...@virgilio.it wrote:

> Thank you very much Shantanu and Anastasia.Now I'm running trac-all but I
> have an error:
>
> niiRead(): error 
openingfile/Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion_tutorial/Diff
001/
> dlabel/mni/lh.cst_AS_roi2.flt.nii.gz
> WARN: Could 
notopen/Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion_tutorial/Diff
001/
> dlabel/mni/lh.cst_AS.flt.trk for reading
> WARN: Error was: Can not open file
> WARN: Skipping to next subject
>
> dmri_train(5801) malloc: *** mmap(size=159744) failed (error code=12)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> MRIalloc(218, 182, 182): could not allocate 158704 bytes for 13th slice
>
> Cannot allocate memory
> Darwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct
18
> 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64
>
> What's meaning?
>
>
> Stefano
>
>
>
> Messaggio originale
> Da: shant...@nmr.mgh.harvard.edu
> Data: 5-feb-2013 21.53
> A: 
> Cc: , 
> Ogg: Re: [Freesurfer] R: Re:  R: Re:  tracula and recon-all
>
> Hi Stefano,
>
> Just use the cp command to move your recon-all directories to the Diff01
> directory and source it from there.
>
> HTH,
> Shantanu
>
>
> On Tue, February 5, 2013 3:38 pm, std...@virgilio.it wrote:
> > Because initially I have run recon-all and trac-all in two separate
> > folder.Now I'd like rerun them in a unique folder.I have put MPRAGE and
> > data.nii.gz in Diff01
> > When I run:recon-all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -sd
> > $SUBJECTS_DIR/Diff01 -all I have:ERROR: must specify a subject id
> > I do not understand as I should placed the my file in the folder.
> >
> > Stefano
> >
> >
> >
> > Messaggio originale
> > Da: ayend...@nmr.mgh.harvard.edu
> > Data: 5-feb-2013 21.08
> > A: 
> > Cc: 
> > Ogg: Re: [Freesurfer] R: Re:  tracula and recon-all
> >
> >
> > Why do you want to rerun recon-all after trac-all? You just need to run
it
> > before trac-all.
> >
> > On Tue, 5 Feb 2013, std...@virgilio.it wrote:
> >
> >> No, I 'm sorry. I try to reformulate my question.
> >> I have a folder called Diff01 in
> >> my $SUBJECTS_DIR (/Applications/freesurfer/subjects/subject_prova)
> >> This folder (Diff01) contains four files: data.nii.gz (DWI), bvecs.txt,
> >> bvals.txt and MPRAGE.nii.gz.
> >>
> >> Which is the exact command line (and the exact files name in the
folder)
> >> that you advise me for running recon-all and after trac-all?
> >>
> >>
> >>
> >> Stefano
> >>
> >>
> >>
> >> You mean the exact command line to delete a folder? It's rm -rf.
> >>
> >> On Tue, 5 Feb 2013, std...@virgilio.it wrote:
> >>
> >> > Thanks. I have a folder called Diff01 in my $SUBJECTS_DIR
> >> > (/Applications/freesurfer/subjects/subject_prova)In Diff01 folder I
> >> have
> >> > data.nii.gz bvecs bvals MPRAGE.nii.gz
> >> >
> >> > If I write on terminal
> >> >
> >> > recon-all -all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -subject
> >> > $SUBJECTS_DIR/Diff01
> >> >
> >> > with this ERROR: You are trying to re-run an existing subject with
> >> > (possibly)
> >> >  new input data (-i). If this is truly new input data, you should
> >> delete
> >> >  the subject folder and re-run, or specify a different subject name.
> >> >  If you are just continuing an analysis of an existing subject, then
> >> >
> >> > How is the exact command line, please?
> >> >
> >> > Thanks,
> >> >
> >> >
> >> > Stefano
> >> >
> >> >  omit all -i flags.The subject name needs to be the same for
recon-all
> >> and
> >> t
> >> > rac-all. There is
> >> > no way for trac-all to guess that hpth_subj01 and Diff01 are the same
> >> > subject.
> >> >
> >> > > Hi Anastasia,
> >> > > my original folder Diff01 in
> >> > > /Applications/freesurfer/subjects/subject_prova/Diff01 now
> >> > > contains:data.nii.gz (DWI), MPRAGE.nii.gz, bvecs, bvals.I have
> >> runned
> >> > > recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject
> >> > > $SUBJECTS_DIR/hpth_subj01 without error and after trac-all -prep -c
> >> > > $FREESURFER_HOME/dmrirc_single_subject but I still have this error:
> >> > > /Applications/freesurfer/bin/dmri_train --outdir
> >> > > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mni
> >

Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: tracula and recon-all

[Shantanu Ghosh]

Seems you have to rename the directory to:  instead of
diffusion_tutorial, maybe that's what is causing the problem, then source
from path/to/diffusion

HTH, S.


On Tue, February 5, 2013 4:28 pm, std...@virgilio.it wrote:
> 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: ayend...@nmr.mgh.harvard.edu
> Data: 5-feb-2013 22.23
> A: 
> Cc: 
> Ogg: Re: R: Re: [Freesurfer] R: Re:  R: Re:  tracula and recon-all
>
>
> It's looking for files in
> /Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion
>
> Does this directory actually exist?
>
> On Tue, 5 Feb 2013, std...@virgilio.it wrote:
>
>> Thank you very much Shantanu and Anastasia.Now I'm running trac-all but
>> I
>> have an error:
>>
>> niiRead(): error 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: shant...@nmr.mgh.harvard.edu
>> Data: 5-feb-2013 21.53
>> A: 
>> Cc: , 
>> Ogg: Re: [Freesurfer] R: Re:  R: Re:  tracula and recon-all
>>
>> Hi Stefano,
>>
>> Just use the cp command to move your recon-all directories to the Diff01
>> directory and source it from there.
>>
>> HTH,
>> Shantanu
>>
>>
>> On Tue, February 5, 2013 3:38 pm, std...@virgilio.it wrote:
>> > Because initially I have run recon-all and trac-all in two separate
>> > folder.Now I'd like rerun them in a unique folder.I have put MPRAGE
>> and
>> > data.nii.gz in Diff01
>> > When I run:recon-all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -sd
>> > $SUBJECTS_DIR/Diff01 -all I have:ERROR: must specify a subject id
>> > I do not understand as I should placed the my file in the folder.
>> >
>> > Stefano
>> >
>> >
>> >
>> > Messaggio originale
>> > Da: ayend...@nmr.mgh.harvard.edu
>> > Data: 5-feb-2013 21.08
>> > A: 
>> > Cc: 
>> > Ogg: Re: [Freesurfer] R: Re:  tracula and recon-all
>> >
>> >
>> > Why do you want to rerun recon-all after trac-all? You just need to
>> run it
>> > before trac-all.
>> >
>> > On Tue, 5 Feb 2013, std...@virgilio.it wrote:
>> >
>> >> No, I 'm sorry. I try to reformulate my question.
>> >> I have a folder called Diff01 in
>> >> my $SUBJECTS_DIR (/Applications/freesurfer/subjects/subject_prova)
>> >> This folder (Diff01) contains four files: data.nii.gz (DWI),
>> bvecs.txt,
>> >> bvals.txt and MPRAGE.nii.gz.
>> >>
>> >> Which is the exact command line (and the exact files name in the
>> folder)
>> >> that you advise me for running recon-all and after trac-all?
>> >>
>> >>
>> >>
>> >> Stefano
>> >>
>> >>
>> >>
>> >> You mean the exact command line to delete a folder? It's rm -rf.
>> >>
>> >> On Tue, 5 Feb 2013, std...@virgilio.it wrote:
>> >>
>> >> > Thanks. I have a folder called Diff01 in my $SUBJECTS_DIR
>> >> > (/Applications/freesurfer/subjects/subject_prova)In Diff01 folder I
>> >> have
>> >> > data.nii.gz bvecs bvals MPRAGE.nii.gz
>> >> >
>> >> > If I write on terminal
>> >> >
>> >> > recon-all -all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -subject
>> >> > $SUBJECTS_DIR/Diff01
>> >> >
>> >> > with this ERROR: You are trying to re-run an existing subject with
>> >> > (possibly)
>> >> >  new input data (-i). If this is truly new input data, you should
>> >> delete
>> >> >  the subject folder and re-run, or specify a different subject
>> name.
>> >> >  If you are just continuing an analysis of an existing subject,
>> then
>> >> >
>> >> > How is the exact command line, please?
>> >> >
>> >> > Thanks,
>> >> >
>> >> >
>> >> > Stefano
>> >> >
>> >> >  omit all -i flags.The subject name needs to be the same for
>> recon-all
>> >> and
>> >> t
>> >> > rac-all. There is
>> >> > no way for trac-all to guess that hpth_subj01 and Diff01 are the
>> same
>> >> > subject.
>> >> >
>> >> > > Hi Anastasia,
>> >> > > my original folder Diff01 in
>> >> > > /Applications/freesurfer/subjects/subject_prova/Diff01 now
>> >> > > contains:data.nii.gz (DWI), MPRAGE.nii.gz, bvecs, bvals.I have
>> >> runned
>> >> > > recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject
>> >> > > $SUBJECTS_DIR/hpth_subj01 without error and after trac-all -prep
>> -c
>> >> > > $FREESURFER_HOME/dmrirc_single_subject but I still have this
>> error:
>> >> > > /Applications/fr

[Freesurfer] R: Re: R: Re: R: Re: R: Re: tracula and recon-all

[stdp82]

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: ayend...@nmr.mgh.harvard.edu
Data: 5-feb-2013 22.23
A: 
Cc: 
Ogg: Re: R: Re: [Freesurfer] R: Re:  R: Re:  tracula and recon-all


It's looking for files in 
/Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion

Does this directory actually exist?

On Tue, 5 Feb 2013, std...@virgilio.it wrote:

> Thank you very much Shantanu and Anastasia.Now I'm running trac-all but I
> have an error:
> 
> niiRead(): error 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: shant...@nmr.mgh.harvard.edu
> Data: 5-feb-2013 21.53
> A: 
> Cc: , 
> Ogg: Re: [Freesurfer] R: Re:  R: Re:  tracula and recon-all
> 
> Hi Stefano,
> 
> Just use the cp command to move your recon-all directories to the Diff01
> directory and source it from there.
> 
> HTH,
> Shantanu
> 
> 
> On Tue, February 5, 2013 3:38 pm, std...@virgilio.it wrote:
> > Because initially I have run recon-all and trac-all in two separate
> > folder.Now I'd like rerun them in a unique folder.I have put MPRAGE and
> > data.nii.gz in Diff01
> > When I run:recon-all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -sd
> > $SUBJECTS_DIR/Diff01 -all I have:ERROR: must specify a subject id
> > I do not understand as I should placed the my file in the folder.
> >
> > Stefano
> >
> >
> >
> > Messaggio originale
> > Da: ayend...@nmr.mgh.harvard.edu
> > Data: 5-feb-2013 21.08
> > A: 
> > Cc: 
> > Ogg: Re: [Freesurfer] R: Re:  tracula and recon-all
> >
> >
> > Why do you want to rerun recon-all after trac-all? You just need to run it
> > before trac-all.
> >
> > On Tue, 5 Feb 2013, std...@virgilio.it wrote:
> >
> >> No, I 'm sorry. I try to reformulate my question.
> >> I have a folder called Diff01 in
> >> my $SUBJECTS_DIR (/Applications/freesurfer/subjects/subject_prova)
> >> This folder (Diff01) contains four files: data.nii.gz (DWI), bvecs.txt,
> >> bvals.txt and MPRAGE.nii.gz.
> >>
> >> Which is the exact command line (and the exact files name in the folder)
> >> that you advise me for running recon-all and after trac-all?
> >>
> >>
> >>
> >> Stefano
> >>
> >>
> >>
> >> You mean the exact command line to delete a folder? It's rm -rf.
> >>
> >> On Tue, 5 Feb 2013, std...@virgilio.it wrote:
> >>
> >> > Thanks. I have a folder called Diff01 in my $SUBJECTS_DIR
> >> > (/Applications/freesurfer/subjects/subject_prova)In Diff01 folder I
> >> have
> >> > data.nii.gz bvecs bvals MPRAGE.nii.gz
> >> >
> >> > If I write on terminal
> >> >
> >> > recon-all -all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -subject
> >> > $SUBJECTS_DIR/Diff01
> >> >
> >> > with this ERROR: You are trying to re-run an existing subject with
> >> > (possibly)
> >> >  new input data (-i). If this is truly new input data, you should
> >> delete
> >> >  the subject folder and re-run, or specify a different subject name.
> >> >  If you are just continuing an analysis of an existing subject, then
> >> >
> >> > How is the exact command line, please?
> >> >
> >> > Thanks,
> >> >
> >> >
> >> > Stefano
> >> >
> >> >  omit all -i flags.The subject name needs to be the same for recon-all
> >> and
> >> t
> >> > rac-all. There is
> >> > no way for trac-all to guess that hpth_subj01 and Diff01 are the same
> >> > subject.
> >> >
> >> > > Hi Anastasia,
> >> > > my original folder Diff01 in
> >> > > /Applications/freesurfer/subjects/subject_prova/Diff01 now
> >> > > contains:data.nii.gz (DWI), MPRAGE.nii.gz, bvecs, bvals.I have
> >> runned
> >> > > recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject
> >> > > $SUBJECTS_DIR/hpth_subj01 without error and after trac-all -prep -c
> >> > > $FREESURFER_HOME/dmrirc_single_subject but I still have this error:
> >> > > /Applications/freesurfer/bin/dmri_train --outdir
> >> > > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mni
> >> --out
> >> > > lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt
> >> lh.ilf_AS_avg33_mni_flt
> >> > > rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt
> >> rh.unc_AS_avg33_mni_flt
> >> > > fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt
> >> lh.atr_PP_avg33_mni_flt
> >> > > rh.atr_PP_avg33_mn

Re: [Freesurfer] R: Re: R: Re: R: Re: tracula and recon-all

[Anastasia Yendiki]

It's looking for files in 
/Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion


Does this directory actually exist?

On Tue, 5 Feb 2013, std...@virgilio.it wrote:


Thank you very much Shantanu and Anastasia.Now I'm running trac-all but I
have an error:

niiRead(): error 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: shant...@nmr.mgh.harvard.edu
Data: 5-feb-2013 21.53
A: 
Cc: , 
Ogg: Re: [Freesurfer] R: Re:  R: Re:  tracula and recon-all

Hi Stefano,

Just use the cp command to move your recon-all directories to the Diff01
directory and source it from there.

HTH,
Shantanu


On Tue, February 5, 2013 3:38 pm, std...@virgilio.it wrote:
> Because initially I have run recon-all and trac-all in two separate
> folder.Now I'd like rerun them in a unique folder.I have put MPRAGE and
> data.nii.gz in Diff01
> When I run:recon-all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -sd
> $SUBJECTS_DIR/Diff01 -all I have:ERROR: must specify a subject id
> I do not understand as I should placed the my file in the folder.
>
> Stefano
>
>
>
> Messaggio originale
> Da: ayend...@nmr.mgh.harvard.edu
> Data: 5-feb-2013 21.08
> A: 
> Cc: 
> Ogg: Re: [Freesurfer] R: Re:  tracula and recon-all
>
>
> Why do you want to rerun recon-all after trac-all? You just need to run it
> before trac-all.
>
> On Tue, 5 Feb 2013, std...@virgilio.it wrote:
>
>> No, I 'm sorry. I try to reformulate my question.
>> I have a folder called Diff01 in
>> my $SUBJECTS_DIR (/Applications/freesurfer/subjects/subject_prova)
>> This folder (Diff01) contains four files: data.nii.gz (DWI), bvecs.txt,
>> bvals.txt and MPRAGE.nii.gz.
>>
>> Which is the exact command line (and the exact files name in the folder)
>> that you advise me for running recon-all and after trac-all?
>>
>>
>>
>> Stefano
>>
>>
>>
>> You mean the exact command line to delete a folder? It's rm -rf.
>>
>> On Tue, 5 Feb 2013, std...@virgilio.it wrote:
>>
>> > Thanks. I have a folder called Diff01 in my $SUBJECTS_DIR
>> > (/Applications/freesurfer/subjects/subject_prova)In Diff01 folder I
>> have
>> > data.nii.gz bvecs bvals MPRAGE.nii.gz
>> >
>> > If I write on terminal
>> >
>> > recon-all -all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -subject
>> > $SUBJECTS_DIR/Diff01
>> >
>> > with this ERROR: You are trying to re-run an existing subject with
>> > (possibly)
>> >  new input data (-i). If this is truly new input data, you should
>> delete
>> >  the subject folder and re-run, or specify a different subject name.
>> >  If you are just continuing an analysis of an existing subject, then
>> >
>> > How is the exact command line, please?
>> >
>> > Thanks,
>> >
>> >
>> > Stefano
>> >
>> >  omit all -i flags.The subject name needs to be the same for recon-all
>> and
>> t
>> > rac-all. There is
>> > no way for trac-all to guess that hpth_subj01 and Diff01 are the same
>> > subject.
>> >
>> > > Hi Anastasia,
>> > > my original folder Diff01 in
>> > > /Applications/freesurfer/subjects/subject_prova/Diff01 now
>> > > contains:data.nii.gz (DWI), MPRAGE.nii.gz, bvecs, bvals.I have
>> runned
>> > > recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject
>> > > $SUBJECTS_DIR/hpth_subj01 without error and after trac-all -prep -c
>> > > $FREESURFER_HOME/dmrirc_single_subject but I still have this error:
>> > > /Applications/freesurfer/bin/dmri_train --outdir
>> > > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mni
>> --out
>> > > lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt
>> lh.ilf_AS_avg33_mni_flt
>> > > rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt
>> rh.unc_AS_avg33_mni_flt
>> > > fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt
>> lh.atr_PP_avg33_mni_flt
>> > > rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt
>> rh.cab_PP_avg33_mni_flt
>> > > lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt
>> lh.slfp_PP_avg33_mni_flt
>> > > rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt
>> rh.slft_PP_avg33_mni_flt
>> > > --slist /tmp/subj33.Diff01.21529.txt --trk
>> dlabel/mni/lh.cst_AS.flt.trk
>> > > dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk
>> > > dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk
>> > > dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk
>> > > dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk
>> > > dlabel/mni/rh.atr

[Freesurfer] R: Re: R: Re: R: Re: tracula and recon-all

[stdp82]

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: shant...@nmr.mgh.harvard.edu
Data: 5-feb-2013 21.53
A: 
Cc: , 
Ogg: Re: [Freesurfer] R: Re:  R: Re:  tracula and recon-all

Hi Stefano,

Just use the cp command to move your recon-all directories to the Diff01
directory and source it from there.

HTH,
 Shantanu


On Tue, February 5, 2013 3:38 pm, std...@virgilio.it wrote:
> Because initially I have run recon-all and trac-all in two separate
> folder.Now I'd like rerun them in a unique folder.I have put MPRAGE and
> data.nii.gz in Diff01
> When I run:recon-all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -sd
> $SUBJECTS_DIR/Diff01 -all I have:ERROR: must specify a subject id
> I do not understand as I should placed the my file in the folder.
>
> Stefano
>
>
>
> Messaggio originale
> Da: ayend...@nmr.mgh.harvard.edu
> Data: 5-feb-2013 21.08
> A: 
> Cc: 
> Ogg: Re: [Freesurfer] R: Re:  tracula and recon-all
>
>
> Why do you want to rerun recon-all after trac-all? You just need to run it
> before trac-all.
>
> On Tue, 5 Feb 2013, std...@virgilio.it wrote:
>
>> No, I 'm sorry. I try to reformulate my question.
>> I have a folder called Diff01 in
>> my $SUBJECTS_DIR (/Applications/freesurfer/subjects/subject_prova)
>> This folder (Diff01) contains four files: data.nii.gz (DWI), bvecs.txt,
>> bvals.txt and MPRAGE.nii.gz.
>>
>> Which is the exact command line (and the exact files name in the folder)
>> that you advise me for running recon-all and after trac-all?
>>
>>
>>
>> Stefano
>>
>>
>>
>> You mean the exact command line to delete a folder? It's rm -rf.
>>
>> On Tue, 5 Feb 2013, std...@virgilio.it wrote:
>>
>> > Thanks. I have a folder called Diff01 in my $SUBJECTS_DIR
>> > (/Applications/freesurfer/subjects/subject_prova)In Diff01 folder I
>> have
>> > data.nii.gz bvecs bvals MPRAGE.nii.gz
>> >
>> > If I write on terminal
>> >
>> > recon-all -all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -subject
>> > $SUBJECTS_DIR/Diff01
>> >
>> > with this ERROR: You are trying to re-run an existing subject with
>> > (possibly)
>> >  new input data (-i). If this is truly new input data, you should
>> delete
>> >  the subject folder and re-run, or specify a different subject name.
>> >  If you are just continuing an analysis of an existing subject, then
>> >
>> > How is the exact command line, please?
>> >
>> > Thanks,
>> >
>> >
>> > Stefano
>> >
>> >  omit all -i flags.The subject name needs to be the same for recon-all
>> and
>> t
>> > rac-all. There is
>> > no way for trac-all to guess that hpth_subj01 and Diff01 are the same
>> > subject.
>> >
>> > > Hi Anastasia,
>> > > my original folder Diff01 in
>> > > /Applications/freesurfer/subjects/subject_prova/Diff01 now
>> > > contains:data.nii.gz (DWI), MPRAGE.nii.gz, bvecs, bvals.I have
>> runned
>> > > recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject
>> > > $SUBJECTS_DIR/hpth_subj01 without error and after trac-all -prep -c
>> > > $FREESURFER_HOME/dmrirc_single_subject but I still have this error:
>> > > /Applications/freesurfer/bin/dmri_train --outdir
>> > > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mni
>> --out
>> > > lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt
>> lh.ilf_AS_avg33_mni_flt
>> > > rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt
>> rh.unc_AS_avg33_mni_flt
>> > > fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt
>> lh.atr_PP_avg33_mni_flt
>> > > rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt
>> rh.cab_PP_avg33_mni_flt
>> > > lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt
>> lh.slfp_PP_avg33_mni_flt
>> > > rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt
>> rh.slft_PP_avg33_mni_flt
>> > > --slist /tmp/subj33.Diff01.21529.txt --trk
>> dlabel/mni/lh.cst_AS.flt.trk
>> > > dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk
>> > > dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk
>> > > dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk
>> > > dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk
>> > > dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk
>> > > dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk
>> > > dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk
>> > >

Re: [Freesurfer] R: Re: R: Re: tracula and recon-all

[Shantanu Ghosh]

Hi Stefano,

Just use the cp command to move your recon-all directories to the Diff01
directory and source it from there.

HTH,
 Shantanu


On Tue, February 5, 2013 3:38 pm, std...@virgilio.it wrote:
> Because initially I have run recon-all and trac-all in two separate
> folder.Now I'd like rerun them in a unique folder.I have put MPRAGE and
> data.nii.gz in Diff01
> When I run:recon-all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -sd
> $SUBJECTS_DIR/Diff01 -all I have:ERROR: must specify a subject id
> I do not understand as I should placed the my file in the folder.
>
> Stefano
>
>
>
> Messaggio originale
> Da: ayend...@nmr.mgh.harvard.edu
> Data: 5-feb-2013 21.08
> A: 
> Cc: 
> Ogg: Re: [Freesurfer] R: Re:  tracula and recon-all
>
>
> Why do you want to rerun recon-all after trac-all? You just need to run it
> before trac-all.
>
> On Tue, 5 Feb 2013, std...@virgilio.it wrote:
>
>> No, I 'm sorry. I try to reformulate my question.
>> I have a folder called Diff01 in
>> my $SUBJECTS_DIR (/Applications/freesurfer/subjects/subject_prova)
>> This folder (Diff01) contains four files: data.nii.gz (DWI), bvecs.txt,
>> bvals.txt and MPRAGE.nii.gz.
>>
>> Which is the exact command line (and the exact files name in the folder)
>> that you advise me for running recon-all and after trac-all?
>>
>>
>>
>> Stefano
>>
>>
>>
>> You mean the exact command line to delete a folder? It's rm -rf.
>>
>> On Tue, 5 Feb 2013, std...@virgilio.it wrote:
>>
>> > Thanks. I have a folder called Diff01 in my $SUBJECTS_DIR
>> > (/Applications/freesurfer/subjects/subject_prova)In Diff01 folder I
>> have
>> > data.nii.gz bvecs bvals MPRAGE.nii.gz
>> >
>> > If I write on terminal
>> >
>> > recon-all -all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -subject
>> > $SUBJECTS_DIR/Diff01
>> >
>> > with this ERROR: You are trying to re-run an existing subject with
>> > (possibly)
>> >  new input data (-i). If this is truly new input data, you should
>> delete
>> >  the subject folder and re-run, or specify a different subject name.
>> >  If you are just continuing an analysis of an existing subject, then
>> >
>> > How is the exact command line, please?
>> >
>> > Thanks,
>> >
>> >
>> > Stefano
>> >
>> >  omit all -i flags.The subject name needs to be the same for recon-all
>> and
>> t
>> > rac-all. There is
>> > no way for trac-all to guess that hpth_subj01 and Diff01 are the same
>> > subject.
>> >
>> > > Hi Anastasia,
>> > > my original folder Diff01 in
>> > > /Applications/freesurfer/subjects/subject_prova/Diff01 now
>> > > contains:data.nii.gz (DWI), MPRAGE.nii.gz, bvecs, bvals.I have
>> runned
>> > > recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject
>> > > $SUBJECTS_DIR/hpth_subj01 without error and after trac-all -prep -c
>> > > $FREESURFER_HOME/dmrirc_single_subject but I still have this error:
>> > > /Applications/freesurfer/bin/dmri_train --outdir
>> > > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mni
>> --out
>> > > lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt
>> lh.ilf_AS_avg33_mni_flt
>> > > rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt
>> rh.unc_AS_avg33_mni_flt
>> > > fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt
>> lh.atr_PP_avg33_mni_flt
>> > > rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt
>> rh.cab_PP_avg33_mni_flt
>> > > lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt
>> lh.slfp_PP_avg33_mni_flt
>> > > rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt
>> rh.slft_PP_avg33_mni_flt
>> > > --slist /tmp/subj33.Diff01.21529.txt --trk
>> dlabel/mni/lh.cst_AS.flt.trk
>> > > dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk
>> > > dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk
>> > > dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk
>> > > dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk
>> > > dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk
>> > > dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk
>> > > dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk
>> > > dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk
>> > > dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz
>> --cmask
>> > > dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0
>> 0 0
>> 0
>> > > 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz
>> > > dlabel/mni/lh.cst_AS_roi2.flt.nii.gz
>> dlabel/mni/rh.cst_AS_roi1.flt.nii.gz
>> > > dlabel/mni/rh.cst_AS_roi2.flt.nii.gz
>> dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz
>> > > dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz
>> dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz
>> > > dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz
>> dlabel/mni/lh.unc_AS_roi1.flt.nii.gz
>> > > dlabel/mni/lh.unc_AS_roi2.flt.nii.gz
>> dlabel/mni/rh.unc_AS_roi1.flt.nii.gz
>> > > dlabel/mni/rh.unc_AS_roi2.flt.nii.gz
>> dlabel/mni/fmajor_PP_roi1.flt.nii.gz
>> > > dlabel/mni/fmajor_PP_roi2.flt.nii.gz
>> dlabel/mni/fminor_PP_roi1.flt.nii.gz
>> > > dlabel/mni/fminor_PP_roi2.flt.nii.gz
>> dlabel/mni/lh.atr_PP_roi1.flt.nii.gz
>> > > dlabel/mni/lh.atr_PP_roi2.flt.nii.gz
>> dlabe

Re: [Freesurfer] R: Re: R: Re: tracula and recon-all

[Anastasia Yendiki]

You could just move the recon-all output directories from the location 
where they was originally generated into the Diff01 directory. For the 
purposes of running trac-all this should not make a difference.


On Tue, 5 Feb 2013, std...@virgilio.it wrote:


Because initially I have run recon-all and trac-all in two separate
folder.Now I'd like rerun them in a unique folder.
I have put MPRAGE and data.nii.gz in Diff01

When I run:
recon-all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -sd $SUBJECTS_DIR/Diff01
-all I have:
ERROR: must specify a subject id

I do not understand as I should placed the my file in the folder.


Stefano


Messaggio originale
Da: ayend...@nmr.mgh.harvard.edu
Data: 5-feb-2013 21.08
A: 
Cc: 
Ogg: Re: [Freesurfer] R: Re:  tracula and recon-all


Why do you want to rerun recon-all after trac-all? You just need to run it
before trac-all.

On Tue, 5 Feb 2013, std...@virgilio.it wrote:

> No, I 'm sorry. I try to reformulate my question. 
> I have a folder called Diff01 in
> my $SUBJECTS_DIR (/Applications/freesurfer/subjects/subject_prova)
> This folder (Diff01) contains four files: data.nii.gz (DWI), bvecs.txt,
> bvals.txt and MPRAGE.nii.gz.
>
> Which is the exact command line (and the exact files name in the folder)
> that you advise me for running recon-all and after trac-all?
>
>
>
> Stefano
>
>
>
> You mean the exact command line to delete a folder? It's rm -rf.
>
> On Tue, 5 Feb 2013, std...@virgilio.it wrote:
>
> > Thanks. I have a folder called Diff01 in my $SUBJECTS_DIR
> > (/Applications/freesurfer/subjects/subject_prova)In Diff01 folder I have
> > data.nii.gz bvecs bvals MPRAGE.nii.gz
> >
> > If I write on terminal 
> >
> > recon-all -all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -subject
> > $SUBJECTS_DIR/Diff01
> >
> > with this ERROR: You are trying to re-run an existing subject with
> > (possibly)
> >  new input data (-i). If this is truly new input data, you should delete
> >  the subject folder and re-run, or specify a different subject name.
> >  If you are just continuing an analysis of an existing subject, then 
> >
> > How is the exact command line, please?
> >
> > Thanks,
> >
> >
> > Stefano
> >
> >  omit all -i flags.The subject name needs to be the same for recon-all
and
> t
> > rac-all. There is
> > no way for trac-all to guess that hpth_subj01 and Diff01 are the same
> > subject.
> >
> > > Hi Anastasia,
> > > my original folder Diff01 in
> > > /Applications/freesurfer/subjects/subject_prova/Diff01 now
> > > contains:data.nii.gz (DWI), MPRAGE.nii.gz, bvecs, bvals.I have runned
> > > recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject
> > > $SUBJECTS_DIR/hpth_subj01 without error and after trac-all -prep -c
> > > $FREESURFER_HOME/dmrirc_single_subject but I still have this error:
> > > /Applications/freesurfer/bin/dmri_train --outdir
> > > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mni
--out
> > > lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt
lh.ilf_AS_avg33_mni_flt
> > > rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt
rh.unc_AS_avg33_mni_flt
> > > fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt
lh.atr_PP_avg33_mni_flt
> > > rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt
rh.cab_PP_avg33_mni_flt
> > > lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt
lh.slfp_PP_avg33_mni_flt
> > > rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt
> rh.slft_PP_avg33_mni_flt
> > > --slist /tmp/subj33.Diff01.21529.txt --trk
dlabel/mni/lh.cst_AS.flt.trk
> > > dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk
> > > dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk
> > > dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk
> > > dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk
> > > dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk
> > > dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk
> > > dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk
> > > dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk
> > > dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz
--cmask
> > > dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0
0
> 0
> > > 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz
> > > dlabel/mni/lh.cst_AS_roi2.flt.nii.gz
> dlabel/mni/rh.cst_AS_roi1.flt.nii.gz
> > > dlabel/mni/rh.cst_AS_roi2.flt.nii.gz
> dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz
> > > dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz
> dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz
> > > dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz
> dlabel/mni/lh.unc_AS_roi1.flt.nii.gz
> > > dlabel/mni/lh.unc_AS_roi2.flt.nii.gz
> dlabel/mni/rh.unc_AS_roi1.flt.nii.gz
> > > dlabel/mni/rh.unc_AS_roi2.flt.nii.gz
> dlabel/mni/fmajor_PP_roi1.flt.nii.gz
> > > dlabel/mni/fmajor_PP_roi2.flt.nii.gz
> dlabel/mni/fminor_PP_roi1.flt.nii.gz
> > > dlabel/mni/fminor_PP_roi2.flt.nii.gz
> dlabel/mni/lh.atr_PP_roi1.flt.nii.gz
> > > dlabel/mni/lh.atr_PP_roi2.flt.nii.gz
> dlabel/mni/rh.atr_PP_roi1.flt.nii.gz
> > > dlabel/mni/rh.atr_PP_roi2.flt.nii.gz
> dlabel/mni/lh.cab_PP_roi1.fl

[Freesurfer] R: Re: R: Re: tracula and recon-all

[stdp82]

Because initially I have run recon-all and trac-all in two separate folder.Now 
I'd like rerun them in a unique folder.I have put MPRAGE and data.nii.gz in 
Diff01
When I run:recon-all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -sd 
$SUBJECTS_DIR/Diff01 -all I have:ERROR: must specify a subject id
I do not understand as I should placed the my file in the folder.

Stefano



Messaggio originale
Da: ayend...@nmr.mgh.harvard.edu
Data: 5-feb-2013 21.08
A: 
Cc: 
Ogg: Re: [Freesurfer] R: Re:  tracula and recon-all


Why do you want to rerun recon-all after trac-all? You just need to run it 
before trac-all.

On Tue, 5 Feb 2013, std...@virgilio.it wrote:

> No, I 'm sorry. I try to reformulate my question. 
> I have a folder called Diff01 in
> my $SUBJECTS_DIR (/Applications/freesurfer/subjects/subject_prova)
> This folder (Diff01) contains four files: data.nii.gz (DWI), bvecs.txt,
> bvals.txt and MPRAGE.nii.gz.
> 
> Which is the exact command line (and the exact files name in the folder)
> that you advise me for running recon-all and after trac-all?
> 
> 
> 
> Stefano
> 
> 
> 
> You mean the exact command line to delete a folder? It's rm -rf.
> 
> On Tue, 5 Feb 2013, std...@virgilio.it wrote:
> 
> > Thanks. I have a folder called Diff01 in my $SUBJECTS_DIR
> > (/Applications/freesurfer/subjects/subject_prova)In Diff01 folder I have
> > data.nii.gz bvecs bvals MPRAGE.nii.gz
> >
> > If I write on terminal 
> >
> > recon-all -all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -subject
> > $SUBJECTS_DIR/Diff01
> >
> > with this ERROR: You are trying to re-run an existing subject with
> > (possibly)
> >  new input data (-i). If this is truly new input data, you should delete
> >  the subject folder and re-run, or specify a different subject name.
> >  If you are just continuing an analysis of an existing subject, then 
> >
> > How is the exact command line, please?
> >
> > Thanks,
> >
> >
> > Stefano
> >
> >  omit all -i flags.The subject name needs to be the same for recon-all and
> t
> > rac-all. There is
> > no way for trac-all to guess that hpth_subj01 and Diff01 are the same
> > subject.
> >
> > > Hi Anastasia,
> > > my original folder Diff01 in
> > > /Applications/freesurfer/subjects/subject_prova/Diff01 now
> > > contains:data.nii.gz (DWI), MPRAGE.nii.gz, bvecs, bvals.I have runned
> > > recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject
> > > $SUBJECTS_DIR/hpth_subj01 without error and after trac-all -prep -c
> > > $FREESURFER_HOME/dmrirc_single_subject but I still have this error:
> > > /Applications/freesurfer/bin/dmri_train --outdir
> > > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mni --out
> > > lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt
> > > rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt
> > > fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt
> > > rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt
> > > lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt
> > > rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt
> rh.slft_PP_avg33_mni_flt
> > > --slist /tmp/subj33.Diff01.21529.txt --trk dlabel/mni/lh.cst_AS.flt.trk
> > > dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk
> > > dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk
> > > dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk
> > > dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk
> > > dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk
> > > dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk
> > > dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk
> > > dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk
> > > dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask
> > > dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0
> 0
> > > 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz
> > > dlabel/mni/lh.cst_AS_roi2.flt.nii.gz
> dlabel/mni/rh.cst_AS_roi1.flt.nii.gz
> > > dlabel/mni/rh.cst_AS_roi2.flt.nii.gz
> dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz
> > > dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz
> dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz
> > > dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz
> dlabel/mni/lh.unc_AS_roi1.flt.nii.gz
> > > dlabel/mni/lh.unc_AS_roi2.flt.nii.gz
> dlabel/mni/rh.unc_AS_roi1.flt.nii.gz
> > > dlabel/mni/rh.unc_AS_roi2.flt.nii.gz
> dlabel/mni/fmajor_PP_roi1.flt.nii.gz
> > > dlabel/mni/fmajor_PP_roi2.flt.nii.gz
> dlabel/mni/fminor_PP_roi1.flt.nii.gz
> > > dlabel/mni/fminor_PP_roi2.flt.nii.gz
> dlabel/mni/lh.atr_PP_roi1.flt.nii.gz
> > > dlabel/mni/lh.atr_PP_roi2.flt.nii.gz
> dlabel/mni/rh.atr_PP_roi1.flt.nii.gz
> > > dlabel/mni/rh.atr_PP_roi2.flt.nii.gz
> dlabel/mni/lh.cab_PP_roi1.flt.nii.gz
> > > dlabel/mni/lh.cab_PP_roi2.flt.nii.gz
> dlabel/mni/rh.cab_PP_roi1.flt.nii.gz
> > > dlabel/mni/rh.cab_PP_roi2.flt.nii.gz
> dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz
> > > dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz
> dlabel/mni/rh.ccg_PP_roi1.flt.nii.

Re: [Freesurfer] R: Re: tracula and recon-all

[Bruce Fischl]

recon-all would be:


recon-all -i MPRAGE.nii.gz -s Diff01 -sd  -all

that will name your subject Diff01 and run recon-all on it. Depending on 
your hardware it will take 10-20 hours


cheers
Bruce

On Tue, 5 Feb 2013, std...@virgilio.it wrote:


No, I 'm sorry. I try to reformulate my question. 
I have a folder called Diff01 in my $SUBJECTS_DIR 
(/Applications/freesurfer/subjects/subject_prova)
This folder (Diff01) contains four files: data.nii.gz (DWI), bvecs.txt, 
bvals.txt and MPRAGE.nii.gz.

Which is the exact command line (and the exact files name in the folder) that 
you advise me for running recon-all and
after trac-all?



Stefano



You mean the exact command line to delete a folder? It's rm -rf.

On Tue, 5 Feb 2013, std...@virgilio.it wrote:

> Thanks. I have a folder called Diff01 in my $SUBJECTS_DIR
> (/Applications/freesurfer/subjects/subject_prova)In Diff01 folder I have
> data.nii.gz bvecs bvals MPRAGE.nii.gz
>
> If I write on terminal 
>
> recon-all -all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -subject
> $SUBJECTS_DIR/Diff01
>
> with this ERROR: You are trying to re-run an existing subject with
> (possibly)
>  new input data (-i). If this is truly new input data, you should delete
>  the subject folder and re-run, or specify a different subject name.
>  If you are just continuing an analysis of an existing subject, then 
>
> How is the exact command line, please?
>
> Thanks,
>
>
> Stefano
>
>  omit all -i flags.The subject name needs to be the same for recon-all and t
> rac-all. There is
> no way for trac-all to guess that hpth_subj01 and Diff01 are the same
> subject.
>
> > Hi Anastasia,
> > my original folder Diff01 in
> > /Applications/freesurfer/subjects/subject_prova/Diff01 now
> > contains:data.nii.gz (DWI), MPRAGE.nii.gz, bvecs, bvals.I have runned
> > recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject
> > $SUBJECTS_DIR/hpth_subj01 without error and after trac-all -prep -c
> > $FREESURFER_HOME/dmrirc_single_subject but I still have this error:
> > /Applications/freesurfer/bin/dmri_train --outdir
> > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mni --out
> > lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt
> > rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt
> > fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt
> > rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt
> > lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt
> > rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt
> > --slist /tmp/subj33.Diff01.21529.txt --trk dlabel/mni/lh.cst_AS.flt.trk
> > dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk
> > dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk
> > dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk
> > dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk
> > dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk
> > dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk
> > dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk
> > dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk
> > dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask
> > dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0
> > 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz
> > dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz
> > dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz
> > dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz
> > dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz
> > dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz
> > dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz
> > dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz
> > dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz
> > dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz
> > dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz
> > dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz
> > dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz
> > dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz
> > dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz
> > dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz
> > dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz
> > dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz
> > dlabel/mni/lh.slft_PP_roi1.flt.nii.gz
> > dlabel/mni/lh.slft_PP_roi2.flt.nii.gz
> > dlabel/mni/rh.slft_PP_roi1.flt.nii.gz
> > dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask
> > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mni/lowb_bra
> in_mask.flt.nii.gz
> > --fa
> > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/mni/dtifit_FA.
> flt.nii.gz
> > --ncpts 5 --debugERROR: 

Re: [Freesurfer] R: Re: tracula and recon-all

[Anastasia Yendiki]

Why do you want to rerun recon-all after trac-all? You just need to run it 
before trac-all.


On Tue, 5 Feb 2013, std...@virgilio.it wrote:


No, I 'm sorry. I try to reformulate my question. 
I have a folder called Diff01 in
my $SUBJECTS_DIR (/Applications/freesurfer/subjects/subject_prova)
This folder (Diff01) contains four files: data.nii.gz (DWI), bvecs.txt,
bvals.txt and MPRAGE.nii.gz.

Which is the exact command line (and the exact files name in the folder)
that you advise me for running recon-all and after trac-all?



Stefano



You mean the exact command line to delete a folder? It's rm -rf.

On Tue, 5 Feb 2013, std...@virgilio.it wrote:

> Thanks. I have a folder called Diff01 in my $SUBJECTS_DIR
> (/Applications/freesurfer/subjects/subject_prova)In Diff01 folder I have
> data.nii.gz bvecs bvals MPRAGE.nii.gz
>
> If I write on terminal 
>
> recon-all -all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -subject
> $SUBJECTS_DIR/Diff01
>
> with this ERROR: You are trying to re-run an existing subject with
> (possibly)
>  new input data (-i). If this is truly new input data, you should delete
>  the subject folder and re-run, or specify a different subject name.
>  If you are just continuing an analysis of an existing subject, then 
>
> How is the exact command line, please?
>
> Thanks,
>
>
> Stefano
>
>  omit all -i flags.The subject name needs to be the same for recon-all and
t
> rac-all. There is
> no way for trac-all to guess that hpth_subj01 and Diff01 are the same
> subject.
>
> > Hi Anastasia,
> > my original folder Diff01 in
> > /Applications/freesurfer/subjects/subject_prova/Diff01 now
> > contains:data.nii.gz (DWI), MPRAGE.nii.gz, bvecs, bvals.I have runned
> > recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject
> > $SUBJECTS_DIR/hpth_subj01 without error and after trac-all -prep -c
> > $FREESURFER_HOME/dmrirc_single_subject but I still have this error:
> > /Applications/freesurfer/bin/dmri_train --outdir
> > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mni --out
> > lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt
> > rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt
> > fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt
> > rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt
> > lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt
> > rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt
rh.slft_PP_avg33_mni_flt
> > --slist /tmp/subj33.Diff01.21529.txt --trk dlabel/mni/lh.cst_AS.flt.trk
> > dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk
> > dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk
> > dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk
> > dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk
> > dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk
> > dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk
> > dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk
> > dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk
> > dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask
> > dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0
0
> > 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz
> > dlabel/mni/lh.cst_AS_roi2.flt.nii.gz
dlabel/mni/rh.cst_AS_roi1.flt.nii.gz
> > dlabel/mni/rh.cst_AS_roi2.flt.nii.gz
dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz
> > dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz
dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz
> > dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz
dlabel/mni/lh.unc_AS_roi1.flt.nii.gz
> > dlabel/mni/lh.unc_AS_roi2.flt.nii.gz
dlabel/mni/rh.unc_AS_roi1.flt.nii.gz
> > dlabel/mni/rh.unc_AS_roi2.flt.nii.gz
dlabel/mni/fmajor_PP_roi1.flt.nii.gz
> > dlabel/mni/fmajor_PP_roi2.flt.nii.gz
dlabel/mni/fminor_PP_roi1.flt.nii.gz
> > dlabel/mni/fminor_PP_roi2.flt.nii.gz
dlabel/mni/lh.atr_PP_roi1.flt.nii.gz
> > dlabel/mni/lh.atr_PP_roi2.flt.nii.gz
dlabel/mni/rh.atr_PP_roi1.flt.nii.gz
> > dlabel/mni/rh.atr_PP_roi2.flt.nii.gz
dlabel/mni/lh.cab_PP_roi1.flt.nii.gz
> > dlabel/mni/lh.cab_PP_roi2.flt.nii.gz
dlabel/mni/rh.cab_PP_roi1.flt.nii.gz
> > dlabel/mni/rh.cab_PP_roi2.flt.nii.gz
dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz
> > dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz
dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz
> > dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz
dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz
> > dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz
> > dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz
> > dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz
> > dlabel/mni/lh.slft_PP_roi1.flt.nii.gz
> > dlabel/mni/lh.slft_PP_roi2.flt.nii.gz
> > dlabel/mni/rh.slft_PP_roi1.flt.nii.gz
> > dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask
> >
/Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mni/lowb_bra
> in_mask.flt.nii.gz
> > --fa
> >
/Applications/freesurfer/subjects/subject_prova/Diff01/dmri/mni/dtifit_FA.
> flt.nii.gz
> > --ncpts 5 --debugERROR: fio_pushd:
> > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mniERROR:
> > must specify br

[Freesurfer] R: Re: tracula and recon-all

[stdp82]

No, I 'm sorry. I try to reformulate my question. 
I have a folder called Diff01 in my $SUBJECTS_DIR 
(/Applications/freesurfer/subjects/subject_prova)
This folder (Diff01) contains four files: data.nii.gz (DWI), bvecs.txt, 
bvals.txt and MPRAGE.nii.gz.
Which is the exact command line (and the exact files name in the folder) that 
you advise me for running recon-all and after trac-all?


Stefano


You mean the exact command line to delete a folder? It's rm -rf.

On Tue, 5 Feb 2013, std...@virgilio.it wrote:

> Thanks. I have a folder called Diff01 in my $SUBJECTS_DIR
> (/Applications/freesurfer/subjects/subject_prova)In Diff01 folder I have
> data.nii.gz bvecs bvals MPRAGE.nii.gz
> 
> If I write on terminal 
> 
> recon-all -all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -subject
> $SUBJECTS_DIR/Diff01
> 
> with this ERROR: You are trying to re-run an existing subject with
> (possibly)
>  new input data (-i). If this is truly new input data, you should delete
>  the subject folder and re-run, or specify a different subject name.
>  If you are just continuing an analysis of an existing subject, then 
> 
> How is the exact command line, please?
> 
> Thanks,
> 
> 
> Stefano
> 
>  omit all -i flags.The subject name needs to be the same for recon-all and t
> rac-all. There is
> no way for trac-all to guess that hpth_subj01 and Diff01 are the same
> subject.
> 
> > Hi Anastasia,
> > my original folder Diff01 in
> > /Applications/freesurfer/subjects/subject_prova/Diff01 now
> > contains:data.nii.gz (DWI), MPRAGE.nii.gz, bvecs, bvals.I have runned
> > recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject
> > $SUBJECTS_DIR/hpth_subj01 without error and after trac-all -prep -c
> > $FREESURFER_HOME/dmrirc_single_subject but I still have this error:
> > /Applications/freesurfer/bin/dmri_train --outdir
> > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mni --out
> > lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt
> > rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt
> > fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt
> > rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt
> > lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt
> > rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt
> > --slist /tmp/subj33.Diff01.21529.txt --trk dlabel/mni/lh.cst_AS.flt.trk
> > dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk
> > dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk
> > dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk
> > dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk
> > dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk
> > dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk
> > dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk
> > dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk
> > dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask
> > dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0
> > 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz
> > dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz
> > dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz
> > dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz
> > dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz
> > dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz
> > dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz
> > dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz
> > dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz
> > dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz
> > dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz
> > dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz
> > dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz
> > dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz
> > dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz
> > dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz
> > dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz
> > dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz
> > dlabel/mni/lh.slft_PP_roi1.flt.nii.gz
> > dlabel/mni/lh.slft_PP_roi2.flt.nii.gz
> > dlabel/mni/rh.slft_PP_roi1.flt.nii.gz
> > dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask
> > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mni/lowb_bra
> in_mask.flt.nii.gz
> > --fa
> > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/mni/dtifit_FA.
> flt.nii.gz
> > --ncpts 5 --debugERROR: fio_pushd:
> > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mniERROR:
> > must specify brain mask volume for output subjectDarwin
> > iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18
> > 12:13:47 PDT 2012

Re: [Freesurfer] tracula and recon-all

[Anastasia Yendiki]

You mean the exact command line to delete a folder? It's rm -rf.

On Tue, 5 Feb 2013, std...@virgilio.it wrote:


Thanks. I have a folder called Diff01 in my $SUBJECTS_DIR
(/Applications/freesurfer/subjects/subject_prova)In Diff01 folder I have
data.nii.gz bvecs bvals MPRAGE.nii.gz

If I write on terminal 

recon-all -all -i $SUBJECTS_DIR/Diff01/MPRAGE.nii.gz -subject
$SUBJECTS_DIR/Diff01

with this ERROR: You are trying to re-run an existing subject with
(possibly)
 new input data (-i). If this is truly new input data, you should delete
 the subject folder and re-run, or specify a different subject name.
 If you are just continuing an analysis of an existing subject, then 

How is the exact command line, please?

Thanks,


Stefano

 omit all -i flags.The subject name needs to be the same for recon-all and t
rac-all. There is
no way for trac-all to guess that hpth_subj01 and Diff01 are the same
subject.

> Hi Anastasia,
> my original folder Diff01 in
> /Applications/freesurfer/subjects/subject_prova/Diff01 now
> contains:data.nii.gz (DWI), MPRAGE.nii.gz, bvecs, bvals.I have runned
> recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject
> $SUBJECTS_DIR/hpth_subj01 without error and after trac-all -prep -c
> $FREESURFER_HOME/dmrirc_single_subject but I still have this error:
> /Applications/freesurfer/bin/dmri_train --outdir
> /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mni --out
> lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt
> rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt
> fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt
> rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt
> lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt
> rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt
> --slist /tmp/subj33.Diff01.21529.txt --trk dlabel/mni/lh.cst_AS.flt.trk
> dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk
> dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk
> dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk
> dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk
> dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk
> dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk
> dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk
> dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk
> dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask
> dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0
> 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz
> dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz
> dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz
> dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz
> dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz
> dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz
> dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz
> dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz
> dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz
> dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz
> dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz
> dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz
> dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz
> dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz
> dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz
> dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz
> dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz
> dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz
> dlabel/mni/lh.slft_PP_roi1.flt.nii.gz
> dlabel/mni/lh.slft_PP_roi2.flt.nii.gz
> dlabel/mni/rh.slft_PP_roi1.flt.nii.gz
> dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask
> /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mni/lowb_bra
in_mask.flt.nii.gz
> --fa
> /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/mni/dtifit_FA.
flt.nii.gz
> --ncpts 5 --debugERROR: fio_pushd:
> /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mniERROR:
> must specify brain mask volume for output subjectDarwin
> iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18
> 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64
> trac-preproc exited with ERRORS at Tue Feb  5 07:54:09 CET 2013
> Why? Can it depends from the files in the original folder Diff01? Please,
> if yes, may you explain which is the better arrangement of the MPRAGE and
> DWI in the folders.
> Thank you very much,
>
> Stefano
>
>
>
>
> Messaggio originale
> Da: ayend...@nmr.mgh.harvard.edu
> Data: 4-feb-2013 4.48
> A: 
> Cc: 
> Ogg: Re: [Freesurfer] R: Re:  tracula bvecs error
>
>
> No, putting your T1 in a folder is not the same as running freesurfer on
> it. Y

[Freesurfer] tracula and recon-all

[stdp82]

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...@nmr.mgh.harvard.edu
> Data: 4-feb-2013 4.48
> A: 
> Cc: 
> 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 wi

Re: [Freesurfer] cannot find eddy_correct

[Anastasia Yendiki]

In general the FSLDIR variable needs to be set up for freesurfer scripts 
to find FSL executables. Others on the list will be more qualified than me 
to address the VM aspects of this.


On Tue, 5 Feb 2013, Varghese Chikku wrote:


Hi Anastasia,
First of all,thanks  for your mail and  forgive my ignorance again.
I have  now  downloaded FSL on VMplayer I also have FS running on Oracle
VM.So my question is if I run dti_recon,will  freesurfer  automatically
detect FSL,which is   running on a  different VM.-
Many thanks for  your help,
Chikku  

On 4 February 2013 16:39, Anastasia Yendiki 
wrote:

  Yes.

  On Mon, 4 Feb 2013, Varghese Chikku wrote:

Dear Team,
   I tried to run dt_recon and  the  systems
says  cannot find
eddy_correct,Make  sure FSL is installed. So ,do I
need to  install the
whole FSL package to run this.
In Thanks
Chikku




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Re: [Freesurfer] intracranial volume

[Bruce Fischl]

Hi Linn

the ICV is estimated as part of the recon-all process and ends up in one 
of the stats files. Is that good enough?
Bruce
On Tue, 5 Feb 2013, Linn 
Mittlestein wrote:

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

[Linn Mittlestein]

Hi,

Is there a command that can be used just to extract just the intracranial
volume of all participants?

Many kind regards
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Re: [Freesurfer] Difficult results from our PD data

[Bruce Fischl]

Hi Stan

we have found positive correlations between performance (in this case 
CVLT) and thickness, so it is certainly possible. And negative correlations 
aren't necssarily false - you could certainly imagine that successful 
pruning for example could help performance. Have you visually inspected the 
surfaces for accuracy?


cheers
Bruce


On Tue, 5 Feb 2013, Berg, 
S.F. van den wrote:



 

Dear Freesurfer experts,

 

We investigated the relation between cortical thickness and performance on 
several cognitive tasks within a large group of
Parkinson?s disease patients, but are slightly puzzled by the results. We 
obtained several, both in the vertex-wise analysis
in qdec and in the SPSS analysis in the a-priori parcelated areas, negative 
correlations (i.e. better performance relates
to a thinner cortical area) for all our neuropsychological tasks. These 
negative correlations were unexpected and we are
having a hard time interpreting them. After correcting for multiple 
comparisons, all effects failed to reach the
statistical threshold, rendering no results at all. When we compared our 
patient group on a structural level with healthy
controls, we did find expected results that made sense.

We also ran the exact same analyses (same group, same data) in VBM and there 
found several positive task-related
correlations in expected areas.  

We noticed that in previous literature almost no studies investigated the 
relation between cortical thickness and
cognitive task-performance. This made us wonder whether Freesurfer is suited 
for these correlation-based analyses, or is
it better to be used in between group analyses? And do you have any idea on how 
to explain our negative correlations? Is
it possible we might have done something wrong? 

 

Many thanks,

 

Stan


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[Freesurfer] Difficult results from our PD data

[Berg, S.F. van den]

Dear Freesurfer experts,



We investigated the relation between cortical thickness and performance on 
several cognitive tasks within a large group of Parkinson’s disease patients, 
but are slightly puzzled by the results. We obtained several, both in the 
vertex-wise analysis in qdec and in the SPSS analysis in the a-priori 
parcelated areas, negative correlations (i.e. better performance relates to a 
thinner cortical area) for all our neuropsychological tasks. These negative 
correlations were unexpected and we are having a hard time interpreting them. 
After correcting for multiple comparisons, all effects failed to reach the 
statistical threshold, rendering no results at all. When we compared our 
patient group on a structural level with healthy controls, we did find expected 
results that made sense.

We also ran the exact same analyses (same group, same data) in VBM and there 
found several positive task-related correlations in expected areas.

We noticed that in previous literature almost no studies investigated the 
relation between cortical thickness and cognitive task-performance. This made 
us wonder whether Freesurfer is suited for these correlation-based analyses, or 
is it better to be used in between group analyses? And do you have any idea on 
how to explain our negative correlations? Is it possible we might have done 
something wrong?



Many thanks,



Stan
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Re: [Freesurfer] R: Re: R: Re: tracula bvecs error

[ayendiki]

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...@nmr.mgh.harvard.edu
> Data: 4-feb-2013 4.48
> A: 
> Cc: 
> 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: 
>> Cc: 
>> Ogg: Re: [Freesurfer] tracula bvecs error
>>
>>
>> Do you have a freesurfer recon of your subject's T1 in the
>> $SUBJECTS_DIR?
>>
>> On Sun,

[Freesurfer] R: Re: R: Re: tracula bvecs error

[stdp82]

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...@nmr.mgh.harvard.edu
Data: 4-feb-2013 4.48
A: 
Cc: 
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: 
> Cc: 
> 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: