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
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
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
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 inspecte
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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The inf
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?
>
> Ma
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
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
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
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 exac
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)
Thi
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.
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
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
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 t
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_D
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/Appl
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: tr
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/f
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...@virgil
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
St
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
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
byt
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
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
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
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
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 p
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
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