External Email - Use Caution
Hi Anastasia,
In the past days, we have obtained the original T1s from the original study
and we are running Freesurfer in all of the subjects in order to run
TRACULA correctly so we can avoid all the problems you mention. TRACULA is
running in some of
Have you checked the registration between the structural and diffusion? The
concern here would be that some of your subjects' brains could look more like
bert's brain than others, and the registration could be better for the former
than the latter. You would have to ensure that this doesn't intr
External Email - Use Caution
Hi Anastasia,
thank you for your rapid response. Since I do not have the T1 of my
subjects, I have not run the recon-all. Instead of that, I have copy-pasted
the "mri" folder (including the aparc+aseg.mgz file) located in
$FREESURFER_HOME/freesurfer/su
Hi Ainara - What do you mean by default freesurfer files? Can you describe how
you created each subject's recon-all style directory under SUBJECTS_DIR?
TRACULA looks for $SUBJECTS_DIR/$subjectid/mri/aparc+aseg.mgz for each subject
ID.
a.y
On Jan 11, 2019 8:30 AM, Ainara Gomez wrote:
External Email - Use Caution
Dear Freesurfer experts,
I am trying to run TRACULA as a complementary analysis on a patients and
healthy controls sample. I have read in the tutorial that it is assumed
that FreeSurfer has already been run on all the subjects' T1-weighted data
because
. Any thoughts?
>
> Thanks,
>
> Emily
>
> - Original Message -
> From: ebell...@uwm.edu
> To: "Anastasia Yendiki"
> Cc: "freesurfer"
> Sent: Wednesday, March 5, 2014 3:25:00 PM
> Subject: Re: [Freesurfer] Running Tracula on a cluster
>
> Hi Anast
25:00 PM
Subject: Re: [Freesurfer] Running Tracula on a cluster
Hi Anastasia,
We use SLURM.
I have not personally yet run bedpost off of the cluster, but one of my
colleagues was able to run his data off of our cluster ( the whole pathway
including bedpost) without any problem. However he
for every subject and then made
sure each one got assigned to a different processor in another script.
Thanks,
Emily
- Original Message -
From: "Anastasia Yendiki"
To: ebell...@uwm.edu
Cc: "freesurfer"
Sent: Wednesday, March 5, 2014 3:02:14 PM
Subject: Re: [Freesur
Hi Emily - Which job management system does your cluster run on? Have you
ever tried to run any of the FSL parallelized programs, like bedpostx, on
your cluster?
a.y
On Wed, 5 Mar 2014, ebell...@uwm.edu wrote:
>
> Hello,
>
> I plan on running a batch of subjects (around 80) on a computer clus
Hello,
I plan on running a batch of subjects (around 80) on a computer cluster.
I am assuming that in the dmrirc configuration file, I can enter all of the
subjects in subjlist?
However, do I have to add something to it to make sure that each subject gets
sent to a different processor on the
Can you please send the text files instead of pasting them in the email?
Thanks!
On Fri, 7 Dec 2012, s0675204 wrote:
Hello
I think I spoke to soon!
It ended with errors again.
I get the error message: "bvecs and bvals don't have the same number of entries"
I saw on some older messages on
Hello
I think I spoke to soon!
It ended with errors again.
I get the error message: "bvecs and bvals don't have the same number of entries"
I saw on some older messages on the mail-base you said that we need to
check that the number of entries in the bvals is same as and bvecs is
3 times as muc
Hi Prerona - You need to uncomment the bvecfile and bvalfile definitions
in your configuration file.
Hope this helps,
a.y
On Fri, 7 Dec 2012, s0675204 wrote:
Hello
I am trying to run Tracula on a set of dicoms files. I have run
recon-all previously.
I am getting a message trac-preproc exit
Hello
I am trying to run Tracula on a set of dicoms files. I have run
recon-all previously.
I am getting a message trac-preproc exited with ERRORS
Please can anyone advise me on this?
I have listed all the details (command, error/output, config file) below
Thank you so much for your help
best w
Thanks - appears as if all is well.
On Tue, Apr 24, 2012 at 4:02 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:
>
> Hi Richard - I'd check your bedpostx output files, run mri_info on them to
> make sure they have the right number of slices. The monitoring script that
> produces the
Hi Richard - I'd check your bedpostx output files, run mri_info on them to
make sure they have the right number of slices. The monitoring script that
produces the "slices processed" messages checks only every once in a
while, so you won't see a separate message for each slice.
The warnings f
Hi Anastasia,
I ran bedpost directly: bedpostx dmri
It seemed to run fine, not exiting with any errors. the only thing that
concerned me was that the last output in the terminal was
50 slices processed [when I have 54]
queing post-processing stage
then it exited. It seemed to run rather quicke
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