Hi Vinny - Glad that things worked out. I'll defer to Eugenio about the
thalamic parcellation, but in general mri_binarize --match allows you to create
an ROI from all the voxels in a segmentation map that have a specific
segmentation ID.
a.y
On Sep 25, 2018 7:33 AM, Vinny K <vinit.k.srivast...@gmail.com> wrote:
External Email - Use Caution
Hello Anastasia,
The approach worked great and I was able to get the required TRACULA outputs
from each step. According to the FreeSurfer Lookup Table, there are thalamic
parcellation labels from 8001 - 8014. How can I access and visualize these
thalamic labels?
Thanks/Vinny
On Thu, Sep 20, 2018 at 8:32 AM Vinny K
<vinit.k.srivast...@gmail.com<mailto:vinit.k.srivast...@gmail.com>> wrote:
Thanks Anastasia, I'll give this approach a try.
On Thu, Sep 20, 2018 at 8:31 AM Yendiki, Anastasia
<ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>> wrote:
That's correct! You can source the setup script of whichever version you need
to use.
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Vinny K
<vinit.k.srivast...@gmail.com<mailto:vinit.k.srivast...@gmail.com>>
Sent: Thursday, September 20, 2018 8:25:31 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] error with trac-all -prep
External Email - Use Caution
Hi Anastasia,
Thanks for your reply. I needed the dev version in order to utilize the new
thalamic segmentation nuclei tool: http://freesurfer.net/fswiki/ThalamicNuclei
I'll download the stable one as well and use that one for Tracula.
I'm assuming I can have both the stable and dev versions installed and modify
the .bashrc profile to point to the correct freesurfer version that I wish to
use?
Vinny
On Thu, Sep 20, 2018 at 8:20 AM Yendiki, Anastasia
<ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Vinny - Unless there was a specific reason why you were using a dev version
(a feature that you needed and wasn't working in the stable one), please use
the stable one in general.
Best,
a.y
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Vinny K
<vinit.k.srivast...@gmail.com<mailto:vinit.k.srivast...@gmail.com>>
Sent: Thursday, September 20, 2018 6:57:02 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] error with trac-all -prep
External Email - Use Caution
Hi Anastasia,
A similar post had encountered a similar problem a while back:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-July/046979.html
Should I install the latest stable release of FreeSurfer and run only the
trac-all -prep step using the stable FreeSurfer release? Or should I repeat
entire process starting with recon-all using the stable release?
Thanks,
Vinny
On Wed, Sep 19, 2018 at 8:44 PM Yendiki, Anastasia
<ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Vinny - This error is during the diffusion-to-structural registration. Can
you send the entire log file (scripts/trac-all.log)?
Best,
a.y
On Sep 19, 2018 8:39 PM, Vinny K
<vinit.k.srivast...@gmail.com<mailto:vinit.k.srivast...@gmail.com>> wrote:
External Email - Use Caution
Hi,
I am using 'freesurfer-linux-centos6_x86_64-dev-20180902-a7bb8b4.
I get the following error when running the command: trac-all -prep -c dmrirc.
Any help would be greatly appreciated.
Thanks,
Vinny
/home/Vinit/freesurfer/subjects/diffusion/Subj1
flirt.fsl -ref
/home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/refvol.fslregister.nii
-in
/home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/movvol.fslregister.nii
-bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz
-90 90 -verbose 0 -omat
/home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/fslmat0.trans.mat
-schedule /home/Vinit/freesurfer/bin/fsl.5.0.2.xyztrans.sch -init
/home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/reg.init.dat.fsl.mat0
Wed Sep 19 20:29:11 DST 2018
/home/Vinit/freesurfer/subjects/diffusion/Subj1
flirt.fsl -ref
/home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/refvol.fslregister.nii
-in
/home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/movvol.fslregister.nii
-bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz
-90 90 -verbose 0 -omat
/home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/reg.init.dat.fsl.mat
-init
/home/Vinit/freesurfer/subjects/diffusion/Subj1/PatientA/dmri/xfms/tmp.bbregister.15960/fslregister/fslmat0.trans.mat
-schedule /home/Vinit/freesurfer/bin/flirt.newdefault.20080811.sch
terminate called after throwing an instance of 'NEWMAT::SingularException'
Abort (core dumped)
ERROR: flirt
Linux LAPTOP-VTQVHSSF 4.4.0-17134-Microsoft #285-Microsoft Thu Aug 30 17:31:00
PST 2018 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Wed Sep 19 20:29:14 DST 2018
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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
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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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