Hi Supada,
post-contrast MRI may fail in several recon-all step (or may require
manual edits).
I would:
- run recon-all on the pre-contrast MRI
- use mri_robust_regsiter to co-register the post-contrast MRI to the
pre-contrast one
- I am not too familiar with the tractography pipeline, maybe that is
alrady in the pre-constrast mri space. If not use bb_register.
Cheers, Martin
On 06/08/2015 02:51 PM, Prakkamakul, Supada wrote:
Dear All,
I am relatively new to Freesurfer. I have just started working on
TRACULA in patients with focal enhancing brain lesions.
My first question is How can I overlay *contrast enhanced*T1 MPRAGE
with the tractography output?
I tried running recon-all in both non-enhanced MPRAGE and enhanced
MPRAGE (recon-all -i RawData/patientname/T1/IM-0001-0001.dcm -i
RawData/patientname/T1_post/IM-0001-0001.dcm -s patientname -all), so
that I could get orig file.mgz for both T1 and T1_post that I can
overlay on the tractography output. However, the aparg+aseg did not
come out as nice as the ones ran using only T1 precontrast. I am also
wondering if I ran both T1 pre and T1 post using recon-all, which one
or both of the data will be reflected in the aparg+aseg image.
Is there any other way that I can obtain .mgz file from post contrast
T1 MPRAGE to overlay it with the tractography output?
The second question is how can I measure the distance between the
enhancing lesion and tracts using freeview?
Thank you very much in advance for your help,
Best Regards,
Supada Prakkamakul
[email protected]
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--
Dr. Martin Reuter
Instructor in Neurology
Harvard Medical School
Assistant in Neuroscience
Dept. of Radiology, Massachusetts General Hospital
Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
Computer Science and Artificial Intelligence Lab,
Dept. of Electrical Engineering and Computer Science,
Massachusetts Institute of Technology
A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129
Phone: +1-617-724-5652
Email:
[email protected]
[email protected]
Web : http://reuter.mit.edu
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