Hi Prabesh,
I think this is due to a bug that I found recently and which I'm trying to track down. Has it happened to you with many scans? The failure rate is less than 1% in my data.
Regarding your second question: I'm sure it's not too trivial ;-) but I don't understand exactly what you mean. Do you want to deform the segmentations back to the original T2 space?
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
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From: "Prabesh Kanel" <pk09d@my.fsu.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Wednesday, March 2, 2016 6:07:13 PM
Subject: [Freesurfer] hippocampus subfields
Freesurfer List,
I ran recon-all to segment hippocampus subfield using the development version of freesurfer.V6.Beta. To get the better segmentation, I have used both T1 and T2 images. But for some of the scans, the process stops at a point and doesn't seem to progress further.
That happens in only a few cases and only when the data are run using the flag -hippocampal-subfields-T1T2. I have attached a log file of one of the case in this email.
Another query that I have is to get T2 segmented subfields images (one with intensity values rather than labels). Is there an easier way to get T2 subfields segmented images using the segmentation volumes and T2.FSspace.mgz. Sorry, if this question seems too
trivial.
Regards,
Prabesh
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