OK now I get it ;-) You can simply do: mri_convert T2.FSspace.mgz T2.FSspace.resampled.mgz -odt float -rl [lr]h.hippoSfLabels-T1-T2.v10.mgz The rl flag says: "reslice like the following volume" 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 8:31:17 PM Subject: Re: [Freesurfer] hippocampus subfields
Hi Eugenio,
Thank you, for your quick reply. It has happened to me in 4% of the cases, but my data sample is small like 100 data points.
Addition to the second question: When I segment the hippocampus, I get the discrete segmentation volume at 0.333 mm resolution in the file [lr]h.hippoSfLabels-T2.v10.mgz and [lr]h.hippoSfLabels-T1-T2.v10.mgz . Each voxel is labelled based on the subfield. I can use mri_extract_label or mri_binarize to extract individual subfield. But this segmentation will have voxels with the original label. If I load the file along with the T2.FSspace.mgz in Freeview, I can hover my mouse to a location and get the intensities at this place, I believe the intensity value is from T2.FSspace.mgz. Are those intensities values different from the original T2 images? If not, Is it possible to get those value at each voxel location?
Best Regards,
Prabesh
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Eugenio Iglesias e.iglesias@bcbl.eu Sent: Wednesday, March 2, 2016 12:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampus subfields 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
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
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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