Hi Alan,
If you only want volumes, you can use quantifyHippocampalSubfields.sh. If you want to use the segmentations for something else (eg building ROIs for functional or diffusion), then you need to look into the mgz segmentation files.
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
----- Original Message -----
From: Alan Francis <alandarkenergy@gmail.com>
To: Juan Eugenio Iglesias <eiglesias@bcbl.eu>, Freesurfer <freesurfer@nmr.mgh.harvard.edu>
Sent: Tue, 19 Jan 2016 20:26:13 +0100 (CET)
Subject: Hippocampal subfields
Hi Eugenio:
Hope all is well. I have a question. I have run the HSF algorithm on 32
brains and they ran smoothly without problems. I used only T1 scans. I did
not have T2s. Now to extract the data, do I need to run the following:
*<analysisID>.FSspace.mgz*: the additional scan, rigidly registered to the
T1 data.
*[lr]h.hippoSfLabels-<T1>-<analysisID>.v10.mgz*: they store the discrete
segmentation volume at 0.333 mm resolution in the physical space of the
FreeSurfer <https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer> T1 data
(and therefore of the aligned scan *<analysisID>.FSspace.mgz* as well).
*[lr]h.hippoSfLabels-<T1>-<analysisID>.v10.1mm.mgz*: they store the
discrete segmentation volume in the 1 mm FreeSurfer
<https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer> voxel space.
*[lr]h.hippoSfVolumes-<T1>-<analysisID>.v10.txt*: these text files store
the estimated volumes of the subfields and of the whole hippocampi.
Or can I go directly to :
quantifyHippocampalSubfields.sh <T1>-<analysisID> <output_file>
<OPTIONAL_subject_directory>
Thanks so much,
best regards,
Alan