Thanks Eugenio.

On Thu, Jan 21, 2016 at 5:56 AM, Eugenio Iglesias e.iglesias@bcbl.eu wrote:

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

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----- 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