Thanks Eugenio. On Thu, Jan 21, 2016 at 5:56 AM, Eugenio Iglesias <e.igles...@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 > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > > > ----- Original Message ----- > From: Alan Francis <alandarkene...@gmail.com> > To: Juan Eugenio Iglesias <eigles...@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 > > >
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