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