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 -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| *Alan N. Francis PhD* NIDA T32 Fellow in Computational Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 al...@bwh.harvard.edu <ezra_wegbr...@brown.edu> afran...@mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
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