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 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 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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Alan N. Francis PhD
NIDA T32  Fellow in Computational Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
alanf@bwh.harvard.edu
                                                                                                          
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