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 -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| *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 |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
