Re: [Freesurfer] Hippocampal Subsectioning
Hi, Joshua Just answered this to Mohammad Zia in a previous message and I guess it is useful to you. 1- The name Right-Hippocampus is misleading you. The hippocampal subfields segmentation is atlas based. And the atlas was generated from expert manual segmentation. The problem is that the most posterior part of hippocampal tail is too small to allow a precise segmentation. So they know it was part of hippocampus but not being able to discriminate the subfields in this portion they named as hippocampus. This name in manual segmentation was preserved in FreeSurfer's automated process. So in this list, Rigth-Hippocapus does not mean the whole right hippocampus. It is just the portion of the right hippocampus not segmented in subfields. You can see more details at https://surfer.nmr.mgh.harvard.edu/pub/articles/VanLeemputHippocampus2009.pdf . There you can read: Towards the tail of the hippocampus, the manual delineations no longer discern between the different subfields, but rather lump everything together as simply ‘‘hippocampus,’’ In my own data I renamed this to right hippocampal tail complement just to avoid this confusion. 2- Yes, just divide the volumeInVoxels value by eight (or multiply by 0.125, like Eugenio said) to get the volume in cubic milimeters. Marcos. Em Sex, 2014-07-11 às 11:46 -0400, Joshua S escreveu: Hi, I was doing a hippocampal subsectioning on a data set. Previously recon-all -all was used, and then I did recon-all -hippo-subfields. I then used the script kvlQuantifyHippocampalSubfieldSegmentations.sh to find the volume of the hippocampus and its sub parts. I was confused as to the data I was getting out. The hippocampus seems to large. The voxel size is 0.5 mm * 0.5 mm * 0.5 mm so the hippocampal areas seem to large. Also the subunits of the hippocampus are larger than the actual hippocampus which again does not make sense. I attached one of the output files Thank you for any replies, From Joshua Segaran ___ 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. ___ 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.
[Freesurfer] Hippocampal Subsectioning
Hi, I was doing a hippocampal subsectioning https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation on a data set. Previously recon-all -all was used, and then I did recon-all -hippo-subfields. I then used the script kvlQuantifyHippocampalSubfieldSegmentations.sh to find the volume of the hippocampus and its sub parts. I was confused as to the data I was getting out. The hippocampus seems to large. The voxel size is 0.5 mm * 0.5 mm * 0.5 mm so the hippocampal areas seem to large. Also the subunits of the hippocampus are larger than the actual hippocampus which again does not make sense. I attached one of the output files Thank you for any replies, From Joshua Segaran volume_in_number_of_voxels Right-Hippocampus right_presubiculum right_CA1 right_CA2_3 right_fimbria right_subiculum right_CA4_DG right_hippocampal_fissure ESZC063088.863806.93270.49527.04580.9615662.38 5160.47419.635 ESZC094474.984175.63495.299507.35610.4166002.32 5415.3764.783 ESZC173714.853549.983803.8510407.2236.3766100.06 5702.51498.232 ESZC192747.233018.232794.957421.49385.8454304.76 4006.76320.488 ESZC203651.644114.272849.188566.68679.9615988.08 4780.1270.116 ESZS043969.073151.292902.78127.18124.0435183.18 4956.47160.333 ESZS073839.453542.613582.489566.92644.8365774.21 5276.71308.941 ESZS143224.984186.212500.167324.79532.7775247.57 4348.97140.18 ESZS163153.163417.782777.058924.38917.1625016.83 5038.98129.952 ESZS173358.733223.232767.348336.61346.6285224.47 4779.15275.812 ___ 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.
Re: [Freesurfer] Hippocampal Subsectioning
Hi Joshua, the measurements are in voxels, so you need to multiply them by 0.125 (which is 0.5^3) to obtain values in mm3. 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: Joshua S nitrosomonas...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, July 11, 2014 5:46:59 PM Subject: [Freesurfer] Hippocampal Subsectioning Hi, I was doing a hippocampal subsectioning on a data set. Previously recon-all -all was used, and then I did recon-all -hippo-subfields. I then used the script kvlQuantifyHippocampalSubfieldSegmentations.sh to find the volume of the hippocampus and its sub parts. I was confused as to the data I was getting out. The hippocampus seems to large. The voxel size is 0.5 mm * 0.5 mm * 0.5 mm so the hippocampal areas seem to large. Also the subunits of the hippocampus are larger than the actual hippocampus which again does not make sense. I attached one of the output files Thank you for any replies, From Joshua Segaran ___ 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
