Thanks, Bruce. I pasted the mri_segment and mris_make_surfaces I found in three subjects’ logs. Expert opts would be -seg-wlo and -seg-ghi? Which values would be reasonable? Do they depend on scanning characteristics or do you have a sort of standard parameters for the software? Regards, Pedro Rosa.
Subject 1: #@# WM Segmentation Mon Feb 16 09:08:56 BRST 2015 \n mri_segment brain.mgz wm.seg.mgz \n doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 105.0 +- 4.5 [80.0 --> 125.0] GM (72.0) : 70.1 +- 13.5 [30.0 --> 96.0] setting bottom of white matter range to 83.6 setting top of gray matter range to 97.1 Subject 2: WM (105.0): 105.6 +- 4.6 [80.0 --> 125.0] GM (70.0) : 68.4 +- 13.5 [30.0 --> 96.0] setting bottom of white matter range to 81.9 setting top of gray matter range to 95.4 Subject 3: WM (105.0): 105.6 +- 4.3 [80.0 --> 125.0] GM (71.0) : 69.2 +- 13.9 [30.0 --> 96.0] setting bottom of white matter range to 83.2 setting top of gray matter range to 97.1 —— Subject 1: \n mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs Subject2 lh \n only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /Users/pedrogomesrosa/Desktop/Thin-rerun/Subject2/mri/filled.mgz... reading volume /Users/pedrogomesrosa/Desktop/Thin-rerun/Subject2/mri/brain.finalsurfs.mgz... reading volume /Users/pedrogomesrosa/Desktop/Thin-rerun/Subject2/mri/wm.mgz... 14199 bright wm thresholded. 1723 bright non-wm voxels segmented. reading original surface position from /Users/pedrogomesrosa/Desktop/Thin-rerun/Subject2/surf/lh.orig... computing class statistics... border white: 347738 voxels (2.07%) border gray 336007 voxels (2.00%) WM (95.0): 96.2 +- 6.5 [70.0 --> 110.0] GM (85.0) : 81.4 +- 13.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 57.8 (was 70) setting MAX_BORDER_WHITE to 105.5 (was 105) setting MIN_BORDER_WHITE to 71.0 (was 85) setting MAX_CSF to 44.5 (was 40) setting MAX_GRAY to 92.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 31.3 (was 40) Subject 2: setting MIN_GRAY_AT_WHITE_BORDER to 70.2 (was 70) setting MAX_BORDER_WHITE to 106.6 (was 105) setting MIN_BORDER_WHITE to 84.0 (was 85) setting MAX_CSF to 56.4 (was 40) setting MAX_GRAY to 93.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 77.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 42.5 (was 40) Subject 3: WM (97.0): 97.9 +- 6.2 [70.0 --> 110.0] GM (87.0) : 83.8 +- 13.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 71.5 (was 70) setting MAX_BORDER_WHITE to 107.2 (was 105) setting MIN_BORDER_WHITE to 85.0 (was 85) setting MAX_CSF to 57.9 (was 40) setting MAX_GRAY to 94.8 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 78.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 44.4 (was 40) On Wednesday, February 18, 2015 at 7:58 PM, Bruce Fischl wrote: > can you check mri_segmet and mris_make_surfaces and see if the > auto-detected intensity parameters are reasonable? Things like max gray > at csf border and such. If not, you can set them explicitly using the > expert opts - this usually works > Bruce > On Wed, 18 Feb 2015, Pedro Rosa - Gmail > wrote: > > > Hi, > > I am resending it once I could not find it in the archives. > > Thanks, > > Pedro. > > > > Dear Freesurfers, > > I am working on a 1.5T MPRAGE sample of first-episode psychosis and > > controls, and have found that some subjects end up having thin cortical > > surfaces with frequent unsegmented deep sulci. I think this was worse with > > FreeSurfer 5.3 than with FreeSurfer 5.1. I attached some screen shots of > > aparc+aseg labeling T1.mgz from a few of these subjects. > > This seems to be a widespread cortical issue, although it was heterogeneous > > across subjects (some of them seemed to have the “caudal half" of both > > hemispheres adequately segmented), and trying to simply rerun those > > subjects was not very helpful. Should I manually work on them, rerun > > recon-all with distinct parameters, or just discard them? > > Regards, > > Pedro Rosa. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu (mailto: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. > >
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