Can you send the aseg2feat log file? Also, please remember to post to the list instead of to me personally. thanks! doug
On 11/19/2013 03:17 PM, Sudhin A. Shah wrote: > yes, it looks fine.. > ________________________________________ > From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] > Sent: Tuesday, November 19, 2013 2:50 PM > To: Sudhin A. Shah; Freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Aseg2feat: Missing segmentations > > Those are some big segs. Have you checked the registration? > > > On 11/19/2013 02:41 PM, Sudhin A. Shah wrote: >> yes :) For example in this 1 subject segs ( >> 2005 2008 2010 2011 2013 2021 2023 2025 >> 2029 1005 1008 1011 1013 1021) are all missing.. >> >> The missing segs are not consistent across subjs(i.e. other subjs have >> different segs missing). I chose a list of 86 segs to 'cover' the brain and >> not sure if I was over-reaching..Also some segs are reading with value 100 >> (i.e. all voxels have a value of 100)? >> >> >> >> ________________________________________ >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve >> [gr...@nmr.mgh.harvard.edu] >> Sent: Tuesday, November 19, 2013 2:34 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Aseg2feat: Missing segmentations >> >> there were probably some small segmentations that were lost. Is this >> causing a problem? >> On 11/19/2013 02:22 PM, Sudhin A. Shah wrote: >>> Hello, >>> >>> This is regarding the registration of functional data to freesurfer >>> parcellations >>> (http://freesurfer.net/fswiki/FsTutorial/MapSegmentationsToFunctionalSpace). >>> >>> The rsfMRI is sampled at 2x2x2. >>> >>> After running reg-feat2anat and aseg2feat >>> >>>>> a = MRIread('aparc+aseg'); %Original aparc+aseg output from >>> freesurfer recon-all >>>>> size(unique(a.vol(:))) % 114 segs >>>>> a = MRIread('aparc+aseg'); % this is the output file after aseg2feat >>>>> size(unique(a.vol(:))) % 98 segs >>> Any advice? >>> >>> Thanks >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> 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. >> >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
