External Email - Use Caution but this(bright at back and nose) also seems to be the case with participants that sclimbic did work on..
________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgr...@mgh.harvard.edu> Sent: Tuesday, August 9, 2022 10:34 PM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain There was something a little strange about the cases that were failing -- there were very bright values at the back of the head and around the nose. This probably messes up the normalization in the unet. I ran it with --percentile 99.9 (this eliminates the extreme voxels) and the results looked ok after that. On 7/28/2022 8:58 PM, Miriam Taza wrote: Nothing strange about them. They’re T1w scans 1x1x1mm3 ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu> Sent: Thursday, July 28, 2022 1:25 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain Have you looked at the input volume to see if there is anything strange about them? What kind of scans are you passing to it? What is the resolution? On 7/25/2022 9:03 PM, Miriam Taza wrote: External Email - Use Caution Hello, I noticed 20 out of ~240 subjects left basal forebrain volumes were not picked up after running ScLimbic. These are healthy adults and their scans look good. Also, I noticed often when this occurs NAcc is also 0 or other regions. I am concerned if there is a systematic issue with left volumes ending up smaller than they should relative to right. Thanks, Miriam _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1bdJ7eSEQYRD2FPgV6NRFzLuzQauFkpPX73bP5cDW-fqppDs6bY7vBCvM-_N8SBIwIqwyVRBRmezZs3Zcw4Ey0wyT_fg4hAC_mcA8gcoDJofmViLRBbgEd06MBYauwYT8l6cPjqPxMGhSCkggK6BFzR31Gd2b7Yx9pQhrwq-2gJ0JlJPrYkTCKJFZlhyrwe4kncO9Uyfe-wfT7uXxdnQ-9A6bUhDk-ZsA11lUjScted9rEiWyJWXteSCMHTKDoh69G_X01YzCAgj0Z0CyQUKkdYkVemUAgZnOgkz0K9IfOkV684Da5YZpoXIlLh0nca1D/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1bdJ7eSEQYRD2FPgV6NRFzLuzQauFkpPX73bP5cDW-fqppDs6bY7vBCvM-_N8SBIwIqwyVRBRmezZs3Zcw4Ey0wyT_fg4hAC_mcA8gcoDJofmViLRBbgEd06MBYauwYT8l6cPjqPxMGhSCkggK6BFzR31Gd2b7Yx9pQhrwq-2gJ0JlJPrYkTCKJFZlhyrwe4kncO9Uyfe-wfT7uXxdnQ-9A6bUhDk-ZsA11lUjScted9rEiWyJWXteSCMHTKDoh69G_X01YzCAgj0Z0CyQUKkdYkVemUAgZnOgkz0K9IfOkV684Da5YZpoXIlLh0nca1D/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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