Ok thanks I might try that...that slice shows a couple more errors in the occipital lobe and they show up as clear artifact in the myelin maps. Its not fatal since it basically just means that we can't rely on data in those few spots but of course the perfectionist in me is irked. Thanks for the help
__________________________ gaurav patel [email protected] www.neurofreak.net > On Oct 24, 2014, at 3:19 PM, Harms, Michael <[email protected]> wrote: > > > FWIW, the surface error at the crosshair position in your original > snapshot seemed relatively minor from that single slice. One thing you > could try before bringing the subject back would be to just run the > pipeline using only the better of the two T1w scans that you acquired. > > cheers > -MH > > -- > Michael Harms, Ph.D. > > ----------------------------------------------------------- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: [email protected] > > > > > On 10/24/14 2:05 PM, "Gaurav Patel" <[email protected]> wrote: > >> Thanks...we'll be bring the subject back so we'll reacquire anatomy then >> and see what happens >> >> __________________________ >> gaurav patel >> [email protected] >> www.neurofreak.net >> >> >> >> >>> On Oct 24, 2014, at 3:04 PM, Harms, Michael <[email protected]> wrote: >>> >>> >>> It's not that errors in the surfaces are *never* present, but HCP >>> structurals are indeed overall pretty awesome! :) >>> We work hard to reacquire additional structurals when necessary so that >>> all the HCP subjects have a "good" structural or better. >>> In the small number of cases where there are very localized issues in >>> the >>> surfaces we have just accepted those. >>> In the very small number of cases with larger issues (e.g., due to a >>> problem during FS's topology correction) we have just set those subjects >>> aside (not released them yet) while we focusing on processing other >>> subjects. >>> >>> cheers, >>> -MH >>> >>> -- >>> Michael Harms, Ph.D. >>> >>> ----------------------------------------------------------- >>> Conte Center for the Neuroscience of Mental Disorders >>> Washington University School of Medicine >>> Department of Psychiatry, Box 8134 >>> 660 South Euclid Ave. Tel: 314-747-6173 >>> St. Louis, MO 63110 Email: [email protected] >>> >>> >>> >>> >>> On 10/24/14 1:49 PM, "Gaurav Patel" <[email protected]> wrote: >>> >>>> ok thanks...I was wondering how you guys handle errors like these? Or >>>> are your data so awesome that it never happens? ;-) >>>> >>>> __________________________ >>>> gaurav patel >>>> [email protected] >>>> www.neurofreak.net >>>> >>>> >>>> >>>> >>>> On Oct 24, 2014, at 2:46 PM, Harms, Michael wrote: >>>> >>>>> >>>>> Hi Gaurav, >>>>> As the pipelines currently stand, they haven't yet been extended to >>>>> incorporate manual FS edits. It shouldn't be overly difficult for >>>>> someone familiar with FS editing and the various stages in FS to >>>>> modify >>>>> the pipelines appropriately. >>>>> >>>>> cheers, >>>>> -MH >>>>> >>>>> -- >>>>> Michael Harms, Ph.D. >>>>> ----------------------------------------------------------- >>>>> Conte Center for the Neuroscience of Mental Disorders >>>>> Washington University School of Medicine >>>>> Department of Psychiatry, Box 8134 >>>>> 660 South Euclid Ave. Tel: 314-747-6173 >>>>> St. Louis, MO 63110 Email: [email protected] >>>>> >>>>> From: Gaurav Patel <[email protected]> >>>>> Date: Friday, October 24, 2014 1:37 PM >>>>> To: HCP Users <[email protected]> >>>>> Subject: [HCP-Users] freesurfer errors >>>>> >>>>> Hi! I've run a number of subjects acquired on our GE scanner through >>>>> the pipeline without issue until now. With this particular subject I >>>>> am >>>>> seeing freesurfer segmentation errors where the pial surface estimate >>>>> includes dura (see attached picture--scan was 2x.8mm isotropic FSPGR). >>>>> These errors are present with freesurfer versions 5.2 and 5.3-HCP (I >>>>> haven't tried plain 5.3 yet but my guess is that it would be the >>>>> same). >>>>> I know how to correct these when using freesurfer by itself, but I was >>>>> wondering how you handle this within the pipeline--it seems that I >>>>> would >>>>> have to manually skip the initial parts of the FreeSurfer pipeline to >>>>> incorporate my manual edits which seems messy. Any advice? Thanks! >>>>> >>>>> >>>>> _______________________________________________ >>>>> HCP-Users mailing list >>>>> [email protected] >>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>>> <Screen shot 2014-10-24 at 2.29.37 PM.png> >>>>> >>>>> >>>>> __________________________ >>>>> gaurav patel >>>>> [email protected] >>>>> www.neurofreak.net >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> The materials in this message are private and may contain Protected >>>>> Healthcare Information or other information of a sensitive nature. If >>>>> you are not the intended recipient, be advised that any unauthorized >>>>> use, disclosure, copying or the taking of any action in reliance on >>>>> the >>>>> contents of this information is strictly prohibited. If you have >>>>> received this email in error, please immediately notify the sender via >>>>> telephone or return mail. >>>>> >>>>> <Screen shot 2014-10-24 at 2.29.37 PM.png> >>>> >>> >>> >>> ________________________________ >>> The materials in this message are private and may contain Protected >>> Healthcare Information or other information of a sensitive nature. If >>> you are not the intended recipient, be advised that any unauthorized >>> use, disclosure, copying or the taking of any action in reliance on the >>> contents of this information is strictly prohibited. If you have >>> received this email in error, please immediately notify the sender via >>> telephone or return mail. >> > > > ________________________________ > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you are > not the intended recipient, be advised that any unauthorized use, disclosure, > copying or the taking of any action in reliance on the contents of this > information is strictly prohibited. If you have received this email in error, > please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
