Its the "T1w_restore.nii.gz" image that wb_view defaults to using for volume views--the one that I believe is stored in the MNINonlinear directory (the first screenshot came from wb_view, the second set of unprocessed data screen shots came from fslview). As for fatsat, I'm not sure but I'll check with our sequence programmer. Do you?
__________________________ gaurav patel [email protected] www.neurofreak.net > On Oct 24, 2014, at 3:04 PM, Glasser, Matthew <[email protected]> wrote: > > Is that image you initially sent one of the down sampled FreeSurfer > images? It seems a lot blurrier than your raw images. > > Do you use fatsat in your T1w images? > > Peace, > > Matt. > > 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> >> >> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > ________________________________ > 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
