Yeah, several years back, we started tapering off on the flat views in favor of the inflated or very inflated views. Internally, I think we still use flat maps quite a bit, but for publication purposes, the inflated and very inflated views are more easily understood for many readers.
My guess is that the colin cortical flat maps have been registered to fs_LR via PALS and exist in some dataset, though apparently not in the ones supporting that publication's figures. Yet another guess is that a more general purpose visualization specification for fs_LR will be released within the next year. It feels a bit early to do it right now, though. On Feb 25, 2012, at 1:24 PM, Sergei Bogdanov wrote: > ---------------------------------------- >> From: [email protected] >> Date: Fri, 24 Feb 2012 15:55:47 -0600 >> To: [email protected] >> Subject: Re: [caret-users] FNIRT stereotaxic space >> >> Only the Conte69 surfaces are available for FNIRT mapping; there are no PALS >> surfaces that have been registered using FNIRT -- just FLIRT and the other >> methods listed here: >> >> http://brainvis.wustl.edu/help/pals_volume_normalization/ >> >> The Conte69 surfaces are on the new fs_LR standard mesh (164k vertices), >> which is described in this paper: >> >> http://www.ncbi.nlm.nih.gov/pubmed/22047963 >> >> The datasets for this paper are here: >> >> HUMAN_ATLAS_CC11 >> http://sumsdb.wustl.edu/sums/directory.do?id=8286149 >> >> So you could map to the Conte69 FNIRT surfaces, and then perhaps use one of >> the fs_LR datasets from this paper to visualize your results (e.g., on the >> fs_LR inflated surface). > > .. right .. thank you. I noticed there were no flat maps either in the paper > or the fs_LR datasets. Is there any particular reason to prefer inflated and > very inflated four-hemisphere display (left/right medial lateral views) to > two-hemisphere (left/right) flat maps? Easier to orient on the inflated > cortical surfaces? > .. again, thank you for your help,Sergei >> >> >> On Feb 24, 2012, at 2:44 PM, Sergei Bogdanov wrote: >> >>> >>> Dear list, >>> >>> I downloaded Caret v 5.65 hoping to take advantage of the newly added FNIRT >>> stereotaxic space but when I try to map Volume (Metric FSL processed data >>> in standard MNI space) to Surface, having chosen a couple of volumes, >>> proceeded to Atlas Surface Selection dialog box, selected "FNIRT" under >>> space pulldown, I see only Conte69 mid thickness Left and Right maps and >>> not expected "PALS_B12 Multi-Fid Map Left/Right hemisphere (73730 nodes), >>> MNI 305 (FNIRT) space" or something to that effect a la "FLIRT" pulldown. >>> >>> Am I missing something obvious here? Should I use FLIRT stereotaxic space >>> option to project FLIRT+FNIRT registered SPMs to PALS_B12 atlas? >>> >>> Thanks you, >>> Sergei >>> >>>> >>>> >>>> Caret 5.65 is released. It contains these fixes and added features: >>>> >>>> * WashU 711-2* PALS-B12 left hem mapping only: Fix a problem with PALS_B12 >>>> left case 03 and average fiducial surfaces >>>> (http://brainvis.wustl.edu/help/wustl_origin/align2.2). >>>> * Add an error check in case a file is truncated. >>>> * Add FNIRT stereotaxic space and Conte69 (FNIRT) surfaces as map to atlas >>>> options. >>>> * Add myelin mapping features >>>> (http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/MyelinMapping#Preliminaries:_Producing_brain_surfaces_in_FreeSurfer). >>>> >>>> >>> >>> _______________________________________________ >>> caret-users mailing list >>> [email protected] >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> >> _______________________________________________ >> caret-users mailing list >> [email protected] >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
