Hi FR, This is rather an odd file. I did 3dhistog on it and got this output:
http://brainmap.wustl.edu/pub/donna/SPAIN/BCBL/your_file.3dhistog.txt login pub password download Mostly zeroes, but 14184 voxels set to 32766 (and no voxels set to any values in between 0 and 32766). And when I map this to the PALS atlas, I get nothing on most vertices, but solid yellow over a perisylvian blob. And when I click in the yellow, sure enough the ID window confirms the vertex is set to 32766 intensity. Working as expected, but data a bit off the beaten path. Donna On Jun 21, 2015, at 4:55 PM, Frédéric Roux <f.r...@bcbl.eu> wrote: > Hi Dona, > > thanks for getting back on this. > I am using NIFTI, so nothing rare from that side. > > Just uploaded the file via the link you sent me. > > Thanks for looking into this. > > -- > FR > > ----- Original Message ----- > From: "Donna Dierker" <do...@brainvis.wustl.edu> > To: "SureFit Caret, and SuMS software users" <caret-users@brainvis.wustl.edu> > Sent: Sunday, June 21, 2015 6:37:50 PM > Subject: Re: [caret-users] negative values displayed positive > > I'm not sure what would do this. What format is your volume? NIFTI? Older > .hdr/.img pairs sometimes got x-flipped upon opening under some > circumstances, but nothing I know of (except explicit *(-1) using volume > math) does this. > > You can use something AFNI 3dinfo or 3dhistog to double-check your volume's > values, or you can upload your volume here and I can do so tomorrow: > > http://brainvis.wustl.edu/cgi-bin/upload.cgi > > You can also have a look at the palette format, and just make sure it's not > the palette that is making your values appear to be flipped: > > http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/file_formats.html#paletteFile > > Caret has some built-in palettes (see D/C: Metric Settings menu). > > > On Jun 21, 2015, at 3:55 AM, Frédéric Roux <f.r...@bcbl.eu> wrote: > >> Dear all, >> >> I'm trying to map a functional volume to the PLAS-B12 >> surface but the sign of the values gets flipped so that >> negative values appear as positive ones. >> >> Does anyone know what could be wrong? >> >> Many thanks. >> >> Fred >> >> -- >> FR >> >> ----- Original Message ----- >> From: "Matt Glasser" <m...@ma-tea.com> >> To: "SureFit Caret, and SuMS software users" <caret-users@brainvis.wustl.edu> >> Sent: Saturday, June 20, 2015 11:37:53 PM >> Subject: Re: [caret-users] Missing parts in MyelinMap+Different number of >> nodes! >> >> Yes please use the HCP pipelines for myelin mapping. >> >> Peace, >> >> Matt. >> >> On 6/19/15, 4:17 AM, "Donna Dierker" <do...@brainvis.wustl.edu> wrote: >> >>> Hi Xara, >>> >>> Because you are in the enviable position of having high res T1 AND T2, >>> you may be able to use the Human Connectome Project pipelines on your >>> data, rather than this (older generation) caret-based myelin mapping >>> script: >>> >>> http://www.humanconnectome.org/documentation/HCP-pipelines/ >>> >>> This also has the advantage of writing output files in workbench formats, >>> rather than older caret formats. I have a hunch that Matt Glasser will >>> point you in that direction (he is probably at OHBM conference or on his >>> way home). >>> >>> I confess I am not as familiar with this script as Matt is, but from what >>> I read at the link you sent, it appears the maps are on the native mesh, >>> rather than 164k. And I don't see myelin represented in the list of >>> freesurfer_to_fs_LR output files here: >>> >>> http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/Freesurfer_to_fs >>> _LR/Output >>> >>> (These were independent efforts going on at roughly the same time.) >>> >>> You may already have considered the HCP pipeline route, but if not, it is >>> worth a look -- you've got the T2's at the right res, which is often a >>> hitch. I suspect myelin maps on 164k won't be your only benefit. >>> >>> Donna >>> >>> >>> On Jun 19, 2015, at 8:58 AM, "Shams, Z." <z.sh...@donders.ru.nl> wrote: >>> >>>> Dear users, >>>> >>>> >>>> >>>> I just started working with Caret for creating myelin maps. I used HCP >>>> imaging protocols for data acquisition, both T1 and T2 data have the >>>> voxel size of 0.7mm isotropic. >>>> >>>> I followed the instructions in >>>> http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/MyelinMapping. >>>> >>>> Actually I managed to display the four outputs, but some parts of the >>>> maps are missing when overlaying on a surface(they¹re not complete maps: >>>> either raw or corrected myelin maps). >>>> >>>> Another problem is that I used the freesurfer to fs LR script to >>>> convert all my freesurfer files to the 164k_fs_LR mesh, >>>> >>>> but when I try to show the myelin maps on e.g. very-inflated 164k fs >>>> LR, It fails with the error of containing a different number of nodes >>>> thanŠ . >>>> >>>> >>>> >>>> I¹d appreciate any help and instructions. >>>> >>>> >>>> >>>> Thanks, >>>> >>>> >>>> Xara >>>> >>>> _______________________________________________ >>>> caret-users mailing list >>>> caret-users@brainvis.wustl.edu >>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>> >>> >>> _______________________________________________ >>> caret-users mailing list >>> caret-users@brainvis.wustl.edu >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> >> >> _______________________________________________ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> _______________________________________________ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
