Great, thanks! Claude
On 18.08.2017 16:08, Glasser, Matthew wrote: > For the 32k 2mm average spacing surfaces you can find the standard medial > wall definitions here: > > https://github.com/Washington-University/Pipelines/blob/master/global/templ > ates/91282_Greyordinates/L.atlasroi.32k_fs_LR.shape.gii > https://github.com/Washington-University/Pipelines/blob/master/global/templ > ates/91282_Greyordinates/R.atlasroi.32k_fs_LR.shape.gii > > These are the same as are used to produce the CIFTI files. These are the > definitions of cortex, so you will need to subtract 1 and multiply by -1 > to get a medial wall ROI with ones inside the ROI and zeros for the > cortex. > > Peace, > > Matt. > > On 8/18/17, 8:55 AM, "hcp-users-boun...@humanconnectome.org on behalf of > Claude Bajada" <hcp-users-boun...@humanconnectome.org on behalf of > c.baj...@fz-juelich.de> wrote: > >> Hi all, >> >> I had asked a question on this forum a while ago related to medial wall >> structures in cifti and gifti files and I have a follow-up question. >> >> I have been going through the gifti file format and have learned that >> the medial wall structures are labeled as ??? >> >> Unfortunately, it seems that most programmes do not output these vertex >> indices easily (or at least this is my impression). I tend to use the >> matlab gifti library by Guillaume Flandin >> (https://www.artefact.tk/software/matlab/gifti/) >> >> I need to know the medial wall indices in order to exclude them from >> some tractography seeds that I am generating. >> >> The way I have been retrieving these indices so far is: >> >> 1) locate the file ${side}.aparc.32k_fs_LR.label.gii in folder >> MNINonLinear/fsaverage_LR32k/ >> >> 2) load it in matlab > aparc = gifti('${side}.aparc.32k_fs_LR.label.gii'); >> >> 3) identify the data (aparc.cdata) that are associated with label ??? >> and store the indices >> >> My questions are: >> >> a) are these vertices standard across all of the brain? eg one >> participant has 2425 midline vertices. Should all HCP participants have >> the same vertices or do these differ slightly across subjects? >> >> b) can I just map these indices onto the T1 (32k resampled) vertices, in >> order to exclude these areas from my tractography? >> >> Regards, >> >> Claude >> >> >> >> >> >> -------------------------------------------------------------------------- >> ---------------------- >> -------------------------------------------------------------------------- >> ---------------------- >> Forschungszentrum Juelich GmbH >> 52425 Juelich >> Sitz der Gesellschaft: Juelich >> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 >> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher >> Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), >> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, >> Prof. Dr. Sebastian M. Schmidt >> -------------------------------------------------------------------------- >> ---------------------- >> -------------------------------------------------------------------------- >> ---------------------- >> >> >> _______________________________________________ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
