The instructions in part D of the pdf result in data that is already on the fsaverage standard mesh. If what you are trying to do with mris_preproc is just resample to fsaverage from subject native mesh, you can skip that step entirely.
This step looks suspicious: wb_command -surface-sphere-project-unproject \ $dataDir/$i/MNINonLinear/Native/$i.$hemi.sphere.native.surf.gii \ $spheres_to_project_to $spheres_to_unproject_to $new_native_spheres The instructions say to use the "MSMAll" sphere, but regardless, the input sphere must be one that is registered to fs_LR in some way (if this is not HCP data, so you can't run MSM on it yet, then I think you should use "$i.$hemi.sphere.reg.reg_LR.native.surf.gii"). Tim On Mon, Oct 31, 2016 at 3:48 PM, Timothy Hendrickson <[email protected]> wrote: > Ohh, here is the script with the .txt suffix. > > Once I finish this script I attempt to put my fsavg mapped gifti file: > 41815.R.32k_TJH_fsavg.func.gii into mris_preproc in order to re-sample the > data into the common subject fsaverage. > > mris_preproc --target fsaverage --hemi rh --s 41815 --is > /home/lnpi14-raid1/bryon-data-lnpi14/142_CIFASD/HCP_3.4.0/41 > 815/MNINonLinear/fsaverage_LR32k/41815.R.32k_TJH_fsavg.func.gii --out > 41815.32k.R.Myelin.mgh. > > I suppose I may have to ask the freesurfer mailing list about this. > > -Tim > > Timothy Hendrickson > Department of Psychiatry > University of Minnesota > Mobile: 507-259-3434 (texts okay) > > On Mon, Oct 31, 2016 at 3:33 PM, Timothy Coalson <[email protected]> wrote: > >> While our mailing list decided to remove your script because you didn't >> rename it to end in .txt, I would take a guess that you may be attempting >> to use a fsaverage data file with a native mesh surface, which won't work. >> I'm not sure how you tell freesurfer to analyze on a particular mesh. It >> is also possible to resample fs_LR data onto each subject's native mesh, if >> that is what freesurfer requires. >> >> Tim >> >> >> On Mon, Oct 31, 2016 at 2:28 PM, Timothy Hendrickson <[email protected]> >> wrote: >> >>> WARNING: This e-mail has been altered by MIMEDefang. Following this >>> paragraph are indications of the actual changes made. For more >>> information about your site's MIMEDefang policy, contact >>> MIMEDefang Administrator's Full Name <postmaster@localhost>. For more >>> information about MIMEDefang, see: >>> >>> http://www.roaringpenguin.com/mimedefang/enduser.php3 >>> >>> An attachment named myelinMap_FreeSurferResampling.sh was removed from >>> this document as it >>> constituted a security hazard. If you require this document, please >>> contact >>> the sender and arrange an alternate means of receiving it. >>> >>> >>> _______________________________________________ >>> HCP-Users mailing list >>> [email protected] >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> >>> >>> Hello HCP experts, >>> >>> I have been attempting to maps individual myelin maps to freesurfer >>> using part D of the how to document provided by Coalson and colleagues: >>> https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ. >>> <https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ> >>> Following the conversion I was attempting to utilize the freesurfer >>> mapped myelin maps in a group analysis by first feeding it through the >>> freesurfer command mris_preproc and then mri_surf2surf. >>> >>> Once I did this I received the following error: >>> >>> >>> >>> *ERROR: dimension inconsistency in source data Number of surface >>> vertices = 161845 Number of value vertices = 163842* >>> This may be more of a FreeSurfer mailing list question, but first I was >>> hoping that a HCP expert could take a look at my script to ensure that it >>> is accurate. >>> >>> Respectfully, >>> >>> -Tim >>> >>> Timothy Hendrickson >>> Department of Psychiatry >>> University of Minnesota >>> Mobile: 507-259-3434 (texts okay) >>> >>> _______________________________________________ >>> HCP-Users mailing list >>> [email protected] >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> >>> >> > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
