I would ask on the FreeSurfer mailing list how to convert those file types to GIFTI as we are not familiar with them.
Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of Timothy Coalson <[email protected]<mailto:[email protected]>> Date: Tuesday, September 12, 2017 at 1:43 PM To: Xavier Guell Paradis <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Resampling freesurfer-HCP I am not familiar with the .w format, but it sounds like mris_convert is not actually converting it to gifti format. The second error from the .mgh method sounds like it has the surface geometry in the file, which must be removed - workbench requires geometry files (.surf.gii) and data files (.func.gii) to be separate. You could also start from the unthresholded file instead, which would not have this apparently unusual .w format. We generally don't recommend thresholding, but instead making outlines of what is significant, and showing that on top of the unthresholded beta. Tim On Tue, Sep 12, 2017 at 1:21 PM, Xavier Guell Paradis <[email protected]<mailto:[email protected]>> wrote: I thought it might be useful to add that the initial .w file is thresholded and does not contain values for all cerebral cortical regions. Thank you very much, Xavier. ________________________________________ From: [email protected]<mailto:[email protected]> [[email protected]<mailto:[email protected]>] on behalf of Xavier Guell Paradis [[email protected]<mailto:[email protected]>] Sent: Tuesday, September 12, 2017 2:05 PM To: [email protected]<mailto:[email protected]> Subject: [HCP-Users] Resampling freesurfer-HCP Dear HCP experts, I have an overlay freesurfer file (format is .w) which corresponds to a task activity surface map (group result). I have one .w file for each cerebral hemisphere. I would like to visualize these maps using wb_view, and have tried to follow the instructions you published (https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?). As a first step I would need to convert the .w files into .func.gii files using mris_convert. Then I would use wb_command -metric-resample, as indicated in your instructions. This does not seem to work with my .w file: 1) mris_convert myfile.w myfile.func.gii This generates myfile.func.gii, but when I use wb_command -metric-resample I get the following error: ERROR: Parse error while reading: error occurred while parsing element, line number: 1 column number: 1 2) As an alternative approach, I opened myfile.w using Tksurfer and saved the overlay (myfile.w) with .mgh format (generating a new file: "myfile.mgh"). Then I do the following: mris_convert myfile.mgh myfile.func.gii This generates the myfile.func.gii file, but when I use wb_command -metric-resample with this file I get a different error: ERROR: All data arrays (columns) in the file must have the same number of rows. The first array (column) contains 163842 rows. Array 2 contains 327680 rows. Thank you very much for your help, Xavier. _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
