You want to run MSMAll on sICA+FIX cleaned data for sure. As far as your question about the MSMAll pipeline inputs, I would need to see what you have.
Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Sang-Young Kim <sykim...@gmail.com<mailto:sykim...@gmail.com>> Date: Friday, September 28, 2018 at 6:55 PM To: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> Cc: hcp-users <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Question about Multi-Modal Surface Mapping Thanks for prompt response! Tim! Yes, the volume files are individual results. And this data is not part of HCP S1200 released data, but for the our data. That’s why "SubjID=300" seems to be unclear to you. I have one more quick question. If I want to have MSMAll-registered data for "$StudyFolder/$Subject/MNINonLinear/Results/rfMRI_REST1_AP/rfMRI_REST1_AP_Atlas.dtseries.nii" (which is not FIX-cleaned data), do I have to run MSMAll pipeline with changing input variable name? or is there a simple command for getting that as volume-to-surface-mapping? Thanks again. Sang-Young On Sep 28, 2018, at 7:42 PM, Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> wrote: If the volume files are per-individual results, then mapping them to that individual's own MSMAll surfaces will result in them being accurately registered through multimodal surface matching, yes. I am not clear on the "SubjID=300" line, though. To be clear, group average "subjects" do not count for this process, and any group MNI space volume results for all of cortex can't be accurately mapped to surfaces (the accuracy has already been lost due to volume-based group averaging). However, the typical HCP process is to put the unprocessed (well, preprocessed) individual cortical data onto surfaces via the individual's own surfaces, and then compute results in cifti space, not MNI. We typically use the native mesh surfaces to achieve the most fidelity to the original segmentation, and then resample afterward, but the 32k surfaces are probably good enough. Tim On Fri, Sep 28, 2018 at 6:04 PM, Sang-Young Kim <sykim...@gmail.com<mailto:sykim...@gmail.com>> wrote: Dear Experts: I have a certain kinds of volume maps in MNI space. I would like to mapping this map to surface. I know how to use wb_command -volume-to-surface-mapping. My question is that if I use following command, is this also multi-modal surface matched map? StudyFolder="/Volumes/easystore/projects/HCP" SubjID="300" AtlasFolder="$StudyFolder/$SubjID/MNINonLinear/fsaverage_LR32k" ResultFolder="$StudyFolder/$SubjID/MNINonLinear/Results/rfMRI_REST1_AP" MapName="rfMRI_REST1_AP_map_tstat.nii.gz" # Left hemi /Applications/workbench/bin_macosx64/wb_command -volume-to-surface-mapping \ $ResultFolder/$MapName \ $AtlasFolder/${SubjID}.L.midthickness_MSMAll.32k_fs_LR.surf.gii \ $ResultFolder/L.card_coupling_tstat.32k_fs_LR.func.gii \ -ribbon-constrained $AtlasFolder/${SubjID}.L.white_MSMAll.32k_fs_LR.surf.gii \ $AtlasFolder/${SubjID}.L.pial_MSMAll.32k_fs_LR.surf.gii \ If not, could anyone please let me know how to do that? Thanks in advance. Best, Sang-Young _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
