Thank you,
The problem was that the computer I was using before had an older version of workbench. It works on my current computer. As far as using -cifti-label-to-roi How would that work with files like Human.Brodmann09.32k_fs_LR.dlabel.nii where the ROIs in both hemispheres are under the same key? If I want to look at BA44 in the right hemisphere only, for example, how can I separate it from BA44 in the left hemisphere to look at them separately? Thank you, Michael ________________________________ From: Timothy Coalson <tsc...@mst.edu> Sent: Tuesday, September 27, 2016 4:10:15 PM To: Michael F.W. Dreyfuss Cc: Burgess, Gregory; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data The surface structures in -cifti-separate are much coarser, they represent the cifti file organization, not the parcellation areas. You want CORTEX_LEFT and CORTEX_RIGHT for that command to work. However, the outputs are gifti files, not cifti files - it is a format conversion command, and probably not what you want to do. Instead of separating to gifti files, you should use -cifti-label-to-roi on the dlabel file to get the areas by name as separate ROIs (as dscalar files), and then use -cifti-merge and -cifti-reduce to combine them back into one larger ROI. Tim On Tue, Sep 27, 2016 at 10:36 AM, Michael F.W. Dreyfuss <mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>> wrote: I can get separate the volumetric part of cifti files with a command like: wb_command -cifti-separate ToyNogo_fdr_palm/ToyNogo_results_merged_tstat.dscalar.nii COLUMN -volume ACCUMBENS_RIGHT R_Acc_Beta.nii.gz -roi R_NAcc_ROI.nii.gz But when I try that on surface data I get the error: wb_command -cifti-separate ToyNogo_GlasserParcellation_FLOBS1_fdr_palm/ToyNogo_results_dat_tstat.pscalar.nii COLUMN -label R_IFSp_ROI ToyNogo_R_IFSp_Beta.pscalar.nii -roi R_IFSp_ROI.plabel.nii ERROR: unrecognized structure type The problem seems to be in recognizing the structures name (i.e. R_IFSp_ROI). Do you know how I can reference a specific structure or structures with a command from a label file, or is there another comparable command you would suggest for isolating structures from a label file? Thank you, Michael On Sep 27, 2016, at 10:41 AM, Burgess, Gregory <gburg...@wustl.edu<mailto:gburg...@wustl.edu>> wrote: HCP did not have a task that was geared toward response inhibition. Furthermore, although it’s alluring to believe that a single parcel will encapsulate all of response inhibition, it’s doubtful. Why not select a set of parcels in and near IFG, and correct for multiple comparisons? Use a meta-analysis as your guide (https://urldefense.proofpoint.com/v2/url?u=http-3A__neurosynth.org_analyses_terms_response-2520inhibition_&d=DQIGaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg&m=Pb-c1m96L6xixMU-j16J-GkC6tGV5lAdGNKy-Tj1ht8&s=DxHCajoqQSf0nIWSDbUHyB6J7F2eax1NswvaNpprHaU&e= ). Your statistical power should still benefit from the parcellated analysis and reduced number of multiple comparisons, relative to a whole-brain analysis. --Greg ____________________________________________________________________ Greg Burgess, Ph.D. Staff Scientist, Human Connectome Project Washington University School of Medicine Department of Psychiatry Phone: 314-362-7864<tel:314-362-7864> Email: gburg...@wustl.edu<mailto:gburg...@wustl.edu> On Sep 27, 2016, at 9:26 AM, Michael F.W. Dreyfuss <mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>> wrote: I agree, that’s why I was checking in to see if there was a sub parcel you had identified as being involved in response inhibition from your tasks, such as flanker. There is a lot of background of IFG being involved in response inhibition, particularly on go/nogo tasks,, so I was wondering if you had any information on specifically where within your parcellation that may be most relevant. On Sep 27, 2016, at 9:57 AM, Harms, Michael <mha...@wustl.edu<mailto:mha...@wustl.edu>> wrote: Just a reminder to be careful here to avoid issues of circularity/double-dipping. You indicated that you had a priori hypotheses about IFG involvement, but that doesn’t allow you to then select a particular IFG parcel based on your task activation map. Ideally, you would have selected your parcel(s) for analysis prior to ever computing/viewing your activation map (unless what you showed was a map from an independent, unrelated set of subjects). _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=DQIGaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg&m=Pb-c1m96L6xixMU-j16J-GkC6tGV5lAdGNKy-Tj1ht8&s=Kd8JGIfyDD_MWOgH24WZFrQNLqIT2e2KIaFCaLTw3PM&e= --Greg ____________________________________________________________________ Greg Burgess, Ph.D. Staff Scientist, Human Connectome Project Washington University School of Medicine Department of Psychiatry Phone: 314-362-7864<tel:314-362-7864> Email: gburg...@wustl.edu<mailto:gburg...@wustl.edu> ________________________________ 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<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users<https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=DQMFaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg&m=GLk8ZFeALgLFOe44nmJR8JhUU8AATE8ejixj1y8UUjU&s=sDifBL9DsX7F0QBwdQMXdbM7fJElwLj6-2S2HMo7sBg&e=> _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
