The easier way is to use -cifti-merge (or wb_shortcuts -cifti-concatenate for simpler syntax), then -cifti-reduce. It is possible to do with -cifti-math, but not as convenient.
Tim On Tue, Sep 27, 2016 at 4:37 PM, Michael F.W. Dreyfuss < mid2...@med.cornell.edu> wrote: > Thank you, that works. Then if I want multiple parcels to be collapsed > into a single ROI to make a mask spanning several ROIs that are not > considered separate keys, which command would do that. > > Thank you, > Michael > > > On Sep 27, 2016, at 5:26 PM, Timothy Coalson <tsc...@mst.edu> wrote: > > The easiest way to deal with this is probably to use -cifti-separate to > get them as gifti label files, which are each single-hemisphere. The use > of the same key/name for both hemispheres was an unfortunate choice, which > we intended to avoid in the future. > > Tim > > > On Tue, Sep 27, 2016 at 4:15 PM, Michael F.W. Dreyfuss < > mid2...@med.cornell.edu> wrote: > >> 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> 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_FL >>> OBS1_fdr_palm/ToyNogo_results_dat_tstat.pscalar.nii COLUMN -label >>> R_IFSp_ROI ToyNogo_R_IFSp_Beta.pscalar.ni >>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__ToyNogo-5FR-5FIFSp-5FBeta.pscalar.ni&d=DQMFaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg&m=RNChVFlNku6C4rq5ASbFdbABN7bwTnnLDhy6op63_hY&s=qzxt7r-90CndJvK0gVl2yx_UvsFswqgrT2CDYJdSaLM&e=>i >>> -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> >>> 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__neurosy >>> nth.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 >>> Email: gburg...@wustl.edu >>> >>> On Sep 27, 2016, at 9:26 AM, Michael F.W. Dreyfuss < >>> 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> 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 >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.hu >>> manconnectome.org_mailman_listinfo_hcp-2Dusers&d=DQIGaQ&c=lb >>> 62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=rPclmYysc_z1plf9 >>> 9IoNsmxWf1JolkKMmL6bXnYFSwg&m=Pb-c1m96L6xixMU-j16J-GkC6tGV5l >>> AdGNKy-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 >>> Email: 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 >>> 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
