You do need an actual surface file (e.g. that contains a mesh topology and vertex coordinate locations). Presumably you have some of these if you have gotten this far?
Peace, Matt. From: "Michael F.W. Dreyfuss" <mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>> Date: Tuesday, September 20, 2016 at 12:55 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data When I run wb_command -cifti-find-clusters FoodNogo_results_merged_tfce_tstat_fwep.dscalar.nii 1 1 1 1 COLUMN FoodNogo_results_merged_tfce_tstat_fwep_ROIs.dscalar.nii I get the error: ERROR: left surface required but not provided Then if I add the option: -left-surface FoodNogo_results_L_cort_tfce_tstat_fwep.gii I get ERROR: Number of data arrays MUST be two in a SurfaceFile. I understand that this is a metric file and not a surface file, but 1) I do not know how to convert it, and 2) all the information is contained within the cifti file anyway, so I am unsure what additional information this command is looking for As for the thresholding, I arbitrarily chose 1 just to get this running. Thanks, Michael ________________________________ From: Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> Sent: Tuesday, September 20, 2016 12:57:49 PM To: Michael F.W. Dreyfuss; NEUROSCIENCE tim Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data If you are getting error messages, I recommend posting them. Peace, Matt. From: "Michael F.W. Dreyfuss" <mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>> Date: Tuesday, September 20, 2016 at 10:40 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data Thank you for this. We had explored this option in the past and two issues were 1) there was not a parcellation readily available with subcortical structures and 2) I do not feel a need to constrain activation to parcels rather than swaths of signal as they appear to cluster themselves. I'm sure parcellation is a valid approach, but I would really like to be able to simply report activation as it appears to cluster such as with TFCE, fdr or cluster thresholding (although that is less favored now) as has been typical in fMRI reporting. Are there examples available for these kinds of analysis to eventually relate activation to behavior or other measures? I am grateful for all the help you have all provided. Things are quite close, and I hope to be able to be able to get through these last steps as quickly as possible. ________________________________ From: Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> Sent: Tuesday, September 20, 2016 11:06:10 AM To: Michael F.W. Dreyfuss; NEUROSCIENCE tim Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data As Tim mentions, it sounds like you might want to use a parcellated analysis, as this will be more sensitive/powerful and you’ll know exactly what areas you are finding. The HCP’s multi-modal parcellation is available here: https://balsa.wustl.edu/study/show/RVVG<https://urldefense.proofpoint.com/v2/url?u=https-3A__balsa.wustl.edu_study_show_RVVG&d=DQMF-g&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg&m=41tIMVdkyw4FbaKBCuAemq30kaX7FtpSn1fT4mnNgb4&s=LSobQp1e_k82tOjzxrgaFuayanqOIOB0FPCI128My64&e=> Also, the HCP’s task analysis pipeline will allow you to parcellate before fitting the GLM, rather than afterwards to get the addition SNR benefits from averaging across a parcel. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Michael F.W. Dreyfuss" <mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>> Date: Monday, September 19, 2016 at 9:40 PM To: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> Cc: "Michael F.W. Dreyfuss" <mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data Thank you, Are there any examples available for how to use this, possibly? I have been trying to figure these out, but there are a lot of options and I am just not able to decipher how to use these from the help page alone. The errors I am getting also do not clarify what I need to do to get the output I am looking for. Before using this kind of multi-band data I had been using afni. To give an example of what I would want to do in terms of afni commands (if that’s any help), I would have saved all ROIs and then used 3dmaskave to extract mean beta weights for a given GLM beta for each subject and then I would relate those beta weights so subject’s behavior in R or another stats package. Definitely agree that there’s not much meaning to a peak coordinate per se. I’m just trying to figure out how to report the clusters I am finding. In previous reports we would typically focus on broadmann areas or more general regional nomenclature (i.e. vmPFC, mid temporal lobe, etc.). Some of the clusters I’m finding also cover large areas from motor to visual cortex, so I am trying to consider good ways to report that. At this point I would prefer to use TFCE or some other thresholding method to identify contiguous swaths of volumetric and surface activation. Thank you very much again, Michael On Sep 19, 2016, at 6:41 PM, Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> wrote: On Mon, Sep 19, 2016 at 4:51 PM, Michael F.W. Dreyfuss <mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>> wrote: Thank you, How can I turn the ROIs into a label file? You can use -cifti-find-clusters if you just want spatial contiguity to define where ROIs should be considered separate, then use -cifti-label-import to make them into a dlabel file. Also, how can I simply get a list of the ROIs with some information like cluster extent and peak voxel to be able to identify what part(s) of the brain each ROI is covering? A single coordinate isn't a faithful representation of the cluster. You can make a figure showing the clusters displayed on the brain (for instance, choose two of: beta maps, significance outlines, area outlines), and hopefully also provide the unthresholded beta and z maps for others to use. You can get cluster extent info with -cifti-weighted-stats. If the question you want to ask is "which areas are involved", you could do a parcellated analysis instead of a cluster analysis. Thank you, Michael ________________________________ From: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> Sent: Monday, September 19, 2016 4:48:28 PM To: Michael F.W. Dreyfuss Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data The wb_command -cifti-weighted-stats command with -mean is probably what you want (outputs a number to the command line), though you'll need to have each ROI as a separate file and run it separately for each of them. Alternatively, if you turned the ROIs into a label file, you could get -cifti-parcellate to make a file where each parcel contains the answer for an ROI. Tim On Mon, Sep 19, 2016 at 3:26 PM, Michael F.W. Dreyfuss <mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>> wrote: Hello, I have run palm with TFCE on my group level data successfully for a task based fMRI study (yay!), and I would like to be able to identify ROIs from my cifti data (both surface and volume). I then want to extract subject level beta weights for a given condition from those ROIs to relate those betas to behavior (offline). Are there simple ways to: 1) identify regions implicated on the group level and 2) extract subject-level beta weights from them, such as with wb_command? Thank you, Michael _______________________________________________ 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=owdejnaklI6Db2XSiTgha_Wfo4am5eKBMJpc1pFzI1A&s=Ia4QB3ti2OENrr5FEZXT5gcngkIh2Yh34e_N0EOpfFI&e=> _______________________________________________ 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=DQMF-g&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg&m=41tIMVdkyw4FbaKBCuAemq30kaX7FtpSn1fT4mnNgb4&s=-9ww002FIzbXB56mRLX-twqyvFBmaOjLoF5wqiCRwJE&e=> ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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