Hello, I am trying to extract the mean value form a cifti file using -
cifti-weighted-stats within an ROI I produced from the Brodmann area maps Human.Brodmann09.32k_fs_LR.dlabel.nii. I use the command wb_command -cifti-weighted-stats results_merged_tfce_FLOB1_tstat_fwep.dscalar.nii -roi HCP_S900_GroupAvg_v1/BA47.dscalar.nii -match-maps -mean -spatial-weights -left-area-surf HCP_S900_GroupAvg_v1/S900.L.midthickness_MSMAll.32k_fs_LR.surf.gii -right-area-surf HCP_S900_GroupAvg_v1/S900.R.midthickness_MSMAll.32k_fs_LR.surf.gii but I get the error: ERROR: roi cifti has incompatible mapping along column alternatively, I've looked just within the left hemispheric data using the command: wb_command -metric-weighted-stats results_R_cort_tfce_tstat_fwep.gii -roi HCP_S900_GroupAvg_v1/BA47_Right.label.gii -weight-metric NOGO-GO_results_R_cort_tfce_tstat_fwep.gii -mean With the result: WARNING: Metric File: HCP_S900_GroupAvg_v1/BA47_Right.label.gii contains data array with NIFTI_INTENT_LABEL !!! 0.4116454 Do you know how I can extract mean values from an ROI like this? Is this the appropriate command to use when I have an ROI? Thank you, Michael ________________________________ From: Timothy Coalson <tsc...@mst.edu> Sent: Tuesday, September 27, 2016 6:37:42 PM To: Michael F.W. Dreyfuss Cc: Burgess, Gregory; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data Actually, -cifti-math will output a dlabel file with an improper label table, which will look empty (it is not a proper dlabel file, but it does have the ROI you want in it). You should then use -cifti-change-mapping with -scalar on that output to make it into a viewable ROI file (you could also do this on the restricted dlabel file before -cifti-math). Basically, there are several ways to go about the task, and you took a different path than I expected. By starting with -cifti-label-to-roi, you can avoid the need to manually edit a text file for the purpose of extracting the labels you want (and it also avoids doing math on label files, which has some rough edges). Tim On Tue, Sep 27, 2016 at 5:29 PM, Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> wrote: If you already have a dlabel file that excludes the things you aren't interested in, you don't need to bother with the -cifti-reduce I described. Since "unlabeled" is generally represented as 0, you can use -cifti-math with 'x > 0' to generate a combined binary ROI from that restricted dlabel file. Tim On Tue, Sep 27, 2016 at 5:26 PM, Michael F.W. Dreyfuss <mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>> wrote: The command I was using was : wb_command -cifti-reduce Brodmann_Bilateral_IFG.dlabel.nii MAX Brodmann_Bilateral_IFG_Merged.dscalar.nii Where Brodmann_Bilateral_IFG.dlabel.nii contains two labels. Again, this command does not seem to the production of a label file directly. Thanks On Sep 27, 2016, at 6:20 PM, Michael F.W. Dreyfuss <mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>> wrote: I’m sorry, but this is still not clear to me. It seems this function is meant to perform an operation to produce a scalar file, but what is produced when I use MAX for example is just a scalar file where the value for the key each labeled region had in the label file is not the value in that scalar file. so BA44 was 65, BA45 was 66, and now there are two regions with values 65 and 66. What I am trying to do is to merge regions together into one region as a label file to use as a single mask. Is this possible with this function? I’m sorry if I’m missing something here. Thank you, Michael On Sep 27, 2016, at 5:57 PM, Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> wrote: http://www.humanconnectome.org/software/workbench-command.php?function=-cifti-reduce<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.humanconnectome.org_software_workbench-2Dcommand.php-3Ffunction-3D-2Dcifti-2Dreduce&d=DQMFaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg&m=Xs5EfvmcgCd1YzshFEix8oFIzx34876b06vXtA_UXVI&s=KS6IGgzKif6PPGEjorzvQDKDv09VSeiBIXSHw-xZrAI&e=> It is a simple reduction across columns (by default, anyway) in the file. For these kinds of files, that means it isn't reducing across space. MAX is one of the options it can calculate, and for binary ROIs, that is equivalent to boolean OR, which is what we want. The commands are generally written to perform small, specific actions, such that they could be suitable for multiple tasks. Tim On Tue, Sep 27, 2016 at 4:49 PM, Michael F.W. Dreyfuss <mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>> wrote: How would this work with -cifti-reduce? If I have a cifti with BA44 and BA45 for example and I want those two regions to be merged into one, how would -cifti-reduce do that? Wouldn’t it be more suited to calculating something (i.e. mean, mode, etc.) within each of those parcels? Thank you On Sep 27, 2016, at 5:40 PM, Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> wrote: wb_shortcuts _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
