Not quite, you still need to do -cifti-merge to concatenate across subjects to get one matrix that reflects data from all subjects.
Per subject, with a little bit of pattern matching magic: 1) wb_shortcuts -cifti-demean -normalize <subject-output-dir>/all_normalized.dtseries.nii rfMRI_REST?*/rfMRI_REST*Atlas.dtseries.nii 2) wb_command -cifti-parcellate Once, across all subjects: 3) wb_command -cifti-merge (or wb_shortcuts -cifti-concatenate, which is a friendlier front-end to the same command - due to a bug, you'd need the latest version, here: https://github.com/Washington-University/wb_ shortcuts/raw/master/wb_shortcuts) 4) wb_command -cifti-correlation Tim On Wed, Jan 4, 2017 at 4:09 PM, Shearrer, Grace <[email protected]> wrote: > Hi Tim, yes I am planning on concatenating all subjects. Okay so new work > flow to make sure I understand: > > > 1) wb_shortcuts -cifti-demean -normalize output.dtseries.nii > input.dtseries.nii #do this on each subject where the input would be the > 4 resting states runs > > 2) wb_command -cifti-parcellate #on each subject > > 3) wb_command -cifit-correlation #this will create a 360x360 matrix for > further analysis > > > Thanks so much for tips. I am brand new to workbench so I need all the > help I can get. > > Grace > ------------------------------ > *From:* Timothy Coalson <[email protected]> > *Sent:* Wednesday, January 4, 2017 7:00 PM > *To:* Shearrer, Grace > *Cc:* Glasser, Matthew; Elam, Jennifer; [email protected]; > [email protected] > > *Subject:* Re: [HCP-Users] Creating Group Average Resting State fMRI > > Are you planning to concatenate the timeseries across all subjects? If > so, I would suggest parcellating in each subject before concatenating (so, > swap steps 4 and 5), so that the merged file isn't enormous, and so that > the parcellation can be done in parallel on a cluster. The result of > concatenating before vs after parcellation should be the same if you use > the same arguments to -cifti-parcellate, but on the other hand, > parcellating in each subject would make it possible to use individual > subject parcellations instead of a group parcellation. > > Side note, wb_shortcuts has a -cifti-demean function that can do steps 1 > through 3 for you (assuming you don't want to keep the mean and stdev dense > maps around - also note that the mean and stdev files should actually be > dscalar.nii files, not dtseries.nii): > > wb_shortcuts -cifti-demean -normalize output.dtseries.nii > input.dtseries.nii > > This command can also merge files, so you could for instance merge the 4 > runs of each subject after normalizing them by specifying all of them as > inputs to that one command, and then only need to do -cifti-parcellate on > one file per subject. > > There is also some explanatory text for the cifti format in the > information options of wb_command: > > http://www.humanconnectome.org/software/workbench- > command.php?function=-cifti-help > > Tim > > > On Wed, Jan 4, 2017 at 3:28 PM, Shearrer, Grace <[email protected]> > wrote: > >> Ah! Most excellent. Thank you again for your prompt reply. >> >> >> 1) wb_command -cifti-reduce <input> MEAN mean.dtseries.nii >> >> 2) wb_command -cifti-reduce <input> STDEV stdev.dtseries.nii >> >> 3) wb_command -cifti-math '(x - mean) / stdev' <output> -fixnan 0 -var x >> <input> -var mean mean.dtseries.nii -select 1 1 -repeat -var stdev >> stdev.dtseries.nii -select 1 1 -repeat >> 4) wb_command -cifit-merge >> 5) wb_command -cifti-parcellate >> >> 6) wb_command -cifit-correlation >> >> >> Grace >> ------------------------------ >> *From:* Glasser, Matthew <[email protected]> >> *Sent:* Wednesday, January 4, 2017 6:22 PM >> *To:* Shearrer, Grace; Elam, Jennifer; [email protected]; >> [email protected] >> >> *Subject:* Re: [HCP-Users] Creating Group Average Resting State fMRI >> >> I would insert the parcellation between steps 5 and 6. The result if you >> use the file I suggested below will be a 360 X 360 cortical area >> correlation matrix. >> >> Peace, >> >> Matt. >> >> From: "Shearrer, Grace" <[email protected]> >> Date: Wednesday, January 4, 2017 at 4:16 PM >> To: Matt Glasser <[email protected]>, "Elam, Jennifer" <[email protected]>, >> "[email protected]" <[email protected]>, "[email protected]" < >> [email protected]> >> Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI >> >> Hi Matt, thanks so much for all your work on HCP and for replying to my >> email, I really appreciate it (thank you to Jenn too!). I want to make sure >> I understand the sequence quickly: >> >> 1) wb_command -cifti-parcellate >> >> 2) wb_command -cifti-reduce <input> MEAN mean.dtseries.nii >> >> 3) wb_command -cifti-reduce <input> STDEV stdev.dtseries.nii >> >> 4) wb_command -cifti-math '(x - mean) / stdev' <output> -fixnan 0 -var x >> <input> -var mean mean.dtseries.nii -select 1 1 -repeat -var stdev >> stdev.dtseries.nii -select 1 1 -repeat >> 5) wb_command -cifit-merge >> >> 6) wb_command -cifit-correlation >> >> And then I would take this (giant) matrix and run my analyses on it with >> the brain connectivity toolbox (or the like). >> >> Thank you for your patience, >> >> Grace >> >> ------------------------------ >> *From:* Glasser, Matthew <[email protected]> >> *Sent:* Wednesday, January 4, 2017 5:54 PM >> *To:* Elam, Jennifer; Shearrer, Grace; [email protected]; >> [email protected] >> *Subject:* Re: [HCP-Users] Creating Group Average Resting State fMRI >> >> You will need to parcellate the data first using wb_command >> -cifti-parcellate. >> >> A parcellation is available here: >> >> https://balsa.wustl.edu/file/show/3VLx >> >> Peace, >> >> Matt. >> >> From: <[email protected]> on behalf of "Elam, >> Jennifer" <[email protected]> >> Date: Wednesday, January 4, 2017 at 3:47 PM >> To: "Shearrer, Grace" <[email protected]>, "[email protected]" < >> [email protected]>, "[email protected]" < >> [email protected]> >> Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI >> >> Hi Grace, >> >> This is a grayordinate x grayordinate "dense" connectome and it will be a >> large (30GB) resulting file. Grayordinates are surface vertices for both >> hemispheres + subcortical voxels (total of 91,282 grayordinates in our >> case). To learn more about this and CIFTI, I would look at Glasser et >> al. 2013. >> <http://www.sciencedirect.com/science/article/pii/S1053811913005053> >> >> >> <http://www.sciencedirect.com/science/article/pii/S1053811913005053> >> >> Best, >> >> Jenn >> >> >> Jennifer Elam, Ph.D. >> Scientific Outreach, Human Connectome Project >> Washington University School of Medicine >> Department of Neuroscience, Box 8108 >> 660 South Euclid Avenue >> St. Louis, MO 63110 >> 314-362-9387 >> [email protected] >> www.humanconnectome.org >> >> ------------------------------ >> *From:* Shearrer, Grace <[email protected]> >> *Sent:* Wednesday, January 4, 2017 2:16:48 PM >> *To:* Elam, Jennifer; [email protected]; [email protected] >> *Subject:* Re: [HCP-Users] Creating Group Average Resting State fMRI >> >> >> Hi Jenn, oops the User list verification was going to my junk email. I >> just signed up though. I did see the wiki and it was helpful, I like this >> script though since it appears to loop through all the directories. I just >> wanted to make sure I was getting the final connectivity matrix. One other >> question, is the connectivity matrix voxelwise? Or is it connectivity based >> on a parcelation scheme? >> >> Thank you, >> >> Grace >> >> >> Grace Shearrer, PhD >> Post Doctoral Researcher >> Neuropsychology of Ingestive Behavior Lab >> University of North Carolina Chapel Hill >> ------------------------------ >> *From:* Elam, Jennifer <[email protected]> >> *Sent:* Wednesday, January 4, 2017 4:57 PM >> *To:* Shearrer, Grace; [email protected]; [email protected] >> *Subject:* Re: [HCP-Users] Creating Group Average Resting State fMRI >> >> >> Hi Grace, >> >> You might also want to check out the instructions for creating individual >> and group average dense rfMRI connectomes in item #3 in the HCP Users FAQ >> on our wiki: https://wiki.humanconnectome.org/display/PublicData/ >> HCP+Users+FAQ#HCPUsersFAQ-3.IseethatHCPdistributesgroupavera >> gedenseconnectomefiles.Doyoualsoprovideconnectivitymatricesf >> orindividualsubjects? >> >> >> >> <https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-3.IseethatHCPdistributesgroupaveragedenseconnectomefiles.Doyoualsoprovideconnectivitymatricesforindividualsubjects?> >> >> Also, sign up for the HCP-Users list >> <https://www.humanconnectome.org/contact/#subscribe> to learn from other >> users and stay in the discussion. >> >> >> Best, >> >> Jenn >> >> >> Jennifer Elam, Ph.D. >> Scientific Outreach, Human Connectome Project >> Washington University School of Medicine >> Department of Neuroscience, Box 8108 >> 660 South Euclid Avenue >> St. Louis, MO 63110 >> 314-362-9387 >> [email protected] >> www.humanconnectome.org >> >> ------------------------------ >> *From:*[email protected] < >> [email protected]> on behalf of Shearrer, Grace < >> [email protected]> >> *Sent:* Wednesday, January 4, 2017 1:24:49 PM >> *To:* [email protected]; [email protected] >> *Subject:* Re: [HCP-Users] Creating Group Average Resting State fMRI >> >> >> >> Hi Dr. Bari, >> >> thank you so much for script this is very helpful. I just want to check >> that I understand. I would use your script to get the mean time series, >> standard deviation, and then demean the data. Then I would use a command >> like: >> >> >> wb_command -cifit-merge >> >> >> to then merge all my demeaned data into a a single file, then I would >> use: >> >> >> wb_command -cifit-correlation >> >> >> to get a correlation matrix from which I could begin to use a graph >> theory toolkit (like brain connectivity tool box). >> >> >> Does this make sense? This is my first time using CIFTI files and I am >> still trying to wrap my head around it. >> >> >> Thanks, >> >> Grace >> >> >> This question is based on the following thread: http://www.mail-archiv >> e.com/[email protected]/msg00448.html >> >> >> Grace Shearrer, PhD >> Post Doctoral Researcher >> Neuropsychology of Ingestive Behavior Lab >> University of North Carolina Chapel Hill >> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> 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. 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