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.IseethatHCPdistributesgroupave > ragedenseconnectomefiles.Doyoualsoprovideconnectivityma > tricesforindividualsubjects? > > > > <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] <hcp-users-bounces@ > humanconnectome.org> 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- > archive.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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