The -cifti-merge command does not have that type of option (it is not intended to do as many things as melodic - wb_command commands are building blocks, not pipelines). You could accomplish something similar with shell tricks (though it isn't safe with regards to spaces in filenames):
$ cat inputsfile.txt -cifti input1.dtseries.nii -cifti input2.dtseries.nii $ wb_command -cifti-merge output.dtseries.nii `cat inputsfile.txt` The wb_shortcuts script uses a safer way to do this (arrays), so you can use a command like this instead to concatenate some file across all subjects in a directory: wb_shortcuts -cifti-concatenate output.dtseries.nii $subjdir/*/<some-path-to-subject-file>/subjectinput.dtseries.nii If you only want a subset of subjects, you can use a loop to build the list of files in an array variable, or a string if you don't use spaces in file or folder names. Tim On Fri, Jan 6, 2017 at 10:57 AM, Shearrer, Grace <[email protected]> wrote: > Hi Tim, I have a follow up question about the cifti-merge command. Given > I will be merging upwards of 500 subjects does the cifti-merge command have > the ability to take a .txt listing the paths to all the parcellated files? > Similar to the fsl's group ica function which allows: > > melodic -i inputlist_clean.txt -o groupmelodic_fix.ica -v --nobet > --bgthreshold=10 --tr=2.000 --report -d 25 --mmthresh=0.5 --Ostats -a concat > > Thanks, > > Grace > ------------------------------ > *From:* Timothy Coalson <[email protected]> > *Sent:* Wednesday, January 4, 2017 8:43 PM > > *To:* Shearrer, Grace > *Cc:* Glasser, Matthew; Elam, Jennifer; [email protected]; > [email protected] > *Subject:* Re: [HCP-Users] Creating Group Average Resting State fMRI > > 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/Washi > ngton-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.humanconnec >>> tome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-3.Isee >>> thatHCPdistributesgroupaveragedenseconnectomefiles.Doyoualso >>> provideconnectivitymatricesforindividualsubjects? >>> >>> >>> >>> <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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If you have received this email >>> in error, please immediately notify the sender via telephone or return mail. >>> >>> _______________________________________________ >>> 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
