Re: [HCP-Users] Creating Group Average Resting State fMRI
FSLNets wants the parcellated timeseries.
Matt.
From: "Shearrer, Grace" <grac...@email.unc.edu<mailto:grac...@email.unc.edu>>
Date: Thursday, January 12, 2017 at 2:27 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>,
"HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>"
<HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>>, "Harms,
Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>
Cc: Jennifer Elam <jse...@gmail.com<mailto:jse...@gmail.com>>, Timothy Coalson
<tsc...@mst.edu<mailto:tsc...@mst.edu>>
Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI
Hi again, let me reiterate how helpful everyone has been. I really appreciate
it and I have been able to create a 360x360 correlation matrix for test sample
of 10 HCP subjects. I was looking at the wb_command -cifti-correlation and
noticed you can make a covariance matrix, and I was wondering what method you
recommend using to get the inverse covariance matrix? I read Smith et al 2011,
where they recommend
http://www.cs.ubc.ca/~schmidtm/Software/L1precision.html.<http://www.cs.ubc.ca/~schmidtm/Software/L1precision.html>
I have also seen fslNETs used (which I believe uses the same L1 precision). I
read that Dr. Harms suggested and provided input on how to use fslNETs
http://www.mail-archive.com/hcp-users@humanconnectome.org/msg01341.html (as
well as suggested on this thread to compute a separate matrix for each
subject). Is there a way to input a correlation or covariance matrix into
fslNETs? (this might be a question of the fsl list serv)
Thank you again,
Grace
Grace Shearrer, PhD
Post Doctoral Researcher
Neuropsychology of Ingestive Behavior Lab
University of North Carolina Chapel Hill
From: Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Sent: Sunday, January 8, 2017 1:09 PM
To: Shearrer, Grace
Cc: Jennifer Elam; NEUROSCIENCE tim
Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI
Hi Grace,
Have a look at wb_command -cifti-help
Matt.
From: "Shearrer, Grace" <grac...@email.unc.edu<mailto:grac...@email.unc.edu>>
Date: Sunday, January 8, 2017 at 11:06 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, Timothy
Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI
Hi TIm and Matt, thank you so much for your help again. This might be a silly
question, but is there any documentation on the different file types (eg
.dseries.nii vs .dscalar.nii vs .ptseries.nii)? As I am doing my analysis I am
trying to understand each step in a thoughtful manner so hopefully I can teach
grad students in my lab in the future. I searched the HCP documentation but
couldn't find anything about the different file types, I may have missed it
though.
Thank you,
Grace
Grace Shearrer, PhD
Post Doctoral Researcher
Neuropsychology of Ingestive Behavior Lab
University of North Carolina Chapel Hill
____________
From: Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Sent: Friday, January 6, 2017 9:35 PM
To: NEUROSCIENCE tim
Cc: Shearrer, Grace
Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI
Thanks Tim.
Matt.
From: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Date: Friday, January 6, 2017 at 7:33 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "Shearrer, Grace" <grac...@email.unc.edu<mailto:grac...@email.unc.edu>>
Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI
Well, I wrote it as an option to the -*-concatenate functions, and doing so has
warned me not to do it that way again in the future - the script file has
almost doubled in size, as each of the one-line loops in those commands is now
50 lines (error checking, avoiding reading a data file into shell memory if the
user mistypes things...). I also didn't add it to -cifti-demean (that could be
a bit messier).
You can try it by getting the latest version here:
https://github.com/Washington-University/wb_shortcuts
There is equivalent shell magic to do it (with whitespace safety) without using
this option, but it will choke on empty lines in the text file:
readarray -t filelist < filelist.txt
wb_shortcuts -cifti-concatenate output.dtseries.nii "${filelist[@]}"
If someone asks how to do it for -cifti-demean, I think this shell incantation
may be the better answer.
Tim
On Fri, Jan 6, 2017 at 4:30 PM, Glasser, Matthew
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
Whatever is most convenient.
Matt.
From: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Date: Friday, January 6, 2017 a
Re: [HCP-Users] Creating Group Average Resting State fMRI
Hi again, let me reiterate how helpful everyone has been. I really appreciate
it and I have been able to create a 360x360 correlation matrix for test sample
of 10 HCP subjects. I was looking at the wb_command -cifti-correlation and
noticed you can make a covariance matrix, and I was wondering what method you
recommend using to get the inverse covariance matrix? I read Smith et al 2011,
where they recommend
http://www.cs.ubc.ca/~schmidtm/Software/L1precision.html.<http://www.cs.ubc.ca/~schmidtm/Software/L1precision.html>
I have also seen fslNETs used (which I believe uses the same L1 precision). I
read that Dr. Harms suggested and provided input on how to use fslNETs
http://www.mail-archive.com/hcp-users@humanconnectome.org/msg01341.html (as
well as suggested on this thread to compute a separate matrix for each
subject). Is there a way to input a correlation or covariance matrix into
fslNETs? (this might be a question of the fsl list serv)
Thank you again,
Grace
Grace Shearrer, PhD
Post Doctoral Researcher
Neuropsychology of Ingestive Behavior Lab
University of North Carolina Chapel Hill
From: Glasser, Matthew <glass...@wustl.edu>
Sent: Sunday, January 8, 2017 1:09 PM
To: Shearrer, Grace
Cc: Jennifer Elam; NEUROSCIENCE tim
Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI
Hi Grace,
Have a look at wb_command -cifti-help
Matt.
From: "Shearrer, Grace" <grac...@email.unc.edu<mailto:grac...@email.unc.edu>>
Date: Sunday, January 8, 2017 at 11:06 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, Timothy
Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI
Hi TIm and Matt, thank you so much for your help again. This might be a silly
question, but is there any documentation on the different file types (eg
.dseries.nii vs .dscalar.nii vs .ptseries.nii)? As I am doing my analysis I am
trying to understand each step in a thoughtful manner so hopefully I can teach
grad students in my lab in the future. I searched the HCP documentation but
couldn't find anything about the different file types, I may have missed it
though.
Thank you,
Grace
Grace Shearrer, PhD
Post Doctoral Researcher
Neuropsychology of Ingestive Behavior Lab
University of North Carolina Chapel Hill
From: Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Sent: Friday, January 6, 2017 9:35 PM
To: NEUROSCIENCE tim
Cc: Shearrer, Grace
Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI
Thanks Tim.
Matt.
From: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Date: Friday, January 6, 2017 at 7:33 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "Shearrer, Grace" <grac...@email.unc.edu<mailto:grac...@email.unc.edu>>
Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI
Well, I wrote it as an option to the -*-concatenate functions, and doing so has
warned me not to do it that way again in the future - the script file has
almost doubled in size, as each of the one-line loops in those commands is now
50 lines (error checking, avoiding reading a data file into shell memory if the
user mistypes things...). I also didn't add it to -cifti-demean (that could be
a bit messier).
You can try it by getting the latest version here:
https://github.com/Washington-University/wb_shortcuts
There is equivalent shell magic to do it (with whitespace safety) without using
this option, but it will choke on empty lines in the text file:
readarray -t filelist < filelist.txt
wb_shortcuts -cifti-concatenate output.dtseries.nii "${filelist[@]}"
If someone asks how to do it for -cifti-demean, I think this shell incantation
may be the better answer.
Tim
On Fri, Jan 6, 2017 at 4:30 PM, Glasser, Matthew
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
Whatever is most convenient.
Matt.
From: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Date: Friday, January 6, 2017 at 5:29 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "Shearrer, Grace" <grac...@email.unc.edu<mailto:grac...@email.unc.edu>>
Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI
It might be able to fit into the -*-concatenate parsing (people shouldn't name
files starting with '-'). It could also be a separate shortcut.
Tim
On Fri, Jan 6, 2017 at 4:10 PM, Glasser, Matthew
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
That functionality might be a good candidate for wb_shortcuts.
If you are merging that many subjects, you might consider how large your file
will be. You might want to make use of an algorithm like MIGP to do the
combination.
Matt.
From: "Shear
Re: [HCP-Users] Creating Group Average Resting State fMRI
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/*//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 <grac...@email.unc.edu> 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 <tsc...@mst.edu> > *Sent:* Wednesday, January 4, 2017 8:43 PM > > *To:* Shearrer, Grace > *Cc:* Glasser, Matthew; Elam, Jennifer; aus...@gmail.com; > HCP-Users@humanconnectome.org > *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 > /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 <grac...@email.unc.edu> > 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 <tsc...@mst.edu> >> *Sent:* Wednesday, January 4, 2017 7:00 PM >> *To:* Shearrer, Grace >> *Cc:* Glasser, Matthew; Elam, Jennifer; aus...@gmail.com; >> HCP-Users@humanconnectome.org >> >> *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. >
Re: [HCP-Users] Creating Group Average Resting State fMRI
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 <tsc...@mst.edu> Sent: Wednesday, January 4, 2017 8:43 PM To: Shearrer, Grace Cc: Glasser, Matthew; Elam, Jennifer; aus...@gmail.com; HCP-Users@humanconnectome.org 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 /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 <grac...@email.unc.edu<mailto:grac...@email.unc.edu>> 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 <tsc...@mst.edu<mailto:tsc...@mst.edu>> Sent: Wednesday, January 4, 2017 7:00 PM To: Shearrer, Grace Cc: Glasser, Matthew; Elam, Jennifer; aus...@gmail.com<mailto:aus...@gmail.com>; HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> 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 <grac...@email.unc.edu<mailto:grac...@email.unc.edu>> wrote: Ah! Most excellent. Thank you again for your prompt reply. 1) wb_command -cifti-reduce MEAN mean.dtseries.nii 2) wb_command -cifti-reduce STDEV stdev.dtseries.nii 3) wb_command -cifti-math '(x - mean) / stdev' -fixnan 0 -var x -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 <glass...@wustl.edu<mailto:glass...@wustl.edu>> Sent: Wednesday, January 4, 2017 6:22 PM To: Shearrer, Grace; Elam, Jennifer; aus...@gmail.com<mailto:aus...@gmail.com>; HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> 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" <grac...@email.unc.edu<mailto:grac...@email.unc.edu>> Date:
Re: [HCP-Users] Creating Group Average Resting State fMRI
Hi Tim and Michael, thanks so much for clarifying (I needed the hand holding walk through) and giving me an additional option! I will give this a go and most certainly be back on the list serv asking more questions. Grace Grace Shearrer, PhD Post Doctoral Researcher Neuropsychology of Ingestive Behavior Lab University of North Carolina Chapel Hill From: Harms, Michael <mha...@wustl.edu> Sent: Thursday, January 5, 2017 1:09 AM To: NEUROSCIENCE tim; Shearrer, Grace Cc: HCP-Users@humanconnectome.org; aus...@gmail.com Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI Just to throw another variant into the mix, you can also compute a separate network matrix for each run of each subject, Fisher transform those, and then average those generate a representative network matrix for each subject, which you can then average across subjects if you want a group average network matrix. We’ve found that computing a separate network matrix for each run and then averaging can generate slightly better estimates. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> Date: Wednesday, January 4, 2017 at 5:43 PM To: "Shearrer, Grace" <grac...@email.unc.edu<mailto:grac...@email.unc.edu>> Cc: "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>" <HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>>, "aus...@gmail.com<mailto:aus...@gmail.com>" <aus...@gmail.com<mailto:aus...@gmail.com>> 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 /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 <grac...@email.unc.edu<mailto:grac...@email.unc.edu>> 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 <tsc...@mst.edu<mailto:tsc...@mst.edu>> Sent: Wednesday, January 4, 2017 7:00 PM To: Shearrer, Grace Cc: Glasser, Matthew; Elam, Jennifer; aus...@gmail.com<mailto:aus...@gmail.com>; HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> 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
Re: [HCP-Users] Creating Group Average Resting State fMRI
Just to throw another variant into the mix, you can also compute a separate network matrix for each run of each subject, Fisher transform those, and then average those generate a representative network matrix for each subject, which you can then average across subjects if you want a group average network matrix. We’ve found that computing a separate network matrix for each run and then averaging can generate slightly better estimates. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> Date: Wednesday, January 4, 2017 at 5:43 PM To: "Shearrer, Grace" <grac...@email.unc.edu<mailto:grac...@email.unc.edu>> Cc: "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>" <HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>>, "aus...@gmail.com<mailto:aus...@gmail.com>" <aus...@gmail.com<mailto:aus...@gmail.com>> 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 /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 <grac...@email.unc.edu<mailto:grac...@email.unc.edu>> 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 <tsc...@mst.edu<mailto:tsc...@mst.edu>> Sent: Wednesday, January 4, 2017 7:00 PM To: Shearrer, Grace Cc: Glasser, Matthew; Elam, Jennifer; aus...@gmail.com<mailto:aus...@gmail.com>; HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> 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 <grac...@email.unc.edu<mailto:grac...@email.unc.edu>> wrote: Ah! Most excellent. Thank you again for your prompt reply. 1) wb_command -cifti-reduce MEAN mean.dtseries.nii 2) wb_command -cifti-reduce STDEV stdev.dtseries.nii 3) wb_command -cifti-math '(x - mean) / stdev' -fixnan 0 -var x -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
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 /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 <grac...@email.unc.edu> 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 <tsc...@mst.edu> > *Sent:* Wednesday, January 4, 2017 7:00 PM > *To:* Shearrer, Grace > *Cc:* Glasser, Matthew; Elam, Jennifer; aus...@gmail.com; > HCP-Users@humanconnectome.org > > *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 <grac...@email.unc.edu> > wrote: > >> Ah! Most excellent. Thank you again for your prompt reply. >> >> >> 1) wb_command -cifti-reduce MEAN mean.dtseries.nii >> >> 2) wb_command -cifti-reduce STDEV stdev.dtseries.nii >> >> 3) wb_command -cifti-math '(x - mean) / stdev' -fixnan 0 -var x >> -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 <glass...@wustl.edu> >> *Sent:* Wednesday, January 4, 2017 6:22 PM >> *To:* Shearrer, Grace; Elam, Jennifer; aus...@gmail.com; >> HCP-Users@humanconnectome.org >> >> *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" <grac...@email.unc.edu> >> Date: Wednesday, January 4, 2017 at 4:16 PM >> To: Matt Glasser <glass...@wustl.edu>, "Elam, Jennifer" <e...@wustl.edu>, >> "aus...@gmail.com" <aus...@gmail.com>, "HCP-Users@humanconnectome.org" < >> HCP-Users@humanconnectome.org> >> 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 real
Re: [HCP-Users] Creating Group Average Resting State fMRI
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 <tsc...@mst.edu> Sent: Wednesday, January 4, 2017 7:00 PM To: Shearrer, Grace Cc: Glasser, Matthew; Elam, Jennifer; aus...@gmail.com; HCP-Users@humanconnectome.org 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 <grac...@email.unc.edu<mailto:grac...@email.unc.edu>> wrote: Ah! Most excellent. Thank you again for your prompt reply. 1) wb_command -cifti-reduce MEAN mean.dtseries.nii 2) wb_command -cifti-reduce STDEV stdev.dtseries.nii 3) wb_command -cifti-math '(x - mean) / stdev' -fixnan 0 -var x -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 <glass...@wustl.edu<mailto:glass...@wustl.edu>> Sent: Wednesday, January 4, 2017 6:22 PM To: Shearrer, Grace; Elam, Jennifer; aus...@gmail.com<mailto:aus...@gmail.com>; HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> 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" <grac...@email.unc.edu<mailto:grac...@email.unc.edu>> Date: Wednesday, January 4, 2017 at 4:16 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "Elam, Jennifer" <e...@wustl.edu<mailto:e...@wustl.edu>>, "aus...@gmail.com<mailto:aus...@gmail.com>" <aus...@gmail.com<mailto:aus...@gmail.com>>, "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>" <HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>> 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 MEAN mean.dtseries.nii 3) wb_command -cifti-reduce STDEV stdev.dtseries.nii 4) wb_command -cifti-math '(x - mean) / stdev' -fixnan 0 -var x -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 <glass...@wustl.edu<mailto:glass...@wustl.edu>> Sent: Wednesday, January 4, 2017 5:54 PM To: Elam, Jennifer; Shearrer, Grace; aus...@gmail.com<mailto:aus...@gmail.com>; HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> Subject: Re: [HCP-Users] Creating Group Ave
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 <grac...@email.unc.edu> wrote: > Ah! Most excellent. Thank you again for your prompt reply. > > > 1) wb_command -cifti-reduce MEAN mean.dtseries.nii > > 2) wb_command -cifti-reduce STDEV stdev.dtseries.nii > > 3) wb_command -cifti-math '(x - mean) / stdev' -fixnan 0 -var x > -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 <glass...@wustl.edu> > *Sent:* Wednesday, January 4, 2017 6:22 PM > *To:* Shearrer, Grace; Elam, Jennifer; aus...@gmail.com; > HCP-Users@humanconnectome.org > > *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" <grac...@email.unc.edu> > Date: Wednesday, January 4, 2017 at 4:16 PM > To: Matt Glasser <glass...@wustl.edu>, "Elam, Jennifer" <e...@wustl.edu>, > "aus...@gmail.com" <aus...@gmail.com>, "HCP-Users@humanconnectome.org" < > HCP-Users@humanconnectome.org> > 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 MEAN mean.dtseries.nii > > 3) wb_command -cifti-reduce STDEV stdev.dtseries.nii > > 4) wb_command -cifti-math '(x - mean) / stdev' -fixnan 0 -var x > -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 <glass...@wustl.edu> > *Sent:* Wednesday, January 4, 2017 5:54 PM > *To:* Elam, Jennifer; Shearrer, Grace; aus...@gmail.com; > HCP-Users@humanconnectome.org > *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: <hcp-users-boun...@humanconnectome.org> on behalf of "Elam, > Jennifer" <e...@wustl.edu> > Date: Wednesday, January 4, 2017 at 3:47 PM > To: "Shearrer, Grace" <grac...@email.unc.edu>, "aus...@gmail.com" < > aus...@gmail.com>, "HCP-Users@humanconnectome.org" < > HCP-Users@humanconnectome.org> > 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). T
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" <grac...@email.unc.edu<mailto:grac...@email.unc.edu>> Date: Wednesday, January 4, 2017 at 4:16 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "Elam, Jennifer" <e...@wustl.edu<mailto:e...@wustl.edu>>, "aus...@gmail.com<mailto:aus...@gmail.com>" <aus...@gmail.com<mailto:aus...@gmail.com>>, "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>" <HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>> 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 MEAN mean.dtseries.nii 3) wb_command -cifti-reduce STDEV stdev.dtseries.nii 4) wb_command -cifti-math '(x - mean) / stdev' -fixnan 0 -var x -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 <glass...@wustl.edu<mailto:glass...@wustl.edu>> Sent: Wednesday, January 4, 2017 5:54 PM To: Elam, Jennifer; Shearrer, Grace; aus...@gmail.com<mailto:aus...@gmail.com>; HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> 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: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Elam, Jennifer" <e...@wustl.edu<mailto:e...@wustl.edu>> Date: Wednesday, January 4, 2017 at 3:47 PM To: "Shearrer, Grace" <grac...@email.unc.edu<mailto:grac...@email.unc.edu>>, "aus...@gmail.com<mailto:aus...@gmail.com>" <aus...@gmail.com<mailto:aus...@gmail.com>>, "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>" <HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>> 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 e...@wustl.edu<mailto:e...@wustl.edu> www.humanconnectome.org<http://www.humanconnectome.org/> ____________ From: Shearrer, Grace <grac...@email.unc.edu<mailto:grac...@email.unc.edu>> Sent: Wednesday, January 4, 2017 2:16:48 PM To: Elam, Jennifer; aus...@gmail.com<mailto:aus...@gmail.com>; HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> 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 <e...@wustl.edu<mailto:e...@wustl.edu>> Sent: Wednesday, January 4, 2017 4:57 PM To: Shearrer, Grace; aus...@gmail.com<mailto:aus...@gmail.com>; HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> 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
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 MEAN mean.dtseries.nii 3) wb_command -cifti-reduce STDEV stdev.dtseries.nii 4) wb_command -cifti-math '(x - mean) / stdev' -fixnan 0 -var x -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 <glass...@wustl.edu> Sent: Wednesday, January 4, 2017 5:54 PM To: Elam, Jennifer; Shearrer, Grace; aus...@gmail.com; HCP-Users@humanconnectome.org 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: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Elam, Jennifer" <e...@wustl.edu<mailto:e...@wustl.edu>> Date: Wednesday, January 4, 2017 at 3:47 PM To: "Shearrer, Grace" <grac...@email.unc.edu<mailto:grac...@email.unc.edu>>, "aus...@gmail.com<mailto:aus...@gmail.com>" <aus...@gmail.com<mailto:aus...@gmail.com>>, "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>" <HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>> 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 e...@wustl.edu<mailto:e...@wustl.edu> www.humanconnectome.org<http://www.humanconnectome.org/> From: Shearrer, Grace <grac...@email.unc.edu<mailto:grac...@email.unc.edu>> Sent: Wednesday, January 4, 2017 2:16:48 PM To: Elam, Jennifer; aus...@gmail.com<mailto:aus...@gmail.com>; HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> 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 <e...@wustl.edu<mailto:e...@wustl.edu>> Sent: Wednesday, January 4, 2017 4:57 PM To: Shearrer, Grace; aus...@gmail.com<mailto:aus...@gmail.com>; HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> 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.IseethatHCPdistributesgroupaveragedenseconnectomefiles.Doyoualsoprovideconnectivitymatricesforindividualsubjects? <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 e...@wustl.edu<mailto:e...@wustl.edu> www.humanconnectome.org<http://www.humanconnect
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: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Elam, Jennifer" <e...@wustl.edu<mailto:e...@wustl.edu>> Date: Wednesday, January 4, 2017 at 3:47 PM To: "Shearrer, Grace" <grac...@email.unc.edu<mailto:grac...@email.unc.edu>>, "aus...@gmail.com<mailto:aus...@gmail.com>" <aus...@gmail.com<mailto:aus...@gmail.com>>, "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>" <HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>> 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 e...@wustl.edu<mailto:e...@wustl.edu> www.humanconnectome.org<http://www.humanconnectome.org/> From: Shearrer, Grace <grac...@email.unc.edu<mailto:grac...@email.unc.edu>> Sent: Wednesday, January 4, 2017 2:16:48 PM To: Elam, Jennifer; aus...@gmail.com<mailto:aus...@gmail.com>; HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> 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 <e...@wustl.edu<mailto:e...@wustl.edu>> Sent: Wednesday, January 4, 2017 4:57 PM To: Shearrer, Grace; aus...@gmail.com<mailto:aus...@gmail.com>; HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> 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.IseethatHCPdistributesgroupaveragedenseconnectomefiles.Doyoualsoprovideconnectivitymatricesforindividualsubjects? <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 e...@wustl.edu<mailto:e...@wustl.edu> www.humanconnectome.org<http://www.humanconnectome.org/> From: hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org> <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Shearrer, Grace <grac...@email.unc.edu<mailto:grac...@email.unc.edu>> Sent: Wednesday, January 4, 2017 1:24:49 PM To: aus...@gmail.com<mailto:aus...@gmail.com>; HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> 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
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 e...@wustl.edu<mailto:e...@wustl.edu> www.humanconnectome.org<http://www.humanconnectome.org/> From: Shearrer, Grace <grac...@email.unc.edu> Sent: Wednesday, January 4, 2017 2:16:48 PM To: Elam, Jennifer; aus...@gmail.com; HCP-Users@humanconnectome.org 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 <e...@wustl.edu> Sent: Wednesday, January 4, 2017 4:57 PM To: Shearrer, Grace; aus...@gmail.com; HCP-Users@humanconnectome.org 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.IseethatHCPdistributesgroupaveragedenseconnectomefiles.Doyoualsoprovideconnectivitymatricesforindividualsubjects? <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 e...@wustl.edu<mailto:e...@wustl.edu> www.humanconnectome.org<http://www.humanconnectome.org/> From: hcp-users-boun...@humanconnectome.org <hcp-users-boun...@humanconnectome.org> on behalf of Shearrer, Grace <grac...@email.unc.edu> Sent: Wednesday, January 4, 2017 1:24:49 PM To: aus...@gmail.com; HCP-Users@humanconnectome.org 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/hcp-users@humanconnectome.org/msg00448.html Grace Shearrer, PhD Post Doctoral Researcher Neuropsychology of Ingestive Behavior Lab University of North Carolina Chapel Hill ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
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 <e...@wustl.edu> Sent: Wednesday, January 4, 2017 4:57 PM To: Shearrer, Grace; aus...@gmail.com; HCP-Users@humanconnectome.org 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.IseethatHCPdistributesgroupaveragedenseconnectomefiles.Doyoualsoprovideconnectivitymatricesforindividualsubjects? <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 e...@wustl.edu<mailto:e...@wustl.edu> www.humanconnectome.org<http://www.humanconnectome.org/> From: hcp-users-boun...@humanconnectome.org <hcp-users-boun...@humanconnectome.org> on behalf of Shearrer, Grace <grac...@email.unc.edu> Sent: Wednesday, January 4, 2017 1:24:49 PM To: aus...@gmail.com; HCP-Users@humanconnectome.org 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/hcp-users@humanconnectome.org/msg00448.html Grace Shearrer, PhD Post Doctoral Researcher Neuropsychology of Ingestive Behavior Lab University of North Carolina Chapel Hill ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
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.IseethatHCPdistributesgroupaveragedenseconnectomefiles.Doyoualsoprovideconnectivitymatricesforindividualsubjects? <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 e...@wustl.edu<mailto:e...@wustl.edu> www.humanconnectome.org<http://www.humanconnectome.org/> From: hcp-users-boun...@humanconnectome.org <hcp-users-boun...@humanconnectome.org> on behalf of Shearrer, Grace <grac...@email.unc.edu> Sent: Wednesday, January 4, 2017 1:24:49 PM To: aus...@gmail.com; HCP-Users@humanconnectome.org 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/hcp-users@humanconnectome.org/msg00448.html Grace Shearrer, PhD Post Doctoral Researcher Neuropsychology of Ingestive Behavior Lab University of North Carolina Chapel Hill ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
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/hcp-users@humanconnectome.org/msg00448.html Grace Shearrer, PhD Post Doctoral Researcher Neuropsychology of Ingestive Behavior Lab University of North Carolina Chapel Hill ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Creating Group Average Resting State fMRI
Ok that is something I tried recently actually - to merge all the runs across all the subjects and then do a correlation with fisher-z transform. The results didn't feel right in that they didn't look like typical resting state images. That is why I wanted to double check I was doing it the right way. As an alternative could I merge the within subject runs together with -merge and do a within-subject correlation and then average across subjects? Is there any downside to this other than the huge amount of storage space that would be required (32GB per subject)? -Ausaf On Mon, May 19, 2014 at 10:04 PM, Glasser, Matthew glass...@wusm.wustl.eduwrote: The simplest way is to concatenate the timeseries with wb_command -cifti-merge. You could do this for all runs of all subjects, or all runs for each subject (and then z-transform and average the connectomes across subjects). There will be a better way in the future. Peace, Matt. From: Timothy Coalson tsc...@mst.edu Date: Monday, May 19, 2014 at 10:48 PM To: Ausaf Bari aus...@gmail.com Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI Averaging together timepoints does not make sense for resting state data, it does not use stimuli, so there is no temporal correspondence between runs or across subjects. You should do the correlation before any averaging. I'm not sure what method our pipelines use, so I'll let someone else respond as to what the recommended method is (you probably don't need to correlate each file by itself, which would use up lots of disk space). Tim On Mon, May 19, 2014 at 8:22 PM, Ausaf Bari aus...@gmail.com wrote: I am trying to create a resting state fMRI average over 10 subjects to view in connectome workbench. For each HCP subject, I found the following 4 files: rfMRI_REST1_RL_Atlas_hp2000_clean.dtseries.nii rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii rfMRI_REST2_RL_Atlas_hp2000_clean.dtseries.nii rfMRI_REST2_LR_Atlas_hp2000_clean.dtseries.nii So for 10 subjects, I will have 40 total files. Am I correct to assume that I can use the command line tool wb_command -cifti-average to average over all 40 files and then wb_command -cifti-correlation to create a dense connectome? -Ausaf -- Ausaf A. Bari MD PhD Resident Physician UCLA Medical Center Department of Neurosurgery Email: aus...@gmail.com ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org 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. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. -- Ausaf A. Bari MD PhD Resident Physician UCLA Medical Center Department of Neurosurgery Phone: 617-642-1929 Email: aus...@gmail.com ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Creating Group Average Resting State fMRI
Hi - One important point - you should never temporally concatenate without first demeaning the individual timeseries. Cheers. On 20 May 2014, at 10:14, Ausaf Bari aus...@gmail.com wrote: Ok that is something I tried recently actually - to merge all the runs across all the subjects and then do a correlation with fisher-z transform. The results didn't feel right in that they didn't look like typical resting state images. That is why I wanted to double check I was doing it the right way. As an alternative could I merge the within subject runs together with -merge and do a within-subject correlation and then average across subjects? Is there any downside to this other than the huge amount of storage space that would be required (32GB per subject)? -Ausaf On Mon, May 19, 2014 at 10:04 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote: The simplest way is to concatenate the timeseries with wb_command -cifti-merge. You could do this for all runs of all subjects, or all runs for each subject (and then z-transform and average the connectomes across subjects). There will be a better way in the future. Peace, Matt. From: Timothy Coalson tsc...@mst.edu Date: Monday, May 19, 2014 at 10:48 PM To: Ausaf Bari aus...@gmail.com Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI Averaging together timepoints does not make sense for resting state data, it does not use stimuli, so there is no temporal correspondence between runs or across subjects. You should do the correlation before any averaging. I'm not sure what method our pipelines use, so I'll let someone else respond as to what the recommended method is (you probably don't need to correlate each file by itself, which would use up lots of disk space). Tim On Mon, May 19, 2014 at 8:22 PM, Ausaf Bari aus...@gmail.com wrote: I am trying to create a resting state fMRI average over 10 subjects to view in connectome workbench. For each HCP subject, I found the following 4 files: rfMRI_REST1_RL_Atlas_hp2000_clean.dtseries.nii rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii rfMRI_REST2_RL_Atlas_hp2000_clean.dtseries.nii rfMRI_REST2_LR_Atlas_hp2000_clean.dtseries.nii So for 10 subjects, I will have 40 total files. Am I correct to assume that I can use the command line tool wb_command -cifti-average to average over all 40 files and then wb_command -cifti-correlation to create a dense connectome? -Ausaf -- Ausaf A. Bari MD PhD Resident Physician UCLA Medical Center Department of Neurosurgery Email: aus...@gmail.com ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org 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. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. -- Ausaf A. Bari MD PhD Resident Physician UCLA Medical Center Department of Neurosurgery Phone: 617-642-1929 Email: aus...@gmail.com ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users --- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) st...@fmrib.ox.ac.ukhttp://www.fmrib.ox.ac.uk/~steve --- Stop the cultural destruction of Tibet ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Creating Group Average Resting State fMRI
Should you also normalize so that the standard deviations of each timeseries match? Tim On Tue, May 20, 2014 at 12:24 PM, Stephen Smith st...@fmrib.ox.ac.ukwrote: Hi - One important point - you should never temporally concatenate without first demeaning the individual timeseries. Cheers. On 20 May 2014, at 10:14, Ausaf Bari aus...@gmail.com wrote: Ok that is something I tried recently actually - to merge all the runs across all the subjects and then do a correlation with fisher-z transform. The results didn't feel right in that they didn't look like typical resting state images. That is why I wanted to double check I was doing it the right way. As an alternative could I merge the within subject runs together with -merge and do a within-subject correlation and then average across subjects? Is there any downside to this other than the huge amount of storage space that would be required (32GB per subject)? -Ausaf On Mon, May 19, 2014 at 10:04 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote: The simplest way is to concatenate the timeseries with wb_command -cifti-merge. You could do this for all runs of all subjects, or all runs for each subject (and then z-transform and average the connectomes across subjects). There will be a better way in the future. Peace, Matt. From: Timothy Coalson tsc...@mst.edu Date: Monday, May 19, 2014 at 10:48 PM To: Ausaf Bari aus...@gmail.com Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI Averaging together timepoints does not make sense for resting state data, it does not use stimuli, so there is no temporal correspondence between runs or across subjects. You should do the correlation before any averaging. I'm not sure what method our pipelines use, so I'll let someone else respond as to what the recommended method is (you probably don't need to correlate each file by itself, which would use up lots of disk space). Tim On Mon, May 19, 2014 at 8:22 PM, Ausaf Bari aus...@gmail.com wrote: I am trying to create a resting state fMRI average over 10 subjects to view in connectome workbench. For each HCP subject, I found the following 4 files: rfMRI_REST1_RL_Atlas_hp2000_clean.dtseries.nii rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii rfMRI_REST2_RL_Atlas_hp2000_clean.dtseries.nii rfMRI_REST2_LR_Atlas_hp2000_clean.dtseries.nii So for 10 subjects, I will have 40 total files. Am I correct to assume that I can use the command line tool wb_command -cifti-average to average over all 40 files and then wb_command -cifti-correlation to create a dense connectome? -Ausaf -- Ausaf A. Bari MD PhD Resident Physician UCLA Medical Center Department of Neurosurgery Email: aus...@gmail.com ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org 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. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. -- Ausaf A. Bari MD PhD Resident Physician UCLA Medical Center Department of Neurosurgery Phone: 617-642-1929 Email: aus...@gmail.com ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users --- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) st...@fmrib.ox.ac.ukhttp://www.fmrib.ox.ac.uk/~steve --- Stop the cultural destruction of Tibet http://smithinks.net ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Creating Group Average Resting State fMRI
Tim - minor correction in your cifti-math formula: I think you need the cifti-output right after the expression. On Tue, May 20, 2014 at 1:00 PM, Timothy Coalson tsc...@mst.edu wrote: It isn't too hard with -cifti-reduce and -cifti-math (though it does need -select and -repeat): wb_command -cifti-reduce input MEAN mean.dtseries.nii wb_command -cifti-reduce input STDEV stdev.dtseries.nii wb_command -cifti-math '(x - mean) / stdev' -fixnan 0 -var x input -var mean mean.dtseries.nii -select 1 1 -repeat -var stdev stdev.dtseries.nii -select 1 1 -repeat If there are places with 0 stdev in all concatenated timeseries, the correlation will probably give back NaNs, which will have to be fixed. Tim On Tue, May 20, 2014 at 2:44 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote: Demean and normalize functionality might be useful things to add to wb_command -cifti-merge, unless there is a simple wb_command way to do this already (we generally do this in matlab now). Matt. From: Timothy Coalson tsc...@mst.edu Date: Tuesday, May 20, 2014 at 12:19 PM To: Stephen Smith st...@fmrib.ox.ac.uk Cc: Ausaf Bari aus...@gmail.com, hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI Should you also normalize so that the standard deviations of each timeseries match? Tim On Tue, May 20, 2014 at 12:24 PM, Stephen Smith st...@fmrib.ox.ac.ukwrote: Hi - One important point - you should never temporally concatenate without first demeaning the individual timeseries. Cheers. On 20 May 2014, at 10:14, Ausaf Bari aus...@gmail.com wrote: Ok that is something I tried recently actually - to merge all the runs across all the subjects and then do a correlation with fisher-z transform. The results didn't feel right in that they didn't look like typical resting state images. That is why I wanted to double check I was doing it the right way. As an alternative could I merge the within subject runs together with -merge and do a within-subject correlation and then average across subjects? Is there any downside to this other than the huge amount of storage space that would be required (32GB per subject)? -Ausaf On Mon, May 19, 2014 at 10:04 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote: The simplest way is to concatenate the timeseries with wb_command -cifti-merge. You could do this for all runs of all subjects, or all runs for each subject (and then z-transform and average the connectomes across subjects). There will be a better way in the future. Peace, Matt. From: Timothy Coalson tsc...@mst.edu Date: Monday, May 19, 2014 at 10:48 PM To: Ausaf Bari aus...@gmail.com Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI Averaging together timepoints does not make sense for resting state data, it does not use stimuli, so there is no temporal correspondence between runs or across subjects. You should do the correlation before any averaging. I'm not sure what method our pipelines use, so I'll let someone else respond as to what the recommended method is (you probably don't need to correlate each file by itself, which would use up lots of disk space). Tim On Mon, May 19, 2014 at 8:22 PM, Ausaf Bari aus...@gmail.com wrote: I am trying to create a resting state fMRI average over 10 subjects to view in connectome workbench. For each HCP subject, I found the following 4 files: rfMRI_REST1_RL_Atlas_hp2000_clean.dtseries.nii rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii rfMRI_REST2_RL_Atlas_hp2000_clean.dtseries.nii rfMRI_REST2_LR_Atlas_hp2000_clean.dtseries.nii So for 10 subjects, I will have 40 total files. Am I correct to assume that I can use the command line tool wb_command -cifti-average to average over all 40 files and then wb_command -cifti-correlation to create a dense connectome? -Ausaf -- Ausaf A. Bari MD PhD Resident Physician UCLA Medical Center Department of Neurosurgery Email: aus...@gmail.com ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org 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. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. -- Ausaf A. Bari MD PhD Resident
Re: [HCP-Users] Creating Group Average Resting State fMRI
On a similar note, I also want to find the group average of a particular task fMRI such as the emotion task fMRI. I found a .dscalar.nii CIFTI file for each task for each subject. Can I average the .dscalar.nii files together across subjects with cifti-average since these are just CIFTI scalars files with a z-statistic column? -Ausaf On Mon, May 19, 2014 at 10:04 PM, Glasser, Matthew glass...@wusm.wustl.eduwrote: The simplest way is to concatenate the timeseries with wb_command -cifti-merge. You could do this for all runs of all subjects, or all runs for each subject (and then z-transform and average the connectomes across subjects). There will be a better way in the future. Peace, Matt. From: Timothy Coalson tsc...@mst.edu Date: Monday, May 19, 2014 at 10:48 PM To: Ausaf Bari aus...@gmail.com Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI Averaging together timepoints does not make sense for resting state data, it does not use stimuli, so there is no temporal correspondence between runs or across subjects. You should do the correlation before any averaging. I'm not sure what method our pipelines use, so I'll let someone else respond as to what the recommended method is (you probably don't need to correlate each file by itself, which would use up lots of disk space). Tim On Mon, May 19, 2014 at 8:22 PM, Ausaf Bari aus...@gmail.com wrote: I am trying to create a resting state fMRI average over 10 subjects to view in connectome workbench. For each HCP subject, I found the following 4 files: rfMRI_REST1_RL_Atlas_hp2000_clean.dtseries.nii rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii rfMRI_REST2_RL_Atlas_hp2000_clean.dtseries.nii rfMRI_REST2_LR_Atlas_hp2000_clean.dtseries.nii So for 10 subjects, I will have 40 total files. Am I correct to assume that I can use the command line tool wb_command -cifti-average to average over all 40 files and then wb_command -cifti-correlation to create a dense connectome? -Ausaf -- Ausaf A. Bari MD PhD Resident Physician UCLA Medical Center Department of Neurosurgery Email: aus...@gmail.com ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org 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. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Creating Group Average Resting State fMRI
I created a unix bash script that will automatically perform the demeaning on the cleaned dense time series files over multiple subject directories. Place this in your favorite scripts folder and update your .bash_profile to include the script directory in you $PATH variable. If you have any questions feel free to contact me. #!/bin/bash #This sript will recursively search the subject directories for the resting state clean #dense time series files, calculate the mean and standard deviation for each time series #and then demean the the data and output this as a dmean_dtseries.nii file. # #Created by Ausaf Bari, 3/20/2014 # for filepath in $(find . -iname '*clean.dtseries.nii') do f=$(basename $filepath) dir=$(dirname $filepath) echo Processing $filepath wb_command -cifti-reduce $filepath MEAN $dir/mean_$f wb_command -cifti-reduce $filepath STDEV $dir/stdev_$f wb_command -cifti-math '(x-mean)/stdev' $dir/demean_$f -fixnan 0 -var x $filepath -var mean $dir/mean_$f -select 1 1 -repeat -var stdev $dir/stdev_$f -select 1 1 -repeat done On Tue, May 20, 2014 at 1:17 PM, Timothy Coalson tsc...@mst.edu wrote: Wups, yeah, forgot that bit. Nice catch. Tim On Tue, May 20, 2014 at 3:12 PM, Ausaf Bari aus...@gmail.com wrote: Tim - minor correction in your cifti-math formula: I think you need the cifti-output right after the expression. On Tue, May 20, 2014 at 1:00 PM, Timothy Coalson tsc...@mst.edu wrote: It isn't too hard with -cifti-reduce and -cifti-math (though it does need -select and -repeat): wb_command -cifti-reduce input MEAN mean.dtseries.nii wb_command -cifti-reduce input STDEV stdev.dtseries.nii wb_command -cifti-math '(x - mean) / stdev' -fixnan 0 -var x input -var mean mean.dtseries.nii -select 1 1 -repeat -var stdev stdev.dtseries.nii -select 1 1 -repeat If there are places with 0 stdev in all concatenated timeseries, the correlation will probably give back NaNs, which will have to be fixed. Tim On Tue, May 20, 2014 at 2:44 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote: Demean and normalize functionality might be useful things to add to wb_command -cifti-merge, unless there is a simple wb_command way to do this already (we generally do this in matlab now). Matt. From: Timothy Coalson tsc...@mst.edu Date: Tuesday, May 20, 2014 at 12:19 PM To: Stephen Smith st...@fmrib.ox.ac.uk Cc: Ausaf Bari aus...@gmail.com, hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI Should you also normalize so that the standard deviations of each timeseries match? Tim On Tue, May 20, 2014 at 12:24 PM, Stephen Smith st...@fmrib.ox.ac.ukwrote: Hi - One important point - you should never temporally concatenate without first demeaning the individual timeseries. Cheers. On 20 May 2014, at 10:14, Ausaf Bari aus...@gmail.com wrote: Ok that is something I tried recently actually - to merge all the runs across all the subjects and then do a correlation with fisher-z transform. The results didn't feel right in that they didn't look like typical resting state images. That is why I wanted to double check I was doing it the right way. As an alternative could I merge the within subject runs together with -merge and do a within-subject correlation and then average across subjects? Is there any downside to this other than the huge amount of storage space that would be required (32GB per subject)? -Ausaf On Mon, May 19, 2014 at 10:04 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote: The simplest way is to concatenate the timeseries with wb_command -cifti-merge. You could do this for all runs of all subjects, or all runs for each subject (and then z-transform and average the connectomes across subjects). There will be a better way in the future. Peace, Matt. From: Timothy Coalson tsc...@mst.edu Date: Monday, May 19, 2014 at 10:48 PM To: Ausaf Bari aus...@gmail.com Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI Averaging together timepoints does not make sense for resting state data, it does not use stimuli, so there is no temporal correspondence between runs or across subjects. You should do the correlation before any averaging. I'm not sure what method our pipelines use, so I'll let someone else respond as to what the recommended method is (you probably don't need to correlate each file by itself, which would use up lots of disk space). Tim On Mon, May 19, 2014 at 8:22 PM, Ausaf Bari aus...@gmail.com wrote: I am trying to create a resting state fMRI average over 10 subjects to view in connectome workbench. For each HCP subject, I found the following 4 files: rfMRI_REST1_RL_Atlas_hp2000_clean.dtseries.nii rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii rfMRI_REST2_RL_Atlas_hp2000_clean.dtseries.nii
Re: [HCP-Users] Creating Group Average Resting State fMRI
You could do that if you just want a heuristic map of the group activation. But I wouldn’t use that for anything that requires meaningful statistics. To compute proper Level 3 task maps what we do currently is convert the CIFTI copes/varcopes to NIFTI, merge them into a 4D NIFTI file, and then use those as inputs to 'flameo' in a mixed effects analysis. (And then convert those outputs back to CIFTI). cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Ausaf Bari aus...@gmail.com Date: Tuesday, May 20, 2014 5:56 PM To: Matt Glasser glass...@wusm.wustl.edu Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI On a similar note, I also want to find the group average of a particular task fMRI such as the emotion task fMRI. I found a .dscalar.nii CIFTI file for each task for each subject. Can I average the .dscalar.nii files together across subjects with cifti-average since these are just CIFTI scalars files with a z-statistic column? -Ausaf On Mon, May 19, 2014 at 10:04 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote: The simplest way is to concatenate the timeseries with wb_command -cifti-merge. You could do this for all runs of all subjects, or all runs for each subject (and then z-transform and average the connectomes across subjects). There will be a better way in the future. Peace, Matt. From: Timothy Coalson tsc...@mst.edu Date: Monday, May 19, 2014 at 10:48 PM To: Ausaf Bari aus...@gmail.com Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI Averaging together timepoints does not make sense for resting state data, it does not use stimuli, so there is no temporal correspondence between runs or across subjects. You should do the correlation before any averaging. I'm not sure what method our pipelines use, so I'll let someone else respond as to what the recommended method is (you probably don't need to correlate each file by itself, which would use up lots of disk space). Tim On Mon, May 19, 2014 at 8:22 PM, Ausaf Bari aus...@gmail.com wrote: I am trying to create a resting state fMRI average over 10 subjects to view in connectome workbench. For each HCP subject, I found the following 4 files: rfMRI_REST1_RL_Atlas_hp2000_clean.dtseries.nii rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii rfMRI_REST2_RL_Atlas_hp2000_clean.dtseries.nii rfMRI_REST2_LR_Atlas_hp2000_clean.dtseries.nii So for 10 subjects, I will have 40 total files. Am I correct to assume that I can use the command line tool wb_command -cifti-average to average over all 40 files and then wb_command -cifti-correlation to create a dense connectome? -Ausaf -- Ausaf A. Bari MD PhD Resident Physician UCLA Medical Center Department of Neurosurgery Email: aus...@gmail.com ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org 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. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org 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. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___HCP-Users mailing listHCP-Users@humanconnectome.orghttp://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Creating Group Average Resting State fMRI
Thanks. I will try that. -Ausaf On Tue, May 20, 2014 at 8:25 PM, Harms, Michael mha...@wustl.edu wrote: You could do that if you just want a heuristic map of the group activation. But I wouldn’t use that for anything that requires meaningful statistics. To compute proper Level 3 task maps what we do currently is convert the CIFTI copes/varcopes to NIFTI, merge them into a 4D NIFTI file, and then use those as inputs to 'flameo' in a mixed effects analysis. (And then convert those outputs back to CIFTI). cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Ausaf Bari aus...@gmail.com Date: Tuesday, May 20, 2014 5:56 PM To: Matt Glasser glass...@wusm.wustl.edu Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI On a similar note, I also want to find the group average of a particular task fMRI such as the emotion task fMRI. I found a .dscalar.nii CIFTI file for each task for each subject. Can I average the .dscalar.nii files together across subjects with cifti-average since these are just CIFTI scalars files with a z-statistic column? -Ausaf On Mon, May 19, 2014 at 10:04 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote: The simplest way is to concatenate the timeseries with wb_command -cifti-merge. You could do this for all runs of all subjects, or all runs for each subject (and then z-transform and average the connectomes across subjects). There will be a better way in the future. Peace, Matt. From: Timothy Coalson tsc...@mst.edu Date: Monday, May 19, 2014 at 10:48 PM To: Ausaf Bari aus...@gmail.com Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI Averaging together timepoints does not make sense for resting state data, it does not use stimuli, so there is no temporal correspondence between runs or across subjects. You should do the correlation before any averaging. I'm not sure what method our pipelines use, so I'll let someone else respond as to what the recommended method is (you probably don't need to correlate each file by itself, which would use up lots of disk space). Tim On Mon, May 19, 2014 at 8:22 PM, Ausaf Bari aus...@gmail.com wrote: I am trying to create a resting state fMRI average over 10 subjects to view in connectome workbench. For each HCP subject, I found the following 4 files: rfMRI_REST1_RL_Atlas_hp2000_clean.dtseries.nii rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii rfMRI_REST2_RL_Atlas_hp2000_clean.dtseries.nii rfMRI_REST2_LR_Atlas_hp2000_clean.dtseries.nii So for 10 subjects, I will have 40 total files. Am I correct to assume that I can use the command line tool wb_command -cifti-average to average over all 40 files and then wb_command -cifti-correlation to create a dense connectome? -Ausaf -- Ausaf A. Bari MD PhD Resident Physician UCLA Medical Center Department of Neurosurgery Email: aus...@gmail.com ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org 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. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org 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. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. -- Ausaf A. Bari MD PhD Resident Physician UCLA Medical Center Department of Neurosurgery Phone: 617-642-1929 Email: aus...@gmail.com ___ HCP
Re: [HCP-Users] Creating Group Average Resting State fMRI
The simplest way is to concatenate the timeseries with wb_command -cifti-merge. You could do this for all runs of all subjects, or all runs for each subject (and then z-transform and average the connectomes across subjects). There will be a better way in the future. Peace, Matt. From: Timothy Coalson tsc...@mst.edu Date: Monday, May 19, 2014 at 10:48 PM To: Ausaf Bari aus...@gmail.com Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Creating Group Average Resting State fMRI Averaging together timepoints does not make sense for resting state data, it does not use stimuli, so there is no temporal correspondence between runs or across subjects. You should do the correlation before any averaging. I'm not sure what method our pipelines use, so I'll let someone else respond as to what the recommended method is (you probably don't need to correlate each file by itself, which would use up lots of disk space). Tim On Mon, May 19, 2014 at 8:22 PM, Ausaf Bari aus...@gmail.com wrote: I am trying to create a resting state fMRI average over 10 subjects to view in connectome workbench. For each HCP subject, I found the following 4 files: rfMRI_REST1_RL_Atlas_hp2000_clean.dtseries.nii rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii rfMRI_REST2_RL_Atlas_hp2000_clean.dtseries.nii rfMRI_REST2_LR_Atlas_hp2000_clean.dtseries.nii So for 10 subjects, I will have 40 total files. Am I correct to assume that I can use the command line tool wb_command -cifti-average to average over all 40 files and then wb_command -cifti-correlation to create a dense connectome? -Ausaf -- Ausaf A. Bari MD PhD Resident Physician UCLA Medical Center Department of Neurosurgery Email: aus...@gmail.com ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org 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. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___HCP-Users mailing listHCP-Users@humanconnectome.orghttp://lists.humanconnectome.org/mailman/listinfo/hcp-users
