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

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 wrote: > Ok that is something I tried recently actually - to merge all the runs across > all the subjects and then do a correlati

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 wrote: > Hi - One important point - you should never temporally concatenate without > first demeaning the individual timeseries. > Cheers. > > > > On 20 May 2

Re: [HCP-Users] Creating Group Average Resting State fMRI

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 Date: Tuesday, May 20, 2014 at 12:19 PM To: Stephen Smi

Re: [HCP-Users] Creating Group Average Resting State fMRI

That was going to be my next question. I was going to try wb_command -cifti-math or -cifti-reduce. Do you have an available matlab script? -Ausaf On Tue, May 20, 2014 at 12:44 PM, Glasser, Matthew wrote: > Demean and normalize functionality might be useful things to add to > wb_command -cifti-

Re: [HCP-Users] Creating Group Average Resting State fMRI

It isn't too hard with -cifti-reduce and -cifti-math (though it does need -select and -repeat): wb_command -cifti-reduce MEAN mean.dtseries.nii wb_command -cifti-reduce STDEV stdev.dtseries.nii wb_command -cifti-math '(x - mean) / stdev' -fixnan 0 -var x -var mean mean.dtseries.nii -select 1 1

Re: [HCP-Users] Creating Group Average Resting State fMRI

Tim - minor correction in your cifti-math formula: I think you need the right after the expression. On Tue, May 20, 2014 at 1:00 PM, Timothy Coalson wrote: > It isn't too hard with -cifti-reduce and -cifti-math (though it does need > -select and -repeat): > > wb_command -cifti-reduce MEAN mea

Re: [HCP-Users] Creating Group Average Resting State fMRI

Wups, yeah, forgot that bit. Nice catch. Tim On Tue, May 20, 2014 at 3:12 PM, Ausaf Bari wrote: > Tim - minor correction in your cifti-math formula: I think you need the > right after the expression. > > > On Tue, May 20, 2014 at 1:00 PM, Timothy Coalson wrote: > >> It isn't too hard with

Re: [HCP-Users] Creating Group Average Resting State fMRI

Is there any advantage to doing the group resting state analysis with MELODIC ( using multi-session temporal concatenation) instead of the wb commands? -Ausaf On Tue, May 20, 2014 at 1:12 PM, Ausaf Bari wrote: > Tim - minor correction in your cifti-math formula: I think you need the > right a

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 fi

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 ques

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,

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 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 w