Thanks Doug,
Hi,
I am wondering if you would give some input on this:
When we run the buckner scripts for functional connectivity analysis, those
scripts:
1. Obtain correlation maps of individual subjects, and convert them to
individual subject z-maps using Fisher's r-to-z transformation.
2. Obtain group-averaged correlation z-maps ( averaged across all subjects in
the group )
3. Apply an inverse Fisher's r-to-z transformation to the group-averaged
correlation z-map, yielding a group-averaged correlation map.
Using the fsFAST scripts I can:
1. Obtain the individual z maps (but these are converted from the sig.mgh map
not a correlation map).
2. Then I can concat all the individual z maps using isxconcat-sess by adding
the -map z flag. I get a group z.nii.gz map.
3. Now I am uncertain what to do for the within group analysis. The mri_glmfit
command can use the z.nii.gz file and the output is the sig.mgh file. This is
not analogous to the buckner scripts, as I am not converting back to a
correlation map, but am I getting the same result?
When I compare a within group analysis I get similar results if I use the
z.nii.gz or the ces.nii.gz as the input.
mri_glmfit --y ces.nii.gz --osgm --glmdir lh.wls.ces.ogsm --wls cesvar.nii.gz
--cortex --surf fsaverage lh --mask ../mask.nii.gz
When I compare the maps obtained during a regression analysis using the
z.nii.gz file and the ces.nii.gz file I get different results, so I'm not sure
which one to use.
mri_glmfit --y z.nii.gz --fsgd TAQ_ctl_blDIPS2008anatseed.fsgd --surf fsaverage
lh --glmdir lh.TAQ_ctl.glmdir --C ../slope.mtx --C ../intercept.mtx --cortex
Which map should I use?
Thank you
Tracy
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, March 25, 2015 3:37 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] functional connectivity maps (correlation and z maps)
cd glmdir/contrast
(could be sig.nii or sig.nii.gz)
matlab
sig = MRIread('sig.mgh');
p = (10.^-abs(sig.vol))/2;
z = sig;
z.vol = sign(sig.vol).*fast_p2z(p);
MRIwrite(z,'z.mgh')
On 03/25/2015 10:26 AM, Barbour, Tracy,M.D. wrote:
>
> Hello,
>
> I am doing a functional connectivity analysis. I want to make
> individual pearson correlation maps for each subject (correlation
> between the seed region and all other voxels in the brain) and then
> convert them to a map of z-scores using a Fisher's z transformation. I
> want to then get an averaged group z map.
>
> I know there is an -m z option for isxconcat. From where are the z
> values calculated from (Are the z values calculated from the ces map
> or the pcc map)? How do I get the group z map?
>
> Thank you in advance
>
> Tracy
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
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