I think that the ces is the better map to use, but there's not a
consensus. For some reason that I don't understand, people starting
using the z-map or the correlation coefficient as the input to the group
level in contradiction to everything that had ever been done in
task-based analysis. In tests that I have done with task-based analysis,
I did not see much difference in using ces, cespct, z, pcc, or t.
doug
On 03/26/2015 09:21 AM, Barbour, Tracy,M.D. wrote:
> 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
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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>
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> 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
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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