What do you mean by normalized? The intensity is normalized in both, ces
to the grand mean over the brain, and cespct to the voxel mean. I've
done experiments with both and can't find a big difference (though I've
not looked in resting state). I usually just use ces
doug
On 03/27/2015 03:21 PM, Barbour, Tracy,M.D. wrote:
> Thanks! Are both the ces and cespct normalized? Is there a reason you would
> use one over the other?
>
> 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: Friday, March 27, 2015 3:15 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] functional connectivity maps (correlation and z
> maps)
>
> The statistic maps (z, t, correlation coefficient) depend on the noise
> of the individual analysis, ie, two subjects could have identical
> correlation but have different correlation coefficient or z because one
> is noisier than the other (eg, moves more, physio is different). This
> means that you can find difference between groups because one group is
> noisier than the other. The ces and cespct do not have this problem (or,
> rather, it is much reduced).
>
> doug
>
> On 03/27/2015 01:53 PM, Barbour, Tracy,M.D. wrote:
>> Thanks! Would you please explain why you think ces is the better map (vs z
>> or correlation coefficient)?
>>
>> 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: Friday, March 27, 2015 12:28 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] functional connectivity maps (correlation and z
>> maps)
>>
>> 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
>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>> _______________________________________________
>>> 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
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> _______________________________________________
>> 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
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> _______________________________________________
> 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
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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