Thanks Dr. Greve.

Regarding 2nd question, I am not sure how authors in this paper: http://www.sciencedirect.com/science/article/pii/S0166432815001837 performed FRD correction?
If we do not run FDR, then is sig.mgh output already FDR corrected as shown in this paper?

Thanks for your valuable time.

On Mon, May 15, 2017 at 9:26 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
I think your command lines are correct. I would not expect that swapping
the y and pvr to give the same results. sig=-log10(p)=30 is not totally
unreasonable. I don't understand #2. Why are you running FDR and cluster
correction?


On 05/11/2017 06:39 PM, Martin Juneja wrote:
> In addition to that: I am always getting positive correlations (when I
> load sig.mgh) every time i.e. even when I correlated thickness and
> gyrification. None of the voxels/areas showing negative correlation
> between any of the structural measures
>
> On Thu, May 11, 2017 at 11:26 AM, Martin Juneja <mj70481@gmail.com
> <mailto:mj70481@gmail.com>> wrote:
>
>     Hi Dr. Greve,
>
>     I doubt these results because of following:
>
>     (1). When I compare sig.mgh files created using following two
>     commands i.e. correlation between LGI and CV versus CV and LGI:
>     mri_glmfit --y Corr_CV_LGI/lh.LGI.10.mgh --fsgd CV_LGI.fsgd dods
>     --C Corr-VL-cor.mtx --surf fsaverage lh --cortex --glmdir
>     Corr_CV_LGI/lh.VL.glmdir --pvr Corr_CV_LGI/lh.CV.10.mgh
>     and
>     mri_glmfit --y Corr_CV_LGI/lh.vol.10.mgh --fsgd CV_LGI.fsgd dods
>     --C Corr-VL-cor.mtx --surf fsaverage lh --cortex --glmdir
>     Corr_CV_LGI/lh.VL.glmdir --pvr Corr_CV_LGI/lh.LGI.10.mgh
>
>     (a). I do not get identical maps. Please find attached screen shot.
>     (b). Here, colorbar showing a value of around 30, does that
>     reflect -log10(p)? I am not sure if thats normal?
>
>     (2). Assuming magnitude from colorbar is normal then I performed
>     FDR correction- I am assuming its same command as following as
>     mentioned in FS manual:
>     mri_glmfit-sim --glmdir Corr_CV_LGI/lh.VL.glmdir --cache 1.3 pos
>     --cwp 0.01 --2spaces
>
>     After running FDR correction, cache.th13.pos.sig.cluster.mgh and
>     cache.th13.neg.sig.cluster.mgh, none of these are showing me any
>     significant clusters, instead its showing a constant magnitude
>     (same color) over whole brain?
>
>     Thanks.
>     ​
>
>
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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Fax: 617-726-7422

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