You can do FDR or you can co cluster correction, but you can't do both.
It looks like that paper only did FDR. If you want to do FDR, you can
use mri_fdr. Run with --help for more info
On 5/15/17 12:33 PM, Martin Juneja wrote:
Thanks Dr. Greve.
Regarding 2nd question, I am not sure how autho
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.
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 th
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 wrot
mri_glmfit will not generate a pcc file with --pvr. I think I just did
not get around to adding support for this. What about the sig does not
look right? You can often get funny looking maps because each voxel is a
different design matrix.
On 05/09/2017 03:15 PM, Martin Juneja wrote:
> Dear Dr
Dear Dr. Greve,
I created two stacks: one with volume and the other with LGI using mris
commands as following:
mris_preproc --fsgd CV_LGI.fsgd --target fsaverage --hemi lh --meas volume
--out Corr_CV_LGI/lh.vol.mgh
mris_preproc --fsgd CV_LGI.fsgd --target fsaverage --hemi lh --meas
pial_lgi --out
To use the PVR, you need to create a stack of the measures that you want
to use (eg, lGI). This will be the same size as the stack you want to
correlate with. Eg, if you use mris_preproc to create a thickness stack,
you would use the same command to create the lGI stack. Create your FSGD
file a
Hi Dr. Greve,
I did not find --help option very helpful here and also I could not find
much help from the previous FreeSurfer posts. Could you please share more
details here e.g. how to set up fsgd and contrast file and how to run
mri_glmfit command here (e.g. what inputs should be provided here?)
You have to use the --pvr option to mri_glmfit. Run it with --help to
get more info and write back if you still have questions
On 04/26/2017 08:33 PM, Martin Juneja wrote:
> Hello FreeSurfer experts,
>
> I came across a paper:
> http://www.sciencedirect.com/science/article/pii/S0166432815001837
Hello FreeSurfer experts,
I came across a paper:
http://www.sciencedirect.com/science/article/pii/S0166432815001837
where correlation maps between volume and gyrification are reported.
I am familiar with GLM in FreeSurfer i.e. correlating behavioral measures
with volume and gyrification but I was
10 matches
Mail list logo
