On 09/15/2017 02:13 PM, Martin Juneja wrote:
> Hi experts,
>
> I have three questions. I would really appreciate any help.
>
> (1). I ran following commands to estimate relationships between LGI
> and Behav data:
>
>  mris_preproc --fsgd Behav.fsgd --target fsaverage --hemi lh --meas
> pial_lgi --out lh.Behav_LGI.mgh
>
> mri_surf2surf --hemi lh --s fsaverage --sval lh.Behav_LGI.mgh --fwhm
> 10 --cortex --tval lh.Behav_LGI.10.mgh
>
> mri_glmfit --y lh.Behav_LGI.10.mgh --fsgd Behav.fsgd dods --C
> Corr-Behav-cor1.mtx --surf fsaverage lh --cortex --glmdir
> lh.Behav_LGI_P.glmdir --eres-save
>
> mri_glmfit-sim_nonortho --glmdir lh.Behav_LGI_P.glmdir --sim perm 2000
> 1.3 permcsd --sim-sign pos --cwpvalthresh .05 --perm-resid --overwrite
>
> Finally, cluster summary gives me one clusters with peak at the
> fusiform gyrus as following:
> ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZ    CWP
>  CWPLow    CWPHi   NVtxs    WghtVtx   Annot
>    1       -4.045   10153  32101.81    -36.5  -39.5  -15.1  0.00050
>  0.00000  0.00100  64731  -106698.82  fusiform
>
> As you can see number of voxels is 64731, so I when I viewed the
> results in FreeView, its showing me a big cluster, almost all over the
> brain (please see attached screen shot).
>
> Could you please tell me why I am getting these sort of results, and
> how can I fix this? If I change cluster forming threshold from 1.3 to
> 3, would that work? I wanted to make sure before I re-run the analysis
> because mri_glmfit-sim_nonortho command takes about a day to finish.

I don't know whether it would work, but it would make it better. You can
also just load the sig.mgh file and change the voxel-wise thresholds
until you get reasonably sized clusters, then run using that threshold.
If you do this, set the glmfti-sim threshold to the value your selected
during viewing but add 0.3 (needed because you are using a positive sign).
>
> (2). How can I save output cluster e.g. fusiform gyrus in above
> example in NIFTI MNI volume space so that I can use this cluster for
> functional connectivity analysis?
You're probably better of doing your fmri analysis in surface space
because mapping back and forth is a little tricky. But if you want to do
it, you can do
something like
mri_label2vol --annot /path/to/annot/in/glmfit/dir --temp
$FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg
$FREESURFER_HOME/average/mni152.register.dat --fill-ribbon --subject
fsaverage --hemi lh --o output.segmentation.in.mni152space.nii.gz

The output segmenation will have all the clusters from the annot file.
Remember, this mapping is an approximation

>
> (3). If I want to use fusiform gyrus from standard FreeSurfer
> parcellation rather than from my results, how can I save that in
> standard MNI volume space?
same as above
>
> Thank you so much !
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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