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Dear Doug,

Thanks for your quick response.

I am now able to get roifile (i.e., Volume_Subcortical) from asegstats2table, which shows cortical volume values of all the subcortical regions. Next when I run:

mri_glmfit --table Volume_Subcortical --fsgd Subs.fsgd dods --C Corr-cor.mtx --surf fsaverage lh --cortex --glmdir lh.sub_vol.glmdir (everything else here is same as I used for cortical volume calculations, but now just replaced --y volumefile with --table roifile)

Now, I get following in the terminal window:

Measure:volume                    Corr-cor 

Left-Lateral-Ventricle             -3.025 

Left-Inf-Lat-Vent                  -2.273 

Left-Cerebellum-White-Matter       -0.407 

Left-Cerebellum-Cortex              0.027 

Left-Thalamus-Proper                0.280 

Left-Caudate                        0.618 

Left-Putamen                        0.038 

Left-Pallidum                      -0.383 

3rd-Ventricle                      -0.839 

4th-Ventricle                      -0.465 

Brain-Stem                         -0.710 

Left-Hippocampus                    0.225 

Left-Amygdala                       0.342 

CSF                                -0.189 

Left-Accumbens-area                -0.007 

Left-VentralDC                     -0.950 

Left-vessel                        -0.146 

Left-choroid-plexus                -0.788 

Right-Lateral-Ventricle            -1.839 

Right-Inf-Lat-Vent                 -1.150 

Right-Cerebellum-White-Matter      -0.537 

Right-Cerebellum-Cortex             0.025 

Right-Thalamus-Proper              -0.015 

Right-Caudate                       0.197 

Right-Putamen                       0.045 

Right-Pallidum                     -0.278 

Right-Hippocampus                  -0.222 

Right-Amygdala                     -0.204 

Right-Accumbens-area                0.226 

Right-VentralDC                    -1.486 

Right-vessel                       -1.099 

Right-choroid-plexus               -0.675 

5th-Ventricle                       0.187 

WM-hypointensities                 -0.300 

Left-WM-hypointensities             0.000 

Right-WM-hypointensities            0.000 

non-WM-hypointensities              0.880 

Left-non-WM-hypointensities         0.000 

Right-non-WM-hypointensities        0.000 

Optic-Chiasm                       -0.458 

CC_Posterior                       -0.192 

CC_Mid_Posterior                   -0.208 

CC_Central                         -0.061 

CC_Mid_Anterior                     0.067 

CC_Anterior                        -1.261 

BrainSegVol                         0.002 

BrainSegVolNotVent                  0.079 

BrainSegVolNotVentSurf              0.081 

lhCortexVol                         0.239 

rhCortexVol                         0.384 

CortexVol                           0.310 

lhCerebralWhiteMatterVol           -0.125 

rhCerebralWhiteMatterVol           -0.045 

CerebralWhiteMatterVol             -0.084 

SubCortGrayVol                     -0.028 

TotalGrayVol                        0.268 

SupraTentorialVol                   0.016 

SupraTentorialVolNotVent            0.097 

SupraTentorialVolNotVentVox         0.100 

MaskVol                             0.154 

BrainSegVol-to-eTIV                 0.011 

MaskVol-to-eTIV                     0.339 

lhSurfaceHoles                      0.092 

rhSurfaceHoles                     -0.023 

SurfaceHoles                        0.035 

EstimatedTotalIntraCranialVol       0.019 

I assume I am running this correctly up to this point. But after this, when I run:

mri_glmfit-sim --glmdir lh.sub_vol.glmdir --cache 3 abs --cwp 0.05 --2spaces

ERROR: cannot find lh.sub_vol.glmdir/fwhm.dat

This is because replacing --y volumefile with --table roifile in mri_glmfit doesn't generate a fwhm.dat file. I guess I am doing something wrong with may be mri_glmfit (or may be mri_glmfit-sim command.

Thanks.

On Tue, Jun 30, 2020 at 9:13 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

On 6/29/2020 8:45 PM, Martin Juneja wrote:

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Hello experts,

I am following these instructions https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis to analyze the association between IQ and whole brain cortical thickness of brain areas (which by default uses Desikan atlas of 34 regions).

I was wondering how:

(1). To do the similar analysis to identify sub-cortical regions which show significant association between thickness and IQ.

I assume you mean volume since subcortical structures do not have thickness. You would use mri_glmfit the same as with the whole brain above, but instead of --y thicknessfile, you would use --table roifile, where roifile is one of the outputs from asegstats2table or aparcstats2table. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI

(2). To use other atlases here i.e., replace Desikan atlas with 7 or 17 network Yeo atlas to identify which network shows the association with IQ.

You would have to map the Yeo atlas into the individual subject, then run mris_anatomical_stats. I think Yeo has a page on this. Then use aparcstats2table and mri_glmfit

I know how to extract thickness etc from sub-cortical areas (i.e., aseg stats) and use Yeo atlas outside these instructions, but I am not sure how to do this in above described instructions i.e., replace Desikan with sub-cortical and Yeo atlases etc.

Any help would be really appreciated.

Thanks !

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