External Email - Use Caution 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 <dgr...@mgh.harvard.edu> wrote: > > > On 6/29/2020 8:45 PM, Martin Juneja wrote: > > External Email - Use Caution > 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 ! > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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
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