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. (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.
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 !
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%C2%A0to 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 list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 dgreve@mgh.harvard.edu wrote:
On 6/29/2020 8:45 PM, Martin Juneja wrote:
External Email - Use CautionHello 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 listFreesurfer@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
You can't run mri_glmfit-sim on ROI output. mri_glmfit-sim is for correcting multiple comparisons on maps. For ROIs, you'll have to leave them uncorrecrted or correct with Bonferonni or FDR. In theory, you could use permutation.
On 6/30/2020 9:54 PM, Martin Juneja wrote:
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:volumeCorr-cor
Left-Lateral-Ventricle -3.025
Left-Inf-Lat-Vent-2.273
Left-Cerebellum-White-Matter -0.407
Left-Cerebellum-Cortex0.027
Left-Thalamus-Proper0.280
Left-Caudate0.618
Left-Putamen0.038
Left-Pallidum-0.383
3rd-Ventricle-0.839
4th-Ventricle-0.465
Brain-Stem -0.710
Left-Hippocampus0.225
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-area0.226
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-hypointensities0.000
non-WM-hypointensities0.880
Left-non-WM-hypointensities 0.000
Right-non-WM-hypointensities0.000
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
BrainSegVolNotVent0.079
BrainSegVolNotVentSurf0.081
lhCortexVol 0.239
rhCortexVol 0.384
CortexVol 0.310
lhCerebralWhiteMatterVol -0.125
rhCerebralWhiteMatterVol -0.045
CerebralWhiteMatterVol -0.084
SubCortGrayVol -0.028
TotalGrayVol0.268
SupraTentorialVol 0.016
SupraTentorialVolNotVent0.097
SupraTentorialVolNotVentVox 0.100
MaskVol 0.154
BrainSegVol-to-eTIV 0.011
MaskVol-to-eTIV 0.339
lhSurfaceHoles0.092
rhSurfaceHoles -0.023
SurfaceHoles0.035
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 mailto:dgreve@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_glmfitI 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 list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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