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I would like to know what other modification I should make to my script to
run --grf (volume analysis):
- mris_preproc ??
- mri_glmfit (--surf in white)
- mri_glmfit-sim ??
Thanks.
Diogenes Bispo
diogenesdi...@gmail.com
Em sáb., 29 de mai. de 2021 às 03:14, Diógenes Bispo <
diogenesdi...@gmail.com> escreveu:
> Hi Freesurfer team.
>
> I made the following command:
>
> #!/bin/tcsh
> setenv study $argv[1]
> foreach hemi (lh rh)
> foreach smoothing (10)
> foreach meas (volume)
> mris_preproc --fsgd FSGD/{$study}.fsgd \
> --cache-in {$meas}.fwhm{$smoothing}.fsaverage \
> --target fsaverage \
> --hemi {$hemi} \
> --out {$hemi}.{$meas}.{$study}.{$smoothing}.mgh
> end
> end
> end
> ----
> #!/bin/tcsh
> set study = $argv[1]
> foreach hemi (lh rh)
> foreach smoothness (10)
> foreach meas (volume)
> mri_glmfit \
> --y {$hemi}.{$meas}.{$study}.{$smoothness}.mgh \
> --fsgd FSGD/{$study}.fsgd dods \
> --C Contrasts/Contrast-1_group.diff.mtx \
> --C Contrasts/Contrast-2_group-x-age.mtx \
> --C Contrasts/Contrast-3_group-x-icv.mtx \
> --C Contrasts/Contrast-4_group-x-age-x-icv.mtx \
> --C Contrasts/Contrast-5_GCCV.intercept.mtx \
> --C Contrasts/Contrast-6_GCCV.age.mtx \
> --surf fsaverage {$hemi} \
> --cortex \
> --glmdir {$hemi}.{$meas}.{$study}.{$smoothness}.glmdir \
> --eres-save
> end
> end
> end
> ----
> #!/bin/tcsh
> setenv study $argv[1]
> foreach meas (volume)
> foreach hemi (lh rh)
> foreach smoothness (10)
> foreach dir ({$hemi}.{$meas}.{$study}.{$smoothness}.glmdir)
> mri_glmfit-sim \
> --glmdir {$dir} \
> --grf 2.0 neg \
> --cwp 0.05 \
> --2spaces \
> end
> end
> end
> end
>
> I have the following error:
> ...
>
> mri_surfcluster --in
> rh.volume.covid.10.glmdir/Contrast-1_group.diff/sig.mgh --mask
> rh.volume.covid.10.glmdir/mask.mgh --cwsig
> rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.cluster.mgh
> --sum
> rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.cluster.summary
> --ocn
> rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.ocn.mgh
> --annot aparc --cwpvalthresh 0.05 --o
> rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.masked.mgh
> --no-fixmni --csd-out
> rh.volume.covid.10.glmdir/csd/all.grf.th2.0.neg-Contrast-1_group.diff.csd
> --fwhm 13.965488 --hemi rh --subject fsaverage --thmin 2.0 --sign neg
> --oannot
> rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.ocn.annot
> --bonferroni 2 --surf white
>
> ERROR: need --csd with --csd-out
>
> How should I proceed to solve this problem?
>
> Thanks
>
> Diógenes Bispo
> diogenesdi...@gmail.com
>
>
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