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

diogenesdiego@gmail.com