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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