look at the tutorial
On 6/1/2021 12:00 AM, Diógenes Bispo wrote:
External Email - Use Caution
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 <mailto:diogenesdi...@gmail.com>
Em sáb., 29 de mai. de 2021 às 03:14, Diógenes Bispo
<diogenesdi...@gmail.com <mailto: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 <mailto:diogenesdi...@gmail.com>
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