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 diogenesdiego@gmail.com mailto:diogenesdiego@gmail.com

Em sáb., 29 de mai. de 2021 às 03:14, Diógenes Bispo <diogenesdiego@gmail.com mailto:diogenesdiego@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
diogenesdiego@gmail.com <mailto:diogenesdiego@gmail.com>

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