processing-scripts
processing-scripts > RE: Nuisance signal regression- 3dDecon/3dREM
Aug 8, 2012 12:08 PM | veena nair
RE: Nuisance signal regression- 3dDecon/3dREM
Hi, I was hoping somebody with
expertise in afni and fsl could respond-
I tried running afni commands 3dDeconvolve and 3dREMLfit(shown below in previous post) to get nuisance matrix and get the residuals. Then I demean and add 100, similar to nitrc script #5. For the most part these work fine; however for some subjects and for certain rois, my output file from 3dREMLfit seems to have little or no data such that when using 3dROIstats to extract time-series, I get mostly values clustered around 100 (99.999 or 100.xx etc). I checked the rois and they lie within the brain and nothing looks weird.Not sure how to fix this.
Appreciate any thoughts/suggestions,
-thanks
Veena.
Originally posted by veena nair:
I tried running afni commands 3dDeconvolve and 3dREMLfit(shown below in previous post) to get nuisance matrix and get the residuals. Then I demean and add 100, similar to nitrc script #5. For the most part these work fine; however for some subjects and for certain rois, my output file from 3dREMLfit seems to have little or no data such that when using 3dROIstats to extract time-series, I get mostly values clustered around 100 (99.999 or 100.xx etc). I checked the rois and they lie within the brain and nothing looks weird.Not sure how to fix this.
Appreciate any thoughts/suggestions,
-thanks
Veena.
Originally posted by veena nair:
Hi all, thanks for this forum and all the
helpful posts!
I was looking up afni commands to compute the nuisance matrix and residuals for doing resting fc-MRI and found this thread; just wondered if somebody had actually followed up on whether the 3dDeconvolve + 3dREMLfit steps shown below produce results similar to the ones produced using the nitrc script #5? Below are commands from my script:($file is the preprocessed resting func file, $cor is the type of correction with or w/out motion, wm/csf/glob etc); wonder if anyone has used something similar?
3dDeconvolve \
-input $file+orig -polort 0 \
-mask Mask.Brain.$file+orig \
-num_stimts $n \
-stim_file 1 $nuisance/dm.0.$MotionFile -stim_label 1 mot0 -stim_base 1 \
-stim_file 2 $nuisance/dm.1.$MotionFile -stim_label 2 mot1 -stim_base 2 \
-stim_file 3 $nuisance/dm.2.$MotionFile -stim_label 3 mot2 -stim_base 3 \
-stim_file 4 $nuisance/dm.3.$MotionFile -stim_label 4 mot3 -stim_base 4 \
-stim_file 5 $nuisance/dm.4.$MotionFile -stim_label 5 mot4 -stim_base 5 \
-stim_file 6 $nuisance/dm.5.$MotionFile -stim_label 6 mot5 -stim_base 6 \
-stim_file 7 $nuisance/ts.WM.$sid.rest.oxrtfsd.1D -stim_label 7 WM -stim_base 7 \
-stim_file 8 $nuisance/ts.CSF.$sid.rest.oxrtfsd.1D -stim_label 8 CSF -stim_base 8 \
# -stim_file 9 $nuisance/ts.global.$sid.rest.oxrtfsd.1D -stim_label 10 global -stim_base 9 \
-x1D $nuisance/nuisance.$cor.$file \
-x1D_stop
echo "Running 3dREMlfit to get residuals"
3dREMLfit -input $file+orig \
-matrix $nuisance/nuisance.$cor.$file.xmat.1D \
-mask Mask.Brain.$file+orig \
-Rerrts $nuisance/res4d.$cor.nii.gz \
-GOFORIT
echo "Demeaning residuals and adding 100"
3dTstat -mean -prefix $nuisance/res4d_mean.$cor.nii.gz $nuisance/res4d.$cor.nii.gz
3dcalc -a $nuisance/res4d.$cor.nii.gz -b $nuisance/res4d_mean.$cor.nii.gz -expr '(a-b)+100' -prefix $file.$cor.nii
echo "Resampling residuals to TLRC space"
@auto_tlrc -apar $sid.brain+tlrc -suffix res2std -input $file.$cor.nii
-thanks,
veena
I was looking up afni commands to compute the nuisance matrix and residuals for doing resting fc-MRI and found this thread; just wondered if somebody had actually followed up on whether the 3dDeconvolve + 3dREMLfit steps shown below produce results similar to the ones produced using the nitrc script #5? Below are commands from my script:($file is the preprocessed resting func file, $cor is the type of correction with or w/out motion, wm/csf/glob etc); wonder if anyone has used something similar?
3dDeconvolve \
-input $file+orig -polort 0 \
-mask Mask.Brain.$file+orig \
-num_stimts $n \
-stim_file 1 $nuisance/dm.0.$MotionFile -stim_label 1 mot0 -stim_base 1 \
-stim_file 2 $nuisance/dm.1.$MotionFile -stim_label 2 mot1 -stim_base 2 \
-stim_file 3 $nuisance/dm.2.$MotionFile -stim_label 3 mot2 -stim_base 3 \
-stim_file 4 $nuisance/dm.3.$MotionFile -stim_label 4 mot3 -stim_base 4 \
-stim_file 5 $nuisance/dm.4.$MotionFile -stim_label 5 mot4 -stim_base 5 \
-stim_file 6 $nuisance/dm.5.$MotionFile -stim_label 6 mot5 -stim_base 6 \
-stim_file 7 $nuisance/ts.WM.$sid.rest.oxrtfsd.1D -stim_label 7 WM -stim_base 7 \
-stim_file 8 $nuisance/ts.CSF.$sid.rest.oxrtfsd.1D -stim_label 8 CSF -stim_base 8 \
# -stim_file 9 $nuisance/ts.global.$sid.rest.oxrtfsd.1D -stim_label 10 global -stim_base 9 \
-x1D $nuisance/nuisance.$cor.$file \
-x1D_stop
echo "Running 3dREMlfit to get residuals"
3dREMLfit -input $file+orig \
-matrix $nuisance/nuisance.$cor.$file.xmat.1D \
-mask Mask.Brain.$file+orig \
-Rerrts $nuisance/res4d.$cor.nii.gz \
-GOFORIT
echo "Demeaning residuals and adding 100"
3dTstat -mean -prefix $nuisance/res4d_mean.$cor.nii.gz $nuisance/res4d.$cor.nii.gz
3dcalc -a $nuisance/res4d.$cor.nii.gz -b $nuisance/res4d_mean.$cor.nii.gz -expr '(a-b)+100' -prefix $file.$cor.nii
echo "Resampling residuals to TLRC space"
@auto_tlrc -apar $sid.brain+tlrc -suffix res2std -input $file.$cor.nii
-thanks,
veena
Threaded View
| Title | Author | Date |
|---|---|---|
| Lisa Eyler | Jun 8, 2010 | |
| cirong liu | Nov 1, 2011 | |
| Maarten Mennes | Nov 1, 2011 | |
| Xi-Nian Zuo | Jun 14, 2010 | |
| Maarten Mennes | Jun 14, 2010 | |
| Lisa Eyler | Jun 14, 2010 | |
| veena nair | Aug 4, 2012 | |
| veena nair | Aug 8, 2012 | |
| Maarten Mennes | Aug 8, 2012 | |
| veena nair | Aug 8, 2012 | |
| Zarrar Shehzad | Aug 9, 2011 | |
| Clare Kelly | Jun 16, 2010 | |