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help > RE: ROI problem (csf)
Feb 17, 2016 04:02 AM | Alfonso Nieto-Castanon - Boston University
RE: ROI problem (csf)
Hi Jalmar,
Yes, the thresholding/erosion steps are only applied to the White matter and CSF ROIs (not to the gray matter ROIs). The rationale is that erosion helps keep the "noise" ROIs used in aCompCor conservative (without potential inclusion of gray matter voxels). If you prefer to also apply these steps to your gray matter mask you could do that perhaps simply changing the lines in conn_process.m that read:
for nroi=intersect(validrois,2:3),
ERODE=ERODEall(max(1,min(numel(ERODEall),nroi-1)));
THR=THRall(max(1,min(numel(THRall),nroi-1)));
to:
for nroi=intersect(validrois,1:3),
ERODE=ERODEall(max(1,min(numel(ERODEall),nroi)));
THR=THRall(max(1,min(numel(THRall),nroi)));
Then, if you are using the batch.Setup.cwthreshold field to define your threshold and number of erosion steps keep in mind that after this modification this field will be expected to have 6 values instead of 4, now representing the threshold and number of erosion steps for Gray, White, and CSF areas (instead of the original White and CSF areas only)
Hope this helps
Alfonso
Originally posted by Jalmar Teeuw:
Yes, the thresholding/erosion steps are only applied to the White matter and CSF ROIs (not to the gray matter ROIs). The rationale is that erosion helps keep the "noise" ROIs used in aCompCor conservative (without potential inclusion of gray matter voxels). If you prefer to also apply these steps to your gray matter mask you could do that perhaps simply changing the lines in conn_process.m that read:
for nroi=intersect(validrois,2:3),
ERODE=ERODEall(max(1,min(numel(ERODEall),nroi-1)));
THR=THRall(max(1,min(numel(THRall),nroi-1)));
to:
for nroi=intersect(validrois,1:3),
ERODE=ERODEall(max(1,min(numel(ERODEall),nroi)));
THR=THRall(max(1,min(numel(THRall),nroi)));
Then, if you are using the batch.Setup.cwthreshold field to define your threshold and number of erosion steps keep in mind that after this modification this field will be expected to have 6 values instead of 4, now representing the threshold and number of erosion steps for Gray, White, and CSF areas (instead of the original White and CSF areas only)
Hope this helps
Alfonso
Originally posted by Jalmar Teeuw:
Hi Alfonso,
Thanks for the reply. We'll try to set the line "if ERODE>0" to "if 1" for our projects. This part of the code only affects the CSF and WM ROIs, right? Is it possible no thresholding is applied to the GM mask either? We checked the ROI time series stored in the CONN files and they appear to have the same issue where almost the entire brain volume was used to compute these mean time series. I'm not sure if it is used anywhere other than the column appended to the ROI-to-ROI matrix, but it may change the interpretation of 'GM' if voxels other than 'GM' are included in calculating the correlations.
Regards,
Jalmar
Thanks for the reply. We'll try to set the line "if ERODE>0" to "if 1" for our projects. This part of the code only affects the CSF and WM ROIs, right? Is it possible no thresholding is applied to the GM mask either? We checked the ROI time series stored in the CONN files and they appear to have the same issue where almost the entire brain volume was used to compute these mean time series. I'm not sure if it is used anywhere other than the column appended to the ROI-to-ROI matrix, but it may change the interpretation of 'GM' if voxels other than 'GM' are included in calculating the correlations.
Regards,
Jalmar
Threaded View
| Title | Author | Date |
|---|---|---|
| sherihane Bensemmane | Nov 30, 2015 | |
| Alfonso Nieto-Castanon | Nov 30, 2015 | |
| sherihane Bensemmane | Dec 1, 2015 | |
| Alfonso Nieto-Castanon | Dec 1, 2015 | |
| sherihane Bensemmane | Dec 2, 2015 | |
| sherihane Bensemmane | Dec 2, 2015 | |
| Alfonso Nieto-Castanon | Dec 2, 2015 | |
| Jalmar Teeuw | Dec 2, 2015 | |
| Alfonso Nieto-Castanon | Dec 3, 2015 | |
| Jalmar Teeuw | Feb 8, 2016 | |
| Alfonso Nieto-Castanon | Feb 13, 2016 | |
| Jalmar Teeuw | Feb 15, 2016 | |
| Alfonso Nieto-Castanon | Feb 17, 2016 | |
| Bob Kraft | Jun 14, 2016 | |
| Alfonso Nieto-Castanon | Jun 14, 2016 | |
| Bob Kraft | Jun 22, 2016 | |
| Jalmar Teeuw | Dec 4, 2015 | |
| sherihane Bensemmane | Dec 3, 2015 | |