sdm-help-list
77 Subscribers 
sdm-help-list > White matter activation/inclusive masking
Showing 1-2 of 2 posts
Oct 24, 2014 10:10 AM | Nobody
White matter activation/inclusive masking
Hello,
We are in the process of finalising the data for our meta-analysis using SDM. Many thanks for all of the help and support throughout this. However, we note that some of the peak co-ordinates, whilst neighbouring regions of interest, are within white-matter. Is this something that people have encountered before? It seems likely given the variability between studies. I guess this might also reflect different smoothing thresholds as well as different analysis software versions (e.g. SPM 2 - 8, FSL etc.) Therefore, we would like to know:
1) Is there a way to get the peak coordinates for the closest grey matter region, rather than just the peak coordinate as outputted in the html report?
2) Has anyone used an inclusive binary mask before that only includes the grey matter regions? What could be used to generate this to ensure it is read correctly by SDM? Can anyone foresee any problems with this or suggest alternatives?
Many thanks
Jack
We are in the process of finalising the data for our meta-analysis using SDM. Many thanks for all of the help and support throughout this. However, we note that some of the peak co-ordinates, whilst neighbouring regions of interest, are within white-matter. Is this something that people have encountered before? It seems likely given the variability between studies. I guess this might also reflect different smoothing thresholds as well as different analysis software versions (e.g. SPM 2 - 8, FSL etc.) Therefore, we would like to know:
1) Is there a way to get the peak coordinates for the closest grey matter region, rather than just the peak coordinate as outputted in the html report?
2) Has anyone used an inclusive binary mask before that only includes the grey matter regions? What could be used to generate this to ensure it is read correctly by SDM? Can anyone foresee any problems with this or suggest alternatives?
Many thanks
Jack
Oct 27, 2014 01:10 PM | Nobody
RE: White matter activation/inclusive masking
Dear Jack,
current SDM software does not report the closest gray matter region, but you can find it with other software such as MRICroN (open e.g. the AAL atlas). Regarding masks, note that you may use your own one, just name the file "mask_WHATEVER.nii.gz" and copy it in the "share" folder.
With the best wishes,
current SDM software does not report the closest gray matter region, but you can find it with other software such as MRICroN (open e.g. the AAL atlas). Regarding masks, note that you may use your own one, just name the file "mask_WHATEVER.nii.gz" and copy it in the "share" folder.
With the best wishes,