Pipeline Release and Morphometry Measurements
Posted: Tue Mar 11, 2014 3:20 pm
Hi,
In my datasets, the morphologist pipelines 2007 and 2012 have been applied to dbA and dbB, respectively. When computing sulcal depth (with my own piece of software), I have larger sulcal depth in dbB (2012) than in dbA (2007). This could be due to many issues, including a change of software or hemispheric brain volume differences between subjects in dbB compared to subects in dbA.
In order to better understand these sulcal depth differences, I took one subject to which I applied both pipelines. Here are the differences I noticed:
1) despite identical AC-PC coordinates, the normalization transformation is surprisingly slightly different: in the common Talairach space, the MRI is more compressed along the X (sagittal) axis in 2012 than 2007, whereas it is more dilated along the Z (axial) axis in 2012 than 2007.
2) the hemispheric brain volume is 7.5% larger in 2012 than in 2007, which approximately matches a 0.5mm volume inflation (half a voxel) between 2007 and 2012.
3) According to this assumed volume inflation, the superior temporal sulcus is on average deeper in 2012 than in 2007 (using the Morphometry Statistics tool). The depth increase is of 0.9mm (almost one voxel).
My understanding is that I should not use two different pipelines to compute morphometric features. I probably have to re-run dbA with pipeline 2012 to have all measures with the same pipeline (2012). This is fine with me.
However, I deal with databases that have been processed by different labs so that I don't easily know which pipeline has been applied to it. How can I check the pipeline release that has been used? For example, is there a flag in the dataset that says which pipeline has been applied to it, eg pipeline 2007, 2011, 2012 or 2013?
Furthermore, I think this is important to know when and why measurements of hemispheric volume or sulcal features change in a software release. For example, we might have to re-run the new pipeline over an old dataset to comfirm a set of results. Is there some documentation about those changes?
In particular, the brainvisa sulci seem to get closer to the brain envelope/hull in the latest release than in the older ones. When loading together the hemispheric brain volume and the sulci graph, the sulci are more visible in the latest release than in the older ones. Do you confirm this feeling I have and if so, when did that occur?
Thanks so much for your help,
Francois
In my datasets, the morphologist pipelines 2007 and 2012 have been applied to dbA and dbB, respectively. When computing sulcal depth (with my own piece of software), I have larger sulcal depth in dbB (2012) than in dbA (2007). This could be due to many issues, including a change of software or hemispheric brain volume differences between subjects in dbB compared to subects in dbA.
In order to better understand these sulcal depth differences, I took one subject to which I applied both pipelines. Here are the differences I noticed:
1) despite identical AC-PC coordinates, the normalization transformation is surprisingly slightly different: in the common Talairach space, the MRI is more compressed along the X (sagittal) axis in 2012 than 2007, whereas it is more dilated along the Z (axial) axis in 2012 than 2007.
2) the hemispheric brain volume is 7.5% larger in 2012 than in 2007, which approximately matches a 0.5mm volume inflation (half a voxel) between 2007 and 2012.
3) According to this assumed volume inflation, the superior temporal sulcus is on average deeper in 2012 than in 2007 (using the Morphometry Statistics tool). The depth increase is of 0.9mm (almost one voxel).
My understanding is that I should not use two different pipelines to compute morphometric features. I probably have to re-run dbA with pipeline 2012 to have all measures with the same pipeline (2012). This is fine with me.
However, I deal with databases that have been processed by different labs so that I don't easily know which pipeline has been applied to it. How can I check the pipeline release that has been used? For example, is there a flag in the dataset that says which pipeline has been applied to it, eg pipeline 2007, 2011, 2012 or 2013?
Furthermore, I think this is important to know when and why measurements of hemispheric volume or sulcal features change in a software release. For example, we might have to re-run the new pipeline over an old dataset to comfirm a set of results. Is there some documentation about those changes?
In particular, the brainvisa sulci seem to get closer to the brain envelope/hull in the latest release than in the older ones. When loading together the hemispheric brain volume and the sulci graph, the sulci are more visible in the latest release than in the older ones. Do you confirm this feeling I have and if so, when did that occur?
Thanks so much for your help,
Francois