Back to PLS Helpgray matter mask
Posted on 09/02/09 13:24:12
Number of posts: 34
Hi.
I have a gray matter mask I created using SPM5 and I applied it to the same Task analysis (I read somewhere that masks can be applied during the creation of Datamat files which is what I thought I did) I performed before without the mask - the 2 analyses look completely different, with different sets of LV's/activated brain regions. I thought the mask would simply "mask" out the white matter and include only the same activated regions in the gray matter - it did that but the activated areas were far more spread out in a scattered fashion in the masked analysus. I'd like to send someone an image of the masked vs non-masked analysis to ask if this was done correctly - would somebody let me know where to send it to? Thanks so much in advance!
-Miyoung
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I'm Online
Posted on 09/02/09 16:13:19
Number of posts: 229
The quick answer is that if your 'brainmask' region that shows up in the PLS results window looks like a cortical rim, then you have masked the data correctly
If yes, it could well be that the variance structure changes substantially without the contributions from CSF/WM voxels - if that is the case, new patterns would be expected for both the brain and design saliences
nancy
If yes, it could well be that the variance structure changes substantially without the contributions from CSF/WM voxels - if that is the case, new patterns would be expected for both the brain and design saliences
nancy
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Posted on 09/02/09 18:46:41
Number of posts: 34
quote:
The quick answer is that if your 'brainmask' region that shows up in the PLS results window looks like a cortical rim, then you have masked the data correctly
If yes, it could well be that the variance structure changes substantially without the contributions from CSF/WM voxels - if that is the case, new patterns would be expected for both the brain and design saliences
nancy
Thank you for the clarification Nancy! If by "cortical rim" you mean the cortex is outlined by specks of colors (spectrum from red to blue) then I think I masked it correctly. I'm assuming it's a matter of where I set the +/- BSR threshold values now to determine what I want to filter out. It makes total sense that removing those voxels could alter the variance structure - would you say it's more "correct" to analyze WITH the gray matter mask than WITHOUT it? Please let me know what you think - and thanks once again for your time!!
-Miyoung
The quick answer is that if your 'brainmask' region that shows up in the PLS results window looks like a cortical rim, then you have masked the data correctly
If yes, it could well be that the variance structure changes substantially without the contributions from CSF/WM voxels - if that is the case, new patterns would be expected for both the brain and design saliences
nancy
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I'm Online
Posted on 09/03/09 09:37:27
Number of posts: 229
quote:
Thank you for the clarification Nancy! If by "cortical rim" you mean the cortex is outlined by specks of colors (spectrum from red to blue) then I think I masked it correctly. I'm assuming it's a matter of where I set the +/- BSR threshold values now to determine what I want to filter out. It makes total sense that removing those voxels could alter the variance structure - would you say it's more "correct" to analyze WITH the gray matter mask than WITHOUT it? Please let me know what you think - and thanks once again for your time!! -Miyoung
If it is 'speckled', I would be a bit concerned - if when you set the thresholds to zero, you see smoothly varying bootstrap ratios or brain saliences (depending on which window is opened), then you are good to go..Thank you for the clarification Nancy! If by "cortical rim" you mean the cortex is outlined by specks of colors (spectrum from red to blue) then I think I masked it correctly. I'm assuming it's a matter of where I set the +/- BSR threshold values now to determine what I want to filter out. It makes total sense that removing those voxels could alter the variance structure - would you say it's more "correct" to analyze WITH the gray matter mask than WITHOUT it? Please let me know what you think - and thanks once again for your time!! -Miyoung
Masking - this is your choice. Some T2* signal changes in white matter could be important (e.g., Neuroimage. 45(1):83-8, 2009; PLoS ONE [Electronic Resource]. 4(1):e4257, 2009).
Untitled Post
Posted on 09/03/09 13:37:41
Number of posts: 34
Thanks so much for your recommendations Nancy - I did set the BSR to 0 and I think it does look like smoothly varying BSR's. :)
Cheers!
-Miyoung
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