Hi Doug,
Thanks for your response. I implemented what you suggested, but I'm unclear as to what I should use as the value for --min when i use mri_binarize? At first I used 1.3, but that masked out almost all the activation. I lowered it to 0.1 just to see what would happen. That looked overall more reasonable (i.e. showing differences where there is activation and not where there are differences in deactivation). However, there are a couple of very small regions that are still showing up as having a significant difference between Condition A and Condition B, when in fact that difference is due to differences in deactivation (i.e. more deactivation in Condition B than Condition A --> shows up as A greater than B).
I'd like to know what a reasonable value for the --min flag and if you have any insight into why I am still seeing some regions that show differences in deactivation.
Here's what I ran:
mri_binarize --i CONDITION_Avpassive/ces.nii.gz --mask CONDITION_Bvpassive/ces.nii.gz --mask-thresh 0.00001 --o ConditionAvsConditionB/point1.ces.nii --min 0.1
mri_glmfit --y ConditionAvsConditionB/ces.nii.gz --osgm --mask ConditionAvsConditionB/point1.ces.nii --glmdir point1_masked.rfx --nii --surf fsaverage lh
Thanks for the help!
Maya
Message: 1 Date: Tue, 10 Sep 2013 15:37:01 -0400 From: Maya Rosen mayalrosen@gmail.com Subject: [Freesurfer] statistically truncate negative values To: freesurfer@nmr.mgh.harvard.edu Message-ID: CAJzkiyGEMzm1GUke-XV0Ko5qYH3QdQAuPmZWO8Rqm-0RyTOiew@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"
Hi All,
I have two conditions of interest in my GLM analysis, Condition A and Condition B. I would like to make a contrast of Condition A and Condition B that includes only those vertices that are significantly positively activated when compared to the Passive Viewing baseline. In other words, I would like to mask anything that is Passive > Condition A or Passive > Condition B and only include Condition A > Passive and Condition B > Passive when contrasting Condition A and Condition B, so as to limit my contrast to changes in *activation *in the two conditions, not *deactivation *.
I see that in an older version, when isxavg-re-sess was used, there was a flag --trunc that would allow you to set the negative values to 0. If there is a way to do this in the v 5.1.0, I could then perform a second level contrast of positively activated Condition A and Positively activated condition B.
Is there a way to exclude the negatively activated voxels from the Condition A vs Passive and Condition B vs Passive contrasts when looking at Condition A vs Condition B? I would like to do this statistically, not just at the map level.
Thank you for your help!
Maya