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Dear AFNI users-
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely, AFNI HQ
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
https://discuss.afni.nimh.nih.gov
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely, AFNI HQ
| October 18, 2019 09:45AM | |
Hello,
I'm a new user to AFNI, so please forgive me if there's an obvious error on my part. I am trying to do a 2-sample t-test with 3dttest++ and want to use ETAC for cluster correction. I have two groups: depressed (MDD) and control (HC) subjects, so this group analysis compares the mean difference MDD - HC.
When I look at the 3dttest++ output file, specifically the BRIK that displays the mean difference between groups -- (MDD - HC) -- there are both positive and negative differences across the brain. See image below (apologies for its large size):
Specifically, in the voxel selected, the difference is positive between MDD - HC. However, this same voxel is included as a significant voxel in the 1-sided t-test 1neg mask that ETAC gave:
and there are no voxels that are significant for the 1-sided positive 1pos t-test mask that ETAC creates:
I checked the 3dttest++ outputs from the smoothed data to see if this is an artifact of smoothing, but this particular voxel seems to have positive differences at the smoothing levels I gave to ETAC (0, 4, 6, 8).
This is the command I used to run the code:
command = ("3dttest++ -setA {0} ".format(MDD_subj_str) +
"-setB {0} ".format(HC_subj_str) +
"-prefix {0}/ses-03_minus_ses-01/ses-03_minus_ses-01_stats_{1}_ACC_dlPFC_mask.ttest.nii.gz ".format(second_level,BRIK_KEY[BRIK]) +
"-AminusB "
"-mask {0} ".format(dlPFC_mask) +
"-covariates {0} ".format(covar_file) +
"-prefix_clustsim ses-03_minus_ses-01_stats_{0}_ACC_dlPFC_mask ".format(BRIK_KEY[BRIK]) +
"-ETAC -ETAC_blur 0 4 6 8 " +
"-ETAC_opt NN=2:sid=1:hpow=0:name=test1:pthr=0.01/0.001/10:fpr=5"
)
Is there something I'm missing here?
Thanks so much!
I'm a new user to AFNI, so please forgive me if there's an obvious error on my part. I am trying to do a 2-sample t-test with 3dttest++ and want to use ETAC for cluster correction. I have two groups: depressed (MDD) and control (HC) subjects, so this group analysis compares the mean difference MDD - HC.
When I look at the 3dttest++ output file, specifically the BRIK that displays the mean difference between groups -- (MDD - HC) -- there are both positive and negative differences across the brain. See image below (apologies for its large size):
Specifically, in the voxel selected, the difference is positive between MDD - HC. However, this same voxel is included as a significant voxel in the 1-sided t-test 1neg mask that ETAC gave:
and there are no voxels that are significant for the 1-sided positive 1pos t-test mask that ETAC creates:
I checked the 3dttest++ outputs from the smoothed data to see if this is an artifact of smoothing, but this particular voxel seems to have positive differences at the smoothing levels I gave to ETAC (0, 4, 6, 8).
This is the command I used to run the code:
command = ("3dttest++ -setA {0} ".format(MDD_subj_str) +
"-setB {0} ".format(HC_subj_str) +
"-prefix {0}/ses-03_minus_ses-01/ses-03_minus_ses-01_stats_{1}_ACC_dlPFC_mask.ttest.nii.gz ".format(second_level,BRIK_KEY[BRIK]) +
"-AminusB "
"-mask {0} ".format(dlPFC_mask) +
"-covariates {0} ".format(covar_file) +
"-prefix_clustsim ses-03_minus_ses-01_stats_{0}_ACC_dlPFC_mask ".format(BRIK_KEY[BRIK]) +
"-ETAC -ETAC_blur 0 4 6 8 " +
"-ETAC_opt NN=2:sid=1:hpow=0:name=test1:pthr=0.01/0.001/10:fpr=5"
)
Is there something I'm missing here?
Thanks so much!
