Show all posts by user
Dear AFNI users-
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
History of AFNI updates
Page 1 of 1 Pages: 1
Results 1 - 10 of 10
Hi AFNI Experts,
I would like to run 3dttest++ to look at the difference between two groups on a statistical contrast map ConditionA>ConditionB. I would like to restrict the search for significant voxels using an ROI for the amygdala, and also to correct for multiple comparisons using 3dClustSim.
I am using Peter's blog as a guide: blog.cogneurostats.com/?p=196 but I am very stuck a
by
christinapf
-
AFNI Message Board
My appologies for the misunderstanding; here is the command and output to the screen (for a volunteer who generated a lot of -1's):
3dFWHMx -mask mask+orig -input residual_error.fit+orig -detrend
++ 3dFWHMx: AFNI version=AFNI_2011_12_21_1014 (Jun 11 2013) [32-bit]
++ Authored by: The Bob
++ Number of voxels in mask = 33969
*+ WARNING: removed 237 voxels from mask because they are cons
by
christinapf
-
AFNI Message Board
Hi Rick,
See my answers below:
rick reynolds Wrote:
-------------------------------------------------------
> How many voxels are in the mask?
3dinfo -nijk mask+orig
Output: 163840
>Are they contiguous or separated?
Mostly contiguous, but some separations in inferior regions.
> Does the mask include all zero time series?
No
> Would you report the actual outp
by
christinapf
-
AFNI Message Board
Any ideas on how to correct the -1 values? The mask+orig files do appear to contain data.
Any advice would be greatly appreciated.
by
christinapf
-
AFNI Message Board
Thank you, Peter; you've been incredibly helpful!
I do believe I have aligned the EPI and anatomical datasets during my re-construction stage, using the -rotobrick command for Fred Tam's siemenstoafni script.
by
christinapf
-
AFNI Message Board
Ah ha! I think you have caught it for me, Peter!
It appears I have NOT warped the masks to standard space... and in fact, I am wondering whether I have used the wrong data to create the group mask?
I have used the results from my data pre-processing steps; that is, the functional data (after having corrected it for motion, normalized signal, and concatenated the runs then run 3dAutomask on
by
christinapf
-
AFNI Message Board
Hi Rick,
Thank you - I now notice the three values that I was looking for!
In terms of the mask+orig datasets, they appear to contain brain masks. I created a mask for each volunteer with their physiologic/motion corrected, signal normalized, concatenated functional runs using 3dAutomask. Looking at each mask+orig dataset in the AFNI viewer I do see images.
by
christinapf
-
AFNI Message Board
Hi AFNI Experts,
I am trying to run a multiple comparison correction for an ANOVA.
I have generated an average group mask (using each volunteer's brain mask after being warped to standardized space) as follows:
3dMean –prefix avg_group_mask mask_sub1+orig mask_sub2+orig mask_sub3+orig…
→ Output: avg_group_mask+orig.{HEAD|BRIK}
I checked to see whether the mask had the same dimensi
by
christinapf
-
AFNI Message Board
Good afternoon,
I have run into this same issue and am hoping someone may be able to resolve this question at this time.
I am trying to run 3dFWHMx on the residual time series (errts) from 3dDeconvolve. I am using a mask dataset created from 3dAutomask. The command I am using is as follows:
3dFWHMx –mask mask+orig –input residual_error.fit+orig –detrend –out ResidualError_fwhm.txt
If
by
christinapf
-
AFNI Message Board