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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:
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
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Hi!
Thank you very much for replying and sorry for the late reply. I had thought no one could answer.
3dDeconvolve -input m1.nii -nfirst 0 -polort 0 -mask brain_mask.nii \
-fitts fit_m1.nii -errts residual_m1.nii -num_stimts 1 -stim_file 1 $stim -stim_label 1 Visual -x1D X_m1.1D -xjpeg X_m1.jpg \
-tout -bucket stats_m1.nii.gz;
Here is what I run with a representative mouse 1 dataset i
by
kbandrew
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AFNI Message Board
Hello
I work with rodent fMRI and when using 3dDeconvolve, I use a custom-made stimulus file as a regressor/model. Also, I normalize each rodent's dataset to the baseline before inputting it into 3dDeconvolve. However, when I plot the -fitts output file, I notice that the fit'ed model doesn't start at 0. I am comparing multiple conditions and was wondering if this baseline shift
by
kbandrew
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AFNI Message Board
Hello great people of AFNI
I have come to find out that the stim file we have been using for rodent fMRI in 3dDeconvolve isn't an ideal shape and am needing to create a new stim file. I was told to deconvolve the "real" signal with a double gamma function and was wondering if I could do such a thing with afni. Tutorials I see all seem to create an HRF based on the onset of stimu
by
kbandrew
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AFNI Message Board
Thank you very much for the resources and the constant help both of you have given!
by
kbandrew
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AFNI Message Board
Thank you so much! I see now that the number in front of *step is indicating what value to put for that value now.
On a similar note, is there a general rule of thumb on what value I want to threshold for the (a-3) expression? I use the value that is shown after I set my p-value. And now that I think about it.. since I'm using the Ttest results, if I want to find similar voxels based on T
by
kbandrew
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AFNI Message Board
Hello
I have two conditions and have calculated a t-map from 3dttrest++ for each. I now want to create a mask that shows which voxels are active for both conditions. I used the following command based on 3dcalcs help file.
3dcalc -a 'A' -b 'B' -expr '3*step(a-3)'+3*step(b-3)' -prefix common_mask
A and B are the results from my 3dttest++. I thresholded i
by
kbandrew
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AFNI Message Board
Thank you two for your suggestions. I have gotten the overlay to work with both your suggestions.
As for my atlas, it was a custom made using the allen brain atlas for the ROIs. I see many papers claiming they are using an atlas from the Allen brain atlas, but they don't have an actual atlas file to download when I checked.
Thank you for the codes as it helped me learn more on how to
by
kbandrew
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AFNI Message Board
Thank you so much! I am using an in-house template which may be why it's in ORIG space. After converting my normalized functional to ORIG space, I am able to overlay my results on top of the templates (left image). However, if I use my template as an overlay on top of my normalized anatomical image, the template becomes undersampled (right image). I believe it's due to the template havi
by
kbandrew
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AFNI Message Board
Hello. I work with mouse fMRI. After normalizing my functional images with SPM, I am able to see that my normalized results after 3ddeconvolve or 3dttest++, the areas align well with the template crosshair (when opened in new AFNI window) However, I want to be able to align my template ROIs over my functional results instead of using photoshop to try align it properly. I asked before how to resam
by
kbandrew
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AFNI Message Board
Hello. I'm new to analyzing fMRI data, and have been learning how to use AFNI. I also work with mouse data.
Is there a way to resize my template so I can overlay the obtained statistical map from deconvolve and ttest++ on it? I normalize my images using SPM, but when I display both the template and normalized image, the crosshair overlaps well. I'm assuming I can't overlay it si
by
kbandrew
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AFNI Message Board