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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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Great! Thank you. Is this documented somewhere and I missed it?
by
cdurisko
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AFNI Message Board
Hi,
In the documentation for 3dDeconvolve in the model 'BLOCK(d,p)' it says, " = 1 parameter block stimulus of duration 'd'". I do not see anything specifying whether this duration is in seconds or TRs. Based on the rest of the documentation, I assume seconds. Is this correct?
Thanks,
Corrie
by
cdurisko
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AFNI Message Board
Perhaps I did not actually have to rename the images; however, when I used to3d, the dimon process, or medcon with the images not renamed it took the slices out of order and our images looked jumbled because you might have images from higher or lower interspersed incorrectly because of how it was reading the names of the files. I did not know another way to handle the naming to ensure that the s
by
cdurisko
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AFNI Message Board
Rick,
Thank you for having me check the extent. Once I checked this and looked up what it meant, I realized that the information in the header was in fact incorrect. I had used medcon to convert my images to analyze and then 3dcopy to convert to afni. This is where the incorrect information came from.
I was able to fix the issue by renaming the dicom files and then converting using th
by
cdurisko
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AFNI Message Board
Rick,
One additional thing that I did not mention in my original posts is that this data was also taken on a 32-channel coil vs. other studies were done with a 12-channel coil. I do not think that this matters - but I thought I should give you as much info as possible.
Here is the information from 3dinfo:
1. 3dinfo hf01_mprage_ss+orig.| grep -e extent -e orient
++ 3dinfo: AFNI versio
by
cdurisko
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AFNI Message Board
I should also mention that I have tried to de-oblique the data both at the beginning and mid-stream (to determine if this is actually the issue), but there was no change.
I have also tried adjusting the alignment using the following:
1) 3dresample -orient RAI -prefix reorient_mprage -inset mprage_ss+orig
2) align_epi_anat.py -anat reorient_mprage -epi func+orig -epi_base 0 -cost LPC
B
by
cdurisko
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AFNI Message Board
Thank you for your time and help in advance!
I have started to analyze a new research study using the afni_proc.py script. I have used the same script (with minor modifications for names on several other datasets). I have included the script that we are using below. When I went to check the pre-processed images. I cannot get the functional images to overlay on the mprage (even after they ha
by
cdurisko
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AFNI Message Board