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
Thanks a lot, Paul for providing useful information.
I used run_01_ALFF+tlrc as underlay and final_anat as the overlay in the image that I have shared with you.
Once again thank you so much, Paul, for your regular replies.
Regards
-Korann
by
korannvit
-
AFNI Message Board
Thanks, Paul.
We are using the MRICron for visual inspection of fMRI data.
" Well, that looks like it could just be the CSF in the midsagittal part of the brain"
Above statement of yours is scaring me because of the whole intention of doing all these steps is to retain the brain activities present in the whole brain for extracting ALFF values.
My main concern is why the sk
by
korannvit
-
AFNI Message Board
Thanks, Paul for the information.
The file which I shared was 'run_01_ALFF+tlrc.BRIK' generated from the RSFC function. My question is that it looks like the skull is sitting on the EPI image which was never the case with the earlier afni_proc.py file. It was showing only after I used @SSwarper function to correct the normalization. I wanted to confirm before proceeding with the extr
by
korannvit
-
AFNI Message Board
This message was originally part of a separate thread:
which was very much a discussion of alignment in processing; this is really a very separate question. It has been migrated to a new thread here.
--pt
---------------------------------------------------- original message ----------------------------------------
Hi Paul,
I have one doubt regarding the RSFC results. The final r
by
korannvit
-
AFNI Message Board
Thanks, Paul for assisting on a regular basis.
After updating AFNI to a new version, now things are fine. One sincere suggestion from my side is that why don't you people incorporate @SSwarper along with afni proc in example 11 and since eg. 11 does not do the intended job properly. So it would be helpful for others if you could club @SSwarper and example 11 together.
I also attached t
by
korannvit
-
AFNI Message Board
Sure Rick will update the AFNI to it's the newest version.
I Hope that the new AFNI version will sort our issue.
Thank you Rick
Regards
-Korann
by
korannvit
-
AFNI Message Board
Thanks, Paul for the continuous assistance.
@SSwarper code for your reference
@SSwarper CSRI-004-1-Structural.nii -base MNI152_2009_template_SSW.nii.gz -subid CSRI004
I followed your steps and the issue remains the same. Here is the modified code
afni_proc.py -subj_id CSRI004 \
-blocks despike tshift align tlrc volreg blur mask scale regress \
-copy_anat anatSS.-base.nii \
-a
by
korannvit
-
AFNI Message Board
Thanks, Paul for the suggestion.
Here is the afni_proc code for preprocessing.
afni_proc.py -subj_id 004 \
-blocks despike tshift align tlrc volreg blur mask scale regress \
-copy_anat 004_SurfVol.nii \
-anat_follower_ROI aaseg anat aparc.a2009s+aseg.nii \
-anat_follower_ROI aeseg epi aparc.a2009s+aseg.nii \
-anat_follower_ROI FSvent epi 001_vent.nii \
-anat_follower_ROI FSWe
by
korannvit
-
AFNI Message Board
Thanks, Paul for the detailed explanation.
I'm using Version AFNI_18.0.05.
I followed your steps for aligning the anatomical image to the standard template. But it threw an error in the warping. Below I have given the afni proc file for the same along with the error message.
#########afni_proc #############
afni_proc.py -subj_id 004 \
-blocks despike tshift align tlrc volreg b
by
korannvit
-
AFNI Message Board
Dear AFNI experts,
I'm trying to extract the ALFF values from the resting data of Schizophrenia patients. When I'm checking the data quality, I found that the normalization has not happened properly as it intended to be. Below I have attached the codes along with the pictures of overlay of MNI152 template with RSFC file.
#here is the afni proc file
afni_proc.py -subj_id INSP00
by
korannvit
-
AFNI Message Board