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 - 14 of 14
Both are perfectly acceptable answers and work fine. For my purposes, it does seem 3dNwarpXYZ is more straightforward.
As always, your help is much appreciated!
Brady
by
wilxl8
-
AFNI Message Board
Hi,
I am using 3dUndump to create 66 spherical ROIs at various coordinates with the following command:
3dUndump -prefix Targets_MNI.nii -master T1_allineate_Q.nii -xyz coords.txt
After, I am trying to apply the inverse of warping the subject's T1 to MNI space to get the ROIs in subject space:
3dAllineate -prefix T1_allineate.nii -base MNI152_T1_2009c+tlrc. -source anat_brain.nii
by
wilxl8
-
AFNI Message Board
Hi,
I have some results from an analysis that I performed outside of AFNI in the form of a text file with centrality values for each region in a parcellation. I used the Brainnetome atlas so I have one value for each of the 246 regions. I know the regions are labeled in the atlas in the same order as in the text file that I have. How do I go about assigning these values back onto the atlas an
by
wilxl8
-
AFNI Message Board
Thank you again for your time. That all makes sense. I looked through the script and maybe missed the point at which the motion outliers based on a specified threshold were identified and noted in the outcount text file. I will go through it again though.
For the second point, I was referring to Peter's comment on visualizing the activity of an active voxel versus the design. Maybe I mis
by
wilxl8
-
AFNI Message Board
Hi all,
I am so sorry for neglecting to include which image this is! I thought I had it in there but seemed to overlook it. This is a result from a GLT of a verb generation condition minus a noise condition (beta as overlay and t-stat as threshold) with blue (low)-red (high) coloring. I can see that I sounded like a bit of a novice in the post and I apologize. I have experience with this type
by
wilxl8
-
AFNI Message Board
Hi,
I am running through an analysis with afni_proc.py and keep getting a similar problem with all of the subjects that I run. The afni_proc.py command is the following:
afni_proc.py -subj_id subj -dsets verbs.nii -copy_anat T1_ss_orig_vol.nii \
-anat_has_skull no -blocks despike tshift align tlrc volreg blur mask \
scale regress -volreg_align_to MIN_OUTLIER -volreg_align_e2a
by
wilxl8
-
AFNI Message Board
Thanks for checking out the data. Yes you are correct, the original ROIs are in MNI space but in the processing script, I used 3dAllineate with the inverse of the @auto_tlrc matrix for the T1 to align them to subject space and then use 3dresample with the DWI as the master to make sure they have the same resolution. However, the orientation may be the problem. The thing that confuses me the most
by
wilxl8
-
AFNI Message Board
Brian,
The upload was successful. Thanks for fixing the issue so quickly!
Paul,
I just uploaded the directory, called BradyWilliamson.tgz. I included the raw DWI data, bvecs, bvals, the T1 anatomical, a script with the steps I used to process the data, and a script I used to rotate the bvecs (taken from another afni message board post).
Thanks so much for the help,
Brady
by
wilxl8
-
AFNI Message Board
I tried to upload the file to the link that you sent me but for some reason it keeps coming up with an error message. The error message is:
Our apologies...
The item you requested does not exist on this server or cannot be served.
Please double check the web address or use the search function on this page to find what you are looking for.
If you know you have the correct web address bu
by
wilxl8
-
AFNI Message Board
Hi,
Thanks so much for your quick reply! I ran the whole brain tractography and there were still 0 tracks found so I think there may be a deeper issue here. The output of 3dDWItoDT looks good when overlaid onto the anatomical in subject space, i.e. good alignment and all data within white matter tracts. I used 3dAutomask to create a whole brain mask for the command. The command I used was the
by
wilxl8
-
AFNI Message Board
Thanks so much for your quick reply!
The ROIs are actually from a method used in a previous study in the lab in which I work. The random 200 parcel Craddock parcellation was used and then restricted to certain functional clusters and thresholded for clusters > 10 voxels. The ROI map obtained from this method is in MNI space so I used @auto_tlrc to put the Skull Stripped anatomical into MNI
by
wilxl8
-
AFNI Message Board
Hello,
I recently started doing tractography analysis on a DTI dataset and I ran into a problem. I processed the data up through 3dDWItoDT and the data looks great. However, when I try to run 3dTrackID, no fibers or connections are found with AND or OR logic in the deterministic mode. The ROIs I am looking at involve many core structures in the language network so I know there should be some
by
wilxl8
-
AFNI Message Board