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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
History of AFNI updates
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Hi Paul,
Sorry for the delay. I successfully ran through all those steps you outlined and everything appears to be working on my end with the newest AFNI version! Thanks-- I'll definitely be passing along these instructions to my lab mates!
Circling back to the preprocessing issue with the data I sent, have you had a chance to explore those data/processing steps any further?
Thanks
by
cnweis
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AFNI Message Board
Yes that'd be great! Have you had a chance yet to take a look at the files I uploaded to Box?
Carissa
by
cnweis
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AFNI Message Board
Hey Paul,
I've run the suggested lines of code you sent and this is the updated output of "afni_system_check.py -check_all"
I didn't realize you could update binaries in my home directory! That helps a ton!
Carissa
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release:
by
cnweis
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AFNI Message Board
I know... it's quite upsetting and I have very little sway in our cluster administration...
Here's that output:
afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 3.10.0-1160.24.1.el7.x86_64
version: #1 SMP Thu Apr 8 19:51:47
by
cnweis
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AFNI Message Board
Hi Paul,
I've uploaded the afni_proc.py script used for preprocessing as well as preprocessing outputs for 3 subjects. Our cluster at UWM is missing a dependency to generate the HTML outputs for QCing, but the @ss* scripts are still generated. I believe I copied over everything for each subject. Let me know if I can send anything else!
Thanks for your help!
Carissa
by
cnweis
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AFNI Message Board
Hi Paul!
We used a "standard" afni_proc.py script for preprocessing with SSWarper run before afni_proc.py. Only minor changes were use of a different cost function for a handful of subjects who had more difficult alignment. To QC, I used the @ss* programs. Is there something in particular I can share from those QC outputs?
Thanks,
Carissa
by
cnweis
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AFNI Message Board
Hello!
This is more of a conceptual question about MRI voxel signal issues. We have a dataset of ~150 subjects who completed a variety of tasks as well as resting state. Across the whole sample, signal just isn't very robust at the voxel level. Even for well established task paradigms (and even resting state), basic contrasts in expected regions are not surviving correction (expected regi
by
cnweis
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AFNI Message Board
Hello all!
I'm doing a gPPI analysis with a task that has 4 conditions and 4 runs. There were only 2 conditions per run and each condition is only presented twice across all runs. The counterbalancing was pseudorandom so that we didn't have 2 of the same condition in a given run.
I've made it most of the way through the PPI documentation on AFNI. However I'm stumped on c
by
cnweis
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AFNI Message Board
Hello,
I'm struggling to get my 3dLME to run. I keep getting stuck at the model test, with the suggestion that there's inappropriate coding in -model, -qVars, or -gltCode. I've combed through the message board and tried various things other people have had problems with but I can't seem to come to any resolution. Any insights as to what I may be doing wrong?
*I know the
by
cnweis
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AFNI Message Board
Hello everyone! I’m having some issues combining masks. I have a set of masks of segmentations from Freesurfer, and a hand drawn PAG mask that was drawn on an MNI template. For example, the amygdala ROI from freesurfer is in NIFTI format and aligns to both +orig and +tlrc volumes of my anatomy. The PAG only aligns to +tlrc (since that where it was drawn). All of my analyses at this point are in
by
cnweis
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AFNI Message Board
Hey Gang,
I'm having trouble with my 3dMVM script below. I'm trying to run an ANCOVA with functional connectivity maps of 3 seed ROIs (BNST, BLA, CEN) as repeated measures for each subject. The first 3 glt's are to look at just functional connectivity of each ROI while controlling for the other 2. Then the next 6 glt's are to look at how each ROI is related to one of two an
by
cnweis
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AFNI Message Board
Am I only missing the cluster size thresholds from this error? If I have the *.5percent file with the z-score FPR values is this sufficient for thresholding purposes? Do I need anything else output from this step?
Thanks,
Carissa
by
cnweis
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AFNI Message Board
Hello,
I'm looking to use the ClustSim option in 3dttest++ to do some corrections for partial axial coverage resting state 7T data. I keep getting an error that says "dataset grid too big--must recompile to use shorts as indexes" and then the program crashes. Do you think this has to do with the fact that this is 7T data?
My command was:
3dttest++ -setA AMY_CEN {insert sub
by
cnweis
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AFNI Message Board
I'm not entirely sure why, but it did have to do with the AFNI version I was using. I was using the AFNI_2011_12_21_1014 version. However switching to the AFNI_17.2.09 version works just fine.
Perhaps other people will run into this problem so I'll still give you the outputs.
The command I'm using is: 3dTrackID -mode MINIP -dti_in dt -netrois RH_Masks.nii -prefix RH_miniP5_un
by
cnweis
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AFNI Message Board
Hello,
I'm using 3dTrackID -mode MINIP to be able to visualize the tracts running through my ROIs. What does it mean that there are 0 tracks in net[0], but pairwise connections in netw[0]=1? If there are pairwise connections shouldn't there be tracts to make those connections? What is the distinction between those values?
Thanks,
Carissa
by
cnweis
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AFNI Message Board
I started out using -afni_proc.py and when the alignment failed I looked specifically at options I could change in 3dAllineate on its own. Once those didn't work out then I moved to the 3dQwarp command and tried various options there.
by
cnweis
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AFNI Message Board
Hey there,
I'm having some alignment issues when I transform my epi data from orig space to MNI space. I preprocessed about 50 subjects worth of data through the proc script and about 7 of them appear to have the same alignment issues. The epi aligns no problem to the skull stripped anatomy in orig space, and the anatomy seems to transform to MNI space with no problems. However, when the
by
cnweis
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AFNI Message Board