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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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Pages: 123
Results 61 - 80 of 80
Hi AFNI Experts,
I have a question about using timing_tool.py for converting my 'stim_events.1D' files to a 'TR-based .1D' file. My original 'stim_events.1D' file makes use of duration modulation to help model the duration of my stimuli because they vary from trial to trial. I am wondering if I can use these stim_event.1D files for conversion to the TRs (1s, 0s si
by
Danny
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AFNI Message Board
Hi Rick,
Thanks for the info.
I now have to decide which method would be easier for me to set-up. I think either method will be a bit tedious, but as long as they work similarly, then it should not matter.
Thanks,
Danny
by
Danny
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AFNI Message Board
Hi AFNI Experts,
I have a follow-up question to the older posts regarding using dmBLOCK (w/AM1) to account for duration of a stimulus.
For a set of events, I am using the 'BLOCK (1,2.5)' command to model an event that stays on the screen for 2.5 seconds. I am wondering whether using the 'dmBLOCK' command with 'time:2.5' in the timing file would be similar to t
by
Danny
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AFNI Message Board
Hi Bob,
I used the AFNI_proc.py command: '-tlrc_NL_warp' on a skull-stripped brain. Out of the two subjects I ran this on, only 1 of them had the "droopy" anatomy issue.
I am assuming I am using the default 3dQwarp parameters. How would you recommend I change them within the python script? From what I understand the penalty function changes at each step?
Thanks,
D
by
Danny
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AFNI Message Board
Hello AFNI,
I ran 3dQwarp within AFNI_proc.py on a couple of subjects. I noticed that in one subject, the anat_final output the quality looks a tad suspect. Specifically, in a couple of slices, mostly posterior the brain looks "droopy." I am using the Nov 6th binaries, so I figured I have the updated penalty fix for this command. I am wondering, how I can best tweak the penalty or ot
by
Danny
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AFNI Message Board
The blur is run through the AFNI_proc.py command: ' -blur_size 6'.
Looking at ClustSim output after AFNI_proc.py, my blur estimates are approximately: 10.45 9.99 9.34...
by
Danny
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AFNI Message Board
Hi Rick,
I am actually doing a parallel analysis using AFNI_proc.py with the non-linear warp to compare with FSL's non-linear warp. Needless to say, it is taking quite a bit of time to run both of these...
I do notice that the non-linear warp in AFNI_proc.py does keep the functional data in its original space (3.5mm^3). So this is a non-issue and I will run the Monte Carlo Simulations
by
Danny
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AFNI Message Board
I have a highly similar question about this.
My stats were conducted in 3.5^3 space with AFNI_proc.py. However, the stats were later resampled and standardized to 1mm^3 space in FSL's FLIRT/FNIRT to the MNI152_1mm brain. I plan to do group analysis on this resampled data.
After reading the above threads and if I am understanding it correctly, I should be using ClustSim with the 3.5^3
by
Danny
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AFNI Message Board
Nevermind...I found everything. Just had to do some extra digging...
by
Danny
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AFNI Message Board
Hi Rick,
I just ran the AFNI_proc.py script with Qwarp and from looking at the terminal it seems it completed successfully. However, when I try to look at the output files, it did not seem that the files were created. When I look at the output text file from proc.py, it also did not write anything.
I am not sure what happened as the terminal looked like it completed and wrote the appropriat
by
Danny
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AFNI Message Board
Hi Rick,
Yes, I did not do the non-linear warp in the old script that worked with the mounted network. It was the affine transformation to tlrc space that worked.
That being said, I tried downloading the data on a hard drive and run it directly off the computer rather than a network. So far, it made to 3dQwarp which is good. Now I will wait for a while until it is done to see if any new err
by
Danny
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AFNI Message Board
After looking at output scripts I have ran before with this dataset that did not include the nonlinear warping, it does look like it has called upon a similar pathway as the "share" with the spaces and worked successfully, the proceeded to finish the remainder of the script.
So I am not sure if the spaces in there are causing this problem unless it is specific to the Nov 6 AFNI?
C
by
Danny
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AFNI Message Board
Hi Rick,
This mount issue is new to me. I have ran this script before without it calling upon the "share" pathway before. Instead it calls upon the pathway I set from the terminal.
If you look at the 'proc_sub205.WMC_OurModel_Correct_Trials_Qwarp' file I sent you in the e-mail, there is no mention of the "share" pathway with the spaces. So I am not sure why it
by
Danny
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AFNI Message Board
I just sent the files to your e-mail.
It does seem odd that it creates a file: 'anat.sub205_uni_RPI+orig ./anat.nii' when I do not have datasets with that extension that includes both .orig and .nii.
Danny
by
Danny
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AFNI Message Board
I have attempted the script using a skull-stripped brain (tried both in AFNI and .nii format) and I get the following error:
3dcopy /stout/study/sub205/sub205.WMC_OurModel_Correct_Trials_Qwarp.results/anat_final.sub205_uni.nii_RPI+orig ./anat.nii
++ 3dcopy: AFNI version=AFNI_2011_12_21_1014 (Nov 6 2013) [64-bit]
** FATAL ERROR: 3dcopy only takes one input AND one output filename after opti
by
Danny
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AFNI Message Board
I will try it on a skull-stripped brain and see what error I get.
Also, since I am using an MNI template in NIFTI format, would I need to convert all files from AFNI to NIFTI before running AFNI_proc.py?
I am working on getting the library installed. Hopefully I can get that done soon. That way I won't have to worry about getting that error.
Thanks,
Danny
by
Danny
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AFNI Message Board
Hi Rick,
If I were to start out with a skull-stripped (and unifized anatomy), could I bypass this skull-strip error by using the '-tlrc_no_ss' command?
Thanks,
Danny
by
Danny
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AFNI Message Board
I am working on a fix that worked before (i.e., installing the gsl-1.13 package) to see if that changes the error message.
by
Danny
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AFNI Message Board
Hi AFNI Experts,
I have tried running the 3dQwarp within AFNI_proc.py but am running into some errors. Below is the primary error I have been getting:
"3dSkullStrip: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory
** ERROR: Could not strip skull"
I have this version of AFNI: Version AFNI_2011_12_21_1014 [].
I could
by
Danny
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AFNI Message Board
Hi Bob,
I am using the @toMNI_Qwarpar scripts to run this non-linear warp and create a study specific template. I am wondering how to implement the new penalty changes in this script using "penfac ff"?
As of now, the script does not have a penality function, therefore I am not sure what values to set them at for each level (A - E).
Thanks,
Danny
by
Danny
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AFNI Message Board
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Pages: 123