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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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Thank you, that is helpful. I'm still not exactly sure how to actually implement that in 3dMEMA - would the code be something like this?
3dMEMA -prefix 2_by_2_example \
-set Condition_1_A \
Subj001 Subj001+tlrc'' Subj001+tlrc'' \
Subj002 Subj002+tlrc'' Subj002+tlrc'
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nlanderson9
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AFNI Message Board
My question is hopefully fairly easy to answer, but unfortunately I haven't been able to find what I'm looking for in any AFNI documentation so far.
My experiment is set up with 2 different factors, each of which have two levels. These are all within subjects (that is, I don't have any groups).
From reading here (Two-Way Within-Subject ANOVA), my understanding is that I can u
by
nlanderson9
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AFNI Message Board
Thank you both for the advice! I just threw quotes around the offending filename and it worked fine....file_tool didn't reveal any bad characters after that.
Thanks!
by
nlanderson9
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AFNI Message Board
I've been running a script on another machine that hasn't had any issues. I recently moved to a new machine and attempted to run the same script, with the following error:
3dNwarpApply -source anat_mprage_unif_ns_shft+orig -master anat_final.ERwD001+tlrc -ainterp wsinc5 -nwarp anat.aff.qw_WARP.nii anat.aff.Xat.1D anat_mprage_unif_ns_shft_al_keep_mat.aff12.1D -prefix anat_wo_skull_w
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nlanderson9
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AFNI Message Board
I guess as a follow-up question - is it possible to provide the blur_est file in an argument, so that the estimates are captured in @ss_review_basic? I don't see that option under the list of user variables.
by
nlanderson9
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AFNI Message Board
Rick,
Thanks for your help. I think I've got it 90% working. I'm able to direct it to the majority of the files in the subfolder (including the stats dataset, the errts dataset, etc). However, for some reason I can't get it to recognize the mask dataset. I've triple-checked that I've spelled everything correctly, and each time I get the message "** no mask_dset d
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nlanderson9
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AFNI Message Board
I'm currently attempting to use gen_ss_review_scripts.py with the necessary files located in multiple folders. Basically, what I've done is run the preprocessing steps, and then I have separate sub-folders for each GLM I've run. Therefore, some of the files are in the main folder, and some are in the subfolder. Assuming that just copying the files into the correct folder isn'
by
nlanderson9
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AFNI Message Board
That was super helpful, it looks like it's working now! Thanks so much!
by
nlanderson9
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AFNI Message Board
So I think I've figured out part of the problem. The EPI datasets are from two different sessions with the same individual, 48 hours apart (session 1: runs 1-4, session 2: runs 5-9), and they are being aligned to the same anatomical file (collected at session 1).
I tried switching align_epi_anat.py to align the epi files to the anatomical file instead, but that may have just made it wors
by
nlanderson9
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AFNI Message Board
Thanks for the advice. I've tried the following, and maybe I'm just having trouble getting this right conceptually. I've added this @Align_Centers block but it doesn't seem to help.
# --------------------------------
# Align centers of datasets to template
@Align_Centers -base MNI152_T1_2009c+tlrc \
-dset anat_mprage_unif+orig \
by
nlanderson9
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AFNI Message Board
Hello,
Recently, I've attempted to add non-linear warping via auto_warp.py to our single-subject preprocessing. Given the results below, I've clearly done something very wrong. I'm at a loss for what even happened with this error, so any help would be appreciated!
Below is, in order:
1. The output containing the error text
2. The code that was run - the script also contains
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nlanderson9
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AFNI Message Board
Great, thank you! I was worried that I'd missed something obvious.
And I'm in no rush to get the new package - just working on updating some of our scripts for future use.
Thanks again!
by
nlanderson9
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AFNI Message Board
Hey all,
I'm having an issue with gen_ss_review_scripts.py
Long story short, I've ended up breaking the preprocessing and GLM into separate steps/scripts, and am passing the arguments to gen_ss_review_scripts.py myself because it doesn't know where to find them. That's fine, but it's giving me trouble when I try to specify the final anatomical file. I've verif
by
nlanderson9
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AFNI Message Board