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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
Page 4 of 4
Pages: 1234
Results 91 - 101 of 101
Thanks a lot for the quick response. Could you please check if I have checked correctly? If I am going to look at activation for a single stim file, I don't need to specify the below in the proc py script?
-regress_stim_labels NF \
-regress_basis 'BLOCK(4,1)' \
-regress_censor_motion 0.3 \
-regress_opts_3dD \
-gltsym 'SYM: NF' \
-glt_label 1 NF \
Best,
by
JW
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AFNI Message Board
Hi Rick,
Thanks again for the comment. Can I have one more question? If I'd like to see the activation of only F, not subtraction, is it correct to run the script that looks like this?
-regress_stim_labels F \
-regress_basis 'BLOCK(4,1)' \
-regress_censor_motion 0.3 \
-regress_opts_3dD \
-gltsym 'SYM: F' \
-glt_label 1 F \
And, if I want to see the act
by
JW
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AFNI Message Board
Hi Rick,
Thank you so much for your comment. Could you please let me know how should I edit the script in order to get NF -F?
Best,
Jun
by
JW
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AFNI Message Board
Okay, I'll carefully format SYMboic expression. Thank you so much for your help! Appreciate it!
by
JW
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AFNI Message Board
Hi AFNI users,
I have a question regarding proc.py gltsym. Below is the part of the proc.py script I am using which I intended to subtract brain activation during NF from F (F-NF).
-regress_stim_labels F NF \
-regress_basis 'BLOCK(4,1)' \
-regress_censor_motion 0.3 \
-regress_opts_3dD \
-gltsym 'SYM: +F -NF' \
-glt_label 1 F_vs_NF \
If I&
by
JW
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AFNI Message Board
Hi,
I have a following error message when running proc py. The same script was running successfully for the other condition of this participant, but it continuously shows this error message for this condition. Could you please let me know, what is the issue and how to resolve it?
Warping used up maximum iterations even after doubling number of iterations to 274.
Convergence might not have
by
JW
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AFNI Message Board
Hi Rick,
I got the below result from your instruction. Does it look good? I am wondering if your instruction fixed the problem in the timing file.
file_tool -test -infiles /Volumes/BRAINSMITH_DS/EBH/FNT/Analysis/EBH101/EBH101.T1/timing/EBH101.T1.F.txt -prefix FIXED.txt
-- will fix any bad char check errors in FIXED.txt
file '/Volumes/BRAINSMITH_DS/EBH/FNT/Analysis/EBH101/EBH101.T1/ti
by
JW
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AFNI Message Board
Sorry for the late response. So the code should look like
'file_tool -test -infiles -prefix FIXED.txt /Volumes/BRAINSMITH_DS/EBH/FNT/Analysis/EBH101/EBH101.T1/timing/EBH101.T1.F.txt' ?
It says 'error: unknown option, </Volumes/BRAINSMITH_DS/EBH/FNT/Analysis/EBH101/EBH101.T1/timing/EBH101.T1.F.txt>'
by
JW
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AFNI Message Board
titus% file_tool -test -infiles /Volumes/BRAINSMITH_DS/EBH/FNT/Analysis/EBH101/EBH101.T1/timing/EBH101.T1.F.txt
file '/Volumes/BRAINSMITH_DS/EBH/FNT/Analysis/EBH101/EBH101.T1/timing/EBH101.T1.F.txt': missing final newline
/Volumes/BRAINSMITH_DS/EBH/FNT/Analysis/EBH101/EBH101.T1/timing/EBH101.T1.F.txt has 114 bad characters
-- starting at line 1, position 0
file '/Volumes/BR
by
JW
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AFNI Message Board
'
-- consider use of '-test_stim_files no' if files are OK
------------------------------------------------------------
** script creation failure for block 'regress'
+d generated EPI review script @epi_review.$subj
I can see these two lines below.
Screenshot of timing file that results in error and timing file that doesn't result in errors are attached. Ot
by
JW
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AFNI Message Board
Hi all,
I constantly have the error message below when running proc.py script.
afni_proc.py -anat_has_skull yes -blocks despike tshift align tlrc volreg \
blur mask scale regress -copy_anat mprage/mprage.EBH101.T1+orig -dsets \
/Volumes/BRAINSMITH_DS/EBH/FNT/Analysis/EBH101/EBH101.T1/FNT/fnt.EBH101.T1+orig \
-tcat_remove_first_trs 3 -out_dir re
by
JW
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AFNI Message Board
Page 4 of 4
Pages: 1234