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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,
I would like to ask a follow-up question of this thread. Do you have any suggestion on how to check the quality of warping lesioned brains using @SSWarper?
Thanks,
Joy
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joy0617
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AFNI Message Board
Hi,
I would like to check the alignment of data by looking at the APQC-HTML file, but it only contains three QC blocks: 'regr', 'warns', 'qsumm'. Blocks like 've2a' are missing. Since the same '-html_review_style pythonic' command worked well with the other fMRI dataset of mine, I don't know what's wrong with my code.
The afni_proc.p
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joy0617
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AFNI Message Board
Hi Paul,
May I email you the output of my commands?
Thanks,
Joy
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joy0617
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AFNI Message Board
Hi Paul,
Sorry! I missed one part of the error message. The following proceeds what I have posted last time:
+++ Command Echo:
3dQwarp -lite -base /Users/bl/abin/MNI152_2009_template_SSW.nii.gz[0] -source ./junk.SSwarper.5XAHIpy2lsU_AffSS.nii -iniwarp ./junk.SSwarper.5XAHIpy2lsU_TAL5_AWARP.nii -warpscale 1 -lpa -inilev 1 -maxlev 5 -wtgaus 4.5 -inedge -pblur -workhard:5:5 -nodset -prefix
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joy0617
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AFNI Message Board
This has been split off from a previous thread:
... because this is a separate question. (The previous thread already included multiple subtopics.)
--pt
---------------------------------------------------------------------------------------------------------
Hi Paul,
Sorry that I keep bothering you with so many questions, but I encountered new error messages when running @SSwarper
by
joy0617
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AFNI Message Board
Thank you very much!
Do you have any suggestion for warping to standard space in the situation I described in earlier reply? If I have to complete preprocessing and GLM in native space and then do some other analyses using another software for each subject, is it appropriate to use @auto_tlrc when I want to warp the outcome of the analyses to standard space?
by
joy0617
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AFNI Message Board
This fixed the alignment problem! Thank you!
I have another question regarding to the regression modeling: If I have collected the EPI runs over multiple experimental sessions, is the -regress_motion_per_run option adequate to regress out the effect of session in GLM?
Thanks a lot for your help!
-Joy
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joy0617
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AFNI Message Board
Emmm...I ran the script again. Now there is no error message and I'm able to find the QC images.
Thanks,
Joy
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joy0617
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AFNI Message Board
Hi Pual,
I tried @SSwarper script but got error messages about starting Xvfb like these:
++ SSW Step 7
-- trying to start Xvfb :177
[1] 6174
[1] + Exit 1 Xvfb :177 -screen 0 1024x768x24 >& /dev/null
No matching processes belonging to you were found
...
-- trying to start Xvfb :957
[1] 6338
[1] + Exit 1 Xvfb :957 -screen 0 1024
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joy0617
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AFNI Message Board
Hi Paul,
First point:
You are right. This produces an error:
3dBrickStat -slow -min -max C01_2_t1_tl+tlrc
*** failure while reading from brick file ./C01_2_t1_tl+tlrc.BRIK
*** desired 17060042 bytes but only got 1805258
*** Unix error message: Undefined error: 0
THD_load_datablock
Max_func
3dBrickStat main
** Command line was:
3dBrickStat -slow -min -max C01_2_t1_tl+tlrc
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joy0617
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AFNI Message Board
Hi,
I'm trying to warp my functional dataset to standard space.
The code I'm running is:
@auto_tlrc -base MNI152_T1_2009c+tlrc -suffix _tl -input {$subj}_2_t1+orig
@auto_tlrc -apar {$subj}_2_t1_tl+tlrc -suffix _tl -input {$subj}_vwfa_beta+orig -dxyz 1.5
But I got the following error message:
Applying tlrc warp from ./C01_2_t1_tl+tlrc to C01_vwfa_beta+orig ...
Padding the
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joy0617
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AFNI Message Board
Hi Paul,
I edited the afni_proc.py scripts according to your suggestions but my alignment from QC html looks different from your attachment.
The script:
afni_proc.py \
-subj_id {$subj} \
-script proc.{$subj}.vwfa \
-out_dir {$subj}.VWFA.result
by
joy0617
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AFNI Message Board
Hi pt,
I applied the new afni_proc.py to all subjects and now I have alignment problem with another subject. This time it starts pretty far apart so I tried adding the -giant_move option back. But it still didn't work. Do you have any suggestion?
Thanks,
Joy
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joy0617
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AFNI Message Board
Thank you! I updated afni and removed the two lines you mentioned.The problem is solved.
I have another question. I applied the same afni_proc.py script for other patients and they all seems very well aligned to start and didn't give me the alignment problem I have with this one. Do you recommend me to run the new afni_proc.py script for all of the patients?
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joy0617
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AFNI Message Board
an image overlaying any of the EPI volumes on the anatomical *before* alignment
Underlay: P05_2_t1+orig
Overlay: P05_vwfa_1
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joy0617
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AFNI Message Board
output of afni -ver:
Precompiled binary macos_10.12_local: Jun 13 2019 (Version AFNI_19.1.19 'Caligula')
my afni_proc.py command:
afni_proc.py \
-subj_id P05 \
-script proc.P05.vwfa \
-out_dir P05.VWFA.results
by
joy0617
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AFNI Message Board
Hello,
There is an alignment issue with preprocessing of fMRI data using afni_proc.py and I don't know how to fix it. I didn't get any warning or error message but when visually examine the images, I found that after volreg block, the epi data is clearly not correctly aligned to anatomical image.
The "align_epi_anat.py -anat P05_2_t1+orig -epi P05_vwfa_1+orig -epi_base 0 -gi
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joy0617
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AFNI Message Board
Hi-
And just to note, I split this message from the thread that it was originally posted to here:
... because that thread was already waaaay too long (and should have been separated many times).
This question seemed separate (and, as noted below, I think the issue with updating was distinct
from any of the ones on that other thread).
--pt
----------------------------------------
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joy0617
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AFNI Message Board
I got this:
3dbucket -prefix sub03_betas stats.sub03+orig’[0..$(3)]’
Illegal variable name.
But this other command worked! Thank you very much!
Joy
by
joy0617
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AFNI Message Board
Hi,
I would like to extract beta weights using 3dbucket command but I'm getting this error:
3dbucket -prefix sub03_betas stats.sub03+orig’[1..73(3)]’
Badly placed ()'s.
Then I tried this:
3dbucket -prefix sub03_betas stats.sub03+orig’[1 4 7 10 13 16 19 22 25 28 31 34 37 40 43 46 49 52 55 58 61 64 67 70 73]’
++ 3dbucket: AFNI version=AFNI_19.0.07 (Feb 5 2019) [64-bit]
ca
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joy0617
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AFNI Message Board
Sorry. I mean I have multiple .nii files for each epi run (one for each volume) and I want to concatenate them into single dataset for each run.
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joy0617
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AFNI Message Board
Thank you very much for your reply!
One more naive question:
I want to convert .nii files for each epi run into one single AFNI format dataset with time series info so I can do preprocessing.
How can I achieve that or do I even need to do that for preprocessing?
by
joy0617
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AFNI Message Board
Hi,
I'm totally new with AFNI and working on an old dataset that has been converted to .nii format by SPM.
I thought AFNI could read .nii flies so I tried to3d directly to the structural data but it failed to output brik and head files.
to3d -spgr -session ../ -prefix RSA_S1_t1 20130912_145129t1mpragetranssrs002a1001.nii
++ to3d: AFNI version=AFNI_18.0.25 (Mar 7 2018) [64-bit]
++ A
by
joy0617
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AFNI Message Board