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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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I tried adding the "-giant_move" to the align_epi_anat.py script and that seemed to allow the EPI to align to the anat properly.
Mike
by
mikek
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AFNI Message Board
This is what I got:
3dinfo ANA+orig.HEAD|grep extent
++ 3dinfo: AFNI version=AFNI_22.0.09 (Feb 10 2022) [64-bit]
R-to-L extent: -226.044 -to- -63.544 -step- 2.500 mm [ 66 voxels]
A-to-P extent: -134.651 -to- 83.349 -step- 2.000 mm [110 voxels]
I-to-S extent: -109.816 -to- 108.184 -step- 2.000 mm [110 voxels]
by
mikek
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AFNI Message Board
I ran 3drefit -oblique_recenter on the EPI starting image and something does not look right to me.
3dinfo ANA+orig.HEAD|grep extent (Modified EPI image - ran 3drefit)
++ 3dinfo: AFNI version=AFNI_22.0.09 (Feb 10 2022) [64-bit]
R-to-L extent: 82.500 -to- 245.000 -step- 2.500 mm [ 66 voxels]
A-to-P extent: -124.000 -to- 94.000 -step- 2.000 mm [110 voxels]
I-to-S exte
by
mikek
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AFNI Message Board
The "3drefit -oblique_recenter" or "3drefit -deoblique" command should be run on the starting original images not the computed one (vr_base_min_outlier) is that correct? Thanks for the suggestions.
Mike
by
mikek
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AFNI Message Board
I was running a script generated by afni_proc.py for some 7T scan data and the script fails at the align_epi_anat.py step. Here is the command:
align_epi_anat.py -anat2epi -anat anatSS.XXX+orig \
-save_skullstrip -suffix _al_junk \
-anat_has_skull no \
-epi vr_base_min_outlier+orig -epi_base 0 \
by
mikek
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AFNI Message Board
I just realized I ran the old proc instead of the new one so of course I got the same results. I am running the correct one now. Sorry for my mistake.
by
mikek
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AFNI Message Board
The SSwarper seemed to work perfectly (see attached picture). I modified the cmd file as you suggested (I think i did this correctly) but the final outputted images are as warped as before (see attached picture of anat_final). Maybe the deskulling was not the problem or maybe I did something else wrong. Can you advise me?
Here is my modifed cmd file:
afni_proc.py -subj_id $subj
by
mikek
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AFNI Message Board
Is the ${template} value the same in the afni_proc.py script piece as it was in the SSwarper script?
Mike
by
mikek
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AFNI Message Board
OK thank you for your help. I will give this a try and see how it goes. I hope you are keeping healthy and safe!
by
mikek
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AFNI Message Board
OK here is the actual afni_proc.py cmd file command below. I guess I need more explanation of how I would run the @SSwarper command and then pass those results to the proc command.
Thanks for your help.
=================================================================================================
# run afni_proc.py to create a single subject processing script
afni_proc.py -subj_id
by
mikek
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AFNI Message Board
Well I looked thru the proc generated from afni_proc.py and this looks like the one that does it:
# ================================= align ==================================
# for e2a: compute anat alignment transformation to EPI registration base
# (new anat will be intermediate, stripped, mprage_ns+orig)
align_epi_anat.py -anat2epi -anat mprage+orig \
-save_skullstrip -suffix
by
mikek
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AFNI Message Board
We recently started using the 7T scanner and are having problems with deskulling. The mprage in the directory looks fine but the background noise have values above zero and are different than the 3T data we have been processing. The deskulling is failing and the final image is clearly distorted/warped because of this. The original images in the briks directory are not warped. We are using afni_p
by
mikek
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AFNI Message Board
Such a silly mistake on my part - that is exactly what the problem was. Thank you.
by
mikek
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AFNI Message Board
I was following the DTI analysis using FATCAT steps and I have gotten to the step where you could view the tracking information in AFNI and SUMA but it is failing to connect. Here is the code/script I am using:
# port for AFNI-SUMA communications, and end all other chatter on it
set cport = 12
@Quiet_Talkers -npb_val $cport
# set line thickness of SUMA surfaces sent to AFNI
setenv AFNI_SU
by
mikek
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AFNI Message Board