AFNI Message Board

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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Anonymous User
August 27, 2012 10:17PM
Here is the afni_proc.py command, and 3dinfo for pb00 and original epi (please ignore the line-throughs)

afni_proc.py -subj_id CRD_$1 \
-script proc_CRD.$1 -scr_overwrite \
-blocks tshift align tlrc volreg blur mask scale regress \
-copy_anat /Volumes/H_MRI/MRI_CRD/MRI_raw/CRD.$1/T1_MPRAGE_SAG_ISO_0_9_0013/CRD.$1_anat.nii \
-tcat_remove_first_trs 0 \
-dsets \
/Volumes/H_MRI/MRI_CRD/MRI_raw/CRD.$1/CRD.RUN_1+orig.HEAD \
/Volumes/H_MRI/MRI_CRD/MRI_raw/CRD.$1/CRD.RUN_2+orig.HEAD \
/Volumes/H_MRI/MRI_CRD/MRI_raw/CRD.$1/CRD.RUN_3+orig.HEAD \
/Volumes/H_MRI/MRI_CRD/MRI_raw/CRD.$1/CRD.RUN_4+orig.HEAD \
/Volumes/H_MRI/MRI_CRD/MRI_raw/CRD.$1/CRD.RUN_5+orig.HEAD \
/Volumes/H_MRI/MRI_CRD/MRI_raw/CRD.$1/CRD.RUN_6+orig.HEAD \
/Volumes/H_MRI/MRI_CRD/MRI_raw/CRD.$1/CRD.RUN_7+orig.HEAD \
/Volumes/H_MRI/MRI_CRD/MRI_raw/CRD.$1/CRD.RUN_8+orig.HEAD \
-volreg_align_to last \
-volreg_tlrc_warp \
-blur_size 4.1 \
-regress_stim_times \
/Volumes/H_MRI/MRI_CRD/canonicals/CRD.$1/$1.3.1D \
/Volumes/H_MRI/MRI_CRD/canonicals/CRD.$1/$1.8.1D \
/Volumes/H_MRI/MRI_CRD/canonicals/CRD.$1/$1.10.1D \
/Volumes/H_MRI/MRI_CRD/canonicals/CRD.$1/$1.12.1D \
/Volumes/H_MRI/MRI_CRD/canonicals/CRD.$1/$1.14.1D \
/Volumes/H_MRI/MRI_CRD/canonicals/CRD.$1/$1.18.1D \
/Volumes/H_MRI/MRI_CRD/canonicals/CRD.$1/$1.23.1D \
/Volumes/H_MRI/MRI_CRD/canonicals/CRD.$1/$1.25.1D \
/Volumes/H_MRI/MRI_CRD/canonicals/CRD.$1/$1.27.1D \
/Volumes/H_MRI/MRI_CRD/canonicals/CRD.$1/$1.29.1D \
/Volumes/H_MRI/MRI_CRD/canonicals/CRD.$1/$1.31.1D \
/Volumes/H_MRI/MRI_CRD/canonicals/CRD.$1/$1.32.1D \
-regress_stim_labels \
nogo_err nogo_reward_hi.di_cor nogo_neutral_hi.di_cor \
nogo_reward_lo.di_cor nogo_neutral_lo.di_cor money_err \
money_reward_hi.di_cor money_neutral_hi.di_cor money_reward_lo.di_cor \
money_neutral_lo.di_cor all_nogo_feedback all_money_feedback \
-regress_basis 'BLOCK(.75,1)' \
-regress_censor_motion 0.3 \
-regress_censor_outliers 0.3 \
-regress_opts_3dD -GOFORIT 6 \
-regress_make_ideal_sum sum_ideal.1D \
-regress_est_blur_epits \
-regress_global_times \
-regress_est_blur_errts


Dataset File: pb00.CRD_001.r01.tcat+orig
Identifier Code: XYZ_Jt5e7844hD-AT06EaWjd9A Creation Date: Mon Aug 27 16:35:24 2012
Template Space: ORIG
Dataset Type: Echo Planar (-epan)
Byte Order: LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode: BRIK
Storage Space: 87,552,000 (88 million) bytes
Geometry String: "MATRIX(2.4,0,0,-95.99995,0,1.951442,2.328492,-130.2147,0,-1.397095,3.252403,0.556965):80,80,38"
Data Axes Tilt: Oblique (35.600 deg. from plumb)
Data Axes Approximate Orientation:
first (x) = Right-to-Left
second (y) = Anterior-to-Posterior
third (z) = Inferior-to-Superior [-orient RAI]
R-to-L extent: -96.000 [R] -to- 93.600 [L] -step- 2.400 mm [ 80 voxels]
A-to-P extent: -22.561 [A] -to- 167.039 [P] -step- 2.400 mm [ 80 voxels]
I-to-S extent: -55.327 -to- 92.673 [S] -step- 4.000 mm [ 38 voxels]
Number of time steps = 180 Time step = 2.00000s Origin = 0.00000s Number time-offset slices = 38 Thickness = 4.000



Dataset File: CRD.RUN_1+orig
Identifier Code: XYZ_Fs96xt0tGH0Hs-ERbFaTSQ Creation Date: Mon Aug 27 16:07:03 2012
Template Space: ORIG
Dataset Type: Echo Planar (-epan)
Byte Order: LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode: BRIK
Storage Space: 87,552,000 (88 million) bytes
Geometry String: "MATRIX(2.4,0,0,-95.99995,0,1.951442,2.328492,-130.2147,0,-1.397095,3.252403,0.556965):80,80,38"
Data Axes Tilt: Oblique (35.600 deg. from plumb)
Data Axes Approximate Orientation:
first (x) = Right-to-Left
second (y) = Anterior-to-Posterior
third (z) = Inferior-to-Superior [-orient RAI]
R-to-L extent: -96.000 [R] -to- 93.600 [L] -step- 2.400 mm [ 80 voxels]
A-to-P extent: -22.561 [-] -to- 167.039 [P] -step- 2.400 mm [ 80 voxels]
I-to-S extent: -55.327 -to- 92.673 [S] -step- 4.000 mm [ 38 voxels]
Number of time steps = 180 Time step = 2.00000s Origin = 0.00000s Number time-offset slices = 38 Thickness = 4.000
Subject Author Posted

afni_proc.py - processing speed issue

David August 26, 2012 01:12AM

Re: afni_proc.py - processing speed issue

Peter Molfese August 26, 2012 09:26AM

Re: afni_proc.py - processing speed issue

Daniel Glen August 26, 2012 10:49AM

Re: afni_proc.py - processing speed issue

rick reynolds August 26, 2012 10:44AM

Re: afni_proc.py - processing speed issue

Anonymous User August 27, 2012 02:58AM

Re: afni_proc.py - processing speed issue

Daniel Glen August 27, 2012 07:17AM

Re: afni_proc.py - processing speed issue

rick reynolds August 27, 2012 08:19AM

Re: afni_proc.py - processing speed issue

Anonymous User August 27, 2012 10:17PM

Re: afni_proc.py - processing speed issue

rick reynolds August 28, 2012 11:43AM

Re: afni_proc.py - processing speed issue

Anonymous User August 28, 2012 10:46PM

Re: afni_proc.py - processing speed issue

rick reynolds August 29, 2012 07:54AM

Re: afni_proc.py - processing speed issue

Anonymous User August 29, 2012 08:34PM

Re: afni_proc.py - processing speed issue

rick reynolds August 29, 2012 09:00PM