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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January 05, 2022 05:41PM
Thank you, Rick. This is getting more interesting. 3dcopy give the same error I got before:
3dcopy ${subj}.REML_IMs_reord+tlrc copy_reord.nii.gz
++ 3dcopy: AFNI version=AFNI_21.3.17 (Dec 30 2021) [64-bit]
** ERROR: nifti_image_write_hdr_img: NBL does not match nim

I forgot to say that in these cases a NIFTI file is actually produced. However, when I run 3dinfo on it, this is what happens:
3dinfo copy_reord.nii.gz
++ 3dinfo: AFNI version=AFNI_21.3.17 (Dec 30 2021) [64-bit]
** ERROR (nifti_image_read): short header read '/home/wgraves/data/bsafAG/data/mcwRA/copy_reord.nii.gz'
** FATAL ERROR: Can't open dataset copy_reord.nii.gz
** Program compile date = Dec 30 2021

But the 3dbucket command actually does work to successfully save it as a NIFTI file. Here's the output of 3dinfo on that resulting file:
3dinfo bucket_reord.nii.gz
++ 3dinfo: AFNI version=AFNI_21.3.17 (Dec 30 2021) [64-bit]

Dataset File: /home/wgraves/data/bsafAG/data/mcwRA/bucket_reord.nii.gz
Identifier Code: XYZ_IsUKqzK2tsZ7jPpyjmPHvw Creation Date: Wed Jan 5 17:31:16 2022
Template Space: TT_N27
Dataset Type: Anat Bucket (-abuc)
Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode: NIFTI
Storage Space: 1,060,200,000 (1.1 billion) bytes
Geometry String: "MATRIX(2,0,0,-79,0,2,0,-79,0,0,2,-64):80,95,75"
Data Axes Tilt: Plumb
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Anterior-to-Posterior
third (z) = Inferior-to-Superior [-orient RAI]
R-to-L extent: -79.000 [R] -to- 79.000 [L] -step- 2.000 mm [ 80 voxels]
A-to-P extent: -79.000 [A] -to- 109.000 [P] -step- 2.000 mm [ 95 voxels]
I-to-S extent: -64.000 -to- 84.000 [S] -step- 2.000 mm [ 75 voxels]
Number of values stored at each pixel = 465
-- At sub-brick #0 'allwords#36_Tstat' datum type is float: -8.46264 to 8.56861
statcode = fitt; statpar = 673
-- At sub-brick #1 'allwords#400_Tstat' datum type is float: -4.15827 to 4.30151
statcode = fitt; statpar = 673
-- At sub-brick #2 'allwords#408_Tstat' datum type is float: -4.11308 to 5.13197
statcode = fitt; statpar = 673
** For info on all 465 sub-bricks, use '3dinfo -verb' **

----- HISTORY -----
[wgraves@argus: Wed Oct 13 00:43:56 2021] Matrix source: ; 3dDeconvolve -input 3Dout.words1+orig 3Dout.words2+orig 3Dout.words3+orig 3Dout.words4+orig 3Dout.words5+orig -mask epimask+orig -x1D R.xmat.1D -x1D_stop -polort A -censor Mcensor.1D -CENSORTR '*:0-5' -num_stimts 8 -stim_file 1 'MP.all.1D[1]' -stim_label 1 MP1 -stim_base 1 -stim_file 2 'MP.all.1D[2]' -stim_label 2 MP2 -stim_base 2 -stim_file 3 'MP.all.1D[3]' -stim_label 3 MP3 -stim_base 3 -stim_file 4 'MP.all.1D[4]' -stim_label 4 MP4 -stim_base 4 -stim_file 5 'MP.all.1D[5]' -stim_label 5 MP5 -stim_base 5 -stim_file 6 'MP.all.1D[6]' -stim_label 6 MP6 -stim_base 6 -stim_file 7 ./noise.1D -stim_label 7 noise -stim_base 7 -local_times -stim_times_IM 8 ./regressors/lsstimes.01.1D 'BLOCK(1,1)' -stim_label 8 allwords
[wgraves@argus: Wed Oct 13 00:43:56 2021] {AFNI_21.1.20:linux_ubuntu_16_64} 3dREMLfit -matrix R.xmat.1D -input '3Dout.words1+orig 3Dout.words2+orig 3Dout.words3+orig 3Dout.words4+orig 3Dout.words5+orig' -mask epimask+orig -tout -nobout -Rbuck 2426.REML_IMs -verb
[wgraves@argus: Wed Jan 5 16:35:24 2022] {AFNI_21.3.17:linux_ubuntu_16_64} 3dbucket -fbuc -prefix 2426.REML_IMs_reord.nii.gz '2426.REML_IMs+orig[1dcat reorder.1D]'
[wgraves@hermes: Wed Jan 5 16:38:29 2022] {AFNI_21.3.17:linux_ubuntu_16_64} 3dNwarpApply -nwarp MPRAGE_sag_al_qw_WARP+tlrc -source 2426.REML_IMs_reord.nii.gz -master /usr/lib/afni/bin/TT_N27_SSW.nii.gz -dxyz 2 -prefix /home/wgraves/data/bsafAG/data/mcwRA/2426.REML_IMs_reord+tlrc
[wgraves@hermes: Wed Jan 5 17:31:16 2022] {AFNI_21.3.17:linux_ubuntu_16_64} 3dbucket -prefix bucket_reord.nii.gz 2426.REML_IMs_reord+tlrc

So I guess I'll just stick with your 3dbucket trick (thanks for that!). But it would be nice to know what's going on here.

Best,
Will
Subject Author Posted

problem saving HEAD/BRIK to nii

wgraves January 05, 2022 04:54PM

Re: problem saving HEAD/BRIK to nii

rick reynolds January 05, 2022 05:22PM

Re: problem saving HEAD/BRIK to nii

wgraves January 05, 2022 05:41PM

Re: problem saving HEAD/BRIK to nii

rick reynolds January 06, 2022 12:11PM

Re: problem saving HEAD/BRIK to nii

rick reynolds January 06, 2022 05:51PM

Re: problem saving HEAD/BRIK to nii

wgraves January 07, 2022 04:58PM

Re: problem saving HEAD/BRIK to nii

rick reynolds January 07, 2022 09:27PM

Re: problem saving HEAD/BRIK to nii

wgraves January 11, 2022 09:48AM

Re: problem saving HEAD/BRIK to nii

rick reynolds January 11, 2022 12:26PM