Hi Rosalia,
Alas, I don't really have experience with AFNI formats. That mismatch just stuck out at me. The only other thing I can think of is that I thought AFNI files needed BRIK and HEAD filies, and you don't seem to have HEAD files. But this might be better targeted to the AFNI message board (https://afni.nimh.nih.gov/afni/community/board/list.php?1).
Chris
________________________________________
From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Rosalia Dacosta Aguayo <[log in to unmask]>
Sent: Wednesday, February 28, 2018 2:43:23 PM
To: [log in to unmask]
Subject: Re: [FSL] Problems converting file from AFNI to NIFTI
The same for others...
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/EXERCISE_HELEN_FMRI/data/Rosie_Soha_preprocess/ms02/session_1 $ 3dAFNItoNIFTI sdmt_1_seq3+orig.BRIK.gz -prefix sdmt1Temp.nii
++ 3dAFNItoNIFTI: AFNI version=AFNI_17.3.05 (Nov 27 2017) [64-bit]
** FATAL ERROR: Can't open dataset 'sdmt_1_seq3+orig.BRIK.gz'
** Program compile date = Nov 27 2017
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/EXERCISE_HELEN_FMRI/data/Rosie_Soha_preprocess/ms02/session_1 $
2018-02-28 20:42 GMT+01:00 Rosalia Dacosta Aguayo <[log in to unmask]<mailto:[log in to unmask]>>:
Hi Christopher,
Thank you for answering. I have changed the _ because I had changed it thinking about if the + was a problem. But the warning message is the same....Any idea? This is really weird
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/EXERCISE_HELEN_FMRI/data/Rosie_Soha_preprocess/ms02/session_1 $ ls
mprage+orig.BRIK.gz sdmt_2_seq1+orig.BRIK.gz sdmt_4_seq4+orig.BRIK.gz
sdmt_1_seq3+orig.BRIK.gz sdmt_3_seq2+orig.BRIK.gz
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/EXERCISE_HELEN_FMRI/data/Rosie_Soha_preprocess/ms02/session_1 $ 3dAFNItoNIFTI mprage+orig.BRIK.gz -prefix mprageTem
p.nii
++ 3dAFNItoNIFTI: AFNI version=AFNI_17.3.05 (Nov 27 2017) [64-bit]
** FATAL ERROR: Can't open dataset 'mprage+orig.BRIK.gz'
** Program compile date = Nov 27 2017
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/EXERCISE_HELEN_FMRI/data/Rosie_Soha_preprocess/ms02/session_1 $
2018-02-28 20:30 GMT+01:00 Christopher Markiewicz <[log in to unmask]<mailto:[log in to unmask]>>:
Hi Rosalia,
It looks like the file has an underscore (_) in it, while you're attempting to operate on a file with a plus (+).
--
Chris Markiewicz
Center for Reproducible Neuroscience
Stanford University
________________________________________
From: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> on behalf of Rosalia Dacosta Aguayo <[log in to unmask]<mailto:[log in to unmask]>>
Sent: Wednesday, February 28, 2018 7:46 AM
To: [log in to unmask]<mailto:[log in to unmask]>
Subject: [FSL] Problems converting file from AFNI to NIFTI
Dear FSL'experts,
I am having problems when I try to convert an image from AFNI to NIFTI in order to work with FSL program.
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/EXERCISE_HELEN_FMRI/data/Rosie_Soha_preprocess/ms02/session_1 $ ls
mprage_orig.BRIK.gz sdmt_1_seq3+orig.BRIK.gz sdmt_2_seq1+orig.BRIK.gz sdmt_3_seq2+orig.BRIK.gz sdmt_4_seq4+orig.BRIK.gz
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/EXERCISE_HELEN_FMRI/data/Rosie_Soha_preprocess/ms02/session_1 $ 3dAFNItoNIFTI mprage+orig.BRIK.gz -prefix mprageTemp.nii
++ 3dAFNItoNIFTI: AFNI version=AFNI_17.3.05 (Nov 27 2017) [64-bit]
** FATAL ERROR: Can't open dataset 'mprage+orig.BRIK.gz'
** Program compile date = Nov 27 2017
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/EXERCISE_HELEN_FMRI/data/Rosie_Soha_preprocess/ms02/session_1 $
My colleague has tried with her computer and it seems she does not have any problem, so I wonder if there is something bad with the date of compilation for AFNI and how could I fix it.
Best regards,
Rosie
More info:
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $ afni
Precompiled binary linux_ubuntu_16_64: Nov 27 2017 (Version AFNI_17.3.05)
Thanks go to B Feige for useful feedback
Initializing: X11[The X.Org Foundation v 11804000].. Widgets...... Input files:
** Searching subdirectories of './' for data
session # 1 = ./abin/ ==> 82 datasets
dataset count = 82
Time series = 0 files read
NLfit & NLerr= Optimizer (AFNI_NLFIM_METHOD) is SIMPLEX
NLfit & NLerr= Found 29 models
Plugins = 52 libraries read
++ AFNI is detached from terminal.
rosalia@rosalia-Lenovo-Y520-15IKBN ~ $
++ NOTE: This version of AFNI was built Nov 27 2017 ++
++ NOTE: 'Define Markers' is hidden: right-click 'DataDir' to see it
++ NOTE: Use '-seehidden' option to see which plugins are hidden
** AFNI concludes: Always be patient with the rich and powerful! [282/640]
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