I am trying to turn a bunch of .jpegs into a 3D file. It worked yesterday with fewer files - however I did get this warning and the GUI popped up… but it successfully generated the 3D file through the GUI.
[rossisl@nialbn-01878557 JPEG]$ to3d *.jpg -orient SAL
++ to3d: AFNI version=AFNI_16.1.07 (Apr 25 2016) [64-bit]
++ Authored by: RW Cox
++ It is best to use to3d via the Dimon program.
** Can’t find file -orient
** Can’t find file SAL
++ Counting images: total=546 2D slices
++ Each 2D slice is 2160 X 2560 pixels
++ Image data type = byte
++ Reading images: …
*+ WARNING: *** ILLEGAL INPUTS (cannot save) ***
Axes orientations are not consistent!
++ Making widgets…
Today, with the complete set of files, this is what I’m getting and the GUI won’t pop up - even if I only input the filename.
[rossisl@nialbn-01878557 newborn_neurons]$ to3d *.jpg -orient SAL
++ to3d: AFNI version=AFNI_16.2.18 (Sep 19 2016) [64-bit]
++ Authored by: RW Cox
++ It is best to use to3d via the Dimon program.
** Can’t find file -orient
** Can’t find file SAL
++ Counting images: total=2362 2D slices
++ Each 2D slice is 2160 X 2560 pixels
++ Image data type = byte
++ Reading images:
Fatal Signal 11 (SIGSEGV) received
T3D_read_images
to3d:main
Bottom of Debug Stack
** Command line was:
to3d Aged_10000.jpg Aged_10001.jpg Aged_10002.jpg … -orient SAL
** AFNI version = AFNI_16.2.18 Compile date = Sep 19 2016
** [[Precompiled binary linux_openmp_64: Sep 19 2016]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Crash log is appended to file /home/rossisl/.afni.crashlog
[rossisl@nialbn-01878557 newborn_neurons]$
Do I not have enough memory because there are so many files?
I have 89MB of free RAM. I tried to break these into smaller files and used 3dZcat as I saw someone had done in the past. They can’t be concatenated either and that’s not even all of them
Fatal Signal 11 (SIGSEGV) received
3dZcat main
Bottom of Debug Stack
** Command line was:
3dZcat Aged_100+orig Aged_101+orig Aged_102+orig Aged_103+orig Aged_104+orig Aged_105+orig Aged_106+orig Aged_107+orig -prefix Aged_100_107
** AFNI version = AFNI_16.2.18 Compile date = Sep 19 2016
** [[Precompiled binary linux_openmp_64: Sep 19 2016]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Crash log is appended to file /home/rossisl/.afni.crashlog
I expect 89 MB of free RAM is a typo, though if is it for GB,
that would be a lot!
To be clear, your original command was putting 2160 X 2560 pixel
images together, and there were 2362 of them. Presumably that
means they were 5 mega-pixel images, possibly of RGBA form,
making them 20 MB each, 2362 of which would create almost a
50 GB dataset. Big.
Yes, as Daniel noted, any options (like -prefix) must go first:
I know it is a lot of data - it’s still crashing… Would it work if I resample each 3D output and then concatenate? Do you think that will help before I go through all of these?
Fatal Signal 11 (SIGSEGV) received
3dZcat main
Bottom of Debug Stack
** Command line was:
3dZcat -prefix Aged_100_107 Aged_100+orig.HEAD Aged_101+orig.HEAD Aged_102+orig.HEAD Aged_103+orig.HEAD Aged_104+orig.HEAD Aged_105+orig.HEAD Aged_106+orig.HEAD Aged_107+orig.HEAD
** AFNI version = AFNI_16.2.18 Compile date = Sep 19 2016
** [[Precompiled binary linux_openmp_64: Sep 19 2016]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Crash log is appended to file /home/rossisl/.afni.crashlog
So, I broke them down into about 100 files each so it wouldn’t crash but this is what happens. Then ‘making widgets’ I guess becomes the GUI and after I input the information there (orientation and output file name), it generates the file. But note that my to3d never finds the -orient option (??) don’t know how much that matters.
rossisl@nialbn-01878557 newborn_neurons]$ to3d Aged_100* -orient SAR
++ to3d: AFNI version=AFNI_16.2.18 (Sep 19 2016) [64-bit]
++ Authored by: RW Cox
++ It is best to use to3d via the Dimon program.
** Can’t find file -orient
** Can’t find file SAR
++ Counting images: total=100 2D slices
++ Each 2D slice is 2160 X 2560 pixels
++ Image data type = byte
++ Reading images: …
*+ WARNING: *** ILLEGAL INPUTS (cannot save) ***
Axes orientations are not consistent!
++ Making widgets…
[rossisl@nialbn-01878557 newborn_neurons]$
[rossisl@nialbn-01878557 newborn_neurons]$
[rossisl@nialbn-01878557 newborn_neurons]$
[rossisl@nialbn-01878557 newborn_neurons]$ to3d Aged_101* -orient SAR
++ to3d: AFNI version=AFNI_16.2.18 (Sep 19 2016) [64-bit]
++ Authored by: RW Cox
++ It is best to use to3d via the Dimon program.
** Can’t find file -orient
** Can’t find file SAR
++ Counting images: total=100 2D slices
++ Each 2D slice is 2160 X 2560 pixels
++ Image data type = byte
++ Reading images: …
*+ WARNING: *** ILLEGAL INPUTS (cannot save) ***
Axes orientations are not consistent!
++ Making widgets…
This is similar to the other cases: for to3d, the
options go first, then the input files. Since
-orient SAR option should go before the input
file names, as in:
to3d -orient SAR Aged_101*
But still, if you are eventually putting all of
those together, it will still be huge.
rick
The
National Institute of Mental Health (NIMH) is part of the National Institutes of
Health (NIH), a component of the U.S. Department of Health and Human
Services.
and that’s not even all of them