Fod2fixel does not produce output

1

Hello
I am attempting to follow this tutorial to perform a Fixel-based analysis of a clinical dataset. Previously, the same procedure has been effective for b=1000 images. However, when attempting to analyze a series of b=3000 images, I have experienced several issues. Most notably, any and all attempts to run the fod2fixel command result in mrtrix reporting success, but no output files. This happens regardless of whether thresholds are used or not.

Any advice would be greatly appreciated

2

Hi @MTBernas,

Before we can help here, we would need (a lot) more information – at a minimum:

  • the full command used and its full output, ideally when running with the -debug flag
  • the operating system and hardware you’re running this on (especially if one of the newer mac M1 CPUs).
  • the version of MRtrix used (e.g. fod2fixel -version)
  • information about the destination storage device: internal / external hard drive? Connected via SATA / PCI-E / USB / other? Network share? What file system (ext4 / ZFS / NTFS / FAT / NFS / other?)
  • confirmation that there is sufficient storage on the device you’re writing to

That should be enough to work out what’s going on…
All the best,

Donald.

3

Hello, thank you for your response

The command I am attempting to run is

fod2fixel -mask ../template/template_mask.mif dmd_003/fod_in_template_space_NOT_REORIENTED.mif dmd_003/fixel_in_template_space_NOT_REORIENTED -afd fd.mif -force -debug

Which gives the following output:

fod2fixel: [WARNING] existing output files will be overwritten
fod2fixel: [DEBUG] No config file found at "/etc/mrtrix.conf"
fod2fixel: [DEBUG] No config file found at "/home/cogdmd/.mrtrix.conf"
fod2fixel: [INFO] opening image "dmd_003/fod_in_template_space_NOT_REORIENTED.mif"...
fod2fixel: [DEBUG] reading key/value file "dmd_003/fod_in_template_space_NOT_REORIENTED.mif"...
fod2fixel: [DEBUG] sanitising image information...
fod2fixel: [INFO] image "dmd_003/fod_in_template_space_NOT_REORIENTED.mif" opened with dimensions 145x191x134x45, voxel spacing 1.25x1.25x1.25xnan, datatype Float32LE
fod2fixel: [DEBUG] memory-mapping file "dmd_003/fod_in_template_space_NOT_REORIENTED.mif"...
fod2fixel: [DEBUG] file "dmd_003/fod_in_template_space_NOT_REORIENTED.mif" mapped at 0x7fba4c8da000, size 668003400 (read-only)
fod2fixel: [DEBUG] image "dmd_003/fod_in_template_space_NOT_REORIENTED.mif" loaded
fod2fixel: [DEBUG] image "dmd_003/fod_in_template_space_NOT_REORIENTED.mif" initialised with strides = [ -45 -6525 1246275 1 ], start = 1246230, using direct IO
fod2fixel: [INFO] opening image "../template/template_mask.mif"...
fod2fixel: [DEBUG] reading key/value file "../template/template_mask.mif"...
fod2fixel: [DEBUG] sanitising image information...
fod2fixel: [INFO] image "../template/template_mask.mif" opened with dimensions 145x191x134, voxel spacing 1.25x1.25x1.25, datatype Bit
fod2fixel: [DEBUG] memory-mapping file "../template/template_mask.mif"...
fod2fixel: [DEBUG] file "../template/template_mask.mif" mapped at 0x7fba4c867000, size 463892 (read-only)
fod2fixel: [DEBUG] image "../template/template_mask.mif" loaded
fod2fixel: [DEBUG] image "../template/template_mask.mif" initialised with strides = [ -1 -145 27695 ], start = 27694, using indirect IO
fod2fixel: [DEBUG] initialising threads...
fod2fixel: [DEBUG] launching thread "source"...
fod2fixel: [DEBUG] launching 16 threads "pipe"...
fod2fixel: [  0%] segmenting FODs...
fod2fixel: [DEBUG] launching thread "sink"...
fod2fixel: [DEBUG] waiting for completion of thread "source"...
fod2fixel: [100%] segmenting FODs...
fod2fixel: [DEBUG] no writers left on queue "source->pipe"
fod2fixel: [DEBUG] thread "source" completed OK
fod2fixel: [DEBUG] waiting for completion of threads "pipe"...
fod2fixel: [DEBUG] no writers left on queue "pipe->sink"
fod2fixel: [DEBUG] no readers left on queue "source->pipe"
fod2fixel: [DEBUG] no readers left on queue "pipe->sink"
fod2fixel: [DEBUG] threads "pipe" completed OK
fod2fixel: [DEBUG] waiting for completion of thread "sink"...
fod2fixel: [DEBUG] thread "sink" completed OK
fod2fixel: [100%] segmenting FODs
fod2fixel: [DEBUG] unmapping file "../template/template_mask.mif"
fod2fixel: [DEBUG] image "../template/template_mask.mif" unloaded
fod2fixel: [DEBUG] unmapping file "dmd_003/fod_in_template_space_NOT_REORIENTED.mif"
fod2fixel: [DEBUG] image "dmd_003/fod_in_template_space_NOT_REORIENTED.mif" unloaded

I am running Scientific Linux 7.9 (Nitrogen), kernel version 3.10.0-1160.76.1.el7.x86_64.
The CPU is an Intel Xenon W-1370
The GPU is an Nvidia T1000, 4GB model
I have 64 GB of DDR4 RAM available
The destination disk is an internal SSD, connected via PCI-E. It has sufficient space, and is formatted for ext4.

I am using MRtrix 3.0.3, 64-bit version.

Of note is the fact that I have since attempted to analyze the same data on a different machine, with no results.

4

Hello, have you solved your problem? I face the same problem :joy: