Hi!
We are encountering a strange issue with JIP, please see error in bold below.
Basically, JIP seems to scramble the path to our distortion.nii NIFTI file.
It is a bit mysterious where the path that JIP tries to read originates, definetly not in the align.com file.
This is version 3.1 on Linux.
Any advice would be appreciated.
Thanks! Caspar


[GWDG\ssudman@ug-ukme-cn03 func_scripts]$ jip jip_scripts/register.com ../bold/MOCOVOL/alignTo20180109Phoenix.com ../bold/MOCOVOL/mocovol.nii ../bold/MOCOVOL/mocovola.nii

/neuro_tools/jip/jip/Linux-x86_64/jip
jip > jip >
jip > read ../bold/MOCOVOL/alignTo20180109Phoenix.com
jip > set target-matrix 80 80 43
jip > set target-resolution 1.2 1.2 1.2
jip > set target-origin 44.9511 64.5954 -50.8716
jip > set target-direction -1 -1 1
jip > set source-matrix 80 80 43
jip > set source-resolution 1.2 1.2 1.2
jip > set source-origin 50.3067 66.9567 -53.4317
jip > set source-direction -1 -1 1
jip > set registration-orientation 0 0 0 0
jip > set registration-translations 0.0148761 4.18427 -0.979116
jip > set registration-rotations -0.0601725 0.0363694 -0.177008
jip > set registration-inflations 0.9985 0.999993 1.01028
jip > set registration-skews 0.0104977 -0.0115842 0.000290953
jip > set spinal-x-shift 0 0
jip > set spinal-y-shift 0 0 0
jip > set spinal-rotation 0 0 0 0
jip > set registration-distortions /home/local/GWDG/ssudman/ukme11/ssudman/MRI/functional/20181130Phoenix/bold/MOCOVOL/distortions.nii
Error: cannot open Nifti file /home/local/GWDG/ssudman/ukme11/ssudman/MRI/funcld/MOCO20181130Phoenix/bold/MOCOVOL/distortions.nii.
jip > read ../bold/MOCOVOL/mocovol.nii
The NIFTI header for file ../bold/MOCOVOL/mocovol.nii uses Method 3: affine transformation of voxel indices
magnitude data, short ints, voxels (80,80,43,1), res (1.2,1.2,1.2,2)
1 volume of size 80 x 80 x 43 was read and stored in stack ' ../bold/MOCOVOL/mocovol '
jip > register
Register data using a Lanczos interpolation kernel,
which will not smooth data but will exhibit some ringing.
For downsampling > 2x, a Gaussian kernel will be used instead.
Switch kernels by:
set interpolation-kernel [type] , where type is Gaussian or Lanczos
jip > write ../bold/MOCOVOL/mocovola.nii
selected output format = floats; use 'write-short' to change this1 volume(s) of dimension 80 x 80 x 43 were written to file ../bold/MOCOVOL/mocovola.