How to get functional volume after the registration FSL

Software Support
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1

Summary of what happened:

FSL finished the first level analysis correctly, however, within the outputs I am not able to find the functional volume after the registration. Which in my case should be a .nii.gz file with dimensions 91x109x91x(total time). I need this file to run a custom model.

Screenshots / relevant information:

The registration was executed with the following parameters:

image

files in the reg folder:

ls -lha
 520K ene 11 14:42 example_func2highres_fast_wmedge.nii.gz
 417K ene 11 14:42 example_func2highres_fast_wmseg.nii.gz
  195 ene 11 14:42 example_func2highres_init.mat
  188 ene 11 14:43 example_func2highres.mat
  14M ene 11 14:43 example_func2highres.nii.gz
 2,6M ene 11 14:43 example_func2highres.png
 165K ene 11 14:44 example_func2standard1.png
  196 ene 11 14:44 example_func2standard.mat
1022K ene 11 14:44 example_func2standard.nii.gz
 372K ene 11 14:44 example_func2standard.png
 230K ene 11 14:37 example_func.nii.gz
  192 ene 11 14:43 highres2example_func.mat
  193 ene 11 14:44 highres2standard.mat
 2,5M ene 11 14:44 highres2standard.nii.gz
 506K ene 11 14:44 highres2standard.png
  14M ene 11 14:37 highres_head.nii.gz
  14M ene 11 14:37 highres.nii.gz
  190 ene 11 14:44 standard2example_func.mat
  185 ene 11 14:44 standard2highres.mat
 522K ene 11 14:37 standard.nii.gz

Version:

6.0.7.3

Environment (Docker, Singularity, custom installation):

Linux intel2 6.6.8-2-MANJARO #1 SMP PREEMPT_DYNAMIC Thu Dec 21 16:21:45 UTC 2023 x86_64 GNU/Linux

2

FEAT calculates functional->standard space transformations, but does not necessarily apply them. For a first level analysis, the model fitting is performed in native functional space, and then only results (e.g. COPE images) are transformed/resampled to standard space as needed. If you want the full 4D functional data in standard space you will need to transform/resample it yourself using a command such as:

applywarp -r reg/standard.nii.gz                \
	      -i filtered_func_data.nii.gz          \
	      -o filtered_func_data_standard.nii.gz \
	      --premat=reg/example_func2highres.mat \
          -w reg/highres2standard_warp.nii.gz