Laynii is a set of tools to analyze layer fMRI datasets.

References:

• Huber, L., Poser, B. A., Bandettini, P. A., Arora, K., Wagstyl, K., Cho, S., Goense, J., Nothnagel, N., Morgan, A. T., van den Hurk, J., Mueller A. K., Reynolds, R. C., Glen, D. R., Goebel, R. W., Gulban, O. F. (2021). LayNii: A software suite for layer-fMRI. NeuroImage, 118091.

Allocate an interactive session and run the program.
Sam ple session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load laynii
[user@cn3144 ~]$ cd /data/${USER}
[user@cn3144 ~]$ cp -r ${LAYNII_HOME}/test_data .
[user@cn3144 ~]$ cd test_data
[user@cn3144 ~]$ LN2_LAYER_SMOOTH -input sc_VASO_act.nii.gz -layer_file sc_layers.nii.gz -FWHM 1
=======================
LayNii v2.9.0          
=======================
LN2_LAYER_SMOOTH

    File name: sc_VASO_act.nii.gz
    Image details: 648 X | 648 Y | 15 Z | 1 T 
    Voxel size = 0.200617 x 0.200617 x 0.32
    Datatype = 4

    File name: sc_layers.nii.gz
    Image details: 648 X | 648 Y | 15 Z | 1 T 
    Voxel size = 0.200617 x 0.200617 x 0.32
    Datatype = 4

  Vicinity = 9
  FWHM = 1
  There are 20 layers to smooth within.
  Smoothing in layer, not considering sulci.
    100%
  Smoothing is done. 
    Writing output as:
      sc_VASO_act_layer_smoothed.nii.gz
  Finished.

[user@cn3144 ~]$ LN_LAYER_SMOOTH -input sc_VASO_act.nii.gz -layer_file sc_layers.nii.gz -FWHM 0.3 -NoKissing
I will not smooth across sluci, this might make it longer though
15 slices    648 PhaseSteps     648 Read steps    1 timesteps 
 Voxel size    0.200617 x 0.200617 x 0.32
 datatye 1 = 16
 datatye 2 = 8
debug  2 
 vinc 2
 FWHM_val 0.3
 There are  20 layers/masks to smooth within  
 vinc 2
 FWHM_val 0.3
 starting within sulucal smoothing now  
 106%   smoothing done  
writing as = smoothed_sc_VASO_act.nii.gz

[user@cn3144 ~]$ LN_BOCO -Nulled lo_Nulled_intemp.nii.gz -BOLD lo_BOLD_intemp.nii.gz -trialBOCO 40 -shift
Do a correlation analysis with temporal shifts.
=======================
LayNii v2.9.0          
=======================
LN_BOCO

    File name: lo_Nulled_intemp.nii.gz
    Image details: 162 X | 162 Y | 3 Z | 80 T 
    Voxel size = 0.802469 x 0.802469 x 1.28
    Datatype = 4

    File name: lo_BOLD_intemp.nii.gz
    Image details: 162 X | 162 Y | 3 Z | 80 T 
    Voxel size = 0.802469 x 0.802469 x 1.28
    Datatype = 4

    !!!Warning!!! Input nifti header contains scl_scale !=0.
    Make sure to check the resulting output image.

  Calculating shift = -3
  Calculating shift = -2
  Calculating shift = -1
  Calculating shift = 0
  Calculating shift = 1
  Calculating shift = 2
  Calculating shift = 3
  Doing BOLD correction after trial average...
    Trial duration is 40. This means there are 2 trials recorded here.
    Writing output as:
      VASO_trialAV_LN
    Writing output as:
      BOLD_trialAV_LN
    Writing output as:
      VASO_LN
  Finished.

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. laynii.sh). Example command below:

#!/bin/bash
#SBATCH --cpus-per-task=4
#SBATCH --job-name=laynii-test
#SBATCH --mem=8g
#SBATCH --time=1:00:00
#SBATCH --partition=norm

module load laynii

cd /data/${USER}/test_data
LN2_LAYER_SMOOTH -input sc_VASO_act.nii.gz -layer_file sc_layers.nii.gz -FWHM 1
LN_LAYER_SMOOTH -input sc_VASO_act.nii.gz -layer_file sc_layers.nii.gz -FWHM 0.3 -NoKissing
LN_BOCO -Nulled lo_Nulled_intemp.nii.gz -BOLD lo_BOLD_intemp.nii.gz -trialBOCO 40 -shift

Submit this job using the Slurm sbatch command.

sbatch laynii.sh

Create a swarmfile (e.g. laynii.swarm). For example:

cd /data/${USER}/test_data_01; \
LN2_LAYER_SMOOTH -input sc_VASO_act.nii.gz \
                 -layer_file sc_layers.nii.gz \
                 -FWHM 1; \
LN_LAYER_SMOOTH -input sc_VASO_act.nii.gz \
                -layer_file sc_layers.nii.gz \
                -FWHM 0.3 -NoKissing; \
LN_BOCO -Nulled lo_Nulled_intemp.nii.gz \
                -BOLD lo_BOLD_intemp.nii.gz \
                -trialBOCO 40 \
                -shift
cd /data/${USER}/test_data_02; \
LN2_LAYER_SMOOTH -input sc_VASO_act.nii.gz \
                 -layer_file sc_layers.nii.gz \
                 -FWHM 1; \
LN_LAYER_SMOOTH -input sc_VASO_act.nii.gz \
                -layer_file sc_layers.nii.gz \
                -FWHM 0.3 -NoKissing; \
LN_BOCO -Nulled lo_Nulled_intemp.nii.gz \
                -BOLD lo_BOLD_intemp.nii.gz \
                -trialBOCO 40 \
                -shift
cd /data/${USER}/test_data_03; \
LN2_LAYER_SMOOTH -input sc_VASO_act.nii.gz \
                 -layer_file sc_layers.nii.gz \
                 -FWHM 1; \
LN_LAYER_SMOOTH -input sc_VASO_act.nii.gz \
                -layer_file sc_layers.nii.gz \
                -FWHM 0.3 -NoKissing; \
LN_BOCO -Nulled lo_Nulled_intemp.nii.gz \
                -BOLD lo_BOLD_intemp.nii.gz \
                -trialBOCO 40 \
                -shift

Submit this job using the swarm command.

swarm -f laynii.swarm -g 8 -t 4 --partition norm --module laynii