"Failure" at cutneckapplyautocrop

[raihaan]

Ran into the following issue in the minccalc step of cutneckapplyautocrop

/bin/sh: error importing function definition for `BASH_FUNC_module%%'
Files T2_cutneck//subject5_t2.affine_register_masked.mnc and /opt/quarantine/resources/mni_icbm152_nlin_sym_09c_minc2/mni_icbm152_t1_tal_nlin_sym_09c_headmask.mnc have different sizes of dimensions

Ran with preprocess segment as linear_register + cutneckapplyautocrop

outputs created so far for subject5_t2:

subject5_t2.affine_register_inverse.xfm         subject5_t2.affine_register_masked.xfm  subject5_t2.rough_register.xfm
subject5_t2.affine_register_masked_inverse.xfm  subject5_t2.affine_register.xfm
subject5_t2.affine_register_masked.mnc          subject5_t2.rough_register_inverse.xfm

However, after commenting out minccalc step in the cutneckapplyautocrop segment and rerunning with original command, native autocropped files were produced as desired:

cutneckapplyautocrop = {
    //Alternative implementation of cutneck which applies via autocrop in native space
    //Applies model mask to subject brain in model space
    //exec """
    //minccalc -2 -short -unsigned -clobber -expression A[0]*A[1] ${CUTNECKMODEL}_headmask.mnc $input.mnc $output.mnc
    //"""
...
...

[raihaan]

Pipeline failed! (2) 

Command failed with exit status = 1 : 

minccalc -2 -short -unsigned -clobber -expression A[0]*A[1] /opt/quarantine/resources/mni_icbm152_nlin_sym_09c_minc2/mni_icbm152_t1_tal_nlin_sym_09c_headmask.mnc T2_cutneck//subject5_t2.affine_register_masked.mnc T2_cutneck//subject5_t2.affine_register_masked.cutneckapplyautocrop.mnc

[raihaan]

Input files are here

/data/chamal/projects/raihaan/models/winterburn_hc/T2

command was

bpipe run -d T2_cutneck/ minc-bpipe-library/minc-library.bpipe T2/*mnc

[gdevenyi]

Problem with new headmask, fixed.