I am trying to generate unbiased FOD template using three subjects. I use the command:
population_template fodimage -mask_dir maskimage fod_template.mif
I get error message: "mrregister: [ERROR] Error allocating memory for scratch buffer"
I am working on a system with RAM size 15GB. My system configuration as below:
Memory 15.6 GiB, Disk 928 GB, Graphics: Gallium 0.4 on NVE6, Processor: Intel® Core™ i7-3770 CPU @ 3.40GHz × 8
How I can remove this error, please help!
Here is the extract of the output of my command:---------
population_template: Generating a population-average template from 3 input images
population_template: SH Series detected, performing FOD registration
population_template: Generated temporary directory: /tmp/population_template-tmp-88C99P/
population_template: Changing to temporary directory (/tmp/population_template-tmp-88C99P/)
population_template: Generating initial template
Command: mraverageheader /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/fodimage/118932_fod.mif /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/fodimage/123117_fod.mif /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/fodimage/118730_fod.mif average_header.mif -fill
Command: mrtransform /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/maskimage/118932mask.mif -interp nearest -template average_header.mif masks_transformed/118932mask.mif
Command: mrtransform /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/maskimage/123117mask.mif -interp nearest -template average_header.mif masks_transformed/123117mask.mif
Command: mrtransform /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/maskimage/118730mask.mif -interp nearest -template average_header.mif masks_transformed/118730mask.mif
Command: mrmath masks_transformed/118932mask.mif masks_transformed/123117mask.mif masks_transformed/118730mask.mif max mask_initial.mif
Command: mrcrop average_header.mif -mask mask_initial.mif average_header_cropped.mif
Command: rm -f mask_initial.mif
Command: rm -f average_header.mif
Command: mv average_header_cropped.mif average_header.mif
Command: rm masks_transformed/118932mask.mif
Command: rm masks_transformed/123117mask.mif
Command: rm masks_transformed/118730mask.mif
Command: mrregister /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/fodimage/118932_fod.mif average_header.mif -mask1 /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/maskimage/118932mask.mif -rigid_scale 1 -rigid_niter 0 -type rigid -noreorientation -rigid_init_translation mass -datatype float32 -rigid linear_transforms_initial/118932.txt
Command: mrtransform /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/fodimage/118932_fod.mif -linear linear_transforms_initial/118932.txt -datatype float32 input_transformed/118932_translated.mif
Command: mrtransform /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/maskimage/118932mask.mif -linear linear_transforms_initial/118932.txt -datatype float32 masks_transformed/118932_translated.mif
Command: mrregister /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/fodimage/123117_fod.mif average_header.mif -mask1 /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/maskimage/123117mask.mif -rigid_scale 1 -rigid_niter 0 -type rigid -noreorientation -rigid_init_translation mass -datatype float32 -rigid linear_transforms_initial/123117.txt
Command: mrtransform /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/fodimage/123117_fod.mif -linear linear_transforms_initial/123117.txt -datatype float32 input_transformed/123117_translated.mif
Command: mrtransform /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/maskimage/123117mask.mif -linear linear_transforms_initial/123117.txt -datatype float32 masks_transformed/123117_translated.mif
Command: mrregister /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/fodimage/118730_fod.mif average_header.mif -mask1 /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/maskimage/118730mask.mif -rigid_scale 1 -rigid_niter 0 -type rigid -noreorientation -rigid_init_translation mass -datatype float32 -rigid linear_transforms_initial/118730.txt
Command: mrtransform /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/fodimage/118730_fod.mif -linear linear_transforms_initial/118730.txt -datatype float32 input_transformed/118730_translated.mif
Command: mrtransform /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/maskimage/118730mask.mif -linear linear_transforms_initial/118730.txt -datatype float32 masks_transformed/118730_translated.mif
Command: mraverageheader input_transformed/118932_translated.mif input_transformed/123117_translated.mif input_transformed/118730_translated.mif average_header_tight.mif
Command: mrpad -uniform 10 average_header_tight.mif average_header.mif -force
Command: rm -f average_header_tight.mif
Command: mrtransform masks_transformed/118932_translated.mif masks_transformed/118932.mif -interp nearest -template average_header.mif -datatype float32
Command: mrtransform masks_transformed/123117_translated.mif masks_transformed/123117.mif -interp nearest -template average_header.mif -datatype float32
Command: mrtransform masks_transformed/118730_translated.mif masks_transformed/118730.mif -interp nearest -template average_header.mif -datatype float32
Command: mrmath masks_transformed/118932.mif masks_transformed/123117.mif masks_transformed/118730.mif max mask_translated.mif
Command: rm -f mask_translated_smooth.mif
Command: mrcrop average_header.mif -mask mask_translated.mif average_header_cropped.mif
Command: mrpad -uniform 10 average_header_cropped.mif -force average_header.mif
Command: rm -f average_header_cropped.mif
Command: mrtransform masks_transformed/118932_translated.mif masks_transformed/118932.mif -interp nearest -template average_header.mif -datatype float32 -force
Command: rm -f masks_transformed/118932_translated.mif
Command: mrtransform masks_transformed/123117_translated.mif masks_transformed/123117.mif -interp nearest -template average_header.mif -datatype float32 -force
Command: rm -f masks_transformed/123117_translated.mif
Command: mrtransform masks_transformed/118730_translated.mif masks_transformed/118730.mif -interp nearest -template average_header.mif -datatype float32 -force
Command: rm -f masks_transformed/118730_translated.mif
Command: rm -f mask_translated.mif
Command: mrtransform input_transformed/118932_translated.mif input_transformed/118932.mif -interp linear -template average_header.mif -datatype float32
Command: rm -f input_transformed/118932_translated.mif
Command: mrtransform input_transformed/123117_translated.mif input_transformed/123117.mif -interp linear -template average_header.mif -datatype float32
Command: rm -f input_transformed/123117_translated.mif
Command: mrtransform input_transformed/118730_translated.mif input_transformed/118730.mif -interp linear -template average_header.mif -datatype float32
Command: rm -f input_transformed/118730_translated.mif
Command: mrmath input_transformed/118932.mif input_transformed/118730.mif input_transformed/123117.mif mean initial_template.mif
population_template: Optimising template with linear registration
Command: mrregister /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/fodimage/118932_fod.mif initial_template.mif -force -mask1 /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/maskimage/118932mask.mif -affine_scale 0.3 -affine_niter 500 -affine_lmax 2 -type affine -datatype float32 -affine linear_transforms_0/118932.txt
Command: transformcalc linear_transforms_0/118932.txt decompose linear_transforms_0/118932.txtdecomp
Command: mrregister /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/fodimage/123117_fod.mif initial_template.mif -force -mask1 /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/maskimage/123117mask.mif -affine_scale 0.3 -affine_niter 500 -affine_lmax 2 -type affine -datatype float32 -affine linear_transforms_0/123117.txt
Command: transformcalc linear_transforms_0/123117.txt decompose linear_transforms_0/123117.txtdecomp
Command: mrregister /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/fodimage/118730_fod.mif initial_template.mif -force -mask1 /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/maskimage/118730mask.mif -affine_scale 0.3 -affine_niter 500 -affine_lmax 2 -type affine -datatype float32 -affine linear_transforms_0/118730.txt
Command: transformcalc linear_transforms_0/118730.txt decompose linear_transforms_0/118730.txtdecomp
Command: transformcalc linear_transforms_0/123117.txt linear_transforms_0/118932.txt linear_transforms_0/118730.txt average linear_transform_average.txt -force -quiet
Command: transformcalc linear_transform_average.txt invert linear_transform_average_inv.txt -force -quiet
Command: mrtransform /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/fodimage/118932_fod.mif -template initial_template.mif -linear linear_transforms_0/118932.txt input_transformed/118932.mif -datatype float32 -force
Command: mrtransform /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/fodimage/123117_fod.mif -template initial_template.mif -linear linear_transforms_0/123117.txt input_transformed/123117.mif -datatype float32 -force
Command: mrtransform /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/fodimage/118730_fod.mif -template initial_template.mif -linear linear_transforms_0/118730.txt input_transformed/118730.mif -datatype float32 -force
Command: mrmath input_transformed/118932.mif input_transformed/118730.mif input_transformed/123117.mif mean linear_template0.mif -force
Command: mrregister /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/fodimage/118932_fod.mif linear_template0.mif -force -affine_init_matrix linear_transforms_0/118932.txt -mask1 /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/maskimage/118932mask.mif -affine_scale 0.4 -affine_niter 500 -affine_lmax 2 -type affine -datatype float32 -affine linear_transforms_1/118932.txt
Command: transformcalc linear_transforms_1/118932.txt decompose linear_transforms_1/118932.txtdecomp
Command: mrregister /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/fodimage/123117_fod.mif linear_template0.mif -force -affine_init_matrix linear_transforms_0/123117.txt -mask1 /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/maskimage/123117mask.mif -affine_scale 0.4 -affine_niter 500 -affine_lmax 2 -type affine -datatype float32 -affine linear_transforms_1/123117.txt
Command: transformcalc linear_transforms_1/123117.txt decompose linear_transforms_1/123117.txtdecomp
Command: mrregister /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/fodimage/118730_fod.mif linear_template0.mif -force -affine_init_matrix linear_transforms_0/118730.txt -mask1 /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/maskimage/118730mask.mif -affine_scale 0.4 -affine_niter 500 -affine_lmax 2 -type affine -datatype float32 -affine linear_transforms_1/118730.txt
Command: transformcalc linear_transforms_1/118730.txt decompose linear_transforms_1/118730.txtdecomp
Command: transformcalc linear_transforms_1/123117.txt linear_transforms_1/118932.txt linear_transforms_1/118730.txt average linear_transform_average.txt -force -quiet
Command: transformcalc linear_transform_average.txt invert linear_transform_average_inv.txt -force -quiet
Command: mrtransform /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/fodimage/118932_fod.mif -template linear_template0.mif -linear linear_transforms_1/118932.txt input_transformed/118932.mif -datatype float32 -force
Command: mrtransform /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/fodimage/123117_fod.mif -template linear_template0.mif -linear linear_transforms_1/123117.txt input_transformed/123117.mif -datatype float32 -force
Command: mrtransform /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/fodimage/118730_fod.mif -template linear_template0.mif -linear linear_transforms_1/118730.txt input_transformed/118730.mif -datatype float32 -force
Command: mrmath input_transformed/118932.mif input_transformed/118730.mif input_transformed/123117.mif mean linear_template1.mif -force
Command: mrregister /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/fodimage/118932_fod.mif linear_template1.mif -force -affine_init_matrix linear_transforms_1/118932.txt -mask1 /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/maskimage/118932mask.mif -affine_scale 0.6 -affine_niter 500 -affine_lmax 2 -type affine -datatype float32 -affine linear_transforms_2/118932.txt
Command: transformcalc linear_transforms_2/118932.txt decompose linear_transforms_2/118932.txtdecomp
Command: mrregister /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/fodimage/123117_fod.mif linear_template1.mif -force -affine_init_matrix linear_transforms_1/123117.txt -mask1 /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/maskimage/123117mask.mif -affine_scale 0.6 -affine_niter 500 -affine_lmax 2 -type affine -datatype float32 -affine linear_transforms_2/123117.txt
Command: transformcalc linear_transforms_2/123117.txt decompose linear_transforms_2/123117.txtdecomp
Command: mrregister /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/fodimage/118730_fod.mif linear_template1.mif -force -affine_init_matrix linear_transforms_1/118730.txt -mask1 /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/maskimage/118730mask.mif -affine_scale 0.6 -affine_niter 500 -affine_lmax 2 -type affine -datatype float32 -affine linear_transforms_2/118730.txt
Command: transformcalc linear_transforms_2/118730.txt decompose linear_transforms_2/118730.txtdecomp
Command: transformcalc linear_transforms_2/123117.txt linear_transforms_2/118932.txt linear_transforms_2/118730.txt average linear_transform_average.txt -force -quiet
Command: transformcalc linear_transform_average.txt invert linear_transform_average_inv.txt -force -quiet
Command: mrtransform /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/fodimage/118932_fod.mif -template linear_template1.mif -linear linear_transforms_2/118932.txt input_transformed/118932.mif -datatype float32 -force
Command: mrtransform /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/fodimage/123117_fod.mif -template linear_template1.mif -linear linear_transforms_2/123117.txt input_transformed/123117.mif -datatype float32 -force
Command: mrtransform /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/fodimage/118730_fod.mif -template linear_template1.mif -linear linear_transforms_2/118730.txt input_transformed/118730.mif -datatype float32 -force
Command: mrmath input_transformed/118932.mif input_transformed/118730.mif input_transformed/123117.mif mean linear_template2.mif -force
Command: mrregister /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/fodimage/118932_fod.mif linear_template2.mif -force -affine_init_matrix linear_transforms_2/118932.txt -mask1 /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/maskimage/118932mask.mif -affine_scale 0.8 -affine_niter 500 -affine_lmax 4 -type affine -datatype float32 -affine linear_transforms_3/118932.txt
population_template:
population_template: [ERROR] Command failed: mrregister /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/fodimage/118932_fod.mif linear_template2.mif -force -affine_init_matrix linear_transforms_2/118932.txt -mask1 /home/koushik/HCP_Data/12-08-16/output_normalised_dwi/maskimage/118932mask.mif -affine_scale 0.8 -affine_niter 500 -affine_lmax 4 -type affine -datatype float32 -affine linear_transforms_3/118932.txt
population_template: Output of failed command:
mrregister: [ERROR] Error allocating memory for scratch buffer
population_template: Changing back to original directory (/home/koushik/HCP_Data/12-08-16/output_normalised_dwi)
population_template: Deleting temporary directory /tmp/population_template-tmp-88C99P/