Hello AFNI experts,
I am attempting to run epi_b0_correct.py to perform spatial distortion correction of my EPI dataset but I am running into some issues. I am attempting to execute epi_b0_correct.py following as per Example 1 in the documentation. My frequency dataset (fieldmap volume in rad/s) was created using FSL's FUGUE program.
Here is my command:
epi_b0_correct.py \
-epi_pe_echo_sp 0.2 \
-epi_pe_dir PA \
-in_freq fieldmap_rads_regularised.nii.gz \
-in_mask pm2_brain_mask.nii.gz \
-in_magn pm2.nii \
-in_epi eWM.nii \
-prefix b0_corr
I receive the following error:
ERROR: can't have freq dset datum type be 'float' and then
use (def) 'mode' to recenter its values;
see -do_recenter_freq for recentering in other ways
(like 'median'?).
I then tried to addressing this by adding the following option: -do_recenter_freq MEAN
However, I received the following output with another error:
++ EPI and phase have same obliq? True
++ Using PE effective echo spacing to calc BWPP: 0.04901960784313725
++ ================== Start B0 correction ==================
Ver : 2.63
Date : June 3, 2020
++ -------------------- copy inputs -----------------------
wdir: ./__work_B0_corr_oN6KeBMs5PG
+++ Command Echo:
3dcalc -a fieldmap_rads_regularised.nii.gz -expr a -prefix ./__work_B0_corr_oN6KeBMs5PG/fieldmap_rads_regularised.nii.gz
++ 3dcalc: AFNI version=AFNI_21.2.06 (Sep 1 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__work_B0_corr_oN6KeBMs5PG/fieldmap_rads_regularised.nii.gz
+++ Command Echo:
3dcalc -a eWM.nii -expr a -prefix ./__work_B0_corr_oN6KeBMs5PG/eWM.nii
++ 3dcalc: AFNI version=AFNI_21.2.06 (Sep 1 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__work_B0_corr_oN6KeBMs5PG/eWM.nii
+++ Command Echo:
3dcalc -a pm2.nii -expr a -prefix ./__work_B0_corr_oN6KeBMs5PG/pm2.nii
++ 3dcalc: AFNI version=AFNI_21.2.06 (Sep 1 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__work_B0_corr_oN6KeBMs5PG/pm2.nii
+++ Command Echo:
3dcalc -a pm2_brain_mask.nii.gz -expr a -prefix ./__work_B0_corr_oN6KeBMs5PG/pm2_brain_mask.nii.gz
++ 3dcalc: AFNI version=AFNI_21.2.06 (Sep 1 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__work_B0_corr_oN6KeBMs5PG/pm2_brain_mask.nii.gz
++ -------------------- calc B0 corr -----------------------
freq dset: fieldmap_rads_regularised.nii.gz
2381.124618
+++ Command Echo:
3dcalc -a fieldmap_rads_regularised.nii.gz -b pm2_brain_mask.nii.gz -expr (1.0/6.2831853)*(a-(2381.124618))/0.04901960784313725*2.5098*b -datum float -prefix bc_00.nii.gz
++ 3dcalc: AFNI version=AFNI_21.2.06 (Sep 1 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./bc_00.nii.gz
Program 3dmerge
+++ Command Echo:
3dmerge -doall -1blur_sigma 9 -datum float -prefix bc_01_smoo.nii.gz bc_00.nii.gz
3dmerge: edit and combine 3D datasets, by RW Cox
++ editing input dataset in memory (2.5 MB)
.
++ 3dmerge: AFNI version=AFNI_21.2.06 (Sep 1 2021) [64-bit]
++ default -1dindex = 0
++ default -1tindex = 1
-- Wrote edited dataset: ./bc_01_smoo.nii.gz
20.0 -1250.262695 40.0 -57.175697 60.0 584.526978 80.0 1263.749023 100.0 4331.105957
++ 3dWarp: AFNI version=AFNI_21.2.06 (Sep 1 2021) [64-bit]
++ Authored by: RW Cox
** ERROR executing this command in the shell:
3dNwarpApply -echo_edu -warp "mat_obl_epi_freq.aff12.1D PA:1.0:bc_01_smoo.nii.gz" -master eWM.nii -ainterp quintic -prefix bc_02_smoo_wrpd2epi.nii.gz -source bc_01_smoo.nii.gz
** Exit status : 1
** Standard error : ++ 3dNwarpApply: AFNI version=AFNI_21.2.06 (Sep 1 2021) [64-bit]
++ Authored by: Zhark the Warped
++ -master dataset is 'eWM.nii'
++ opened source dataset 'bc_01_smoo.nii.gz'
++ Processing -nwarp ** FATAL ERROR: malloc (out of memory) error for dataset sub-brick #0
** Program compile date = Sep 1 2021
Any guidance on how to address this error is much appreciated.
Thank you!
Michael
