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October 12, 2021 02:26PM
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
Subject Author Posted

epi_b0_correct.py error

mjss October 12, 2021 02:26PM

Re: epi_b0_correct.py error

Daniel Glen October 12, 2021 04:32PM

Re: epi_b0_correct.py error

mjss October 13, 2021 01:20PM

Re: epi_b0_correct.py error

Daniel Glen October 13, 2021 05:17PM

Re: epi_b0_correct.py error

mjss October 13, 2021 08:48PM

Re: epi_b0_correct.py error

Daniel Glen October 14, 2021 05:53PM

Re: epi_b0_correct.py error

mjss October 15, 2021 10:47AM



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