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Resample images to desired resolution #85

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merged 9 commits into from
Nov 15, 2020
Merged

Resample images to desired resolution #85

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49d5adf
resample t2w images to 1x1x1mm
PaulBautin Oct 16, 2020
8e3012e
resample t2w images manual segmentation to 1x1x1mm
PaulBautin Oct 16, 2020
0322ce6
update config_sct_run_batch for compute canada
PaulBautin Oct 16, 2020
d5a9d2e
Merge branch 'master' of https://github.com/sct-pipeline/csa-atrophy …
PaulBautin Nov 10, 2020
482a704
- pull from master
PaulBautin Nov 10, 2020
e260200
- remove local config
PaulBautin Nov 10, 2020
6104cf5
- rename config_script_t2.yml config_script.yml
PaulBautin Nov 15, 2020
1c3c906
- update config_sct_run_batch.yml
PaulBautin Nov 15, 2020
bb4e11f
Improve config_script.yml comments
PaulBautin Nov 15, 2020
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2 changes: 1 addition & 1 deletion config_sct_run_batch.yml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
# config file for sct_run_batch
path_data: /scratch/pabaua/data-multi-subject-p
path_output: /scratch/pabaua/results_csa_t2_2
path_output: /scratch/pabaua/results_csa_t2
script: /home/pabaua/csa-atrophy/process_data.sh
script_args: /home/pabaua/csa-atrophy/config_script_t2.yml
jobs: -1
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7 changes: 4 additions & 3 deletions process_data.sh
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Expand Up @@ -78,10 +78,11 @@ segment_if_does_not_exist(){
local qc=$3
# Update global variable with segmentation file name
FILESEG="${file}_seg"
FILESEGMANUAL="${path_derivatives}/${FILESEG}-manual.nii.gz"
FILESEGMANUAL="${path_derivatives}/${FILESEG}-manual"
if [ -e $FILESEGMANUAL ]; then
echo "Found! Using manual segmentation."
rsync -avzh $FILESEGMANUAL ${FILESEG}.nii.gz
sct_resample -i ${FILESEGMANUAL}.nii.gz -mm $interp -x nn -o ${FILESEGMANUAL}_r.nii.gz
rsync -avzh ${FILESEGMANUAL}_r.nii.gz ${FILESEG}.nii.gz
sct_qc -i ${file}.nii.gz -s ${FILESEG}.nii.gz -p sct_deepseg_sc $qc
else
# Segment spinal cord
Expand Down Expand Up @@ -113,7 +114,7 @@ cd anat
# Reorient to RPI and resample file
if [ $contrast == "t2" ]; then
contrast_str="T2w"
interp="0.8x0.8x0.8"
interp="1x1x1"
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i was suggesting to resample to 1mm iso only for "checking" the effect of this resampling, not for the "stable" release of the pipeline

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Sorry for the confusion, i was thinking of re-running this PR on Compute Canada to put results in the article's supplementary material (It could partly explain differences observed between t1 and t2 results). @jcohenadad, what are your thoughts on that?

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sounds good. IN fact, if we explore the effect of resampling, we probably want to also try other resamplings, e.g. 1.2mm iso

elif [ $contrast == "t1" ]; then
contrast_str="T1w"
interp="1x1x1"
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