Resample images to desired resolution #85
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@@ -82,10 +82,11 @@ segment_if_does_not_exist(){ | |
| local qc=$3 | ||
| # Update global variable with segmentation file name | ||
| FILESEG="${file}_seg" | ||
| FILESEGMANUAL="${path_derivatives}/${FILESEG}-manual" | ||
| if [ -e $FILESEGMANUAL ]; then | ||
| echo "Found! Using manual segmentation." | ||
| sct_resample -i ${FILESEGMANUAL}.nii.gz -mm $interp -x nn -o ${FILESEGMANUAL}_r.nii.gz | ||
| rsync -avzh ${FILESEGMANUAL}.nii.gz ${FILESEG}.nii.gz | ||
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There was a problem hiding this comment. problem here, the resampled There was a problem hiding this comment. Suggestion was implemented in commit: 482a704 |
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| sct_qc -i ${file}.nii.gz -s ${FILESEG}.nii.gz -p sct_deepseg_sc $qc | ||
| else | ||
| # Segment spinal cord | ||
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@@ -117,7 +118,7 @@ cd anat | |
| # Reorient to RPI and resample file | ||
| if [ $contrast == "t2" ]; then | ||
| contrast_str="T2w" | ||
| interp="1x1x1" | ||
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There was a problem hiding this comment. i was suggesting to resample to 1mm iso only for "checking" the effect of this resampling, not for the "stable" release of the pipeline There was a problem hiding this comment. 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? There was a problem hiding this comment. sounds good. IN fact, if we explore the effect of resampling, we probably want to also try other resamplings, e.g. 1.2mm iso |
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| elif [ $contrast == "t1" ]; then | ||
| contrast_str="T1w" | ||
| interp="1x1x1" | ||
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why these changes? they are local (ie specific to your config)
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It is to keep track of the configs i used when i run jobs on compute canada. I will not merge this into master. In the future i will fork the repo for these kinds of PRs.