From 471025aec5e082f6571f3dfb771556d253c38b44 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 13 Aug 2024 13:09:18 -0400
Subject: [PATCH] Update io_spec.json

---
 qsiprep/data/io_spec.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/qsiprep/data/io_spec.json b/qsiprep/data/io_spec.json
index 5313d734..037f1990 100644
--- a/qsiprep/data/io_spec.json
+++ b/qsiprep/data/io_spec.json
@@ -14,13 +14,13 @@
     "default_path_patterns": [
       "[desc-{desc}]_{suffix<qc>}{extension<.json>|.json}",
       "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_space-{space}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|dseg|inplaneT[12]|angio|imtcoreg>}.{extension<nii|nii.gz|json>|nii.gz}",
-      "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}.{extension<txt|h5>}",
+      "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}.{extension<txt|h5|mat>}",
       "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_space-{space}]_desc-{desc}_{suffix<mask>|mask}.{extension<nii|nii.gz|json>|nii.gz}",
       "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_space-{space}]_label-{label}[_desc-{desc}]_{suffix<probseg>|probseg}.{extension<nii|nii.gz|json>|nii.gz}",
       "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_space-{space}][_desc-{desc}]_{suffix<dwiref>|dwiref}.{extension<nii|nii.gz|json>|nii.gz}",
       "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_space-{space}][_desc-{desc}]_{suffix<mask>|mask}.{extension<nii|nii.gz|json>|nii.gz}",
       "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_space-{space}][_desc-{desc}]_{suffix<dwi>|dwi}.{extension<nii|nii.gz|b|b_table.txt|bval|bvec|json>|nii.gz}",
-      "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_space-{space}][_desc-{desc}]_{suffix<confounds|dwi>|confounds}.{extension<tsv|csv|json>|tsv}",
+      "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_space-{space}][_desc-{desc}]_{suffix<confounds|dwi|topupcsv>|confounds}.{extension<tsv|csv|json>|tsv}",
       "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_space-{space}][_desc-{desc}]_{suffix<bvecs|cnr>|bvecs}.{extension<nii|nii.gz|json>|nii.gz}",
       "sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_space-{space}][_desc-{desc}]_{suffix<fmapreg|fmapregvsm|b0ref>|fmapreg}.{extension<nii|nii.gz|json>|nii.gz}",
       "sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_space-{space}][_desc-{desc}]_{suffix<biascorr|denoising|unringing>|biascorr}.{extension<nii|nii.gz|json>|nii.gz}",