fix: correct the position of the echo tag

BrkRaw · Jun 22, 2024 · 894eaa2 · 894eaa2
1 parent 6a02a07
commit 894eaa2
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Showing 2 changed files with 5 additions and 1 deletion.
diff --git a/brkraw/lib/utils.py b/brkraw/lib/utils.py
@@ -404,9 +404,11 @@ def build_bids_json(dset, row, fname, json_path, slope=False, offset=False):
         crop = None
     if dset.is_multi_echo(row.ScanID, row.RecoID):  # multi_echo
         nii_objs = dset.get_niftiobj(row.ScanID, row.RecoID, crop=crop, slope=slope, offset=offset)
+        n_echo = len(nii_objs)
+        n_digit = len(str(n_echo))
         for echo, nii in enumerate(nii_objs):
             # caught a bug here for multiple echo, changed fname to currentFileName
-            currentFileName = '{}_echo-{}_{}'.format(fname, echo + 1, row.modality)
+            currentFileName = fname.replace('echo.index',str(echo + 1).zfill(n_digit))
             output_path = os.path.join(row.Dir, currentFileName)
             nii.to_filename('{}.nii.gz'.format(output_path))
             if json_path:

diff --git a/brkraw/scripts/brkraw.py b/brkraw/scripts/brkraw.py
@@ -705,6 +705,8 @@ def completeFieldsCreateFolders (df, filtered_dset, dset, multi_session, root_pa
         if pd.notnull(row.run):
             if bids_validation(df, i, 'run', row.run, 2):
                 fname = '{}_run-{}'.format(fname, row.run)
+        if dset.is_multi_echo(row.ScanID, row.RecoID):
+            fname = '{}_echo-echo.index'.format(fname)
         if pd.notnull(row.flip):
             if bids_validation(df, i, 'flip', row.flip, 2):
                 fname = '{}_flip-{}'.format(fname, row.flip)