Skip to content

Commit 68c46d1

Browse files
committed
fix tbss_non_FA to match FSL's tbss_non_FA command
Here is the FSL command from their source code: "${FSLDIR}/bin/tbss_skeleton -i mean_FA -p $thresh mean_FA_skeleton_mask_dst ${FSLDIR}/data/standard/LowerCingulum_1mm all_FA all_${ALTIM}skeletonised -a all$ALTIM" where all_${ALTIM} in my example is all_RD. notice all_FA is in the placeholder for the 4d Data file under the -p option, and the -a all_RD is there too. here is what I changed in tbss.py to allow for this: see new inputnode, all_FA_file and see (maskgroup, projectfa, [('out_file', 'alt_data_file')]) step in tbss_non_fa.connect command. This is to get the -a option with the all_RD file.
1 parent 226ff40 commit 68c46d1

File tree

1 file changed

+6
-2
lines changed

1 file changed

+6
-2
lines changed

nipype/workflows/dmri/fsl/tbss.py

Lines changed: 6 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -504,6 +504,7 @@ def create_tbss_non_FA(name='tbss_non_FA'):
504504
>>> tbss_MD.inputs.inputnode.groupmask = './xxx'
505505
>>> tbss_MD.inputs.inputnode.meanfa_file = './xxx'
506506
>>> tbss_MD.inputs.inputnode.distance_map = []
507+
>>> tbss_MD.inputs.inputnode.all_FA_file = './xxx'
507508
508509
Inputs::
509510
@@ -513,6 +514,7 @@ def create_tbss_non_FA(name='tbss_non_FA'):
513514
inputnode.groupmask
514515
inputnode.meanfa_file
515516
inputnode.distance_map
517+
inputnode.all_FA_file
516518
517519
Outputs::
518520
@@ -526,7 +528,8 @@ def create_tbss_non_FA(name='tbss_non_FA'):
526528
'skeleton_thresh',
527529
'groupmask',
528530
'meanfa_file',
529-
'distance_map']),
531+
'distance_map',
532+
'all_FA_file']),
530533
name='inputnode')
531534

532535
# Apply the warpfield to the non FA image
@@ -560,10 +563,11 @@ def create_tbss_non_FA(name='tbss_non_FA'):
560563

561564
(inputnode, maskgroup, [('groupmask', 'in_file2')]),
562565

563-
(maskgroup, projectfa, [('out_file', 'data_file')]),
566+
(maskgroup, projectfa, [('out_file', 'alt_data_file')]),
564567
(inputnode, projectfa, [('skeleton_thresh', 'threshold'),
565568
("meanfa_file", "in_file"),
566569
("distance_map", "distance_map"),
570+
("all_FA_file", 'data_file')
567571
]),
568572
])
569573

0 commit comments

Comments
 (0)