fsl_anatare supported by/available in
nipype, thus you could just "recreate" the pipeline there. However, I'm not sure if that's more feasible than using
functioninterface. I would assume that someone also already looked at that!?
Salutations. Attempting to use
nipype.interfaces.slicer.BRAINSFit in a pipeline, but running into
No command "BRAINSFit" found errors. I have the latest version of Slicer installed at
/opt/Slicer and manually appended that directory and
/opt/Slicer/bin to my path. BRAINSFit runs correctly under bash:
Slicer --launch BRAINSFit
but won't work in nipype. Any ideas?
Traceback (most recent call last):
File "/var/lib/condor/execute/dir_25201/condor_exec.exe", line 355, in <module>
File "/var/lib/condor/execute/dir_25201/condor_exec.exe", line 351, in main
File "/var/lib/condor/execute/dir_25201/condor_exec.exe", line 220, in asl_2d_flirt
File "/usr/local/lib/python3.6/dist-packages/nipype/interfaces/base/core.py", line 434, in run
runtime = self._run_interface(runtime)
File "/usr/local/lib/python3.6/dist-packages/nipype/interfaces/base/core.py", line 829, in _run_interface
File "/usr/local/lib/python3.6/dist-packages/nipype/interfaces/base/core.py", line 760, in raise_exception
flirt -in /mnt/ss_rhb1/s3-mri-general/AFRL-Single_Exposure/processed_data/AE001/SESSION_02/AE001_SESS02_ASL_RESTING.nii.gz -ref /mnt/ss_rhb1/scratch/AFRL-Single_Exposure/processed_data/AE001/SESSION_02/AE001_SESS02_AXIAL_T1_brain.nii.gz -out /mnt/ss_rhb1/scratch/AFRL-Single_Exposure/processed_data/AE001/SESSION_02/AE001_SESS02_ASL_RESTING_highres.nii.gz -omat /mnt/ss_rhb1/scratch/AFRL-Single_Exposure/processed_data/AE001/SESSION_02/AE001_SESS02_ASL_RESTING.reg/tmp.mat -applyxfm -init /mnt/ss_rhb1/scratch/AFRL-Single_Exposure/processed_data/AE001/SESSION_02/AE001_SESS02_ASL_RESTING.reg/example_asl2highres.mat
Return code: 137
fsl.FNIRTdoesn't input in the following block (
fsl.ConvertWarp). Does anyone know if there is any specific options i have to set in order to obtain as output the field_file from FNIRT?