Hi there, thanks for your time. Looking to wrap https://surfer.nmr.mgh.harvard.edu/fswiki/mri_cvs_register. It is 1 line in bash, with the only required flag being subject ID -freesurfer does the rest. Is there any quick way to add this to a work flow without creating a whole interface?
@ramroomh you could use the function interface for that: https://miykael.github.io/nipype_tutorial/notebooks/basic_function_interface.html
@rpbaptista the available
https://nipype.readthedocs.io/en/latest/api/generated/nipype.interfaces.fsl.html
FSL functions are here:https://nipype.readthedocs.io/en/latest/api/generated/nipype.interfaces.fsl.html
workflows that used to be available via
nipype.workflows were migrated to NiFlows and their continued use is discouraged: https://nipype.readthedocs.io/en/latest/interfaces.html#workflows
you could try the
FSLCommand interface: https://nipype.readthedocs.io/en/latest/api/generated/nipype.interfaces.fsl.base.html#fslcommand
AFAIK all the functions in
fsl_anat are 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 FSLCommand or the function interface. I would assume that someone also already looked at that!?
@ramroomh and @rpbaptista, it would be great if you could post
nipype related questions on https://neurostars.org/ to increase FAIR-ness and reach more people
i cant find trans.mat
Hi, I hope this is the correct place to ask simple questions.
How exactly do you handle Nodes that take in lists as inputs within a workflow? Specifically, I'm trying to append the apply_to_files property for the spm.normalization interface from the output of two different nodes.
2 replies
Hi, I hope this is a good place to ask for this question: I'm trying to run a simple Finite Impulse Response model in FSL using Nipype. The beginner's guide makes it seem like it is very possible to run this analysis, but I haven't found a good example of exactly how to do it. I have tried to set the bases function as {'none':None} or {'none':{'none':None}} or {'none':{}}, but they gave the error of saying the EV file (in 3-column format) does not have enough data. Is there an example to set up the model that resembles the "FIR basis functions" convolution setting in FSL GUI? Thanks for any inputs!!
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?
4 replies
Hi, So I am using the SpaceTimeRealigner and was wondering if I can save the motion it has deducted and then use it to remove physiological noise? Also, every 10 frames, in my experiment, subject was pressing a button. I do have exact timing of those button presses as well, is there a good way to regress that out as well?
No such file or directory '/scratch/06953/jes6785/CPT/output/preproc_ses2_scan1/mcflirt/20200207.005.2_func_task-CPTPNND_run-01_dir-AP_20200207181451_15_brain_mcf_mean_reg.nii.gz' for output 'mean_img' of a MCFLIRT interface
when trying to output the mean image
seen this discussion above
hey i am trying to learn how to use nipype for a project i have in my university. It is something that is not clear to me for the nipype package. The nipype package gives you the capabilty to visualize image data and/or recontruct them into 3d visualization? or is it only to process the image data?
hi Guys, i am new to nipype and trying to transform my lab's processing pipeline to nipype workflow. so far i have been able to grab my BIDS validated dataset and axialize my mprage scan by wrapping afni commandline (fat_proc_axialize_anat) and use it's output as a reference to coregister t2 and flair scans. in the coregistration process i use MapNode to perform afni 3dAllineate . my next step is to perform freesurfer recon-all command and i want to use my coreigsitered t2 (as T2_file) input along side my axialized mprage( T1_files). the problem is the recon-all node does not recognize my t2 and throws an error. this is how i am connecting my node reconall = pe.Node(interface=ReconAll(),name="reconall")
reconall.inputs.subjects_dir = freesurfer_dir
reconall.inputs.use_T2 = True
reconall.inputs.directive = 'all'
reconall.inputs.subjects_dir = freesurfer_dir
reconall.inputs.use_T2 = True
reconall.inputs.directive = 'all'
pipeline.connect(subj_infosource, 'subject_id', reconall, 'subject_id')
pipeline.connect(axialized, 'out_file', reconall, 'T1_files')
pipeline.connect(allineate1, 'out_file', reconall, 'T2_file')
pipeline.connect(axialized, 'out_file', reconall, 'T1_files')
pipeline.connect(allineate1, 'out_file', reconall, 'T2_file')
is there anything wrong with the way i am connecting the nodes? does the output of MapNode have a specific format that cant be called like a regular node output?
any suggestion would be greatly apprecited