nipype

nipype copied to clipboard

The function `affine_from_fsl_mat_file` is imported and used here: https://github.com/nipy/nipype/blob/f756b71117493caea093bac79d576207d8f96482/nipype/interfaces/mrtrix/convert.py#L196 However, this function was deleted in https://github.com/dipy/dipy/commit/a700df9805a5a626d4f33aa48d027d229d61042b#diff-24e3afc30f00cdbf9015dffb73ce1d2ab08ae582ebdc519b218361b5ff904e7e I'm not sure what happened to the functionality in dipy, I will try to...

koenhelwegen

Segmentation Fault using fsl.ExtractROI()

7

### Summary I am post-processing fMRI data that has already been run through fMRIPrep. I am trying to use `fsl.ExtractROI()`, but every time I run it, a segmentation fault occurs,...

butellyn

1deval AFNI

2

I was running a script that used 1deval from the afni package. Everytime it runs it gives me an error saying "-prefix = unknown command line option!" even though this...

Racer2055

[enhancement] ICC_rep_anova could be significantly faster than it is when running on images

4

### Summary ICC_rep_anova calculates ICC(3,1) on a table of subjects and repeated measures. Setting up the design matrix is far more computationally expensive than actually calculating ICC from the input...

bbfrederick

I'm using the plugin MultiProc plugin in my workflows and caching results are checked with multiprocessing for the standard nipype interfaces as expected. However when I create my own interface,...

s2334

### Summary The log file of `freesurfer.GLMFit()` / mri_glmfit is not part of `GLMFit().outputs`. In general, I like logfiles to be available, but in this case it's even neccessary to...

0nu

## Summary I added the option of using FDR correction (at the voxel level) and the option to choose between FWEc and FDRc for the clustersize correction (only FDRc was...

ldeangelisphys

ENH: interface for whitestripe normalization

8

## Summary A processing pipeline for MS usually follows these preprocessing steps: 1. N4 correction 2. Registration 3. Skull stripping 4. Intensity normalization nipype provides interfaces for tools for all...

Terf

### Summary I am running the spm interface and trying to calculate the vdm using the FieldMap function. I have given the correct inputs and the error message tells me...

kristian1801

ants.BrainExtraction.run() [ index out of range due to version output in ants has changes]

5

### Summary I am unable to execute bet.run() after the following lines: ``` from nipype.interfaces.ants.segmentation import BrainExtraction import os import sys bet = BrainExtraction() bet.inputs.dimension = 3 bet.inputs.anatomical_image = sstrip_in_fname...

rperea14