Chris Gorgolewski chrisgorgo
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| import nipype.pipeline.engine as pe | |
| from nipype.interfaces.utility import Function | |
| def Hello(): | |
| import os | |
| from nipype import logging | |
| iflogger = logging.getLogger('interface') | |
| message = "Hello " | |
| iflogger.info(message) | |
| return message |
chrisgorgo
/ qsm_registration.py
Last active
August 29, 2015 14:07
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| __author__ = 'lampe' | |
| """ | |
| ============================================= | |
| 1. Registration of T1 to QSM | |
| 2. Apply the xfm to the masks that have been created with the T1, so they are in QSM space | |
| ============================================= | |
| Packages and Data Setup | |
| ======================= | |
| Import necessary modules from nipype. |
chrisgorgo
/ asdf
Created
July 17, 2014 15:09
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| from nilearn.plotting.img_plotting import plot_img | |
| import pylab as plt | |
| import nibabel as nb | |
| import numpy as np | |
| nii = nb.load("/home/raid3/gorgolewski/Downloads/fmap_field_masked.nii.gz") | |
| print nii.get_affine() | |
| scaling_affine = np.array([[-3, 0, 0, 0], |
chrisgorgo
/ gist:d3596f1615d29d75ad65
Created
July 7, 2014 12:35
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| In [4]: !cat /tmp/stefan.py | |
| out_name = "/tmp/bla" | |
| out = open(out_name, 'w') | |
| out.write("asdfasdfasdf\n") #out_str) out.close | |
| out = open(out_name, 'w') | |
| out.write("asdfasdfasdf\n") | |
| out.close() | |
| In [5]: %run /tmp/stefan.py |
chrisgorgo
/ getmipav
Created
June 30, 2014 16:45
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| (devel)adenauer:~$ cd /tmp/ | |
| (devel)adenauer:/tmp$ git clone https://github.com/nipy/nipype.git | |
| Cloning into 'nipype'... | |
| remote: Reusing existing pack: 36611, done. | |
| remote: Total 36611 (delta 0), reused 0 (delta 0) | |
| Receiving objects: 100% (36611/36611), 17.80 MiB | 1.13 MiB/s, done. | |
| Resolving deltas: 100% (22184/22184), done. | |
| (devel)adenauer:/tmp$ cd nipype/ | |
| (devel)adenauer:/tmp/nipype$ git remote | |
| origin |
chrisgorgo
/ get_tr_and_sliceorder_from_dicoms.py
Last active
December 30, 2015 11:19
A little function to get TR and slicetime order from dicoms
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| def get_tr_and_sliceorder(dicom_files, convention="SPM"): | |
| import numpy as np | |
| import dcmstack, dicom | |
| my_stack = dcmstack.DicomStack() | |
| for src_path in dicom_files: | |
| src_dcm = dicom.read_file(src_path) | |
| my_stack.add_dcm(src_dcm) | |
| nii_wrp = my_stack.to_nifti_wrapper() | |
| if convention == "french": |
chrisgorgo
/ partial_correlations.py
Created
June 27, 2013 14:40
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| def partial_correlation_via_inverse(X): | |
| model = GraphLassoCV() | |
| model.fit(X) | |
| prec_ = model.precision_ | |
| return -cov2corr( model.precision_ ) ) | |
| def cov2corr( A ): | |
| """ | |
| covariance matrix to correlation matrix. | |
| """ |
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| #merge maps - condition 1 | |
| fslmerge -t "/scr/adenauer1/workingdir/rs_analysis_group/main_workflow/merge_conn_maps_6_58_0/roi_6_58_0_masked_merged.nii.gz" /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_13261.8d/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_14390.d3/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_14446.fb/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_16090.c9/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_12184.55/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Project/results/volumes/normalized_z_scored_corr_map/_subject_id_15070.25/_roi_6.58.0/_fwhm_5/roi_6_58_0_masked.nii /scr/namibia1/baird/MPI_Projec |
chrisgorgo
/ gist:3795359
Created
September 27, 2012 17:46
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| Process: Python [6691] | |
| Path: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python | |
| Identifier: Python | |
| Version: 2.7.3 (2.7.3) | |
| Code Type: X86-64 (Native) | |
| Parent Process: Python [6670] | |
| User ID: 501 | |
| Date/Time: 2012-09-27 19:40:00.297 +0200 | |
| OS Version: Mac OS X 10.8.2 (12C54) |
chrisgorgo
/ scrip.py
Created
September 25, 2012 18:23
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| def plot_coregistration(): | |
| anat_file = "/Users/filo/data/rs_pipeline/GSDT/anat/mprage.nii" | |
| func_file = "/Users/filo/workdir/rs_preprocessing/preprocess/preproc/take_mean_art/weighted_mean/corr_rest_roi_dtype.nii.gz" | |
| affine_file = '/Users/filo/workdir/rs_preprocessing/preprocess/preproc/getmask/register/mapflow/_register0/corr_rest_roi_dtype_bbreg_recon_all.mat' | |
| from nipy.labs import viz | |
| from nipy.labs.viz_tools import anat_cache | |
| import nibabel as nb | |
| anat = nb.load(anat_file).get_data() | |
| anat_affine = nb.load(anat_file).get_affine() |