GitHub - shanqing-cai/MRI_analysis: Scripts and programs for MRI data analysis

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Name		Name	Last commit message	Last commit date
Latest commit History 134 Commits
3dplots		3dplots
vistools		vistools
.gitignore		.gitignore
LICENSE		LICENSE
README.md		README.md
analyze_parc.py		analyze_parc.py
analyze_pt2_seedOnly_cmat.m		analyze_pt2_seedOnly_cmat.m
analyze_pt2_subcort_cvecs.m		analyze_pt2_subcort_cvecs.m
aparc12.py		aparc12.py
aparc12_FA_analysis.m		aparc12_FA_analysis.m
aparc12_based_fa_analysis_2.py		aparc12_based_fa_analysis_2.py
aparc12_cortical_rois.m		aparc12_cortical_rois.m
aparc12_diff_label_asymm.py		aparc12_diff_label_asymm.py
aparc12_oldVer.py		aparc12_oldVer.py
aparc12_probtrackx_2.py		aparc12_probtrackx_2.py
aparc12_probtrackx_cortical_connmat.py		aparc12_probtrackx_cortical_connmat.py
aparc12_probtrackx_subcortical_connvec.py		aparc12_probtrackx_subcortical_connvec.py
aparc12_surface_stats.py		aparc12_surface_stats.py
aparc12_volumetric_stats.py		aparc12_volumetric_stats.py
batch_seedOnly_ccaw_pt2.py		batch_seedOnly_ccaw_pt2.py
batch_seedOnly_cw_pt2.py		batch_seedOnly_cw_pt2.py
batch_tract_subcort_conn.py		batch_tract_subcort_conn.py
check_masks.py		check_masks.py
compare_cmats.m		compare_cmats.m
conn_mat_circle.py		conn_mat_circle.py
conn_mat_xls.m		conn_mat_xls.m
convert_dcm.py		convert_dcm.py
dtiprep.py		dtiprep.py
dtiprep_qc_xml.py		dtiprep_qc_xml.py
fa2surf_dtiprep.py		fa2surf_dtiprep.py
fill_aparc12_roi_fig.m		fill_aparc12_roi_fig.m
fsav_parc_centers.py		fsav_parc_centers.py
funcloc_demographic_stats.py		funcloc_demographic_stats.py
gen_aparc12_gm_diff_mask.py		gen_aparc12_gm_diff_mask.py
gen_bips_aparc12_time_series.py		gen_bips_aparc12_time_series.py
gen_ccMask.py		gen_ccMask.py
gen_tbss_aparc12_prob_map.py		gen_tbss_aparc12_prob_map.py
gen_tbss_mat_bgc.py		gen_tbss_mat_bgc.py
get_aparc12_cortical_rois.m		get_aparc12_cortical_rois.m
get_aparc12_roi_fig_coords.m		get_aparc12_roi_fig_coords.m
meta_bgComp_linCorr.m		meta_bgComp_linCorr.m
meta_bv_fa2.m		meta_bv_fa2.m
nbs_bct_sc.m		nbs_bct_sc.m
parc_stats.py		parc_stats.py
plot_elisa_speech_network.m		plot_elisa_speech_network.m
qced_dti_analysis.py		qced_dti_analysis.py
read_roi_data.m		read_roi_data.m
read_xml_labels.py		read_xml_labels.py
remove_dtiprep_bad_frames.py		remove_dtiprep_bad_frames.py
resting_roicorr_compare_aparc12.py		resting_roicorr_compare_aparc12.py
roi_name_match.m		roi_name_match.m
rotate_bvecs.py		rotate_bvecs.py
row_col_swap.py		row_col_swap.py
show_2d_mat.m		show_2d_mat.m
show_tract_regionSeg_3d.m		show_tract_regionSeg_3d.m
stutFL_2ndLevel_ROI_aparc12.m		stutFL_2ndLevel_ROI_aparc12.m
stutFL_gen_roi_timecourses_aparc12.m		stutFL_gen_roi_timecourses_aparc12.m
surf_FA_grpAnalysis_2.py		surf_FA_grpAnalysis_2.py
tbss_clusters.py		tbss_clusters.py
tbss_wm_atlas_stats.py		tbss_wm_atlas_stats.py
tract_seg.py		tract_seg.py
tract_seg_grp.m		tract_seg_grp.m
tract_subcort_conn.m		tract_subcort_conn.m
tract_subcort_conn.py		tract_subcort_conn.py
tract_subcort_grp_wta.py		tract_subcort_grp_wta.py
tracula_group_comp.m		tracula_group_comp.m
tracula_path_bv.m		tracula_path_bv.m
tracula_path_stats.m		tracula_path_stats.m
translate_roi_name.m		translate_roi_name.m
writeNodeGraphTheoryMeasTxt.m		writeNodeGraphTheoryMeasTxt.m
write_netw_component_txt.m		write_netw_component_txt.m

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In this repo are a bunch of scripts and programs I wrote for analyzing MRI (Structural, task fMRI, resting-state fMRI, and diffusion) data for various projects at MIT and BU.

Since I use FSL, FreeSurfer and sometime SPM for this kind of analysis, a lot of the scripts here will depend on those software packages.

Contact me at shanqing.cai@gmail.com if you have any questions.

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shanqing-cai/MRI_analysis

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