Working on mrtrix code

README.md

@@ -1,6 +1,6 @@
 ## Vistasoft
 
-This is the main software repository of the [Vista lab](http://vistalab.stanford.edu) at [Stanford University](http://stanford.edu). It contains Matlab code to perform a variety of analysis on MRI data, including functional MRI and diffusion MRI.
+VISTASOFT is the main software repository of the [Vista lab](http://vistalab.stanford.edu) at [Stanford University](http://stanford.edu). It contains Matlab code to perform a variety of analysis on MRI data, including functional MRI and diffusion MRI.
 
 It has the following modules:
 
@@ -22,7 +22,7 @@ External dependencies:
 - Matlab (2009 or newer)
 - SPM8
 
-For documentation, please visit the [lab wiki](http://vistalab.stanford.edu/wiki).
+For documentation, please visit the [VISTA lab wiki](http://vistalab.stanford.edu/wiki).
 
 
 For help with the new mrInit intialization method, please see the [Initialization Page](http://white.stanford.edu/newlm/index.php/Initialization#mrInit).

external/camino/camAlignImageToDTI.m

@@ -9,8 +9,8 @@ function camAlignImageToDTI(dti_ref_filename,high_res_filename,output_filename,p
 
 
 % Experiment with xform
-ni_src = readFileNifti(high_res_filename);
-ni_ref = readFileNifti(dti_ref_filename);
+ni_src = niftiRead(high_res_filename);
+ni_ref = niftiRead(dti_ref_filename);
 
 ref_dim = ni_ref.dim(1:3);
 ref_pixdim = ni_ref.pixdim(1:3);
@@ -38,4 +38,4 @@ function camAlignImageToDTI(dti_ref_filename,high_res_filename,output_filename,p
 % write
 dtiWriteNiftiWrapper(new_data, xform, output_filename);
 
-return
+return

external/camino/camCreateHARDIFitScript.m

@@ -18,7 +18,7 @@ function camCreateHARDIFitScript(scr_modelfit_filename,scr_after_modelfit_filena
     bgthresh = 200;
 end
 % Volumetric information
-raw = readFileNifti(raw_filename);
+raw = niftiRead(raw_filename);
 vol_dim = raw.dim;
 xd = vol_dim(1);
 yd = vol_dim(2);

external/camino/camFA.m

@@ -46,7 +46,7 @@ function camFA(dtfit_filename, fa_filename, raw_nifti_filename)
     display(cmd);
     system(cmd,'-echo');
 
-    raw = readFileNifti(raw_nifti_filename);
+    raw = niftiRead(raw_nifti_filename);
 
     camVoxel2Image( fa_bdouble_filename, fa_nifti_filename, 'double', ...
                     raw.qto_xyz, 1, raw.dim(1:3) );

external/camino/camTrackProjectomeCandidates.m

@@ -33,7 +33,7 @@ function camTrackProjectomeCandidates(cdb_filename,step_size,min_track_length,pd
 
     if ~notDefined('ends_filename')
 
-        ends = readFileNifti(ends_filename);
+        ends = niftiRead(ends_filename);
 
         if max(ends.data(:)>1)
             cmd3 = sprintf('procstreamlines -inputfile %s -mintractlength %f -noresample -endpointfile %s -outputfile %s',t2_filename, min_track_length, ends_filename, cdb_filename);

external/camino/cam_fix_header.m

@@ -5,8 +5,8 @@ function cam_fix_header(file_to_fix,file_to_src,file_out)
 end
 
 %% Load image files
-ni_fix = readFileNifti(file_to_fix);
-ni_src = readFileNifti(file_to_src);
+ni_fix = niftiRead(file_to_fix);
+ni_src = niftiRead(file_to_src);
 
 %% Fix image header
-dtiWriteNiftiWrapper(ni_fix.data, ni_src.qto_xyz, file_out);
+dtiWriteNiftiWrapper(ni_fix.data, ni_src.qto_xyz, file_out);

external/camino/s_cam_compute_track_projections.m

@@ -2,7 +2,7 @@
 s_cam_definitions;
 
 %% Load image for pathway xforms
-ni_seg = readFileNifti(fullfile(mask_dir,seg_filename));
+ni_seg = niftiRead(fullfile(mask_dir,seg_filename));
 % Calc xform from camino space to acpc space
 xform = ni_seg.qto_xyz;
 xform(1:3,1:3) = eye(3);
@@ -16,26 +16,26 @@
 % Needs to be in comparison to how else the fiber is connected
 fiber_cthresh = 0;
 % Gray Matter
-ni_gm = readFileNifti(fullfile(mask_dir,'gm.nii.gz'));
+ni_gm = niftiRead(fullfile(mask_dir,'gm.nii.gz'));
 num_gm_vox = sum(ni_gm.data(:)>0);
 num_fibers_gen = num_gm_vox * 10;
 % Eccentricity
-ni_ecc = readFileNifti(fullfile(mask_dir,'ecc_var_0.1.nii.gz'));
+ni_ecc = niftiRead(fullfile(mask_dir,'ecc_var_0.1.nii.gz'));
 ni_ecc.data(ni_gm.data==0) = 0;
 ecc_vox = ni_ecc.data(ni_ecc.data>0);
 num_ret_vox = numel(ecc_vox);
 ratio_ret_gm = num_ret_vox / num_gm_vox;
 % ROIs
-ni_roi = readFileNifti(fullfile(mask_dir,'rois.nii.gz'));
+ni_roi = niftiRead(fullfile(mask_dir,'rois.nii.gz'));
 ni_roi.data(ni_gm.data==0) = 0;
 roi_vox = ni_roi.data(ni_roi.data>0);
 num_roi_vox = numel(roi_vox);
 ratio_roi_gm = num_roi_vox / num_gm_vox;
 
 %% Occipital exiting connections
 % Considering eccentricity
-ni_fiber_gm_exit = readFileNifti(fullfile(camino_dir,'tracts_mesd_gm_exit_1cm_ends.nii.gz'));
-%ni_fiber_gm = readFileNifti(fullfile(acm_dir,'tracts_pico_gm_1cm_acm_sc.nii.gz'));
+ni_fiber_gm_exit = niftiRead(fullfile(camino_dir,'tracts_mesd_gm_exit_1cm_ends.nii.gz'));
+%ni_fiber_gm = niftiRead(fullfile(acm_dir,'tracts_pico_gm_1cm_acm_sc.nii.gz'));
 num_gm_exit_vox = sum(ni_fiber_gm_exit.data(:)>fiber_cthresh & ni_gm.data(:)>0); 
 ecc_exit_vox = ni_ecc.data(ni_fiber_gm_exit.data>fiber_cthresh & ni_ecc.data>0);
 num_ret_exit_vox = numel(ecc_exit_vox);
@@ -75,8 +75,8 @@
 dtiWriteNiftiWrapper(fdImg, xform_img_to_acpc, fullfile(tract_dir,[file_root '.nii.gz']));
 
 % Some voxel comparisons
-ni_a = readFileNifti(fullfile(camino_dir,'tracts_pico_gm_1cm_ends.nii.gz'));
-ni_e = readFileNifti(fullfile(camino_dir,'tracts_mesd_gm_exit_1cm_ends.nii.gz'));
+ni_a = niftiRead(fullfile(camino_dir,'tracts_pico_gm_1cm_ends.nii.gz'));
+ni_e = niftiRead(fullfile(camino_dir,'tracts_mesd_gm_exit_1cm_ends.nii.gz'));
 a_vox = ni_a.data(ni_a.data>0);
 e_vox = ni_e.data(ni_a.data>0);
 figure, plot(a_vox,e_vox,'.');

external/camino/s_cam_generate_tracking_masks.m

@@ -14,10 +14,10 @@
 end
 
 %% Load all reinterpolated data
-ni_seg = readFileNifti(fullfile(mask_dir,seg_filename));
-ni_var = readFileNifti(fullfile(mask_dir,var_map_filename));
-ni_ecc = readFileNifti(fullfile(mask_dir,ecc_map_filename));
-ni_rois = readFileNifti(fullfile(mask_dir,roi_map_filename));
+ni_seg = niftiRead(fullfile(mask_dir,seg_filename));
+ni_var = niftiRead(fullfile(mask_dir,var_map_filename));
+ni_ecc = niftiRead(fullfile(mask_dir,ecc_map_filename));
+ni_rois = niftiRead(fullfile(mask_dir,roi_map_filename));
 
 %% Gray Matter Mask
 % RH
@@ -102,7 +102,7 @@
 % RH
 ni_occ = ni_seg;
 ni_occ.fname = fullfile(mask_dir,'occ_rh_mask.nii.gz');
-ni_gm = readFileNifti(fullfile(mask_dir,'gm_rh.nii.gz'));
+ni_gm = niftiRead(fullfile(mask_dir,'gm_rh.nii.gz'));
 % Grab only right hemisphere GM and WM
 ni_occ.data(ni_seg.data~=6 & ni_seg.data~=4) = 0;
 ni_occ.data(ni_occ.data>0) = 1;
@@ -116,7 +116,7 @@
 % LH
 ni_occ = ni_seg;
 ni_occ.fname = fullfile(mask_dir,'occ_lh_mask.nii.gz');
-ni_gm = readFileNifti(fullfile(mask_dir,'gm_lh.nii.gz'));
+ni_gm = niftiRead(fullfile(mask_dir,'gm_lh.nii.gz'));
 % Grab only left hemisphere GM and WM
 ni_occ.data(ni_seg.data~=5 & ni_seg.data~=3) = 0;
 ni_occ.data(ni_occ.data>0) = 1;
@@ -128,32 +128,32 @@
 writeFileNifti(ni_occ);
 
 %% Create a background mask in native diffusion space
-%ni_b0 = readFileNifti(fullfile(dti_dir,b0_filename));
+%ni_b0 = niftiRead(fullfile(dti_dir,b0_filename));
 %lowres_pixdim = ni_b0.pixdim;
 %camAlignImageToDTI( fullfile(dti_dir,b0_filename), fullfile(mask_dir,'occ_rh_mask.nii.gz'), fullfile(mask_dir,'bgmask_rh.nii.gz'), lowres_pixdim);
 %camAlignImageToDTI( fullfile(dti_dir,b0_filename), fullfile(mask_dir,'occ_lh_mask.nii.gz'), fullfile(mask_dir,'bgmask_lh.nii.gz'), lowres_pixdim);
 
 %% Define outside occ lobe for exclusion purposes
 % RH
-ni_occ = readFileNifti( fullfile(mask_dir,'occ_rh_mask.nii.gz') );
-ni_not_occ = readFileNifti(fullfile(mask_dir,'occ_rh_mask.nii.gz'));
+ni_occ = niftiRead( fullfile(mask_dir,'occ_rh_mask.nii.gz') );
+ni_not_occ = niftiRead(fullfile(mask_dir,'occ_rh_mask.nii.gz'));
 ni_not_occ.fname = fullfile(mask_dir,'not_occ_rh_mask.nii.gz');
 ni_not_occ.data(ni_occ.data==0) = 1;
 ni_not_occ.data(ni_occ.data==1) = 0;
 writeFileNifti(ni_not_occ);
 % LH
-ni_occ = readFileNifti( fullfile(mask_dir,'occ_lh_mask.nii.gz') );
-ni_not_occ = readFileNifti(fullfile(mask_dir,'occ_lh_mask.nii.gz'));
+ni_occ = niftiRead( fullfile(mask_dir,'occ_lh_mask.nii.gz') );
+ni_not_occ = niftiRead(fullfile(mask_dir,'occ_lh_mask.nii.gz'));
 ni_not_occ.fname = fullfile(mask_dir,'not_occ_lh_mask.nii.gz');
 ni_not_occ.data(ni_occ.data==0) = 1;
 ni_not_occ.data(ni_occ.data==1) = 0;
 writeFileNifti(ni_not_occ);
 
 %% Image that defines the occipital exit plane and GM as two ROIs
 % RH
-ni_occ_exit = readFileNifti(fullfile(mask_dir,'wm_rh_exit.nii.gz'));
+ni_occ_exit = niftiRead(fullfile(mask_dir,'wm_rh_exit.nii.gz'));
 ni_occ_exit.fname = fullfile(mask_dir,'occ_rh_exit.nii.gz');
-ni_gm = readFileNifti(fullfile(mask_dir,'gm_rh.nii.gz'));
+ni_gm = niftiRead(fullfile(mask_dir,'gm_rh.nii.gz'));
 ni_occ_exit.data(ni_gm.data>0) = 2;
 writeFileNifti(ni_occ_exit);
 % Now the mask
@@ -163,9 +163,9 @@
 writeFileNifti(ni_occ_exit_mask);
 
 % LH
-ni_occ_exit = readFileNifti(fullfile(mask_dir,'wm_lh_exit.nii.gz'));
+ni_occ_exit = niftiRead(fullfile(mask_dir,'wm_lh_exit.nii.gz'));
 ni_occ_exit.fname = fullfile(mask_dir,'occ_lh_exit.nii.gz');
-ni_gm = readFileNifti(fullfile(mask_dir,'gm_lh.nii.gz'));
+ni_gm = niftiRead(fullfile(mask_dir,'gm_lh.nii.gz'));
 ni_occ_exit.data(ni_gm.data>0) = 2;
 writeFileNifti(ni_occ_exit);
 % Now the mask
@@ -208,7 +208,7 @@
 % Ecc Ventral
 var = 0.2;
 filename = fullfile(mask_dir,sprintf('atlas_%s_%s_%.2f.nii.gz',ecc_atlas_root,var_atlas_root,var));
-ecc = readFileNifti(filename);
+ecc = niftiRead(filename);
 ecc.data(data==0) = 0;
 filename = fullfile(mask_dir,sprintf('atlas_%s_%s_%s_%.2f.nii.gz',roi_ventral_atlas_root,ecc_atlas_root,var_atlas_root,var));
 dtiWriteNiftiWrapper(ecc.data,ecc.qto_xyz,filename);
@@ -229,7 +229,7 @@
 % Ecc Dorsal
 var = 0.2;
 filename = fullfile(mask_dir,sprintf('atlas_%s_%s_%.2f.nii.gz',ecc_atlas_root,var_atlas_root,var));
-ecc = readFileNifti(filename);
+ecc = niftiRead(filename);
 ecc.data(data==0) = 0;
 filename = fullfile(mask_dir,sprintf('atlas_%s_%s_%s_%.2f.nii.gz',roi_dorsal_atlas_root,ecc_atlas_root,var_atlas_root,var));
 dtiWriteNiftiWrapper(ecc.data,ecc.qto_xyz,filename);
@@ -246,7 +246,7 @@
 filename = fullfile(mask_dir,sprintf('atlas_%s_%s_%.2f.nii.gz',ecc_atlas_root,var_atlas_root,var));
 % C1 ECC
 var = 0.2;
-ecc = readFileNifti(filename);
+ecc = niftiRead(filename);
 ecc.data(data==0) = 0;
 filename = fullfile(mask_dir,sprintf('atlas_%s_%s_%s_%.2f.nii.gz',roi_c1_atlas_root,ecc_atlas_root,var_atlas_root,var));
 dtiWriteNiftiWrapper(ecc.data,ecc.qto_xyz,filename);
@@ -261,7 +261,7 @@
 filename = fullfile(mask_dir,sprintf('atlas_%s_%s_%.2f.nii.gz',ecc_atlas_root,var_atlas_root,var));
 % CMT ECC
 var = 0.2;
-ecc = readFileNifti(filename);
+ecc = niftiRead(filename);
 ecc.data(data==0) = 0;
 filename = fullfile(mask_dir,sprintf('atlas_%s_%s_%s_%.2f.nii.gz',roi_cmt_atlas_root,ecc_atlas_root,var_atlas_root,var));
 dtiWriteNiftiWrapper(ecc.data,ecc.qto_xyz,filename);
@@ -276,7 +276,7 @@
 filename = fullfile(mask_dir,sprintf('atlas_%s_%s_%.2f.nii.gz',ecc_atlas_root,var_atlas_root,var));
 % CVO ECC
 var = 0.2;
-ecc = readFileNifti(filename);
+ecc = niftiRead(filename);
 ecc.data(data==0) = 0;
 filename = fullfile(mask_dir,sprintf('atlas_%s_%s_%s_%.2f.nii.gz',roi_cvo_atlas_root,ecc_atlas_root,var_atlas_root,var));
 dtiWriteNiftiWrapper(ecc.data,ecc.qto_xyz,filename);
@@ -291,7 +291,7 @@
 filename = fullfile(mask_dir,sprintf('atlas_%s_%s_%.2f.nii.gz',ecc_atlas_root,var_atlas_root,var));
 % cv3ab ECC
 var = 0.2;
-ecc = readFileNifti(filename);
+ecc = niftiRead(filename);
 ecc.data(data==0) = 0;
 filename = fullfile(mask_dir,sprintf('atlas_%s_%s_%s_%.2f.nii.gz',roi_cv3ab_atlas_root,ecc_atlas_root,var_atlas_root,var));
 dtiWriteNiftiWrapper(ecc.data,ecc.qto_xyz,filename);
@@ -305,13 +305,13 @@
     hem = hem_names{hh};
     % Load exit wm
     filename = fullfile(mask_dir,sprintf('wm_%s_exit.nii.gz',hem));
-    ni = readFileNifti(filename);
+    ni = niftiRead(filename);
     num_vox_exit = sum(ni.data(:)>0);
     % Go through each variance explained level
     for vv = 1:length(var_thresh)
         var = var_thresh(vv);
         filename = fullfile(mask_dir,sprintf('%s_%s_%d_%s_%.2f_%s.nii.gz',cbs_root,hem,num_tracks,var_atlas_root,var,lbl_post));
-        ni = readFileNifti(filename);
+        ni = niftiRead(filename);
         exit_data(hh,vv) = sum(ni.data(:)>0) / num_vox_exit;
     end
 end

external/camino/s_cam_notes.m

@@ -2,7 +2,7 @@
 s_cam_definitions;
 
 %% Load image for pathway xforms
-ni_seg = readFileNifti(fullfile(mask_dir,seg_filename));
+ni_seg = niftiRead(fullfile(mask_dir,seg_filename));
 % Calc xform from camino space to acpc space
 xform = ni_seg.qto_xyz;
 xform(1:3,1:3) = eye(3);
@@ -14,7 +14,7 @@
 %% Fix image header
 %filename = fullfile(camino_dir,'acm','t_mesd_gm_rh_exit_1cm_acm_sc.nii.gz');
 filename = fullfile(camino_dir,'fa.nii.gz');
-ni = readFileNifti(filename);
+ni = niftiRead(filename);
 dtiWriteNiftiWrapper(ni.data, xform_img_to_acpc, filename);
 
 %% Load generated paths
@@ -36,14 +36,14 @@
 dtiWriteNiftiWrapper(fd_img, xform_img_to_acpc, fullfile(camino_dir,'tracts_occ.nii.gz'));
 % Intersect occ map with cortex
 tracts_filename = 'tracts_occ.nii.gz';
-ni_tracts = readFileNifti(fullfile(camino_dir, tracts_filename));
-ni_c = readFileNifti(fullfile(mask_dir,'gm.nii.gz'));
+ni_tracts = niftiRead(fullfile(camino_dir, tracts_filename));
+ni_c = niftiRead(fullfile(mask_dir,'gm.nii.gz'));
 ni_tracts.fname = fullfile(camino_dir,'tracts_occ_gm.nii.gz');
 ni_tracts.data(ni_c.data==0) = 0;
 writeFileNifti(ni_tracts);
 % Intersect with retinotopic cortex
-ni_tracts = readFileNifti(fullfile(camino_dir, tracts_filename));
-ni_c = readFileNifti(fullfile(mask_dir,'atlas_mask.nii.gz'));
+ni_tracts = niftiRead(fullfile(camino_dir, tracts_filename));
+ni_c = niftiRead(fullfile(mask_dir,'atlas_mask.nii.gz'));
 ni_tracts.fname = fullfile(camino_dir,'tracts_occ_atlas.nii.gz');
 ni_tracts.data(ni_c.data==0) = 0;
 writeFileNifti(ni_tracts);
@@ -58,31 +58,31 @@
 dtiWriteNiftiWrapper(fd_img, xform_img_to_acpc, fullfile(camino_dir,'tracts_occ_exit.nii.gz'));
 % Intersect occ map with cortex
 tracts_filename = 'tracts_occ_exit.nii.gz';
-ni_tracts = readFileNifti(fullfile(camino_dir, tracts_filename));
-ni_c = readFileNifti(fullfile(mask_dir,'gm.nii.gz'));
+ni_tracts = niftiRead(fullfile(camino_dir, tracts_filename));
+ni_c = niftiRead(fullfile(mask_dir,'gm.nii.gz'));
 ni_tracts.fname = fullfile(camino_dir,'tracts_occ_exit_gm.nii.gz');
 ni_tracts.data(ni_c.data==0) = 0;
 writeFileNifti(ni_tracts);
 % Intersect with retinotopic cortex
-ni_tracts = readFileNifti(fullfile(camino_dir, tracts_filename));
-ni_c = readFileNifti(fullfile(mask_dir,'atlas_mask.nii.gz'));
+ni_tracts = niftiRead(fullfile(camino_dir, tracts_filename));
+ni_c = niftiRead(fullfile(mask_dir,'atlas_mask.nii.gz'));
 ni_tracts.fname = fullfile(camino_dir,'tracts_occ_exit_atlas.nii.gz');
 ni_tracts.data(ni_c.data==0) = 0;
 writeFileNifti(ni_tracts);
 
 %% Tract surface measurements
 
 %% Fix residual image
-ni_b0 = readFileNifti(fullfile(dti_dir,'b0.nii.gz'));
-ni = readFileNifti(fullfile(camino_dir,'wdt_rmsqr.nii.gz'));
+ni_b0 = niftiRead(fullfile(dti_dir,'b0.nii.gz'));
+ni = niftiRead(fullfile(camino_dir,'wdt_rmsqr.nii.gz'));
 ni_b0.fname =  fullfile(camino_dir,'wdt_rmsqr.nii.gz');
 ni_b0.data = ni.data;
 %ni_b0.data = ni.data(1:-1:end,:,:);
 writeFileNifti(ni_b0);
 
 %% Examine residuals
-ni_mse = readFileNifti(fullfile(camino_dir,'wdt_rmsqr.nii.gz'));
-ni_std = readFileNifti(fullfile(camino_dir,'wdt_std.nii.gz'));
+ni_mse = niftiRead(fullfile(camino_dir,'wdt_rmsqr.nii.gz'));
+ni_std = niftiRead(fullfile(camino_dir,'wdt_std.nii.gz'));
 ni_std.data(ni_std.data>100) = 100;
 ni_mse.data(ni_mse.data>100) = 100;
 showMontage(ni_std.data)
@@ -93,14 +93,14 @@
 
 % Fix label image
 filename_labels = fullfile(camino_dir,'cbs_labels_1_1_0.nii.gz');
-ni = readFileNifti(filename_labels);
+ni = niftiRead(filename_labels);
 ni_labels = ni_occ;
 ni_labels.fname = filename_labels;
 ni_labels.data = ni.data;
 writeFileNifti(ni_labels);
 
 filename_labels = fullfile(camino_dir,'cbs_labelcp_1_1_0.nii.gz');
-ni = readFileNifti(filename_labels);
+ni = niftiRead(filename_labels);
 ni_labels = ni_occ;
 ni_labels.fname = filename_labels;
 ni_labels.data = ni.data;