From 4f9a01092ec4a0ac0ea4c6f4c29522c7c3ac1d48 Mon Sep 17 00:00:00 2001 From: Zhe Tim Wu Date: Tue, 30 Jan 2024 19:30:28 -0500 Subject: [PATCH] Fixed errors for the generated documentation --- docs/lit/examples/joss_demo.jl | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/docs/lit/examples/joss_demo.jl b/docs/lit/examples/joss_demo.jl index 81bd4cf..69abc7c 100644 --- a/docs/lit/examples/joss_demo.jl +++ b/docs/lit/examples/joss_demo.jl @@ -182,16 +182,16 @@ are merged into `imaging_acq_data`. This step is done through the function `merge_raw_interleaves`, which can be viewed in [utils.jl](@__REPO_ROOT_URL__/utils/utils.jl). -Note that we only do these steps when they have not been done yet or it's specifically required. +Since the loaded/calculated sens maps and B0 maps are in ascending slice order, +they need to be reordered according to the slice order in the spiral RawAcqData + +We only do these steps when they have not been done yet or it's specifically required. =# if reload_spiral_data || !(@isdefined imaging_acq_data) || !(@isdefined slice_idx_array_spiral) @info "Reading spiral data and merging interleaves" imaging_acq_data = merge_raw_interleaves(params_spiral, false) raw_temp = RawAcquisitionData(ISMRMRDFile(params_general[:scan_fullpath][1])) slice_idx_array_spiral = get_slice_order(raw_temp, num_slices, (num_slices+1)*2, 2) - - # The loaded/calculated sens maps and B0 maps are in ascending slice order - # need to reorder them according to spiral RawAcqData b0_maps = b0_maps[:, :, invperm(slice_idx_array_spiral)] cartesian_sensitivity = cartesian_sensitivity[:, :, invperm(slice_idx_array_spiral), :] end @@ -321,8 +321,6 @@ the file [utils.jl](@__REPO_ROOT_URL__/utils/utils.jl). if params_general[:do_save_recon] # TODO: include elements to save as tuple, e.g., ["b0", "sense", "recon"], same for load resolution_tmp = fieldOfView(imaging_acq_data)[1:2] ./ encodingSize(imaging_acq_data) resolution_mm = (resolution_tmp[1], resolution_tmp[2], fieldOfView(imaging_acq_data)[3] * (1 + params_general[:slice_distance_factor_percent] / 100.0)) #for 2D only, since FOV[3] is slice thickness then, but gap has to be observed - - # TODO: use slice ordering from cartesian scan directly! num_slices = numSlices(imaging_acq_data) save_map( params_general[:recon_save_fullpath],