problem with generating vmv file, and running network histograms analysis ?

[ofrag]

Hi,

Thanks for sharing the software. it looks great from the paper.
I succeed in running all the steps up to the network step on your Image1 sample dataset.

However, I encounter few problems for the network step:

1. 'histograms' output fails , with :

Unable to perform assignment because the left and right sides have a different number of elements.

Error in area_histogram_plotter/sort_and_bin_by_statistic (line 96)
        bin_index_limits( ik ) = find( inner_statistics >= bin_limits( ik ), 1, 'first' );

Error in area_histogram_plotter (line 66)
[ x1, dx1, dy1 ] = sort_and_bin_by_statistic( inner_pos_z,            inner_pos_area, number_of_bins,  z_pos_limits, false );

Error in vectorize_V200 (line 3596)
            area_histogram_plotter( strand_subscripts, lumen_radius_in_microns_range, microns_per_voxel, size_of_image, number_of_bins );

Error in vectorization_script_michael (line 91)
        time_stamp = vectorize_V200( name_value_pair_inputs{ 1, : });
 

2. I want to visualize the 3D results with blender as you state in your documentation, but I couldn't find how to generate a .vmv file that I can open with VeMorphoVis in blender.

Thanks
Ofra

[mihelics]

Hi Ofra,

Please excuse the delay in response. Somehow I was unaware of the issues raised on this repository until today. Please also excuse my failure to follow up on our collaboration around the time this issue was posted, I had a lot going on at that time with the birth of my daughter and finishing the PhD.

Since this issue was opened, there have been several notable improvements to the software in two subsequent release versions of the software. I recommend downloading the newest version of the software and seeing if your problems are solved. Otherwise, I am happy to help you resolve your issue, especially if it leads to a better software product.

That is great news that you were able to get the network file. How does it look in the vertex curator or the edge curator (before the final network output)?

Here are some specific comments about your issues:

1. Histograms output failure to define the limits of the boxes used to make the histogram.
   Without more context, it's hard to say why you would get this error here. Which statistic failed and why, I wonder. It is possible that this issue was solved in a later version of the software.

2. According to the documentation (quoted below), the vmv output file should be automatically written to the vectors folder by default (in the latest version of the software at least). If it is not output by default, use the SpecialOutput parameter to specify the vmv file format (i.e. vectorize_v200( ... , 'SpecialOutput', 'vmv' )

% 'SpecialOutput'           'none'           - Does not create any special network outputs.
%                           'histograms'     - Shows strand, length statistic histograms          (defualt) 
%                           'depth-stats'    - Shows depth-resolved statistics.                   (defualt) 
%                           'flow-field'     - Writes x, y, and z component .tif's of flow field.
%                           'depth'          - Shows vectors over raw with color-coded depth.     (defualt)           
%                           'strands'        - Shows vectors over raw with color-coded strands.   (defualt) 
%                           'directions'     - Shows vectors over raw with color-coded direcions. (defualt) 
%                           '3D-strands'     - Shows 3D volume rendering with color-coded strands.
%                           '3D-directions'  - Shows 3D volume rendering with color-coded strand 
%                                              directions.
%                           'original-stats' - Calculates signal, noise, background, etc, from
%                                              network binary. Saves in the network_*.mat vector file.
%                           'casX'           - Creates .casX equivalent representation of strands.
%                                              Format .casX is due to LPPD in Chicago, IL.
%                           'vmv'            - Creates .vmv equivalent representation of strands. (defualt)
%                                              Format .vmv is due to Blue Brain Project in
%                                              Switzerland.
%                           { ... }          - Creates ... (a list of) special network outputs.
%                           'all'            - Creates all special network outputs.

Please let me know here or via email if you continue to have issues. Again, I apologize for failing to respond to this issue earlier. I very much would like to support your research goals moving forward.

Sincerely,
Sam