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sulantha2006 / VoxelStats

A MATLAB package for multi-modal voxel-wise brain image analysis
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Mask read fail #4

Closed dsodums closed 7 years ago

dsodums commented 7 years ago

I tried running a linear model using the GUI method and keep getting errors saying it can't read the mask I have supplied. I have used the "mni_icbm152_t1_tal_nlin_sym_09c_mask.mnc" minc file that has always worked for me when running linear models in RMINC so I'm confused why it is having problems reading the file. I checked the dimensions and they are the same as the preprocessed VBM files I have supplied with a .csv file. Both my input files and the mask are minc V2 files.

Any thoughts? voxelstats_exampleguisetup

I have attached a screenshot of the GUI setup and my CSV file, and here is the error message from Matlab 2015a:

In readMaskSlices (line 5) [mask_slices_n, mask_height, mask_width, mask_slices, voxel_dims, slices_data] = getMaskSlicesMinc(maskFile);

In VoxelStatsLM (line 31) [slices, image_height, image_width, mask_slices, voxel_dims, slices_data] = readMaskSlices(imageType, mask_file);

In runVS (line 21) [ c_struct, slices_p, image_height_p, image_width_p, coeff_vars, voxel_num, df, voxel_dims] = ...

voxelstats_exampleguisetup

sulantha2006 commented 7 years ago

This can be an issue with emma tools not correctly installed. Can you use emma tools to read minc files. Try this command:

mask = openimage(mask_file); mask_slices_n = getimageinfo(mask, 'NumSlices'); mask_file - file path for the mask file.

Let me know if this works.

ykjymkoko commented 3 years ago

Supplementary information: I have the same error messages when using a nifti mask file. The problem was resolved after setting the path for VoxelStats with all subfolders in Matlab.