Index in position 1 exceeds array bounds. Index must not exceed 1.

While I am trying to convert H5 file to mat file I got this error. The code is below:

close all; clear all;
addpath(genpath('.\'));
file_name_data = 'file_brain_AXFLAIR_200_6002425.h5';

info = h5info(file_name_data);
h5disp(file_name_data,'/');
struct_data = h5read(file_name_data,'/kspace');
raw_data = complex(struct_data(1:1:20,:,:,:),struct_data(1:1:20,:,:,:));
raw_data_xyz = fftshift(ifft(raw_data, 640, 4),4);
image_data_xyz = ifft(ifft(ifft(raw_data_xyz,640,4),320,3),20,2);
% figure,imshow(abs(squeeze(raw_data_xfft(6,100,:,:))),[]);
figure,imshow(abs(squeeze(image_data_xyz(6,100,:,:))),[]);



save(strcat(file_name_data,'.mat'),'raw_data_xyz');

output is below:

HDF5 file_brain_AXFLAIR_200_6002425.h5 
Group '/' 
    Attributes:
        'norm':  0.091318
        'max':  0.000427
        'patient_id':  'dcfc3e70496246a709dab23831262b60589f4383d6e05bf5559731ea8d80bb1f'
        'acquisition':  'AXFLAIR'
    Dataset 'ismrmrd_header' 
        Size:  scalar
        Datatype:   H5T_STRING
            String Length: variable
            Padding: H5T_STR_NULLTERM
            Character Set: H5T_CSET_ASCII
            Character Type: H5T_C_S1
        ChunkSize:  []
        Filters:  none
    Dataset 'kspace' 
        Size:  320x640x20x16
        MaxSize:  320x640x20x16
        Datatype:   H5T_COMPOUND
            Member 'r':  H5T_IEEE_F32LE (single)
            Member 'i':  H5T_IEEE_F32LE (single)
        ChunkSize:  []
        Filters:  none
        FillValue:  H5T_COMPOUND
    Dataset 'reconstruction_rss' 
        Size:  320x320x16
        MaxSize:  320x320x16
        Datatype:   H5T_IEEE_F32LE (single)
        ChunkSize:  []
        Filters:  none
        FillValue:  0.000000
Index in position 1 exceeds array bounds. Index must not exceed 1.

Error in h5_to_mat (line 8)
raw_data = complex(struct_data(1:1:20,:,:,:),struct_data(1:1:20,:,:,:));

[Geoff Hayes]

@Gulfam Saju - what are the dimensions of struct_data? Is 1:1:20 valid for this struct?

[Gulfam Saju]

you can check the output. I am not sure whether the dimension is correct in the code.

[Walter Roberson]

To help diagnose the problem, immediately before the assignment to raw_data, insert the line

whos

and then run the code, and show us the results of the whos command.

Question: why are you creating a variable whose real parts and imaginary parts are the same? It would make more sense to me if the code were something like

raw_data = complex(struct_data(1:2:20,:,:,:),struct_data(2:2:20,:,:,:));

[Gulfam Saju]

HDF5 file_brain_AXFLAIR_200_6002425.h5 
Group '/' 
    Attributes:
        'norm':  0.091318
        'max':  0.000427
        'patient_id':  'dcfc3e70496246a709dab23831262b60589f4383d6e05bf5559731ea8d80bb1f'
        'acquisition':  'AXFLAIR'
    Dataset 'ismrmrd_header' 
        Size:  scalar
        Datatype:   H5T_STRING
            String Length: variable
            Padding: H5T_STR_NULLTERM
            Character Set: H5T_CSET_ASCII
            Character Type: H5T_C_S1
        ChunkSize:  []
        Filters:  none
    Dataset 'kspace' 
        Size:  320x640x20x16
        MaxSize:  320x640x20x16
        Datatype:   H5T_COMPOUND
            Member 'r':  H5T_IEEE_F32LE (single)
            Member 'i':  H5T_IEEE_F32LE (single)
        ChunkSize:  []
        Filters:  none
        FillValue:  H5T_COMPOUND
    Dataset 'reconstruction_rss' 
        Size:  320x320x16
        MaxSize:  320x320x16
        Datatype:   H5T_IEEE_F32LE (single)
        ChunkSize:  []
        Filters:  none
        FillValue:  0.000000
  Name                Size                Bytes  Class     Attributes

  file_name_data      1x33                   66  char                
  info                1x1                 20340  struct              
  struct_data         1x1             524288336  struct  

[Geoff Hayes]

@Gulfam Saju - according to the above, struct_data is a 1x1 struct. You are treating it as if it had 3 dimensions. I suspect there is a field/member of that struct which has the data you want.

Answer 1

[Walter Roberson]

Dataset 'kspace'

Size: 320x640x20x16

MaxSize: 320x640x20x16

Datatype: H5T_COMPOUND

Member 'r': H5T_IEEE_F32LE (single)

Member 'i': H5T_IEEE_F32LE (single)

ChunkSize: []

Filters: none

FillValue: H5T_COMPOUND

Notice that it says it is a structure!

You probably need

raw_data = complex(struct_data.r(1:1:20,:,:,:), struct_data.i(1:1:20,:,:,:));

[Gulfam Saju]

Index in position 2 exceeds array bounds. Index must not exceed 20.

Error in h5_to_mat (line 13)
figure,imshow(abs(squeeze(image_data_xyz(6,100,:,:))),[]);
 

I got this error.

[Walter Roberson]

What shows up if you ask

size(struct_data.r)