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

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Gulfam Saju
Gulfam Saju 2022-3-17
评论： Walter Roberson 2022-3-17
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,:,:,:));
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Gulfam Saju
Gulfam Saju 2022-3-17
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
Geoff Hayes 2022-3-17
@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.

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采纳的回答

Walter Roberson
Walter Roberson 2022-3-17
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,:,:,:));
  2 个评论
Gulfam Saju
Gulfam Saju 2022-3-17
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.

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