Hello, for the first time I am working with some files with *.TIFF and DICOM extensions generated by MeVisLab from some colleagues of mine. It is supposed to be a 4-D data (x,y,z and time).
Before that I used to work with *.hdr files and so far it is being way too different and because of that I am having some problems which I will attempt to describe them here.
So, let's say I have files: Filename.tif and Filename.dcm.
If I write:
[im1,map1] = imread('Filename.tif');
it will result in a two dimensional 'im1' (299x306 uint16), empty 'map1', and an error saying:
Warning: Only the first slice will be read from this image with depth 372.
I tried writing:
[im1,map1] = imread('Filename.tif',1);
But it gives the same results, no temporal positions neither z dimension. Changing 1 to 2 i'll obtain:
Invalid TIFF image index specified.
Using the imfinfo command, I obtain the following:
FileModDate: '26-Nov-2006 11:32:30'
FileSize: 76209780
Format: 'tif'
FormatVersion: []
Width: 306
Height: 299
BitDepth: 16
ColorType: 'grayscale'
FormatSignature: [73 73 42 0]
ByteOrder: 'little-endian'
NewSubFileType: 0
BitsPerSample: 16
Compression: 'Uncompressed'
PhotometricInterpretation: 'BlackIsZero'
StripOffsets: []
SamplesPerPixel: 1
RowsPerStrip: 4.2950e+09
StripByteCounts: []
XResolution: 12.8000
YResolution: 12.8000
ResolutionUnit: 'Centimeter'
Colormap: []
PlanarConfiguration: 'Chunky'
TileWidth: 160
TileLength: 80
TileOffsets: [2976x1 double]
TileByteCounts: [2976x1 double]
Orientation: 1
FillOrder: 1
GrayResponseUnit: 0.0100
MaxSampleValue: 132
MinSampleValue: 0
Thresholding: 1
Offset: 76185608
ImageDescription: 'MeVisLab'
Software: 'MFL MeVis File Format Library, TIFF Module'
SampleFormat: 'Unsigned integer'
SMinSampleValue: 0
SMaxSampleValue: 132
ImageDepth: 372
TileDepth: 1
ImageDepth is in fact there, 372 vertical frames are there.. But how can I change this frame? So I went to read and search for answers through Matlab Help, forums, etc, and found out about Tiff command (that uses LibTIFF). Let me be honest, I never used this library before and I don't intend to use that much, I just wanted to plot the signals between temporal positions for all voxels.
However I read the Matlab Help and tried the following:
t = Tiff('Filename.tif','r')
Which returned:
TIFF File: '/etc/Filename.tif'
Mode: 'r'
Current Image Directory: 1
Number Of Tiles: 2976
SubFileType: Tiff.SubFileType.Default
Photometric: Tiff.Photometric.MinIsBlack
ImageLength: 299
ImageWidth: 306
TileWidth: 160
TileLength: 80
BitsPerSample: 16
Compression: Tiff.Compression.None
SampleFormat: Tiff.SampleFormat.UInt
SamplesPerPixel: 1
PlanarConfiguration: Tiff.PlanarConfiguration.Chunky
ImageDescription: MeVisLab
Orientation: Tiff.Orientation.TopLeft
Reading the entire image with:
I'll get a 4-D uint 16 subimage_one. Things look better now, but when I check its size, seems that it has size 299*306*1*372. It is weird to having only 1 temporal position. Because of that, I installed MeVisLab and used the same file. There I confirmed that in fact there are more than one temporal position: it has 6 temporal positions so its size should be 299*306*6*372..
Am I doing something wrong or is there any other way to access all data in the file? Even using imread, it seems that I can't access all data and I'm missing the timecourses.
