dke-questions > Neither Matlab nor dcm2niix can save my data...what should I do?
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May 8, 2018 02:05 PM | Xinman Liu
Neither Matlab nor dcm2niix can save my data...what should I do?
Hello, everyone. As I'm still struggling with my patient data as I
previously posted before. So I think I need to sum up a little bit
about what I have done. There is something wrong with my data that
I cannot run DKE successfully.
One problem is that my sequence name did not contain"ep", so I use Matlab to change the sequence name. But it still doesn't work out.
So I turn to dcm2niix and generate my own bvec files, which is attached. And when I look at the file, I realized that there are altogether 5 ep_b0 files in between. So I make some adjustment in Matlab in order to realize the correspondence with it and then delete the rest 4 b0 files, And then I run DKE, the result was exactly like before, which reads,
command line: dke DKEParameters.dat
Diffusional Kurtosis Estimator (DKE) version 2.6.0, February 2015
Start date and time: May 08, 2018 16:21:14
Diffusional Kurtosis Estimator (DKE) version 2.6.0
Converting input DICOM images to NIfTI... complete.
Co-registering images...
Error using spm_hist2
Wrong number of dims (1).
Error in spm_coreg>optfun (line 165)
Error in spm_coreg (line 88)
Error in spm_powell (line 27)
Error in spm_coreg (line 143)
Error in dke_preprocess_dicom>coregister (line 207)
Error in dke_preprocess_dicom (line 78)
Reading input images... Error using dke_estimate (line 165)
Input NIfTI image F:\PN6\intermediate_processing\combined\rdki does not exist!
Error in dke (line 182)
and then I thought maybe i should extract bo series to another file so that I can put them into different columns in DKE, and then the result showed
command line: dke DKEParameters.dat
Diffusional Kurtosis Estimator (DKE) version 2.6.0, February 2015
Start date and time: May 08, 2018 16:43:06
Diffusional Kurtosis Estimator (DKE) version 2.6.0
Converting input DICOM images to NIfTI... ***************************************************
* The AcquisitionNumber counter does not appear *
* to be changing from one volume to another. *
* Another possible explanation is that the same *
* DICOM slices are used multiple times. *
* The conversion is having to guess how slices *
* should be arranged into volumes. *
* NCH_PROGLIO_001 / 9 / 1
***************************************************
complete.
Co-registering images...
Error using spm_hist2
Wrong number of dims (1).
Error in spm_coreg>optfun (line 165)
Error in spm_coreg (line 88)
Error in spm_powell (line 27)
Error in spm_coreg (line 143)
Error in dke_preprocess_dicom>coregister (line 207)
Error in dke_preprocess_dicom (line 78)
Reading input images... Error using dke_estimate (line 165)
Input NIfTI image F:\P7\intermediate_processing\combined\rdki does not exist!
Error in dke (line 182)
And then I thought maybe I should combine the two folder together and put it all in DKI series Column, and it reads exactly the same like before.
I'm running out of methods...
Best,
Xinman
One problem is that my sequence name did not contain"ep", so I use Matlab to change the sequence name. But it still doesn't work out.
So I turn to dcm2niix and generate my own bvec files, which is attached. And when I look at the file, I realized that there are altogether 5 ep_b0 files in between. So I make some adjustment in Matlab in order to realize the correspondence with it and then delete the rest 4 b0 files, And then I run DKE, the result was exactly like before, which reads,
command line: dke DKEParameters.dat
Diffusional Kurtosis Estimator (DKE) version 2.6.0, February 2015
Start date and time: May 08, 2018 16:21:14
Diffusional Kurtosis Estimator (DKE) version 2.6.0
Converting input DICOM images to NIfTI... complete.
Co-registering images...
Error using spm_hist2
Wrong number of dims (1).
Error in spm_coreg>optfun (line 165)
Error in spm_coreg (line 88)
Error in spm_powell (line 27)
Error in spm_coreg (line 143)
Error in dke_preprocess_dicom>coregister (line 207)
Error in dke_preprocess_dicom (line 78)
Reading input images... Error using dke_estimate (line 165)
Input NIfTI image F:\PN6\intermediate_processing\combined\rdki does not exist!
Error in dke (line 182)
and then I thought maybe i should extract bo series to another file so that I can put them into different columns in DKE, and then the result showed
command line: dke DKEParameters.dat
Diffusional Kurtosis Estimator (DKE) version 2.6.0, February 2015
Start date and time: May 08, 2018 16:43:06
Diffusional Kurtosis Estimator (DKE) version 2.6.0
Converting input DICOM images to NIfTI... ***************************************************
* The AcquisitionNumber counter does not appear *
* to be changing from one volume to another. *
* Another possible explanation is that the same *
* DICOM slices are used multiple times. *
* The conversion is having to guess how slices *
* should be arranged into volumes. *
* NCH_PROGLIO_001 / 9 / 1
***************************************************
complete.
Co-registering images...
Error using spm_hist2
Wrong number of dims (1).
Error in spm_coreg>optfun (line 165)
Error in spm_coreg (line 88)
Error in spm_powell (line 27)
Error in spm_coreg (line 143)
Error in dke_preprocess_dicom>coregister (line 207)
Error in dke_preprocess_dicom (line 78)
Reading input images... Error using dke_estimate (line 165)
Input NIfTI image F:\P7\intermediate_processing\combined\rdki does not exist!
Error in dke (line 182)
And then I thought maybe I should combine the two folder together and put it all in DKI series Column, and it reads exactly the same like before.
I'm running out of methods...
Best,
Xinman