Hi Ruopeng;

I have the following questions:

1) I was wondering whether the Diffusion toolokit supports Mosaic DICOM images.

2) Also, I have DTI data that is repeated 3 times, and I want to know how to load it to the DTK. Do I have to put each repetition in a separate folder or just put all the data in only one folder? How to define the number of b0 images in this case? Thank you

 

Fatma…

Ruopeng said:

Hi,

DTK does support Mosaic Dicom images. Just select one of the dicom files in the series and they will be unpacked automatically.

Multi-repeat data is also supported under the condition that the input data must either be one 4D nifti file, or a series of 3D nifti files or Siemens Mosaic dicom files (meaning, one 3D volume per file). So if your data is a series of single slice files, it will not work. This support is also not built into the default GUI. You need to enter "-nex 3" manually in "Additional options" box.

Best,

Ruopeng

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Thanks for the answer! Ruopeng

However, it seems the "-nex 3" manually in "Additional options" box.

should be "nex 3"

or it appears:

Unrecognized switch '-nex'.

Process aborted due to error.

 

good luck!

Gao

 

Hi Ruopeng,

I concatenated the tables and loaded the NII files  as a series of 3D volumes (each file representes a 3D volume corresponding to a gradient directions). And that 's what I got. The tracks are found only in the middle part of the brain as shown in the image attached. I tried the case of one Nifti 4D volume and I got the same thing. Can you help me to figure out what is happening?

Thank you.

Fatma..

Ruopeng said:

Fatma said:

Hi Ruopeng,

1) I was wondering how DTK works in the case of repeated data? I mean does it perform averaging for the different repetitions or just concatenate them to have a larger set of observations? I am asking this question because I perform registration for my images using other software which gives me: registered DWI volumes and registered gradient tables. Consequently, each repetiton will have its table. So, how can I use DTK in this case?

DTK will average the repeats. In your case that each repetition has its own table. You should concatenate the tables into one and treat the data as one series without repetition.

2) You said that:

" Multi-repeat data is also supported under the condition that the input

data must either be one 4D nifti file"

You mean by a 4D nifti file that the 3rd dimension represents the number of slices in a volume, and the 4th dimension represents the number of gradient directions x number of repetitions. Is this right?

That is correct.

Ruopeng

 

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 Dear Ruopeng,

I just realize that there are two"additional options", and I did put the "nex 3" in the "Tracking" part. However, still there comes another error:

Reading raw data… 1.1%

** nifti_RCI: dims[4] >= nim->dim[4] (93,93) Can not read file C:DOCUME~1ADMINI~1LOCALS~1Tempdtk_tmp10tmp.nii

Process aborted due to error.

 

This error dissappear after I change it to "nex 3", and it works! In fact, I compare the results from two DKT process, with "nex 3" put in either "Reconstruction" or " tracking", and I get the SAME results. I say SAME since i compare the whole track count and ROI track count and get exactly the same result. 

 

I am not sure whether your guys always using command line to process data, for me, always- i can only use GUI to process data, and keep on trying :) Indeed, I like trackVIS a lot, and have used it for one year. But  I don’t understand the meaning of those parameters to adjust, such as “ mask, angle threshold”. Hope that there may come a brief description on these concepts in TrackVIS.

 

Thanks very much again !

Gao

gaolion said:

sorry, my post is related to :

"Are you running the latest version? Also, there are two "Additional Options" boxes in the GUI. One for recon, one for tracking. Did you make sure to put '-nex 3' in the recon one?

Ruopeng"

 

The image shows the parameters in DTK and the error

"

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Ruopeng said:

Does you data have 3 repetitions? If not, you should not apply "-nex" option. The error appears to indicate the nifti file has different dimension information than the program is expecting.

Ruopeng

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Yes, the data includes 3 repetitions, with 3 B0 images. Actually, your Diffusion toolkit can recognize that automatically.

–i tried several times, only "nex 3" is workable, but not "-nex 3".  the results seem good. Strange