[Mrtrix-discussion] empty ROI

[Manuel Blesa Cábez]

Hi Donald,

This is the 'mrinfo roi_CC1.mif'

************************************************
Image:               "roi_CC1.mif"
************************************************
  Format:            MRtrix
  Dimensions:        120 x 110 x 54
  Voxel size:        1.4 x 1.4 x 2.8
  Data type:         32 bit float (little endian)
  Data strides:      [ -1 2 3 ]
  Intensity scaling: offset = 0, multiplier = 1
  Comments:          FSL5.0
  Transform:                    1           0           0   2.788e+04
                               -0           1           0  -3.487e+04
                               -0           0           1  -5.623e+04
                                0           0           0           1

Regards,

Manuel Blesa


2014-06-04 18:33 GMT+02:00 Donald Tournier <jdtournier at gmail.com>:

> Hi Manuel,
>
> Can you post the output of 'mrinfo roi_CC1.mif' ? Would be good to also
> have some info as to how the image was generated. Hopefully that'll help to
> narrow down the problem...
>
> Cheers,
> Donald
>
> --
> Dr J-Donald Tournier (PhD)
>
> Senior Lecturer, Biomedical Engineering
> Division of Imaging Sciences & Biomedical Engineering
> King's College London
>
> A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St
> Thomas' Hospital, London. SE1 7EH
> T: +44 (0)20 7188 7118 ext 53613
> W:
> http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering
>
> On 4 Jun 2014 17:01, "Manuel Blesa Cábez" <mblesac at gmail.com> wrote:
>
>> Hi all,
>>
>> I have a strange problem, I'm sure is easy to solve but I'm stuck on this
>> and I don't find the solution.
>>
>> I want to calculate the tracks for a ROI, and when I run it I obtain the
>> following message:
>>
>> tckgen fod.mif tracks_CC1.tck -algorithm SD_STREAM -grad
>> ag140128a_6_HARDI_WT_ref.b -seed_image roi_CC1.mif -mask mask.mif -number
>> 1000
>>
>> tckgen [ERROR]: Cannot use image roi_CC1.mif as ROI - image is empty
>>
>> I opened the ROI and it looks ok, and is not "outside" of the fod map. I
>> did the same, for another ROI and it works correctly. I don't know way this
>> ROI has this problem, Somebody can help me? Maybe is due to the location of
>> the ROI and the default parameters? Thanks in advance.
>>
>> Best regards,
>>
>> Manuel Blesa
>>
>>
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>>
>>
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