[Mrtrix-discussion] empty ROI

[Manuel Blesa Cábez]

Hi Donald,

This is the mrinfo for the fod:

************************************************
Image:               "fod.mif"
************************************************
  Format:            MRtrix
  Dimensions:        120 x 110 x 54 x 45
  Voxel size:        1.4 x 1.4 x 2.8 x 1
  Data type:         32 bit float (little endian)
  Data strides:      [ 2 3 4 1 ]
  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


The rest of the ROIs, have the same mrinfo that the problematic ROI. I
check it with both programs, fslview and mrview and with both looks ok.

To calculate this ROIs I did it with FSL, because i calculated on the
template after do the TBSS, to see differences betwen groups, and after
this I did the inverse transform to the subject space.  Can some of this
steps affect to the transform of the ROI?

Regards,

Manuel Blesa


2014-06-04 18:54 GMT+02:00 Donald Tournier <jdtournier at gmail.com>:

> Hi Manuel,
>
> The translation column of the transform seems way out - about 30 metres
> off isocentre... Does the ROI overlay properly onto your fod.mif image
> within MRView? Does your fod.mif image have the same translation - what
> does mrinfo report for that image? I expect whatever you used to generate
> the ROI has corrupted the transform. When you said the ROI looks OK on
> visual inspection, was that with fslview or MRView? I think fslview just
> overlays images voxel-wise, with no regard for any differences in the
> transforms. Basically, if the two images don't overlap in scanner
> coordinates, then that would explain your issue...
>
> 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 17:39, "Manuel Blesa Cábez" <mblesac at gmail.com> wrote:
>
>> 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
>>>>
>>>>
>>>> _______________________________________________
>>>> Mrtrix-discussion mailing list
>>>> Mrtrix-discussion at www.nitrc.org
>>>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>>>
>>>>
>>
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