[Mrtrix-discussion] empty ROI

Donald Tournier jdtournier at gmail.com
Wed Jun 4 09:54:37 PDT 2014


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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