[Mrtrix-discussion] empty ROI
Donald Tournier
jdtournier at gmail.com
Wed Jun 4 10:13:17 PDT 2014
Hi Manuel,
OK, I guess the transform wasn't the issue... The only other possibility I
can think of is that the values in the ROI image aren't the expected 0 & 1.
Can you load the ROI image in MRView and check that the intensity values
outside the ROI are zero and those inside the ROI are one?
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 18:06, "Manuel Blesa Cábez" <mblesac at gmail.com> wrote:
> 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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