[Mrtrix-discussion] empty ROI
Donald Tournier
jdtournier at gmail.com
Wed Jun 4 11:00:48 PDT 2014
Hi Manuel,
OK, make sense then. The threshold is 0.5, I think. You can use mrthreshold
to sort this out.
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 18:28, "Manuel Blesa Cábez" <mblesac at gmail.com> wrote:
> Hi Donald,
>
> I checked it for all the ROIs and the values are not 0 and 1. Are 0
> outside the roi and between 0 and 1 in the ROI. Do you think this is the
> motive? How can I make it binary?
>
> Regards,
>
> Manuel Blesa
>
>
> 2014-06-04 19:13 GMT+02:00 Donald Tournier <jdtournier at gmail.com>:
>
>> 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
>>>>>>>
>>>>>>>
>>>>>
>>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.nitrc.org/pipermail/mrtrix-discussion/attachments/20140604/334d10a8/attachment-0001.html>
More information about the Mrtrix-discussion
mailing list