[Mrtrix-discussion] empty ROI
Donald Tournier
jdtournier at gmail.com
Thu Jun 5 07:10:20 PDT 2014
Hi Manuel,
That's up to you - personally if I had any doubts, I would just to make
sure...
Cheers,
Donald.
On Wed, Jun 4, 2014 at 8:54 PM, Manuel Blesa Cábez <mblesac at gmail.com>
wrote:
> Hi Donald,
>
> Thanks! it works perfect with the mrcalc (I didn't try yet with the
> mrtreshold). One last qüestion related with this, should I do this for all
> the rois that aren't binaries? To be sure that used all the voxels of the
> ROI.
>
> Best regards,
>
> Manuel Blesa
>
>
> 2014-06-04 21:05 GMT+02:00 Donald Tournier <jdtournier at gmail.com>:
>
> Hi Manuel,
>>
>> If mrtreshold doesn't work, and the values outside the ROI are exactly
>> zero, you could also use:
>>
>> mrcalc roi_CC1.mif 0 -neq new_roi_CC1.mif
>>
>> 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 19:00, "Donald Tournier" <jdtournier at gmail.com> wrote:
>>
>>> 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
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>>>>>>
>>>>
>
--
*Dr J-Donald Tournier (PhD)*
*Senior Lecturer, **Biomedical Engineering*
*Division of Imaging Sciences & Biomedical EngineeringKing'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
<http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering>*
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