[Mrtrix-discussion] empty ROI
Manuel Blesa Cábez
mblesac at gmail.com
Wed Jun 4 12:54:41 PDT 2014
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
>>>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>
>>>
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