Hi Bruce and Freesurfer developers,

Thank you. Any suggestions on converting a binary .w file to a label would
be very helpful.

Best, Derek 


________________________________________
Derek Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment
Department of Forensic and Neurodevelopmental Sciences
Institute of Psychiatry, Psychology & Neuroscience, King's College London

Telephone: +44 (0)20 7848 5701
Email: derek.andr...@kcl.ac.uk





On 08/11/2016 14:04, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:

>Hi Derek
>
>I'll cc the FS list so others can answer. It depends on the reason the
>holes exist.  It also depends on the size of the holes. The dev version
>of 
>mri_label2labels supports morphological close operations. It takes an
>integer parameter which should be about the radius of the holes you would
>like to fill in. Note that this will also fill in some concavities in the
>boundary of the label.
>
>cheers
>Bruce
>
>
>On Tue, 8 Nov 2016, Andrews, Derek wrote:
>
>> Hi Bruce,
>>
>> Apologies for contacting you directly but I’m not sure if my message is
>> getting through to the list.
>>
>> I have gotten ahold of the dev version of mri_label2label.
>>
>> Currently I have a .w file that I need to “fill in the holes” on. Could
>> you please specify the steps I will need to take to make my .w file an
>> acceptable input for mri_label2label, and any recommendations you may
>>have
>> for the value of N for the —close flag.
>>
>> Any help you could provide would be appreciated.
>>
>> Best, Derek
>>
>>
>>
>>
>> ________________________________________
>> Derek Sayre Andrews, MSc
>> PhD Candidate
>>
>> The Sackler Institute for Translational Neurodevelopment
>> Department of Forensic and Neurodevelopmental Sciences
>> Institute of Psychiatry, Psychology & Neuroscience, King's College
>>London
>>
>> Telephone: +44 (0)20 7848 5701
>> Email: derek.andr...@kcl.ac.uk
>>
>>
>>
>>
>>
>> On 28/10/2016 15:53, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:
>>
>>> Hi Derek
>>>
>>> I think the dev version of mri_label2label supports
>>> open/close/dilate/erode
>>> operations:
>>>
>>> mri_label2label --help
>>> USAGE: mri_label2label.bin
>>>
>>>    --srclabel     input label file
>>>
>>>    --erode  N     erode the label N times before writing
>>>    --open   N     open the label N times before writing
>>>    --close  N     close the label N times before writing
>>>    --dilate  N    dilate the label N times before writing
>>>  .
>>> .
>>> .
>>>
>>> if your version doesn't have these operations let us know and we can
>>>get
>>> you an updated one
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>>
>>> On Fri, 28 Oct 2016,
>>> Andrews, Derek wrote:
>>>
>>>> Hi Bruce,
>>>>
>>>> As always thank you for your prompt reply.
>>>>
>>>> For the morphological close operation, would you suggest using
>>>>mris_fill
>>>> on the surface ROI I created and then running mri_vol2surf again on
>>>>the
>>>> volume output by mris_fill?
>>>>
>>>> Best, Derek
>>>>
>>>>
>>>> ________________________________________
>>>> Derek Sayre Andrews, MSc
>>>> PhD Candidate
>>>>
>>>> The Sackler Institute for Translational Neurodevelopment
>>>> Department of Forensic and Neurodevelopmental Sciences
>>>> Institute of Psychiatry, Psychology & Neuroscience, King's College
>>>> London
>>>>
>>>> Telephone: +44 (0)20 7848 5701
>>>> Email: derek.andr...@kcl.ac.uk
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On 28/10/2016 14:54, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
>>>>wrote:
>>>>
>>>>> p.s. you could remove many/most of these holes using a morphological
>>>>> close operation
>>>>> On Fri, 28 Oct 2016, Andrews, Derek wrote:
>>>>>
>>>>>> Hello Freesurfer Developers and Community,
>>>>>>
>>>>>> I am looking to map a ROI.nii based on the MNI152 template to the
>>>>>> fsaverage
>>>>>> pial surface.
>>>>>>
>>>>>> I have used the following commands
>>>>>>
>>>>>> Bbregister ‹s fsaverage ‹mov MNI152.nii ‹reg register.dat ‹init-fsl
>>>>>> ‹12
>>>>>> ‹t1
>>>>>>
>>>>>> Then
>>>>>>
>>>>>> mri_vol2surf ‹src ROI.nii ‹out ROI.mgh ‹srcreg register.dat ‹hemi lh
>>>>>>
>>>>>> The ROI appears to be in the right place however is very blotchy.
>>>>>> Have I
>>>>>> missed a step? Or is this correct?
>>>>>>
>>>>>> See bellow a picture of the ROI highlighted in FSL and in tksurfer
>>>>>> after
>>>>>> mapped using the above.
>>>>>>
>>>>>> Thank you for your support,
>>>>>>
>>>>>> Best, Derek
>>>>>>
>>>>>> [IMAGE]
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> 
>>>>>>_____________________________________________________________________
>>>>>>__
>>>>>> __
>>>>>> ___
>>>>>>
>>>>>> Derek Sayre Andrews, MSc
>>>>>> PhD Candidate
>>>>>>
>>>>>> The Sackler Institute for Translational Neurodevelopment
>>>>>>
>>>>>> Department of Forensic and Neurodevelopmental Sciences
>>>>>>
>>>>>> Institute of Psychiatry, Psychology & Neuroscience, King's College
>>>>>> London
>>>>>>
>>>>>> Telephone: +44 (0)20 7848 5701
>>>>>> Email: derek.andr...@kcl.ac.uk
>>>>>>
>>>>>>
>>>>>>
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