Apologies I meant from a label to a .mgh

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 17:35, "Andrews, Derek" <derek.andr...@kcl.ac.uk> wrote:

>This sender failed our fraud detection checks and may not be who they
>appear to be. Learn about spoofing at http://aka.ms/LearnAboutSpoofing
>
>Thank you Doug that worked perfectly.
>
>Is it possible then to go back to a .w from a label?
>
>
>________________________________________
>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 16:10, "Douglas Greve" <gr...@nmr.mgh.harvard.edu> wrote:
>
>>Use mri_surf2surf to convert it to an mgh or mgz file, then use
>>mri_cor2label with the --surf option to convert it to a label
>>
>>
>>On 11/8/16 9:41 AM, Andrews, Derek wrote:
>>> 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
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>> Freesurfer mailing list
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