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.Andrews@kcl.ac.uk
On 28/10/2016 15:53, "Bruce Fischl" fischl@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.Andrews@kcl.ac.uk
On 28/10/2016 14:54, "Bruce Fischl" fischl@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.Andrews@kcl.ac.uk
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