Hello Freesurfer Developers, 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. Thank you. 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 >>> Freesurfer@nmr.mgh.harvard.edu >>> >>> https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail. >>> nm >>> >>> r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cderek >>> .a >>> >>> ndrews%40kcl.ac.uk%7C65ef7af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c16 >>> b8 >>> >>> 3c724071654356%7C0&sdata=liaieNpnjB7M4w9favIeZ9B0ZrooUbfDThLvJxmbcuo%3D& >>> re >>> served=0 >>> >>> >>> The information in this e-mail is intended only for the person to whom >>> it >>> is >>> addressed. 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