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 >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> >>>>> >>>>>https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmai >>>>>l. >>>>> nm >>>>> >>>>> >>>>>r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cder >>>>>ek >>>>> .a >>>>> >>>>> >>>>>ndrews%40kcl.ac.uk%7C65ef7af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c >>>>>16 >>>>> b8 >>>>> >>>>> >>>>>3c724071654356%7C0&sdata=liaieNpnjB7M4w9favIeZ9B0ZrooUbfDThLvJxmbcuo%3 >>>>>D& >>>>> re >>>>> served=0 >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to >>>>>whom >>>>> it >>>>> is >>>>> addressed. 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