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 >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> >>>>>>> >>>>>>> >>>>>>>https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fm >>>>>>>ai >>>>>>> l. >>>>>>> nm >>>>>>> >>>>>>> >>>>>>> >>>>>>>r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cd >>>>>>>er >>>>>>> ek >>>>>>> .a >>>>>>> >>>>>>> >>>>>>> >>>>>>>ndrews%40kcl.ac.uk%7C65ef7af2f2c1455a461a08d3ff3a0395%7C8370cf1416f3 >>>>>>>4c >>>>>>> 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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