Not sure. We are trying to get away from .w files for this reason. Can you use something other than a w file?
On 11/8/16 12:35 PM, Andrews, Derek wrote: > 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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