The ROI volume is not binary however I binarized it after mapping to the surface space. Should I have binarized the ROI prior to running mri_vol2surf?
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 15:59, "dgw" <dgwake...@gmail.com> wrote: >another thing to check is that you are using a binary ROI file. The >Volume based image looked like it had a range of values. > >hth >d > >On Fri, Oct 28, 2016 at 10:53 AM, 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%7Cdere >>>>k.a >>>> >>>> >>>>ndrews%40kcl.ac.uk%7C65ef7af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c1 >>>>6b8 >>>> >>>> >>>>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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