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Hi Doug,

The alignment between the original Freesurfer white matter file and the output of mris_convert to gifti is different. Here you can see that the original file is well registered to the anatomical, while the gifti version is misaligned.

Cheers, Mason

Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK

Email: WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU

E-bost: WellsMT1@caerdydd.ac.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@MGH.HARVARD.EDU Reply to: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, 6 July 2020 at 16:53 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_convert error

Do you mean that the inflated is not somehow in line with the pial? They are not supposed to be (and it is not clear what that would mean). The white and pial look aligned On 7/6/20 7:16 AM, Mason Wells wrote:

External Email - Use Caution Hi Experts,

I am using mris_convert to convert native FreeSurfer surf files (inflated, pial and white) to GIFTI files. However, when I view them in Freeview, there seems to be a misalignment/error (attached). The commands I ran followed this structure:

Mris_convert lh.inflated lh.inflated.surf.gii

Any help would be great. Mason

Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK

Email: WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://www.cardiff.ac.uk/people/research-students/view/974214- Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU

E-bost: WellsMT1@caerdydd.ac.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

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