Hi Ali

What directory are you running from?  You need to specify the full paths

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Alison McDonnell
Sent: Thursday, December 9, 2021 11:11 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FREESURFER

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Hi Bruce, 

Thank you for clearing up the differences. Im getting an error to say there is no such file and that couldn't open the file. was wondering if you had any ideas why this would be as I can see the file in the folder. 

Thanks, 

Ali 

On Thu, 9 Dec 2021 at 15:33, Fischl, Bruce <BFISCHL@mgh.harvard.edu> wrote:

Hi Ali

mris_convert converts surface while mri_convert converts volumes (in general these prefixes hold across all our binaries – the mris_ ones do surfaces and the mri_ ones do volumes).

To convert a patch you need to tell mris_convert that it is a patch and not a complete surface by giving the -p flag

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Alison McDonnell
Sent: Thursday, December 9, 2021 9:46 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] FREESURFER

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Hi all, 

I'm trying to use mris_convert and can't get it to work.

current command I'm using:

mris_convert lh.full.flat.patch.3D lh.full.flat.patch.3D.asc

also can't seem to find the difference between mris convert and mri convert so don't know if I should be using that instead.

any advice would be appreciated

thanks, 

Ali 

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