Thanks Bruce, recon-all finished process without error.

Regards,
Anup

Date: Wed, 14 Jun 2017 10:25:20 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all exits with error at
        surf/lh.thickness, mghRead looks for .mgh/.mgz filename extension
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <alpine.LRH.2.20.1706141024260.28087@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed

Hi Anup

I suspect the problem is choosing a subject with ".mgz" in the ID. I
wouldn't include any of ".nii" ".mgz" or ".mgh" in a subject ID. Try
rerunning and just using fsMM

cheers
Bruce


On Wed, 14 Jun 2017, Anup Bidesi wrote:

>
> Hello FreeSurfer Users,
>
> New to Freesurfer, I'm attempting to recon-all using :
>
> recon-all -all -i T1.nii -s op.nii.mgz  (Attached recon-all log)
>
> The automated process begins normally and seems to run Autorecon Prrocessing
>  Stages 1-25, but at step 26
> (I think) and then exits with Error, per log as seen below:
>
> -------------------------------------------------------------
>
> mghRead(/home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/surf/lh.th
> ickness,
> -1): could not open file.
>  Filename extension must be .mgh, .mgh.gz
> or .mgz
>
> -------------------------------------------------------------
>
> Within the subject .mgz folder in Surf there was a tmp.pctsurfcon.14807 fold
> er with
> a file named lh.wm.mgh (size 569 kb).
>
> I ran this process a couple of times and the autorecon process would exit at
>  same step.I
> tried looking up the Archive for any similar previous error messages but did
>  not find any.
> Please advise.
>
> 1) FreeSurfer version:
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>
> 2) Platform: Ubuntu 14.04
>
> 3) uname -a: Linux brainmindengineer-Precision-Tower-7910 3.13.0-117-generic
>  #164-Ubuntu
> SMP Fri Apr 7 11:05:26 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
>
> 4) recon-all.log: see attached
>
> Thanks for your help,
>
> Anup