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