Hi, I convert my files and i get news folders with one file with the extension .mgz in the folder orig. But , when i try to loasd the volume, I get an error -------------[esther@IP132-207-67-224 ~]$ tkmedit 13A orig.mgzmghRead(/home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig.mgz, -1): could not open file
Error: Loading volume orig.mgz Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size.------------------- could you please help me ? VP
From: nicks@nmr.mgh.harvard.edu Date: Thu, 7 Mar 2013 21:11:31 -0500 To: pvaltti@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu; greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Time
yes, if you give it the filename of the first .dcm in the series, the software will find the other slices and create the .mgz.
On Mar 7, 2013, at 9:02 PM, Valtina Pouegue pvaltti@hotmail.com wrote:
Oh yes. It's my mistake. But should I give the adress of the first file of my set for having the result in .mgz. Thanks.
Date: Thu, 7 Mar 2013 16:00:53 -0500 From: greve@nmr.mgh.harvard.edu To: pvaltti@hotmail.com; Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Time
You cannot give recon-all a folder as input. It must be an image file. If you have multiple files, you need multiple -i flags. doug
On 03/07/2013 03:48 PM, Valtina Pouegue wrote:
Hi, Here it is [esther@IP132-207-67-224 ~]$ recon-all -i /home/esther/Freesurfer/freesurfer/subjects/Patient13B -s 13B Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 INFO: SUBJECTS_DIR is /home/esther/Freesurfer/freesurfer/subjects Actual FREESURFER_HOME /home/esther/Freesurfer/freesurfer Linux IP132-207-67-224 3.4.6-2.fc17.x86_64 #1 SMP Thu Jul 19 22:54:16 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux /home/esther/Freesurfer/freesurfer/subjects/13B
mri_convert /home/esther/Freesurfer/freesurfer/subjects/Patient13B /home/esther/Freesurfer/freesurfer/subjects/13B/mri/orig/001.mgz
mri_convert /home/esther/Freesurfer/freesurfer/subjects/Patient13B /home/esther/Freesurfer/freesurfer/subjects/13B/mri/orig/001.mgz corRead(): can't open file /home/esther/Freesurfer/freesurfer/subjects/Patient13B/COR-.info $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/esther/Freesurfer/freesurfer/subjects/Patient13B...
VP
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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