[esther@IP132-207-67-224 ~]$ recon-all -i $SUBJECTS_DIR/Patient13A/IM-0006--2095457776-0001.dcm -s 13A
Linux IP132-207-67-224 3.4.6-2.fc17.x86_64 #1 SMP Thu Jul 19 22:54:16 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
mri_convert /home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--2095457776-0001.dcm /home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig/001.mgz
mri_convert /home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--2095457776-0001.dcm /home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig/001.mgz
reading from /home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--2095457776-0001.dcm...
dcmfile = /home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--2095457776-0001.dcm
Found 21 dicom files in series.
writing to /home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig/001.mgz...
After i executed the tkmedit..........
> Date: Fri, 8 Mar 2013 12:26:14 -0500
> From: greve@nmr.mgh.harvard.edu
> To: pvaltti@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu; nicks@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Time
>
> Does that file exist? What was your command to create the mgz file?
> On 03/08/2013 12:12 PM, Valtina Pouegue wrote:
> > Hi,
> > I convert my files and i get news folders with one file with the
> > extension .mgz in the folder orig. But , when i try to loasd the
> > volume, I get an error
> > -------------
> > [esther@IP132-207-67-224 ~]$ tkmedit 13A orig.mgz
> > mghRead(/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
> > <mailto: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 <mailto:greve@nmr.mgh.harvard.edu>
> > > To: pvaltti@hotmail.com <mailto:pvaltti@hotmail.com>;
> > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu>
> > > Phone Number: 617-724-2358
> > > Fax: 617-726-7422
> > >
> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > >
> > > The information in this e-mail is intended only for the person
> > to whom it is
> > > addressed. If you believe this e-mail was sent to you in error
> > and the e-mail
> > > contains patient information, please contact the Partners
> > Compliance HelpLine at
> > > http://www.partners.org/complianceline . If the e-mail was sent
> > to you in error
> > > but does not contain patient information, please contact the
> > sender and properly
> > > dispose of the e-mail.
> > >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > _______________________________________________ Freesurfer mailing
> > list Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The
> > information in this e-mail is intended only for the person to whom it
> > is addressed. If you believe this e-mail was sent to you in error and
> > the e-mail contains patient information, please contact the Partners
> > Compliance HelpLine at http://www.partners.org/complianceline . If the
> > e-mail was sent to you in error but does not contain patient
> > information, please contact the sender and properly dispose of the e-mail.
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer