OK.

Thanks ! ;)

> Date: Fri, 8 Mar 2013 13:16:10 -0500
> From: greve@nmr.mgh.harvard.edu
> To: pvaltti@hotmail.com
> CC: nicks@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Time
>
>
> No, you can just run tkmedit -f subject/mri/orig/001.mgz
> You do not need to run recon-all to get a volume, you can just run
> mri_convert, eg
> mri_convert /path/to/dicomfile out.mgz
> tkmedit -f out.mgz
>
> doug
>
> On 03/08/2013 12:54 PM, Valtina Pouegue wrote:
> > If i'm right, the command: > recon-all -s 13A -all execute the whole
> > segmentation ( between 20-40 hours).
> > So , if I just want the see the volume, I have to to the segmentation
> > [ absolutely] ?
> > VP
> >
> > > Date: Fri, 8 Mar 2013 12:36:34 -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
> > >
> > > You will need to run the full processing stream. You can do that from
> > > the beginning with
> > >
> > > recon-all -i $SUBJECTS_DIR/Patient13A/IM-0006--2095457776-0001.dcm -s
> > > 13A -all
> > >
> > > but now that you have a file there, you can run
> > >
> > > recon-all -s 13A -all
> > >
> > > doug
> > >
> > >
> > > On 03/08/2013 12:31 PM, Valtina Pouegue wrote:
> > > > I convert my set of DICOM of the folder 'Patient13A'
> > > > ------------
> > > > [esther@IP132-207-67-224 ~]$ recon-all -i
> > > > $SUBJECTS_DIR/Patient13A/IM-0006--2095457776-0001.dcm -s 13A
> > > > 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/13A
> > > >
> > > > 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
> > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> > > > reading from
> > > >
> > /home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--2095457776-0001.dcm...
> > > > Starting DICOMRead2()
> > > > dcmfile =
> > > >
> > /home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--2095457776-0001.dcm
> > > > dcmdir = /home/esther/Freesurfer/freesurfer/subjects/Patient13A
> > > > Ref Series No = 7
> > > > Found 23 files, checking for dicoms
> > > > Found 21 dicom files in series.
> > > > First Sorting
> > > > Computing Slice Direction
> > > > Vs: -0.598129 1.13977 6.88063
> > > > Vs: -0.0854471 0.162824 0.982948
> > > > Second Sorting
> > > > Counting frames
> > > > nframes = 1
> > > > nslices = 21
> > > > ndcmfiles = 21
> > > > PE Dir = ROW (dicom read)
> > > > TransferSyntaxUID: --1.2.840.10008.1.2.1--
> > > > Loading pixel data
> > > > TR=500.00, TE=9.00, TI=0.00, flip angle=90.00
> > > > i_ras = (-0.992199, 0.0759614, 0.0988506)
> > > > j_ras = (-0.0907614, -0.983726, -0.155063)
> > > > k_ras = (0.0854471, -0.162824, 0.982948)
> > > > writing to
> > > > /home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig/001.mgz...
> > > >
> > > > #------------------------------------------
> > > >
> > > > recon-all -s 13A finished without error at Fri Mar 8 11:37:30 EST 2013
> > > > done
> > > > ------------------------------
> > > > After i executed the tkmedit..........
> > > > VP
> > > > > 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
> > >
> > > --
> > > 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/
> > >
>
> --
> 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