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 13ASubject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0INFO: SUBJECTS_DIR is /home/esther/Freesurfer/freesurfer/subjectsActual FREESURFER_HOME /home/esther/Freesurfer/freesurferLinux 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 $reading from /home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--2095457776-0001.dcm...Starting DICOMRead2()dcmfile = /home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--2095457776-0001.dcmdcmdir = /home/esther/Freesurfer/freesurfer/subjects/Patient13ARef Series No = 7Found 23 files, checking for dicomsFound 21 dicom files in series.First SortingComputing Slice DirectionVs: -0.598129 1.13977 6.88063Vs: -0.0854471 0.162824 0.982948Second SortingCounting framesnframes = 1nslices = 21ndcmfiles = 21PE Dir = ROW (dicom read)TransferSyntaxUID: --1.2.840.10008.1.2.1--Loading pixel dataTR=500.00, TE=9.00, TI=0.00, flip angle=90.00i_ras = (-0.992199, 0.0759614, 0.0988506)j_ras = (-0.0907614, -0.983726, -0.155063)k_ras = (0.0854471, -0.162824, 0.982948)writing to /home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig/001.mgz... #------------------------------------------ recon-all -s 13A finished without error at Fri Mar 8 11:37:30 EST 2013done------------------------------After i executed the tkmedit..........VP
Date: Fri, 8 Mar 2013 12:26:14 -0500 From: greve@nmr.mgh.harvard.edu To: pvaltti@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu; nicks@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Time
Does that file exist? What was your command to create the mgz file? On 03/08/2013 12:12 PM, Valtina Pouegue wrote:
Hi, I convert my files and i get news folders with one file with the extension .mgz in the folder orig. But , when i try to loasd the volume, I get an error
[esther@IP132-207-67-224 ~]$ 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