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
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-- 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/
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-- 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/