> From: fischl@nmr.mgh.harvard.edu
> To: greve@nmr.mgh.harvard.edu
> CC: pvaltti@hotmail.com; freesurfer@nmr.mgh.harvard.edu; nicks@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Time
>
> or even
>
> freeview -v /path/to/dicomfile
> On Fri, 8 Mar 2013, Douglas N Greve wrote:
>
> >
> > 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/
> >>>
> >
> >
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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