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/