VP,I try FreeView,, tit<s really nice!I dont really know what going on, i try mri-convert with another subject aand i get this:--------------------[esther@IP132-207-67-224 /]$ mri_convert $SUBJECTS_DIR/Patient3B/IM-0007--2095579184-0001.dcm out.mgzmri_convert /home/esther/Freesurfer/freesurfer/subjects/Patient3B/IM-0007--2095579184-0001.dcm out.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $reading from /home/esther/Freesurfer/freesurfer/subjects/Patient3B/IM-0007--2095579184-0001.dcm...Starting DICOMRead2()dcmfile = /home/esther/Freesurfer/freesurfer/subjects/Patient3B/IM-0007--2095579184-0001.dcmdcmdir = /home/esther/Freesurfer/freesurfer/subjects/Patient3BRef Series No = 9Found 22 files, checking for dicomsFound 20 dicom files in series.First SortingComputing Slice DirectionVs: 0.260945 -0.596504 6.96965Vs: 0.0372779 -0.0852149 0.995665Second SortingCounting framesnframes = 1nslices = 20ndcmfiles = 20PE Dir = ROW (dicom read)TransferSyntaxUID: --1.2.840.10008.1.2.1--Loading pixel dataTR=466.66, TE=9.00, TI=0.00, flip angle=90.00i_ras = (-0.9993, -0, -0.0374158)j_ras = (-0.00317395, -0.996363, 0.0851462)k_ras = (-0.0372779, 0.0852149, 0.995665)writing to out.mgz...mghWrite(out.mgz, -1): could not open fileERROR: failure writing out.mgz[esther@IP132-207-67-224 /]$ ------------------ I thiought that the software automatically created the out.mgz....
Date: Fri, 8 Mar 2013 13:39:51 -0500 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer