Hi Yuko, it will get the bvals and bvecs from a set of tables distributed with FS. But the dicom has to have some information in it that tells it which table to use. It looks like your dicom did not have this information (it is not in the info dump created from the dicom). So you'll have to create text files of the bval/bvecs. The expected format is given in the help. You'll have to ask someone who knows about your sequences as to what the actual values you should use. doug
On 12/9/11 10:09 PM, Yuko Yotsumoto wrote: > Hi Doug, > > Thank you for your reply. >> If so, then it cannot extract the bvecs and bvals. If you supply them in a >> file on the command line > I don't quite understand how --b works with dt_recon. > > I did: > dt_recon --i > /Users/yuko/Documents/FreeSurfer/raw/AGY11ADTI/DTIs/IM-0011-0001.dcm --s > AGY11 --o /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A > > and it stopped after creating dwi.nii and dwi-ec.nii. > I thought dt_recon is the command to compute bvals and bvecs. How do I supply > bvecs and bvals on the command line? > > Yuko > > > On Dec 10, 2011, at 2:24 AM, Douglas N Greve wrote: > >> Hi Yuko, your dicom file might be from a different versioned scanner than >> dt_recon is used to seeing. If so, then it cannot extract the bvecs and >> bvals. If you supply them in a file on the command line, it should run >> properly. >> doug >> >> Yuko Yotsumoto wrote: >>> Hello, >>> >>> I'm having a problem with dt_recon on data scanned by Siemens TrioTim. >>> I'm using v4.5.0, with Mac OS 10.6.8. >>> >>> dt_recon ran for a while, and stopped with an error "ERROR: cannot extract >>> sWiPMemBlock.alFree[8] from >>> /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat" >>> >>> I found the same errors reported to this mailing list, but found no >>> solution. >>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019755.html >>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07935.html >>> >>> In YDTI/YD11A/ folder, I have the following files >>> dt_recon.log >>> dwi-ec.ecclog >>> dwi-ec.nii >>> dwi-infodump.dat >>> dwi.nii >>> mri_glmfit.log >>> >>> In dwi-infodump.dat, I see bunch of lines, but I don't see >>> "sWiPMemBlock.alFree". >>> >>> Please help! >>> Thanks, >>> Yuko Yotsumoto >>> >>> >>> >>> >>> #@#------------------------------- >>> Fitting Tensors >>> Wed Dec 7 10:15:52 JST 2011 >>> cd /Users/yuko/Documents/FreeSurfer/subjects >>> mri_glmfit --y >>> /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii --glmdir >>> /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A --dti >>> /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat >>> >>> $Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $ >>> cwd /Users/yuko/Documents/FreeSurfer/subjects >>> cmdline mri_glmfit --y >>> /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii --glmdir >>> /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A --dti >>> /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat >>> sysname Darwin >>> hostname Yukos-iMac.local >>> machine i386 >>> user yuko >>> FixVertexAreaFlag = 1 >>> UseMaskWithSmoothing 1 >>> OneSampleGroupMean 0 >>> y /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii >>> logyflag 1 >>> X /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat >>> usedti 1 >>> glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A >>> IllCondOK 0 >>> DoFFx 0 >>> Creating output directory >>> /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A >>> Loading y from >>> /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii >>> Using DTI >>> bValue = 700 >>> ERROR: cannot extract sWiPMemBlock.alFree[8] from >>> /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat >>> >>> >>> _______________________________________________ >>> 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 >> gr...@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 >> >> >> >> 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
