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/[email protected]/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 >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [email protected] > 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 [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
