Doug, Never mind. I think I just figured it out!0
Yuko On Dec 12, 2011, at 6:18 PM, Yuko Yotsumoto wrote: > Thanks Doug, > > In the dt_recon help, > >> The bvalues are in a simple text file, one for each direction >> (including b=0). The bvectors (gradient directions) are also in a >> simple text file with three components on each row. These also include >> the b=0 values. There must be as many rows in the bvals/bvecs >> as there are frames in the input. > > > I got the bvectors from Siemens tech. The file looks similar to one in > $FREESURFER_HOME/diffusion/mgh-dti-seqpack > > However, I am still not sure about bvalues. > >> The bvalues are in a simple text file, one for each direction >> (including b=0). > > > I think I'm using b-value=700, and I have 64 directions. > Should I have b-values for each of the 64 directions? Then the text file > should have 64 rows and each row has the same value? > > Thank you for your help! > Yuko > > > On Dec 10, 2011, at 1:42 PM, Douglas Greve wrote: > >> 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
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