Hi Jon - This is the same issue. The reading from the dicom part will work for the Siemens dicoms that we have here but is not guaranteed to work with other dicoms. You'll have to define bvecfile, bvalfile, and nb0. (The first two should be in columns, not rows.)
Let me know if you run into any other problems, a.y On Tue, 12 Feb 2013, Jon Wieser wrote: > i ran the program with the nb0 set to 2 > > i got the following error: it's not finding a bvec files. the document says > that the bevecs are read from the DICOM headers. here's the output of the run > > > : > INFO: SUBJECTS_DIR is /Studies/MJMRI/MJ0012 > INFO: Diffusion root is /Studies/MJMRI/MJ0012 > Actual FREESURFER_HOME /Applications/freesurfer > trac-preproc -c /Studies/MJMRI/MJ0012/freesurfer/scripts/dmrirc.local -log > /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.log -cmd > /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.cmd > #------------------------------------- > /Applications/freesurfer/bin/trac-preproc > #------------------------------------- > #@# Image corrections Tue Feb 12 13:00:35 CST 2013 > mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 > /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz > mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 > /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading from /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1... > Starting DICOMRead2() > dcmfile = /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 > dcmdir = /Studies/MJMRI/MJ0012//s780 > Ref Series No = 13 > Found 3304 files, checking for dicoms > Found 3300 dicom files in series. > First Sorting > Computing Slice Direction > Vs: 0 0 2 > Vs: 0 0 1 > Second Sorting > Counting frames > nframes = 55 > nslices = 60 > ndcmfiles = 3300 > PE Dir = COL (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > jpegUID: --1.2.840.10008.1.2.4-- > Loading pixel data > TR=9300.00, TE=76.20, TI=0.00, flip angle=90.00 > i_ras = (-1, 0, 0) > j_ras = (0, -1, 0) > k_ras = (-0, -0, 1) > writing to /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz... > mri_probedicom --i /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 > > /Studies/MJMRI/MJ0012/freesurfer/dmri/dcminfo.dat > flip4fsl /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz > /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz > INFO: input image orientation is LPS > INFO: input image determinant is 2 > fslswapdim /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz x -y z > /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz > INFO: left-right orientation was flipped by fslswapdim > fslorient -forceradiological > /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz > mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvecs > /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs > mv: rename /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvecs > to /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs: No such file or directory > Darwin psy-cerebellum.uits.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue > Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 > > trac-preproc exited with ERRORS at Tue Feb 12 13:05:29 CST 2013 > > > > > > > ----- Original Message ----- > From: "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu> > To: "Jon Wieser" <wie...@uwm.edu> > Sent: Tuesday, February 12, 2013 11:24:56 AM > Subject: Re: [Freesurfer] trac-all problem > > > Yeah, the tutorial should say "Siemens dicoms" instead of "dicoms". In any > case in the next version this won't be a problem b/c it'll determine the > nb0 from the bvals file. > > On Tue, 12 Feb 2013, Jon Wieser wrote: > >> hi >> our scanner is a GE >> Jon >> >> ----- Original Message ----- >> From: "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu> >> To: "Jon Wieser" <wie...@uwm.edu> >> Cc: freesurfer@nmr.mgh.harvard.edu >> Sent: Tuesday, February 12, 2013 11:14:42 AM >> Subject: Re: [Freesurfer] trac-all problem >> >> >> Sorry, reading stuff from the dicom header will not work for all dicom >> versions. It should work for Siemens dicoms though. >> >> On Tue, 12 Feb 2013, Jon Wieser wrote: >> >>> according to the >>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula >>> >>> nb0 does not need to be specified when using original dicoms. , but i'll >>> try defining the nb0 variable >>> thanks >>> Jon >>> >>> >>> ----- Original Message ----- >>> From: "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu> >>> To: "Jon Wieser" <wie...@uwm.edu> >>> Cc: "freesurfer" <freesurfer@nmr.mgh.harvard.edu> >>> Sent: Tuesday, February 12, 2013 10:49:18 AM >>> Subject: Re: [Freesurfer] trac-all problem >>> >>> >>> Hi Jon - My guess is you didn't define the nb0 variable in your >>> configuration file, see here: >>> http://www.freesurfer.net/fswiki/dmrirc >>> >>> The new version, which will come out in a few days, will be able to figure >>> it out without you having to specify it but with the current version you >>> have to. >>> >>> Hope this helps, >>> a.y >>> >>> On Tue, 12 Feb 2013, Jon Wieser wrote: >>> >>>> hello >>>> >>>> i am trying to process the dti data with trac-all. I am new to tracula >>>> my input images are 3300 dicoms, 60 slices and 55 dti diffusions >>>> i have attached my dmrirc_single_subject file >>>> >>>> >>>> i did the following command: >>>> >>>> trac-all -prep -c /Studies/MJMRI/DTI/dmrirc_single_subject >>>> >>>> and got the result: >>>> >>>> >>>> >>>> INFO: SUBJECTS_DIR is /Studies/MJMRI/MJ0012 >>>> INFO: Diffusion root is /Studies/MJMRI/MJ0012 >>>> Actual FREESURFER_HOME /Applications/freesurfer >>>> trac-preproc -c /Studies/MJMRI/MJ0012/freesurfer/scripts/dmrirc.local -log >>>> /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.log -cmd >>>> /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.cmd >>>> #------------------------------------- >>>> /Applications/freesurfer/bin/trac-preproc >>>> #------------------------------------- >>>> #@# Image corrections Mon Feb 11 12:41:04 CST 2013 >>>> mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 >>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz >>>> mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 >>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz >>>> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ >>>> reading from /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1... >>>> Starting DICOMRead2() >>>> dcmfile = /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 >>>> dcmdir = /Studies/MJMRI/MJ0012//s780 >>>> Ref Series No = 13 >>>> Found 3304 files, checking for dicoms >>>> Found 3300 dicom files in series. >>>> First Sorting >>>> Computing Slice Direction >>>> Vs: 0 0 2 >>>> Vs: 0 0 1 >>>> Second Sorting >>>> Counting frames >>>> nframes = 55 >>>> nslices = 60 >>>> ndcmfiles = 3300 >>>> PE Dir = COL (dicom read) >>>> TransferSyntaxUID: --1.2.840.10008.1.2.1-- >>>> jpegUID: --1.2.840.10008.1.2.4-- >>>> Loading pixel data >>>> TR=9300.00, TE=76.20, TI=0.00, flip angle=90.00 >>>> i_ras = (-1, 0, 0) >>>> j_ras = (0, -1, 0) >>>> k_ras = (-0, -0, 1) >>>> writing to /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz... >>>> mri_probedicom --i /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 > >>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/dcminfo.dat >>>> flip4fsl /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz >>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz >>>> INFO: input image orientation is LPS >>>> INFO: input image determinant is 2 >>>> fslswapdim /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz x -y z >>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz >>>> INFO: left-right orientation was flipped by fslswapdim >>>> fslorient -forceradiological >>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz >>>> INFO: found /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.mghdti.bvals, >>>> converting to FSL format >>>> INFO: found /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.mghdti.bvecs, >>>> converting to FSL format >>>> mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvecs >>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs >>>> mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvals >>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/bvals >>>> eddy_correct /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz >>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz 0 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0000 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0001 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0002 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0003 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0004 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0005 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0006 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0007 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0008 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0009 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0010 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0011 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0012 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0013 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0014 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0015 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0016 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0017 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0018 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0019 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0020 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0021 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0022 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0023 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0024 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0025 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0026 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0027 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0028 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0029 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0030 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0031 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0032 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0033 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0034 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0035 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0036 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0037 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0038 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0039 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0040 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0041 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0042 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0043 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0044 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0045 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0046 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0047 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0048 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0049 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0050 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0051 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0052 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0053 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0054 >>>> mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs >>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs.norot >>>> xfmrot /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.ecclog >>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs.norot >>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs >>>> fslroi /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz >>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/lowb.nii.gz 0 >>>> >>>> Usage: fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> >>>> fslroi <input> <output> <tmin> <tsize> >>>> >>>> fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> >>>> <tmin> <tsize> >>>> Note: indexing (in both time and space) starts with 0 not 1! >>>> Darwin psy-cerebellum.uits.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: >>>> Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 >>>> >>>> trac-preproc exited with ERRORS at Mon Feb 11 13:25:16 CST 2013 >>>> >>>> >>>> can you tell me how to fix this? >>>> Thanks >>>> Jon Wieser >>>> UW-Milwaukee >>>> >>> >>> >>> 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
