Hi Jon - You'll the aparc+aseg.mgz (cortical parcellation + subcortical segmentation). The basis of TRACULA is that it uses the underlying anatomy to reconstruct the tracts.
a.y On Tue, 12 Feb 2013, Jon Wieser wrote: > no i have not run recon-all yet on this dataset, > do i need to run recon-all with -autorecon1 ,-autorecon2, and -autorecon3 > before i analyze the dti data? > > thanks > 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 3:34:19 PM > Subject: Re: [Freesurfer] trac-all problem > > > Hi Jon - Have you run freesurfer (recon-all) on your T1 data? > > a.y > > On Tue, 12 Feb 2013, Jon Wieser wrote: > >> i got past the problem with the bvesc, and bvals, >> >> >> my current output has a new problem: >> here's the last part of the output. >> >> >> >> #@# Tensor fit Tue Feb 12 15:24:51 CST 2013 >> dtifit -k /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz -m >> /Studies/MJMRI/MJ0012/freesurfer/dlabel/diff/lowb_brain_mask.nii.gz -r >> /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs -b >> /Studies/MJMRI/MJ0012/freesurfer/dmri/bvals -o >> /Studies/MJMRI/MJ0012/freesurfer/dmri/dtifit >> 0 256 0 256 0 60 >> 0 slices processed >> 1 slices processed >> 2 slices processed >> 3 slices processed >> 4 slices processed >> 5 slices processed >> 6 slices processed >> 7 slices processed >> 8 slices processed >> 9 slices processed >> 10 slices processed >> 11 slices processed >> 12 slices processed >> 13 slices processed >> 14 slices processed >> 15 slices processed >> 16 slices processed >> 17 slices processed >> 18 slices processed >> 19 slices processed >> 20 slices processed >> 21 slices processed >> 22 slices processed >> 23 slices processed >> 24 slices processed >> 25 slices processed >> 26 slices processed >> 27 slices processed >> 28 slices processed >> 29 slices processed >> 30 slices processed >> 31 slices processed >> 32 slices processed >> 33 slices processed >> 34 slices processed >> 35 slices processed >> 36 slices processed >> 37 slices processed >> 38 slices processed >> 39 slices processed >> 40 slices processed >> 41 slices processed >> 42 slices processed >> 43 slices processed >> 44 slices processed >> 45 slices processed >> 46 slices processed >> 47 slices processed >> 48 slices processed >> 49 slices processed >> 50 slices processed >> 51 slices processed >> 52 slices processed >> 53 slices processed >> 54 slices processed >> 55 slices processed >> 56 slices processed >> 57 slices processed >> 58 slices processed >> 59 slices processed >> #------------------------------------- >> #@# Priors Tue Feb 12 15:26:36 CST 2013 >> /Applications/freesurfer/bin/dmri_train --outdir >> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni --out lh.cst_AS_avg23_mni_flt >> rh.cst_AS_avg23_mni_flt lh.ilf_AS_avg23_mni_flt rh.ilf_AS_avg23_mni_flt >> lh.unc_AS_avg23_mni_flt rh.unc_AS_avg23_mni_flt fmajor_PP_avg23_mni_flt >> fminor_PP_avg23_mni_flt lh.atr_PP_avg23_mni_flt rh.atr_PP_avg23_mni_flt >> lh.cab_PP_avg23_mni_flt rh.cab_PP_avg23_mni_flt lh.ccg_PP_avg23_mni_flt >> rh.ccg_PP_avg23_mni_flt lh.slfp_PP_avg23_mni_flt rh.slfp_PP_avg23_mni_flt >> lh.slft_PP_avg23_mni_flt rh.slft_PP_avg23_mni_flt --slist >> /tmp/subj23.freesurfer.92196.txt --trk dlabel/mni/lh.cst_AS.flt.trk >> dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk >> dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk >> dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk >> dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk >> dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk >> dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk >> dlabel/mni/rh.ccg_PP.flt.trk > dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk > dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg > dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 > 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois > dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz > dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz > dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz > dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz > dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz > dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz > dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz > dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz > dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz > dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dl > abel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2! > .flt.nii > .gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz > dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz > dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz > dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz > dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz > dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz > dlabel/mni/rh.slft_PP_roi1.flt.nii.gz dlabel/mni/rh.slft_PP_roi2.flt.nii.gz > --bmask > /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lowb_brain_mask.flt.nii.gz --fa > /Studies/MJMRI/MJ0012/freesurfer/dmri/mni/dtifit_FA.flt.nii.gz --ncpts 5 > --debug >> ERROR: fio_pushd: /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni >> ERROR: must specify brain mask volume for output subject >> 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 15:26:36 CST 2013 >> >> >> >> >> >> what is the brainmask volume that it is looking for? >> >> >> >> >> ----- 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 1:26:55 PM >> Subject: Re: [Freesurfer] trac-all problem >> >> >> 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
