The memory error was in the -path part, that's what you should try rerunning. What you downloaded will have no effect on bedpostx itself.
> i just downloaded dmri_5.1_snow_leopard.tar.gz: from that web page and > installed the new version of the dmri file in the freessurfer /boin > directory > I'm rerunning trac-all -bedp > thanks for your help > Jon > > ----- Original Message ----- > From: "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu> > To: "Jon Wieser" <wie...@uwm.edu> > Cc: freesurfer@nmr.mgh.harvard.edu > Sent: Monday, February 18, 2013 5:07:38 PM > Subject: Re: [Freesurfer] Fwd: trac-all problem > > > Hi Jon - There was an updated build of the tracula executables > specifically for macos users that was posted a while back. See the tracula > wiki page: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula > > Better yet, wait for 5.2 to be released later this week! > > a.y > > On Mon, 18 Feb 2013, Jon Wieser wrote: > >> >> I'm using freesurfer 5.1 >> >> Jon >> >> ----- Original Message ----- >> From: "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu> >> To: "Jon Wieser" <wie...@uwm.edu> >> Cc: freesurfer@nmr.mgh.harvard.edu >> Sent: Monday, February 18, 2013 4:41:15 PM >> Subject: Re: [Freesurfer] Fwd: trac-all problem >> >> >> Hi Jon - So the files are there but there's to be a memory allocation >> problem. Are you using the updated mac build from the tracula wiki page >> or >> the one that was originally released with freesurfer 5.1? >> >> a.y >> >> On Mon, 18 Feb 2013, Jon Wieser wrote: >> >>> Hi , >>> >>> i have the following files in my dmri.bedpostX directory >>> >>> >>> bvals dyads2.nii.gz >>> mean_f2samples.nii.gz merged_f1samples.nii.gz >>> merged_th2samples.nii.gz >>> bvecs dyads2_dispersion.nii.gz >>> mean_ph1samples.nii.gz merged_f2samples.nii.gz monitor >>> commands.txt logs >>> mean_ph2samples.nii.gz merged_ph1samples.nii.gz >>> nodif_brain_mask.nii.gz >>> dyads1.nii.gz mean_dsamples.nii.gz >>> mean_th1samples.nii.gz merged_ph2samples.nii.gz xfms >>> dyads1_dispersion.nii.gz mean_f1samples.nii.gz >>> mean_th2samples.nii.gz merged_th1samples.nii.gz >>> >>> 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: Monday, February 18, 2013 3:51:40 PM >>> Subject: Re: [Freesurfer] Fwd: trac-all problem >>> >>> >>> Hi Jon - There's a list of all bedpostx output files here: >>> http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_bedpostx.html >>> >>> Do you see these files in the dmri.bedpostX directory? >>> >>> a.y >>> >>> On Mon, 18 Feb 2013, Jon Wieser wrote: >>> >>>> >>>> >>>> >>>> >>>> I ran trac-all -bedp -c /Studies/MJMRI/DTI/dmrirc_single_subject >>>> the end of the output was: >>>> >>>> >>>> 52 slices processed >>>> 52 slices processed >>>> 53 slices processed >>>> 53 slices processed >>>> 54 slices processed >>>> 54 slices processed >>>> 55 slices processed >>>> 55 slices processed >>>> 56 slices processed >>>> 57 slices processed >>>> 58 slices processed >>>> Queuing post processing stage >>>> 60 slices processed >>>> All slices processed >>>> /Applications/freesurfer/bin/bedpostx_seychelles: line 281: kill: >>>> (35687) - No such process >>>> >>>> >>>> >>>> is this normal? >>>> >>>> >>>> >>>> then I ran trac-all -path -c /Studies/MJMRI/DTI/dmrirc_single_subject >>>> >>>> it ended in an error >>>> >>>> Here's the last part of the trac-all -path output: >>>> >>>> Neighbor aseg label ID list: >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.cst_AS_avg23_mni_flt_fsnnids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.cst_AS_avg23_mni_flt_fsnnids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.ilf_AS_avg23_mni_flt_fsnnids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.ilf_AS_avg23_mni_flt_fsnnids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.unc_AS_avg23_mni_flt_fsnnids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.unc_AS_avg23_mni_flt_fsnnids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/fmajor_PP_avg23_mni_flt_fsnnids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/fminor_PP_avg23_mni_flt_fsnnids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.atr_PP_avg23_mni_flt_fsnnids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.atr_PP_avg23_mni_flt_fsnnids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.cab_PP_avg23_mni_flt_fsnnids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.cab_PP_avg23_mni_flt_fsnnids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/l > h >> . >>> ccg_PP_avg23_mni_flt_fsnnids >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.ccg_PP_avg23_mni_flt_fsnnids >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.slfp_PP_avg23_mni_flt_fsnnids >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.slfp_PP_avg23_mni_flt_fsnnids >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.slft_PP_avg23_mni_flt_fsnnids >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.slft_PP_avg23_mni_flt_fsnnids >>>> Local aseg prior: >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.cst_AS_avg23_mni_flt_fsprior >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.cst_AS_avg23_mni_flt_fsprior >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.ilf_AS_avg23_mni_flt_fsprior >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.ilf_AS_avg23_mni_flt_fsprior >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.unc_AS_avg23_mni_flt_fsprior >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.unc_AS_avg23_mni_flt_fsprior >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/fmajor_PP_avg23_mni_flt_fsprior >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/fminor_PP_avg23_mni_flt_fsprior >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.atr_PP_avg23_mni_flt_fsprior >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.atr_PP_avg23_mni_flt_fsprior >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.cab_PP_avg23_mni_flt_fsprior >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.cab_PP_avg23_mni_flt_fsprior >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.ccg_PP_av > g >> 2 >>> 3_mni_flt_fsprior >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.ccg_PP_avg23_mni_flt_fsprior >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.slfp_PP_avg23_mni_flt_fsprior >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.slfp_PP_avg23_mni_flt_fsprior >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.slft_PP_avg23_mni_flt_fsprior >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.slft_PP_avg23_mni_flt_fsprior >>>> Local aseg label ID list: >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.cst_AS_avg23_mni_flt_fsids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.cst_AS_avg23_mni_flt_fsids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.ilf_AS_avg23_mni_flt_fsids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.ilf_AS_avg23_mni_flt_fsids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.unc_AS_avg23_mni_flt_fsids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.unc_AS_avg23_mni_flt_fsids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/fmajor_PP_avg23_mni_flt_fsids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/fminor_PP_avg23_mni_flt_fsids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.atr_PP_avg23_mni_flt_fsids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.atr_PP_avg23_mni_flt_fsids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.cab_PP_avg23_mni_flt_fsids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.cab_PP_avg23_mni_flt_fsids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.ccg_PP_avg23_mni_flt_fsid > s >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.ccg_PP_avg23_mni_flt_fsids >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.slfp_PP_avg23_mni_flt_fsids >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.slfp_PP_avg23_mni_flt_fsids >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.slft_PP_avg23_mni_flt_fsids >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.slft_PP_avg23_mni_flt_fsids >>>> Segmentation map: >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/aparc+aseg.nii.gz >>>> Type of aseg prior: 0 >>>> DWI-to-atlas affine registration: >>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/xfms/diff2mni.flt.mat >>>> Number of burn-in samples: 200 >>>> Number of post-burn-in samples: 5000 >>>> Keep every: 5-th sample >>>> Update proposal every: 0-th sample >>>> Loading spline control points from >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/diff/lh.cst_AS_avg23_mni_flt_cpts_5.txt >>>> Loading spline mask from >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/diff/aparc+aseg_mask.bbr.nii.gz >>>> Creating output directory >>>> /Studies/MJMRI/MJ0012/freesurfer/dpath/5cpts/priormni/seg14/initmni/regflt/lh.cst_AS_avg23_mni_flt >>>> Loading DWIs from /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz >>>> Loading mask from >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/diff/aparc+aseg_mask.bbr.nii.gz >>>> Loading BEDPOST parameter samples from >>>> /Studies/MJMRI/MJ0012/freesurfer/dmri.bedpostX >>>> dmri_paths(38479) malloc: *** mmap(size=262144) failed (error code=12) >>>> *** error: can't allocate region >>>> *** set a breakpoint in malloc_error_break to debug >>>> MRIalloc(256, 256, 60): could not allocate 262144 bytes for 1193th >>>> slice >>>> >>>> Cannot allocate memory >>>> 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-paths exited with ERRORS at Mon Feb 18 09:14:48 CST 2013 >>>> >>>> >>>> >>>> >>>> how can I fix this? >>>> Jon >>>> >>>> >>>> >>>> >>>> ----- Original Message ----- >>>> From: "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu> >>>> To: "Jon Wieser" <wie...@uwm.edu> >>>> Sent: Thursday, February 14, 2013 1:22:02 PM >>>> Subject: Re: [Freesurfer] trac-all problem >>>> >>>> >>>> Great! >>>> >>>> On Thu, 14 Feb 2013, Jon Wieser wrote: >>>> >>>>> Hi Anastasia, >>>>> >>>>> update on my processing. >>>>> I finished recon-all -autorecon1 ,-autorecon2, and -autorecon3 . >>>>> I finished trac -prep with No errors! >>>>> moving on the Trac-all -bedp >>>>> >>>>> >>>>> 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 3:44:59 PM >>>>> Subject: Re: [Freesurfer] trac-all problem >>>>> >>>>> >>>>> 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 > . >> t >>> r >>>> k >>>>>> 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. > g >> z >>>> d >>>>> l >>>>>> 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 >>>> >>>> >>>> >>> >>> >>> >> >> >> > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
