Freesurfer February 2013

freesurfer@nmr.mgh.harvard.edu

136 participants
236 discussions

Re: [Freesurfer] Fwd: trac-all problem
by Anastasia Yendiki 18 Feb '13

18 Feb '13

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" <ayendiki(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu> > Cc: freesurfer(a)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" <ayendiki(a)nmr.mgh.harvard.edu> >> To: "Jon Wieser" <wieser(a)uwm.edu> >> Cc: "freesurfer" <freesurfer(a)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/lh > . >> 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_avg > 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_fsids >> /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" <ayendiki(a)nmr.mgh.harvard.edu> >>> To: "Jon Wieser" <wieser(a)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" <ayendiki(a)nmr.mgh.harvard.edu> >>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>> Cc: freesurfer(a)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" <ayendiki(a)nmr.mgh.harvard.edu> >>>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>>> Cc: freesurfer(a)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" <ayendiki(a)nmr.mgh.harvard.edu> >>>>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>>>> Cc: freesurfer(a)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" <ayendiki(a)nmr.mgh.harvard.edu> >>>>>>> To: "Jon Wieser" <wieser(a)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" <ayendiki(a)nmr.mgh.harvard.edu> >>>>>>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>>>>>> Cc: freesurfer(a)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" <ayendiki(a)nmr.mgh.harvard.edu> >>>>>>>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>>>>>>> Cc: "freesurfer" <freesurfer(a)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(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> >> >> > > >

1 0

Re: [Freesurfer] Fwd: trac-all problem
by Anastasia Yendiki 18 Feb '13

18 Feb '13

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" <ayendiki(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu> > Cc: "freesurfer" <freesurfer(a)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/lh. > 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_avg2 > 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_fsids > /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" <ayendiki(a)nmr.mgh.harvard.edu> >> To: "Jon Wieser" <wieser(a)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" <ayendiki(a)nmr.mgh.harvard.edu> >>> To: "Jon Wieser" <wieser(a)uwm.edu> >>> Cc: freesurfer(a)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" <ayendiki(a)nmr.mgh.harvard.edu> >>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>> Cc: freesurfer(a)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.gz >> 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" <ayendiki(a)nmr.mgh.harvard.edu> >>>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>>> Cc: freesurfer(a)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" <ayendiki(a)nmr.mgh.harvard.edu> >>>>>> To: "Jon Wieser" <wieser(a)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" <ayendiki(a)nmr.mgh.harvard.edu> >>>>>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>>>>> Cc: freesurfer(a)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" <ayendiki(a)nmr.mgh.harvard.edu> >>>>>>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>>>>>> Cc: "freesurfer" <freesurfer(a)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(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > >

1 0

Re: [Freesurfer] TRACULA exited with errors
by Anastasia Yendiki 18 Feb '13

18 Feb '13

Hi Fabricio - Any format that the mri_convert command can take as input is fine, so I'd try it on a sample data set and see. If this doesn't work, you'll have to convert your data to nifti in advance, and provide the gradient table and b-value table as well. Hope this helps, a.y On Sun, 17 Feb 2013, FABRICIO FELTRIN wrote: > Hi Anastasia. > > Can I use REC/PAR files from a 3,0T philips scaner in tracula?? > > Thank you. > > Fabrício Feltrin > > > > >

1 0

Fwd: trac-all problem
by Jon Wieser 18 Feb '13

18 Feb '13

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/lh.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_avg23_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_fsids /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" <ayendiki(a)nmr.mgh.harvard.edu> To: "Jon Wieser" <wieser(a)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" <ayendiki(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu> > Cc: freesurfer(a)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" <ayendiki(a)nmr.mgh.harvard.edu> >> To: "Jon Wieser" <wieser(a)uwm.edu> >> Cc: freesurfer(a)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.tr 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.gz 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" <ayendiki(a)nmr.mgh.harvard.edu> >>> To: "Jon Wieser" <wieser(a)uwm.edu> >>> Cc: freesurfer(a)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" <ayendiki(a)nmr.mgh.harvard.edu> >>>> To: "Jon Wieser" <wieser(a)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" <ayendiki(a)nmr.mgh.harvard.edu> >>>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>>> Cc: freesurfer(a)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" <ayendiki(a)nmr.mgh.harvard.edu> >>>>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>>>> Cc: "freesurfer" <freesurfer(a)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. >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>> >>>> >>>> >>> >>> >>> >> >> >> > > >

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download freesurfer
by merlinva2012＠grannet.grm.sld.cu 18 Feb '13

18 Feb '13

Hi, Could somebody say to me if exists some form by means of which I can download the file "freesurfer-Linux-centos4-stable-pub-v5.1.0.tar.gz" in several smaller parts? Greetings, Merlin Verdecia -- Este mensaje le ha llegado mediante el servicio de correo electronico que ofrece Infomed para respaldar el cumplimiento de las misiones del Sistema Nacional de Salud. La persona que envia este correo asume el compromiso de usar el servicio a tales fines y cumplir con las regulaciones establecidas Infomed: http://www.sld.cu/

2 1

Cortical thickness analysis on data acquired from multiple sites
by Sinead Kelly 18 Feb '13

18 Feb '13

Dear members, I would like to get your opinion on this issue - I have a dataset of over 400 subjects but under half of this data was acquired on a 1.5T scanner and the rest was acquired on a 3T scanner. Would it be acceptable to conduct cortical thickness analysis on the combined dataset? From reading the literature it seems that this is not a major problem but I just wanted to get some more thoughts on this. Thank you for your help, Sinead -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8

4 5

question about MRF
by Zhennan Yan 16 Feb '13

16 Feb '13

Dear freesurfer experts, I have questions about the MRF in Freesurfer: (1) I have a T1 image and sub-cortical segmentation for it (nifti format). But the segmentation is not perfect and I would like to relabel it using the ICM algorithm as shown in fig.8 in paper: Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain, Fischl et al., (2002). How can I do this using Freesurfer? (2) If I have several subjects with labels, how can I train the anisotropic nonstationary MRF prior as equation (9) in the same paper? Can I use that MRF prior elsewhere in my own program? Many thanks! Best, Zhennan -- Zhennan Yan Department of Computer Science Rutgers University

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Job: Postdoctoral researcher ‘Mathematical & Computational Modelling for Multi-modal NeuroImaging data’ (1,0 fte) (fwd)
by Bruce Fischl 16 Feb '13

16 Feb '13

FYI ---------- Forwarded message ---------- Date: Sat, 16 Feb 2013 10:07:12 +0100 From: Christian F. Beckmann <c.beckmann(a)donders.ru.nl> To: "<c.beckmann(a)fcdonders.ru.nl> Beckmann" <c.beckmann(a)fcdonders.ru.nl> Subject: Job: Postdoctoral researcher ?Mathematical & Computational Modelling for Multi-modal NeuroImaging data? (1,0 fte) Dear colleagues, I'm sorry to fill your inboxes, but I'm hoping that you might know of suitable candidates for the position below. If you do then please forward and encourage them to apply. With best wishes Christian --------------------------------------------------------------------------- ------------------------------------------------------------------ Postdoctoral researcher ?Mathematical & Computational Modelling for Multi-modal NeuroImaging data? (1,0 fte) http://www.ru.nl/vacatures/details/details_vacature_0?recid=526098 The Statistical Imaging Neuroscience Group at the Donders Institutein Nijmegen (http://www.ru.nl/donders/research/theme-4-brain/research-group s/statistical-imaging/) jointly with FMRIB and OHBA in Oxford has received a 5-year Wellcome Trust Strategic Award to develop Integrated Brain Imaging for Neuroscience Research and Clinical Practice. We are looking for excellent researchers with a strong technical background, ideally in developing Neuroimaging Analysis Methods for FMRI and other modalities. Relevant experience in other areas of Engineering/Applied Mathematics, Statistics, Computer Science and Physics would be considered. The Position: This post is to be filled by a postdoctoral researcher working on the goals of: 1) Computational modelling and inference of functional brain networks and connectivity from multi-modal neuroimaging data; 2) methodology development for data fusion using multi-modal exploratory analysis techniques like Linked-ICA; 3) Network modelling and inference that simultaneously utilizes information from multimodal data including FMRI, MEG and diffusion MRI. The 5 Applicants leading the project are Smith, Jenkinson, Behrens (FMRIB), Woolrich (FMRIB & OHBA, Oxford MEG Centre) and Beckmann (Oxford, Twente & Donders, Netherlands). This post will be supervised by Prof. Christian Beckmann at the Donders Centre for Cognitive Neuroimaging, with strong involvement with the FMRIB analysis group in Oxford (UK). In addition to the specific goals relating to this project, this post?s research will also interact with related goals in the ongoing NIH-funded Human Connectome Project, in which FMRIB is a major partner. Responsibilities/duties ? Carry out leading-edge theoretical research in the areas outlined above. ? Implement theoretical research as practical proof-of-concept algorithms. ? Evaluate and develop the algorithms with both simulated and real datasets. ? Implement the final algorithms in robust, maintainable software linked to, or as part of, FSL. ? Publish all of the above research and development in leading neuroimaging and image processing journals, and present at the major conferences. ? Interact closely with all other group and project members and collaborators to promote the project goals as a whole. As a candidate for the position you will you will be assessed on the basis of the following selection criteria: Essential ? BSc and PhD degrees (or equivalent) in a relevant technical area ? most likely one of: Mathematical Engineering, Electrical Engineering, Applied Mathematics, Computer Science, Machine Learning, Physics, Statistics or Image Processing ? Experience in relevant research areas ? track record of high-quality reviewed journal publications ? Strong experience in programming, ideally in both Matlab and C/C++ ? Strong written and oral English communication skills ? Ability to work well work in a team, sharing technical know-how and ideas. Desirable ? Experience in Medical Imaging (e.g. NeuroImaging) technical research ? Experience in computational modelling of the brain ? Experience in machine learning and statistical methods (e.g. Bayesian models, Independent Component Analysis, Multi-modal data fusion) ? Capacity for independent research The project will last up to 5 years; this post will in the first instance be offered for the first 3 years of the project, and could potentially be renewed. Depending on experience the gross salary will be between ? 3.195 and ? 4.374. On top of the monthly gross salaries two yearly 8% bonuses will be added (holiday and end-of-year). The Host Institute: The Donders Institute for Brain, Cognition and Behaviour consists of the Centre for Cognition, the Centre for Neuroscience and the Centre for Cognitive Neuroimaging (DCCN). The mission of the Centre for Cognitive Neuroimaging is to conduct cutting-edge fundamental research in neuroimaging methodology and cognitive neuroscience. Much of the rapid progress in this field is being driven by the development of complex neuro-imaging techniques for measuring activity in the human working brain - an area in which the Centre plays a leading role. The research themes cover central cognitive functions, such as perception, action, control, decision making, attention, memory, language, learning and plasticity, mathematical modelling of brain function and MR physics development. The internationally renowned centre currently hosts more than 100 PhD students and post-docs from more than 20 different nationalities, offering a stimulating and multidisciplinary research environment. The centre is equipped with four MRI scanners (7T, 2x3T, 1.5T), a 275 channels MEG system, a EEG-TMS laboratory, several (MR-compatible) EEG systems, and high-performance computational facilities. English is the common language at the centre. You will work within the Statistical Imaging Neuroscience (SIN) group(http://www.ru.nl/donders/research/theme-4-brain/research-groups/statistica l-imaging/) The Application Process: For informal enquiries please contact Prof. Christian Beckmann (c.beckmann(a)donders.ru.nl) You should submit an application letter defining your research interests, a CV, and the names of two persons who can provide references. It is Radboud University Nijmegen's policy to only accept applications by e-mail. Please send your application, stating vacancy number 30.02.13, to vacatures(a)dpo.ru.nl, for the attention of Prof. Christian Beckmann, before 3 March 2013. Recruitment will continue until a suitable candidate has been found. For more information on the application procedure: +31 24 3611173 -- Christian F. Beckmann, DPhil Professor for Neuroimaging Analysis | MIRA Institute for Biomedical Technology and Technical Medicine | University of Twente | The Netherlands Principal Investigator: Statistical Imaging Neuroscience | Donders Centre for Cognitive Neuroimaging | Radboud University Nijmegen | The Netherlands Senior Research Fellow | Oxford Centre for Functional Magnetic Resonance Imaging of the Brain (FMRIB) | University of Oxford | UK Hon. Senior Lecturer in MRI Methodology | Computational, Cognitive and Clinical Neuroscience Lab (C3NL) | Imperial College London | UK Mail: P.O. Box 9101 | NL-6500 HB Nijmegen | The Netherlands Visiting: Kapittelweg 29 | NL-6525 EN Nijmegen | The Netherlands Tel/Fax: +31 24 36 10880 / 10989 | e-mail: c.beckmann(a)donders.ru.nl

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Surface area computation
by Shantanu Ghosh 16 Feb '13

16 Feb '13

Hello FreeSurfer experts, Has algorithm described in Winkler et al. (2012) Neuroimage paper for computation of surface area been incorporated in v5.1, or is it part of the 5.2b implementation? Thanks for your help. Shantanu -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging

2 2

Re: [Freesurfer] Convert aseg.mgz to .nii and into MNI space with FSL dimensions
by Douglas N Greve 15 Feb '13

15 Feb '13

mri_label2vol will take segmentations as an input look at the --help doug On 02/15/2013 04:25 PM, Roderick McColl wrote: > Sorry for the bother, but there isn't a label for L or R WM. > Should I use mri_vol2vol on the aseg.mgz file and the mni152.register.dat > file instead i.e. just register aseg.mgz into MNI152 space? > Not sure how to make this use a nearest neighbor interpolation though. > Thanks > -roddy > > -----Original Message----- > From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] > Sent: Friday, February 15, 2013 3:04 PM > To: Roderick McColl > Subject: Re: Convert aseg.mgz to .nii and into MNI space with FSL dimensions > > In that case, use mri_label2vol with the following reg $FREESURFER_HOME/average/mni152.register.dat > doug > > On 02/14/2013 11:02 AM, Roderick McColl wrote: >> Thanks very much. >> I should have made myself clearer. >> I would like to use $FREESURFER_HOME/subjects/fsaverage/mr/aseg.mgz >> for some analysis in MNI512 (FSL) space. >> So should I use mni152reg on the orig.mgz file in that folder to generate the transform? >> -roddy >> >> ________________________________________ >> From: Douglas N Greve [greve(a)nmr.mgh.harvard.edu] >> Sent: Wednesday, February 13, 2013 4:48 PM >> To: Roderick McColl >> Cc: 'Clark Fisher'; freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: Convert aseg.mgz to .nii and into MNI space with FSL >> dimensions >> >> you can use mni152reg to compute the registration to the MNI152 space. >> Make sure to spec the 1mm target. You can then use mri_label2vol to >> map aseg.mgz to the MNI152 space. >> >> doug >> >> On 02/13/2013 03:40 PM, Roderick McColl wrote: >>> Hello all, >>> I have a need to generate LH and RH WM masks for analysis. >>> I can convert aseg.mgz to aseg.nii but the dims are 256x256x256 and I >>> need to use the FSL MNI format which is 182x218x182. >>> Is there a recipe for cropping / translating etc to match the >>> aseg.mgz atlas with the FSL atlases? >>> Thanks >>> -roddy >>> >>> --------------------------------------------------------------------- >>> --- >>> >>> UT Southwestern Medical Center >>> The future of medicine, today. >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)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 >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> >> >> 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. >> >> >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)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 > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Freesurfer February 2013