Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30091 discussions

Re: [Freesurfer] trac-all problem
by Anastasia Yendiki 12 Feb '13

12 Feb '13

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.trk > dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dl > abel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2! > .flt.nii > .gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz dlabel/mni/rh.slft_PP_roi1.flt.nii.gz dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lowb_brain_mask.flt.nii.gz --fa /Studies/MJMRI/MJ0012/freesurfer/dmri/mni/dtifit_FA.flt.nii.gz --ncpts 5 --debug >> ERROR: fio_pushd: /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni >> ERROR: must specify brain mask volume for output subject >> Darwin psy-cerebellum.uits.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 >> >> trac-preproc exited with ERRORS at Tue Feb 12 15:26:36 CST 2013 >> >> >> >> >> >> what is the brainmask volume that it is looking for? >> >> >> >> >> ----- Original Message ----- >> From: "Anastasia Yendiki" <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. >>>>> >>>>> >>>>> >>>> >>>> >>>> >>> >>> >>> >> >> >> > > >

2 1

Re: [Freesurfer] trac-all problem
by Anastasia Yendiki 12 Feb '13

12 Feb '13

Hi Jon - Have you run freesurfer (recon-all) on your T1 data? a.y On Tue, 12 Feb 2013, Jon Wieser wrote: > i got past the problem with the bvesc, and bvals, > > > my current output has a new problem: > here's the last part of the output. > > > > #@# Tensor fit Tue Feb 12 15:24:51 CST 2013 > dtifit -k /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz -m /Studies/MJMRI/MJ0012/freesurfer/dlabel/diff/lowb_brain_mask.nii.gz -r /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs -b /Studies/MJMRI/MJ0012/freesurfer/dmri/bvals -o /Studies/MJMRI/MJ0012/freesurfer/dmri/dtifit > 0 256 0 256 0 60 > 0 slices processed > 1 slices processed > 2 slices processed > 3 slices processed > 4 slices processed > 5 slices processed > 6 slices processed > 7 slices processed > 8 slices processed > 9 slices processed > 10 slices processed > 11 slices processed > 12 slices processed > 13 slices processed > 14 slices processed > 15 slices processed > 16 slices processed > 17 slices processed > 18 slices processed > 19 slices processed > 20 slices processed > 21 slices processed > 22 slices processed > 23 slices processed > 24 slices processed > 25 slices processed > 26 slices processed > 27 slices processed > 28 slices processed > 29 slices processed > 30 slices processed > 31 slices processed > 32 slices processed > 33 slices processed > 34 slices processed > 35 slices processed > 36 slices processed > 37 slices processed > 38 slices processed > 39 slices processed > 40 slices processed > 41 slices processed > 42 slices processed > 43 slices processed > 44 slices processed > 45 slices processed > 46 slices processed > 47 slices processed > 48 slices processed > 49 slices processed > 50 slices processed > 51 slices processed > 52 slices processed > 53 slices processed > 54 slices processed > 55 slices processed > 56 slices processed > 57 slices processed > 58 slices processed > 59 slices processed > #------------------------------------- > #@# Priors Tue Feb 12 15:26:36 CST 2013 > /Applications/freesurfer/bin/dmri_train --outdir /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni --out lh.cst_AS_avg23_mni_flt rh.cst_AS_avg23_mni_flt lh.ilf_AS_avg23_mni_flt rh.ilf_AS_avg23_mni_flt lh.unc_AS_avg23_mni_flt rh.unc_AS_avg23_mni_flt fmajor_PP_avg23_mni_flt fminor_PP_avg23_mni_flt lh.atr_PP_avg23_mni_flt rh.atr_PP_avg23_mni_flt lh.cab_PP_avg23_mni_flt rh.cab_PP_avg23_mni_flt lh.ccg_PP_avg23_mni_flt rh.ccg_PP_avg23_mni_flt lh.slfp_PP_avg23_mni_flt rh.slfp_PP_avg23_mni_flt lh.slft_PP_avg23_mni_flt rh.slft_PP_avg23_mni_flt --slist /tmp/subj23.freesurfer.92196.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/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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pial surface problem because of dura
by XJ Kang 12 Feb '13

12 Feb '13

Hi FS Experts, I post an email one year ago about problem of the segmentation of GM/WM because of the duram layer. (See https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-February/017251…) I found in the FreeSurfer release notes that the V5.2.0 will have flags to refine the pial surface using T2/FLAIR images. I will test those when the new version is available. What I did so far to solve the problem are: -> Increase TR: CSF darker, dura darker, but scan time longer. -> Increase receiver BW to change TE : TE cannot be changed in MPRage. Increase BW will reduce TE, but also reduce SNR of everything, including dura. As a result, the brain segmentation seems to be good but the scan is longer and SNR is lower. See changes from brain1.jpg to brang2.jpg. brain1.jpg: MPrage, TR=1900ms, TE=2.45ms, Voxel: 1x1x1mm, BW=220Hz/Px brain2.jpg: MPrage, TR=3000ms, TE=1.62ms, Voxel: 1x1x1mm, BW=340Hz/Px Anybody has experiences or comments on this problem? Hopefully the flags "-T2" and "-T2pial" in the new version are a better solutions. XJ Kang

3 2

Re: [Freesurfer] trac-all problem
by Anastasia Yendiki 12 Feb '13

12 Feb '13

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. >>> >>> >>> >> >> >> > > >

1 0

Parallelizing on a different kind of cluster
by Susan Kuo 12 Feb '13

12 Feb '13

Hi TRACULA Experts, Is there a way of parallelizing BEDPOSTX on a cluster, not using the bedpostx_seychelles option since I'm on a non-MGH cluster? Thanks! Susie Kuo

3 4

Basic skullstrip Inquiry
by Gabriel Obregon 12 Feb '13

12 Feb '13

Hi, I'm using the -gcut flag for the first time and I've noticed that the skull stripping process is still leaving small fragments of dura behind. Will this affect my surfaces? Should I manually edit the brainmask volume to remove as much of these fragments as I can? Also, should I only be concerned about the GM and cerebellum edges when checking for over-aggressive cutting, or are other brain structures important as well, e.g. optic chiasm? Thanks, --G

2 1

Freesurfer version for processed data
by krista kelly 12 Feb '13

12 Feb '13

Hello, Is there any way to find out which Freesurfer version I used to process data? Thanks, Krista

2 1

warping results on surface
by Jacobs H (NP) 12 Feb '13

12 Feb '13

Hi FreeSurfer! A colleague has retinotopic results that he would like to overlay on the FS surface (most likely fsaverage). The retinotopic data is in 2mm isotropic resolution. What would be the best way to be able to overlay this data correctly? Should he first warp the volume to the volume of fsaverage and then use vol2surf? Any help is highly appreciated! Best Heidi ================================================ Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jacobs(a)maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ================================================

2 1

Re: [Freesurfer] trac-all problem
by Anastasia Yendiki 12 Feb '13

12 Feb '13

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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Troubleshooting the preproc
by Susan Kuo 12 Feb '13

12 Feb '13

Hi FreeSurfer community, I am currently trying to troubleshoot my preprocessing part of TRACULA with the tutorial dataset (for *Diff001* as the subject, specifically), running *trac-all -corr -c <config dmrirc>*. I am running the commands in * subjectID/scripts/trac-all.cmd* one by one because I've had problems with some of the steps. Specifically, *flip4fsl* didn't work. I instead used *fslswapdim -x -y z* (*flip4fsl* uses *fslswapdim x -y z*, which doesn't generate the correct orientation for FSL in fact), followed by *fslorient -forceradiological*. I successfully ran *eddy_current *thereafter. Now I am stuck again, at FreeSurfer's *xfmrot, *which should look like: * * *xfmrot <transform file> <input vector file> [<output vector file>]* I specifically typed in: *xfmrot /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi.ecclog /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/bvecs.norot /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/bvecs* and received the following iterative errors: * avscale: Command not found. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. * Can any of you help me? Thank you, Susie K

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