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@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Monday, February 18, 2013 4:41:15 PM Subject: Re: [Freesurfer] Fwd: trac-all problem
Hi Jon - So the files are there but there's to be a memory allocation problem. Are you using the updated mac build from the tracula wiki page or the one that was originally released with freesurfer 5.1?
a.y
On Mon, 18 Feb 2013, Jon Wieser wrote:
Hi ,
i have the following files in my dmri.bedpostX directory
bvals dyads2.nii.gz mean_f2samples.nii.gz merged_f1samples.nii.gz merged_th2samples.nii.gz bvecs dyads2_dispersion.nii.gz mean_ph1samples.nii.gz merged_f2samples.nii.gz monitor commands.txt logs mean_ph2samples.nii.gz merged_ph1samples.nii.gz nodif_brain_mask.nii.gz dyads1.nii.gz mean_dsamples.nii.gz mean_th1samples.nii.gz merged_ph2samples.nii.gz xfms dyads1_dispersion.nii.gz mean_f1samples.nii.gz mean_th2samples.nii.gz merged_th1samples.nii.gz
Jon
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Monday, February 18, 2013 3:51:40 PM Subject: Re: [Freesurfer] Fwd: trac-all problem
Hi Jon - There's a list of all bedpostx output files here: http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_bedpostx.html
Do you see these files in the dmri.bedpostX directory?
a.y
On Mon, 18 Feb 2013, Jon Wieser wrote:
I ran trac-all -bedp -c /Studies/MJMRI/DTI/dmrirc_single_subject the end of the output was:
52 slices processed 52 slices processed 53 slices processed 53 slices processed 54 slices processed 54 slices processed 55 slices processed 55 slices processed 56 slices processed 57 slices processed 58 slices processed Queuing post processing stage 60 slices processed All slices processed /Applications/freesurfer/bin/bedpostx_seychelles: line 281: kill: (35687) - No such process
is this normal?
then I ran trac-all -path -c /Studies/MJMRI/DTI/dmrirc_single_subject
it ended in an error
Here's the last part of the trac-all -path output:
Neighbor aseg label ID list: /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.cst_AS_avg23_mni_flt_fsnnids /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.cst_AS_avg23_mni_flt_fsnnids /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.ilf_AS_avg23_mni_flt_fsnnids /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.ilf_AS_avg23_mni_flt_fsnnids /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.unc_AS_avg23_mni_flt_fsnnids /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.unc_AS_avg23_mni_flt_fsnnids /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/fmajor_PP_avg23_mni_flt_fsnnids /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/fminor_PP_avg23_mni_flt_fsnnids /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.atr_PP_avg23_mni_flt_fsnnids /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.atr_PP_avg23_mni_flt_fsnnids /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.cab_PP_avg23_mni_flt_fsnnids /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.cab_PP_avg23_mni_flt_fsnnids /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/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@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@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@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, February 12, 2013 3:44:59 PM Subject: Re: [Freesurfer] trac-all problem
Hi Jon - You'll the aparc+aseg.mgz (cortical parcellation + subcortical segmentation). The basis of TRACULA is that it uses the underlying anatomy to reconstruct the tracts.
a.y
On Tue, 12 Feb 2013, Jon Wieser wrote:
no i have not run recon-all yet on this dataset, do i need to run recon-all with -autorecon1 ,-autorecon2, and -autorecon3 before i analyze the dti data?
thanks Jon
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, February 12, 2013 3:34:19 PM Subject: Re: [Freesurfer] trac-all problem
Hi Jon - Have you run freesurfer (recon-all) on your T1 data?
a.y
On Tue, 12 Feb 2013, Jon Wieser wrote:
i got past the problem with the bvesc, and bvals,
my current output has a new problem: here's the last part of the output.
#@# Tensor fit Tue Feb 12 15:24:51 CST 2013 dtifit -k /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz -m /Studies/MJMRI/MJ0012/freesurfer/dlabel/diff/lowb_brain_mask.nii.gz -r /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs -b /Studies/MJMRI/MJ0012/freesurfer/dmri/bvals -o /Studies/MJMRI/MJ0012/freesurfer/dmri/dtifit 0 256 0 256 0 60 0 slices processed 1 slices processed 2 slices processed 3 slices processed 4 slices processed 5 slices processed 6 slices processed 7 slices processed 8 slices processed 9 slices processed 10 slices processed 11 slices processed 12 slices processed 13 slices processed 14 slices processed 15 slices processed 16 slices processed 17 slices processed 18 slices processed 19 slices processed 20 slices processed 21 slices processed 22 slices processed 23 slices processed 24 slices processed 25 slices processed 26 slices processed 27 slices processed 28 slices processed 29 slices processed 30 slices processed 31 slices processed 32 slices processed 33 slices processed 34 slices processed 35 slices processed 36 slices processed 37 slices processed 38 slices processed 39 slices processed 40 slices processed 41 slices processed 42 slices processed 43 slices processed 44 slices processed 45 slices processed 46 slices processed 47 slices processed 48 slices processed 49 slices processed 50 slices processed 51 slices processed 52 slices processed 53 slices processed 54 slices processed 55 slices processed 56 slices processed 57 slices processed 58 slices processed 59 slices processed #------------------------------------- #@# Priors Tue Feb 12 15:26:36 CST 2013 /Applications/freesurfer/bin/dmri_train --outdir /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni --out lh.cst_AS_avg23_mni_flt rh.cst_AS_avg23_mni_flt lh.ilf_AS_avg23_mni_flt rh.ilf_AS_avg23_mni_flt lh.unc_AS_avg23_mni_flt rh.unc_AS_avg23_mni_flt fmajor_PP_avg23_mni_flt fminor_PP_avg23_mni_flt lh.atr_PP_avg23_mni_flt rh.atr_PP_avg23_mni_flt lh.cab_PP_avg23_mni_flt rh.cab_PP_avg23_mni_flt lh.ccg_PP_avg23_mni_flt rh.ccg_PP_avg23_mni_flt lh.slfp_PP_avg23_mni_flt rh.slfp_PP_avg23_mni_flt lh.slft_PP_avg23_mni_flt rh.slft_PP_avg23_mni_flt --slist /tmp/subj23.freesurfer.92196.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.
t
r
k
dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.g
z
d
l
abel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2! .flt.nii .gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz dlabel/mni/rh.slft_PP_roi1.flt.nii.gz dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lowb_brain_mask.flt.nii.gz --fa /Studies/MJMRI/MJ0012/freesurfer/dmri/mni/dtifit_FA.flt.nii.gz --ncpts 5 --debug
ERROR: fio_pushd: /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni ERROR: must specify brain mask volume for output subject Darwin psy-cerebellum.uits.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Tue Feb 12 15:26:36 CST 2013
what is the brainmask volume that it is looking for?
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, February 12, 2013 1:26:55 PM Subject: Re: [Freesurfer] trac-all problem
Hi Jon - This is the same issue. The reading from the dicom part will work for the Siemens dicoms that we have here but is not guaranteed to work with other dicoms. You'll have to define bvecfile, bvalfile, and nb0. (The first two should be in columns, not rows.)
Let me know if you run into any other problems, a.y
On Tue, 12 Feb 2013, Jon Wieser wrote:
> i ran the program with the nb0 set to 2 > > i got the following error: it's not finding a bvec files. the document says that the bevecs are read from the DICOM headers. here's the output of the run > > > : > INFO: SUBJECTS_DIR is /Studies/MJMRI/MJ0012 > INFO: Diffusion root is /Studies/MJMRI/MJ0012 > Actual FREESURFER_HOME /Applications/freesurfer > trac-preproc -c /Studies/MJMRI/MJ0012/freesurfer/scripts/dmrirc.local -log /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.log -cmd /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.cmd > #------------------------------------- > /Applications/freesurfer/bin/trac-preproc > #------------------------------------- > #@# Image corrections Tue Feb 12 13:00:35 CST 2013 > mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz > mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading from /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1... > Starting DICOMRead2() > dcmfile = /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 > dcmdir = /Studies/MJMRI/MJ0012//s780 > Ref Series No = 13 > Found 3304 files, checking for dicoms > Found 3300 dicom files in series. > First Sorting > Computing Slice Direction > Vs: 0 0 2 > Vs: 0 0 1 > Second Sorting > Counting frames > nframes = 55 > nslices = 60 > ndcmfiles = 3300 > PE Dir = COL (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > jpegUID: --1.2.840.10008.1.2.4-- > Loading pixel data > TR=9300.00, TE=76.20, TI=0.00, flip angle=90.00 > i_ras = (-1, 0, 0) > j_ras = (0, -1, 0) > k_ras = (-0, -0, 1) > writing to /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz... > mri_probedicom --i /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 > /Studies/MJMRI/MJ0012/freesurfer/dmri/dcminfo.dat > flip4fsl /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz > INFO: input image orientation is LPS > INFO: input image determinant is 2 > fslswapdim /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz x -y z /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz > INFO: left-right orientation was flipped by fslswapdim > fslorient -forceradiological /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz > mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvecs /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs > mv: rename /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvecs to /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs: No such file or directory > Darwin psy-cerebellum.uits.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 > > trac-preproc exited with ERRORS at Tue Feb 12 13:05:29 CST 2013 > > > > > > > ----- Original Message ----- > From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu > To: "Jon Wieser" wieser@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@nmr.mgh.harvard.edu >> To: "Jon Wieser" wieser@uwm.edu >> Cc: freesurfer@nmr.mgh.harvard.edu >> Sent: Tuesday, February 12, 2013 11:14:42 AM >> Subject: Re: [Freesurfer] trac-all problem >> >> >> Sorry, reading stuff from the dicom header will not work for all dicom >> versions. It should work for Siemens dicoms though. >> >> On Tue, 12 Feb 2013, Jon Wieser wrote: >> >>> according to the >>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula >>> >>> nb0 does not need to be specified when using original dicoms. , but i'll try defining the nb0 variable >>> thanks >>> Jon >>> >>> >>> ----- Original Message ----- >>> From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu >>> To: "Jon Wieser" wieser@uwm.edu >>> Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu >>> Sent: Tuesday, February 12, 2013 10:49:18 AM >>> Subject: Re: [Freesurfer] trac-all problem >>> >>> >>> Hi Jon - My guess is you didn't define the nb0 variable in your >>> configuration file, see here: >>> http://www.freesurfer.net/fswiki/dmrirc >>> >>> The new version, which will come out in a few days, will be able to figure >>> it out without you having to specify it but with the current version you >>> have to. >>> >>> Hope this helps, >>> a.y >>> >>> On Tue, 12 Feb 2013, Jon Wieser wrote: >>> >>>> hello >>>> >>>> i am trying to process the dti data with trac-all. I am new to tracula >>>> my input images are 3300 dicoms, 60 slices and 55 dti diffusions >>>> i have attached my dmrirc_single_subject file >>>> >>>> >>>> i did the following command: >>>> >>>> trac-all -prep -c /Studies/MJMRI/DTI/dmrirc_single_subject >>>> >>>> and got the result: >>>> >>>> >>>> >>>> INFO: SUBJECTS_DIR is /Studies/MJMRI/MJ0012 >>>> INFO: Diffusion root is /Studies/MJMRI/MJ0012 >>>> Actual FREESURFER_HOME /Applications/freesurfer >>>> trac-preproc -c /Studies/MJMRI/MJ0012/freesurfer/scripts/dmrirc.local -log /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.log -cmd /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.cmd >>>> #------------------------------------- >>>> /Applications/freesurfer/bin/trac-preproc >>>> #------------------------------------- >>>> #@# Image corrections Mon Feb 11 12:41:04 CST 2013 >>>> mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz >>>> mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz >>>> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ >>>> reading from /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1... >>>> Starting DICOMRead2() >>>> dcmfile = /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 >>>> dcmdir = /Studies/MJMRI/MJ0012//s780 >>>> Ref Series No = 13 >>>> Found 3304 files, checking for dicoms >>>> Found 3300 dicom files in series. >>>> First Sorting >>>> Computing Slice Direction >>>> Vs: 0 0 2 >>>> Vs: 0 0 1 >>>> Second Sorting >>>> Counting frames >>>> nframes = 55 >>>> nslices = 60 >>>> ndcmfiles = 3300 >>>> PE Dir = COL (dicom read) >>>> TransferSyntaxUID: --1.2.840.10008.1.2.1-- >>>> jpegUID: --1.2.840.10008.1.2.4-- >>>> Loading pixel data >>>> TR=9300.00, TE=76.20, TI=0.00, flip angle=90.00 >>>> i_ras = (-1, 0, 0) >>>> j_ras = (0, -1, 0) >>>> k_ras = (-0, -0, 1) >>>> writing to /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz... >>>> mri_probedicom --i /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 > /Studies/MJMRI/MJ0012/freesurfer/dmri/dcminfo.dat >>>> flip4fsl /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz >>>> INFO: input image orientation is LPS >>>> INFO: input image determinant is 2 >>>> fslswapdim /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz x -y z /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz >>>> INFO: left-right orientation was flipped by fslswapdim >>>> fslorient -forceradiological /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz >>>> INFO: found /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.mghdti.bvals, converting to FSL format >>>> INFO: found /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.mghdti.bvecs, converting to FSL format >>>> mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvecs /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs >>>> mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvals /Studies/MJMRI/MJ0012/freesurfer/dmri/bvals >>>> eddy_correct /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz 0 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0000 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0001 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0002 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0003 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0004 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0005 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0006 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0007 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0008 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0009 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0010 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0011 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0012 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0013 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0014 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0015 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0016 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0017 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0018 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0019 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0020 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0021 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0022 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0023 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0024 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0025 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0026 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0027 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0028 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0029 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0030 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0031 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0032 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0033 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0034 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0035 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0036 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0037 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0038 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0039 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0040 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0041 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0042 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0043 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0044 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0045 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0046 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0047 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0048 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0049 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0050 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0051 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0052 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0053 >>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0054 >>>> mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs.norot >>>> xfmrot /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.ecclog /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs.norot /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs >>>> fslroi /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz /Studies/MJMRI/MJ0012/freesurfer/dmri/lowb.nii.gz 0 >>>> >>>> Usage: fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> >>>> fslroi <input> <output> <tmin> <tsize> >>>> >>>> fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> <tmin> <tsize> >>>> Note: indexing (in both time and space) starts with 0 not 1! >>>> Darwin psy-cerebellum.uits.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 >>>> >>>> trac-preproc exited with ERRORS at Mon Feb 11 13:25:16 CST 2013 >>>> >>>> >>>> can you tell me how to fix this? >>>> Thanks >>>> Jon Wieser >>>> UW-Milwaukee >>>> >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the e-mail >>> contains patient information, please contact the Partners Compliance HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in error >>> but does not contain patient information, please contact the sender and properly >>> dispose of the e-mail. >>> >>> >>> >> >> >> > > >
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