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.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@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
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and yes, you'll need to run recon-all on your data before running tracula
cheers Bruce On Tue, 12 Feb 2013, Anastasia Yendiki wrote:
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.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@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 >
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