Sorry, reading stuff from the dicom header will not work for all dicom versions. It should work for Siemens dicoms though.
On Tue, 12 Feb 2013, Jon Wieser wrote: > according to the > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula > > nb0 does not need to be specified when using original dicoms. , but i'll > try defining the nb0 variable > thanks > Jon > > > ----- Original Message ----- > From: "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu> > To: "Jon Wieser" <wie...@uwm.edu> > Cc: "freesurfer" <freesurfer@nmr.mgh.harvard.edu> > Sent: Tuesday, February 12, 2013 10:49:18 AM > Subject: Re: [Freesurfer] trac-all problem > > > Hi Jon - My guess is you didn't define the nb0 variable in your > configuration file, see here: > http://www.freesurfer.net/fswiki/dmrirc > > The new version, which will come out in a few days, will be able to figure > it out without you having to specify it but with the current version you > have to. > > Hope this helps, > a.y > > On Tue, 12 Feb 2013, Jon Wieser wrote: > >> hello >> >> i am trying to process the dti data with trac-all. I am new to tracula >> my input images are 3300 dicoms, 60 slices and 55 dti diffusions >> i have attached my dmrirc_single_subject file >> >> >> i did the following command: >> >> trac-all -prep -c /Studies/MJMRI/DTI/dmrirc_single_subject >> >> and got the result: >> >> >> >> INFO: SUBJECTS_DIR is /Studies/MJMRI/MJ0012 >> INFO: Diffusion root is /Studies/MJMRI/MJ0012 >> Actual FREESURFER_HOME /Applications/freesurfer >> trac-preproc -c /Studies/MJMRI/MJ0012/freesurfer/scripts/dmrirc.local -log >> /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.log -cmd >> /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.cmd >> #------------------------------------- >> /Applications/freesurfer/bin/trac-preproc >> #------------------------------------- >> #@# Image corrections Mon Feb 11 12:41:04 CST 2013 >> mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 >> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz >> mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 >> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz >> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ >> reading from /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1... >> Starting DICOMRead2() >> dcmfile = /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 >> dcmdir = /Studies/MJMRI/MJ0012//s780 >> Ref Series No = 13 >> Found 3304 files, checking for dicoms >> Found 3300 dicom files in series. >> First Sorting >> Computing Slice Direction >> Vs: 0 0 2 >> Vs: 0 0 1 >> Second Sorting >> Counting frames >> nframes = 55 >> nslices = 60 >> ndcmfiles = 3300 >> PE Dir = COL (dicom read) >> TransferSyntaxUID: --1.2.840.10008.1.2.1-- >> jpegUID: --1.2.840.10008.1.2.4-- >> Loading pixel data >> TR=9300.00, TE=76.20, TI=0.00, flip angle=90.00 >> i_ras = (-1, 0, 0) >> j_ras = (0, -1, 0) >> k_ras = (-0, -0, 1) >> writing to /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz... >> mri_probedicom --i /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 > >> /Studies/MJMRI/MJ0012/freesurfer/dmri/dcminfo.dat >> flip4fsl /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz >> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz >> INFO: input image orientation is LPS >> INFO: input image determinant is 2 >> fslswapdim /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz x -y z >> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz >> INFO: left-right orientation was flipped by fslswapdim >> fslorient -forceradiological >> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz >> INFO: found /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.mghdti.bvals, >> converting to FSL format >> INFO: found /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.mghdti.bvecs, >> converting to FSL format >> mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvecs >> /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs >> mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvals >> /Studies/MJMRI/MJ0012/freesurfer/dmri/bvals >> eddy_correct /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz >> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz 0 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0000 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0001 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0002 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0003 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0004 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0005 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0006 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0007 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0008 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0009 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0010 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0011 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0012 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0013 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0014 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0015 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0016 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0017 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0018 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0019 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0020 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0021 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0022 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0023 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0024 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0025 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0026 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0027 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0028 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0029 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0030 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0031 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0032 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0033 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0034 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0035 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0036 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0037 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0038 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0039 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0040 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0041 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0042 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0043 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0044 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0045 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0046 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0047 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0048 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0049 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0050 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0051 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0052 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0053 >> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0054 >> mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs >> /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs.norot >> xfmrot /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.ecclog >> /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs.norot >> /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs >> fslroi /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz >> /Studies/MJMRI/MJ0012/freesurfer/dmri/lowb.nii.gz 0 >> >> Usage: fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> >> fslroi <input> <output> <tmin> <tsize> >> >> fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> >> <tmin> <tsize> >> Note: indexing (in both time and space) starts with 0 not 1! >> Darwin psy-cerebellum.uits.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue >> Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 >> >> trac-preproc exited with ERRORS at Mon Feb 11 13:25:16 CST 2013 >> >> >> can you tell me how to fix this? >> Thanks >> Jon Wieser >> UW-Milwaukee >> > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
