Hi Paula, The * at the end of dtifit_FA.nii.gz may have been a problem (since it gives an unkown extension error? Extension: 146 (Uknown extension))
tcsh source /software/Freesurfer/5.1.0/SetUpFreeSurfer.csh freeview -v /mindhive/gablab/users/cpdla/Documents/s1001/dmri/dtifit_FA.nii.gz can you try running the above commands in that order and tell us if you get the same error? Thanks, Priti > hi, > i am trying to visualize the output of my trac-all results. > here is what i did: > cpdla@ba3:/$ tcsh > ba3:/> source /software/Freesurfer/5.1.0/Set > SetUpFreeSurfer.csh* SetUpFreeSurfer.sh* > ba3:/> source /software/Freesurfer/5.1.0/SetUpFreeSurfer.csh > -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /software/Freesurfer/5.1.0/ > FSFAST_HOME /software/Freesurfer/5.1.0/fsfast > FSF_OUTPUT_FORMAT nii > SUBJECTS_DIR /software/Freesurfer/5.1.0/subjects > MNI_DIR /software/Freesurfer/5.1.0//mni > /usr/share/fsl/4.1/etc/fslconf/fslmachtype.sh: Command not found. > FSL_DIR /usr/share/fsl/4.1 > *ba3:/> freeview -v > /mindhive/gablab/users/cpdla/Documents/s1001/dmri/dtifit_FA.nii.gz* > X Error: BadValue (integer parameter out of range for operation) 2 > Extension: 146 (Uknown extension) > Minor opcode: 3 (Unknown request) > Resource id: 0x24 > Abort > *ba3:/> freeview -tv > /mindhive/gablab/users/cpdla/Documents/s1001/dmri/dtifit_FA.nii.gz* > X Error: BadValue (integer parameter out of range for operation) 2 > Extension: 146 (Uknown extension) > Minor opcode: 3 (Unknown request) > Resource id: 0x24 > Abort > ba3:/> > > > On Thu, Dec 8, 2011 at 10:54 AM, Priti Srinivasan < > rspr...@nmr.mgh.harvard.edu> wrote: > >> Hi Paula, >> >> which image are you trying to open? If you're trying to open the merged >> files in freeview, you should use the -tv flag for opening it. Did you >> source the freesurfer environment before opening freeview? Can you give >> us >> the exact commandline you used? >> >> Priti >> >> > hi, >> > i am trying to visualize my results with freeview, and i am running >> into >> > this error. i am using freesurfer 5.1.0. do you know what the problem >> is? >> > : >> > >> > cpdla@ba3:~/Documents/s1001/dmri$ freeview >> > X Error: BadValue (integer parameter out of range for operation) 2 >> > Extension: 146 (Uknown extension) >> > Minor opcode: 3 (Unknown request) >> > Resource id: 0x24 >> > Abort >> > >> > >> > On Wed, Dec 7, 2011 at 12:52 PM, Priti Srinivasan < >> > rspr...@nmr.mgh.harvard.edu> wrote: >> > >> >> Hi Paula, >> >> >> >> Tracula uses anatomical labels/files from freesurfer cortical >> >> reconstruction to build the posterior distribution of the tracts. It >> >> looks >> >> like you may not have run freesurfer recon for your subject. >> >> >> >> To run freesurfer recon for your subject please refer to the >> following >> >> page: >> >> >> >> http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferBeginnersGuide >> >> >> >> Especially, >> >> >> >> recon-all \ >> >> -i <one slice in the anatomical dicom series> \ >> >> -s <subject id that you make up> \ >> >> -sd <directory to put the subject folder in> \ >> >> -all >> >> >> >> Once this finishes processing you can re-run tracula to see if that >> >> solves >> >> the issue. >> >> >> >> Hope that is helpful, >> >> Priti >> >> >> >> >> >> >> >> > Hi. >> >> > >> >> > I am running into the following error: >> >> > ERROR: fio_pushd: >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/mni >> >> > ERROR: must specify brain mask volume for output subject . >> >> > >> >> > I googled this error and it seems like you suggested this to >> someone >> >> else >> >> > : >> >> > "As for your error, it looks like maybe the freesurfer recon wasn't >> >> found, >> >> > so >> >> > it skipped some steps (diffusion-to-anatomical registration and >> mask >> >> > creation). >> >> > Does the freesurfer recon dir /home/ajfurst/Data/WRIISC/014/ exist? >> >> > >> >> > >> >> > a.y" >> >> > >> >> > What is the freesurfer recon dir supposed to look like? Any >> >> > suggestions on how to fix this error? Below is my output. >> >> > >> >> > Thanks, >> >> > C. Paula >> >> > >> >> > >> >> > >> >> > >> >> > ba3:~/Documents> trac-all -prep -c dmrirc_single_subject >> >> > set: Variable name must begin with a letter. >> >> > INFO: SUBJECTS_DIR is >> >> > /mindhive/gablab/users/cpdla/Documents/diffusion_recons >> >> > INFO: Diffusion root is /mindhive/gablab/users/cpdla/Documents/ >> >> > Actual FREESURFER_HOME /software/Freesurfer/5.1.0 >> >> > trac-preproc -c >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/scripts/dmrirc.local >> >> -log >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/scripts/trac-all.log >> >> -cmd >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/scripts/trac-all.cmd >> >> > #------------------------------------- >> >> > /software/Freesurfer/5.1.0//bin/trac-preproc >> >> > #------------------------------------- >> >> > #@# Image corrections Tue Dec 6 22:02:37 EST 2011 >> >> > mri_convert /data/memory/sourcemem//s1001/156000-20-1.dcm >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz >> >> > mri_convert /data/memory/sourcemem//s1001/156000-20-1.dcm >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz >> >> > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ >> >> > reading from /data/memory/sourcemem//s1001/156000-20-1.dcm... >> >> > Getting Series No >> >> > INFO: Found 3207 files in /data/memory/sourcemem//s1001 >> >> > INFO: Scanning for Series Number 20 >> >> > Scanning Directory >> >> > INFO: found 35 files in series >> >> > INFO: loading series header info. >> >> > >> >> > RunNo = 19 >> >> > WARNING: Run 1 appears to be truncated >> >> > Files Found: 35, Files Expected (lRep+1): 60 >> >> > FileName /data/memory/sourcemem//s1001/156000-20-1.dcm >> >> > Identification >> >> > NumarisVer syngo MR B15 >> >> > ScannerModel TrioTim >> >> > PatientName Gab_source_s1001 >> >> > Date and time >> >> > StudyDate 20091119 >> >> > StudyTime 170216.156000 >> >> > SeriesTime 180621.328000 >> >> > AcqTime 180331.855000 >> >> > Acquisition parameters >> >> > PulseSeq ep_b0#1 >> >> > Protocol DIFFUSION_HighRes_Short >> >> > PhEncDir COL >> >> > EchoNo 1 >> >> > FlipAngle 90 >> >> > EchoTime 84 >> >> > InversionTime -1 >> >> > RepetitionTime 7980 >> >> > PhEncFOV 256 >> >> > ReadoutFOV 256 >> >> > Image information >> >> > RunNo 19 >> >> > SeriesNo 20 >> >> > ImageNo 1 >> >> > NImageRows 1024 >> >> > NImageCols 1024 >> >> > NFrames 35 >> >> > SliceArraylSize 64 >> >> > IsMosaic 1 >> >> > ImgPos 863.3041 1153.2142 -113.6526 >> >> > VolRes 2.0000 2.0000 2.0000 >> >> > VolDim 128 128 64 >> >> > Vc -0.9895 -0.1445 0.0066 >> >> > Vr 0.1446 -0.9873 0.0662 >> >> > Vs -0.0031 0.0664 0.9978 >> >> > VolCenter 0.0000 0.0000 0.0000 >> >> > TransferSyntaxUID unknown >> >> > INFO: sorting. >> >> > INFO: (128 128 64), nframes = 35, ismosaic=1 >> >> > Could not parse NUMARIS version string syngo MR B15 >> >> > found in dicom tag 18,1020 (len = 3 != 6) >> >> > Repetition Time = 7980, TR = 7980 ms >> >> > PE Dir COL COL >> >> > AutoAlign matrix detected >> >> > AutoAlign Matrix --------------------- >> >> > 0.989 -0.141 0.034 4.549; >> >> > 0.145 0.949 -0.279 4.841; >> >> > 0.007 0.281 0.960 24.557; >> >> > 0.000 0.000 0.000 1.000; >> >> > >> >> > This looks like an MGH DTI volume >> >> > MGH DTI SeqPack Info >> >> > 0 ep_b0#1 0.000000 1 >> >> > 1 ep_b0#2 0.000000 2 >> >> > 2 ep_b0#3 0.000000 3 >> >> > 3 ep_b0#4 0.000000 4 >> >> > 4 ep_b0#5 0.000000 5 >> >> > 5 ep_b700#1 700.000000 1 >> >> > 6 ep_b700#2 700.000000 2 >> >> > 7 ep_b700#3 700.000000 3 >> >> > 8 ep_b700#4 700.000000 4 >> >> > 9 ep_b700#5 700.000000 5 >> >> > 10 ep_b700#6 700.000000 6 >> >> > 11 ep_b700#7 700.000000 7 >> >> > 12 ep_b700#8 700.000000 8 >> >> > 13 ep_b700#9 700.000000 9 >> >> > 14 ep_b700#10 700.000000 10 >> >> > 15 ep_b700#11 700.000000 11 >> >> > 16 ep_b700#12 700.000000 12 >> >> > 17 ep_b700#13 700.000000 13 >> >> > 18 ep_b700#14 700.000000 14 >> >> > 19 ep_b700#15 700.000000 15 >> >> > 20 ep_b700#16 700.000000 16 >> >> > 21 ep_b700#17 700.000000 17 >> >> > 22 ep_b700#18 700.000000 18 >> >> > 23 ep_b700#19 700.000000 19 >> >> > 24 ep_b700#20 700.000000 20 >> >> > 25 ep_b700#21 700.000000 21 >> >> > 26 ep_b700#22 700.000000 22 >> >> > 27 ep_b700#23 700.000000 23 >> >> > 28 ep_b700#24 700.000000 24 >> >> > 29 ep_b700#25 700.000000 25 >> >> > 30 ep_b700#26 700.000000 26 >> >> > 31 ep_b700#27 700.000000 27 >> >> > 32 ep_b700#28 700.000000 28 >> >> > 33 ep_b700#29 700.000000 29 >> >> > 34 ep_b700#30 700.000000 30 >> >> > bValue = 700 >> >> > nB0 = 5 >> >> > nDir = 30 >> >> > GradFile >> >> > >> >> >> /software/Freesurfer/5.1.0//diffusion/mgh-dti-seqpack/gradient_mgh_dti30.gdt >> >> > FileName /data/memory/sourcemem//s1001/156000-20-35.dcm >> >> > Identification >> >> > NumarisVer syngo MR B15 >> >> > ScannerModel TrioTim >> >> > PatientName Gab_source_s1001 >> >> > Date and time >> >> > StudyDate 20091119 >> >> > StudyTime 170216.156000 >> >> > SeriesTime 180621.328000 >> >> > AcqTime 180804.265000 >> >> > Acquisition parameters >> >> > PulseSeq ep_b700#30 >> >> > Protocol DIFFUSION_HighRes_Short >> >> > PhEncDir COL >> >> > EchoNo 1 >> >> > FlipAngle 90 >> >> > EchoTime 84 >> >> > InversionTime -1 >> >> > RepetitionTime 7980 >> >> > PhEncFOV 256 >> >> > ReadoutFOV 256 >> >> > Image information >> >> > RunNo 19 >> >> > SeriesNo 20 >> >> > ImageNo 35 >> >> > NImageRows 1024 >> >> > NImageCols 1024 >> >> > NFrames 35 >> >> > SliceArraylSize 64 >> >> > IsMosaic 1 >> >> > ImgPos 863.3041 1153.2142 -113.6526 >> >> > VolRes 2.0000 2.0000 2.0000 >> >> > VolDim 128 128 64 >> >> > Vc -0.9895 -0.1445 0.0066 >> >> > Vr 0.1446 -0.9873 0.0662 >> >> > Vs -0.0031 0.0664 0.9978 >> >> > VolCenter 0.0000 0.0000 0.0000 >> >> > TransferSyntaxUID unknown >> >> > sagrev = 0, correv =0, trarev = 0 >> >> > Vs = -0.00309869 0.0664423 0.997786 >> >> > INFO: no Siemens slice order reversal detected (good!). >> >> > TR=7980.00, TE=84.00, TI=-1.00, flip angle=90.00 >> >> > i_ras = (-0.989479, -0.144529, 0.00655128) >> >> > j_ras = (0.144644, -0.987267, 0.0661911) >> >> > k_ras = (-0.00309869, 0.0664423, 0.997786) >> >> > writing to >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz... >> >> > Saving bvals and bvecs >> >> > mri_probedicom --i /data/memory/sourcemem//s1001/156000-20-1.dcm > >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dcminfo.dat >> >> > flip4fsl >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz >> >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.nii.gz >> >> > INFO: input image orientation is LPS >> >> > INFO: input image determinant is 8 >> >> > fslswapdim >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz >> x >> >> -y z >> >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.nii.gz >> >> > INFO: left-right orientation was flipped by fslswapdim >> >> > fslorient -forceradiological >> >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.nii.gz >> >> > INFO: found >> >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.mghdti.bvals, >> >> > converting to FSL format >> >> > INFO: found >> >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.mghdti.bvecs, >> >> > converting to FSL format >> >> > mv -f >> >> > >> >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.mghdti.bvecs >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs >> >> > mv -f >> >> > >> >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.mghdti.bvals >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvals >> >> > eddy_correct >> >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig_flip.nii.gz >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi.nii.gz 0 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0000 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0001 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0002 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0003 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0004 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0005 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0006 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0007 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0008 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0009 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0010 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0011 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0012 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0013 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0014 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0015 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0016 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0017 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0018 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0019 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0020 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0021 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0022 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0023 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0024 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0025 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0026 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0027 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0028 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0029 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0030 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0031 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0032 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0033 >> >> > processing >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_tmp0034 >> >> > mv -f /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs.norot >> >> > xfmrot >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi.ecclog >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs.norot >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs >> >> > fslroi >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi.nii.gz >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb.nii.gz 0 5 >> >> > fslmaths >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb.nii.gz >> >> > -Tmean >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb.nii.gz >> >> > bet /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb.nii.gz >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb_brain.nii.gz >> >> -m >> >> -f >> >> > 0.3 >> >> > mv -f >> >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb_brain_mask.nii.gz >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/diff >> >> > #------------------------------------- >> >> > #@# Inter-subject registration Tue Dec 6 22:15:05 EST 2011 >> >> > flirt -in >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb_brain.nii.gz >> >> -ref >> >> > /usr/share/fsl/4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out >> >> > >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/lowb_brain_mni.nii.gz >> >> > -omat >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/xfms/diff2mni.mat >> >> > -cost mutualinfo >> >> > convert_xfm -omat >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/xfms/mni2diff.mat >> >> > -inverse >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/xfms/diff2mni.mat >> >> > #------------------------------------- >> >> > #@# Masks Tue Dec 6 22:15:47 EST 2011 >> >> > #------------------------------------- >> >> > #@# Tensor fit Tue Dec 6 22:15:47 EST 2011 >> >> > dtifit -k >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi.nii.gz >> >> -m >> >> > >> >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/diff/lowb_brain_mask.nii.gz >> >> > -r /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvecs -b >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/bvals -o >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dtifit >> >> > 0 128 0 128 0 64 >> >> > 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 >> >> > 60 slices processed >> >> > 61 slices processed >> >> > 62 slices processed >> >> > 63 slices processed >> >> > #------------------------------------- >> >> > #@# Priors Tue Dec 6 22:15:54 EST 2011 >> >> > /software/Freesurfer/5.1.0//bin/dmri_train --outdir >> >> > /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/mni --out >> >> > lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt >> >> lh.ilf_AS_avg33_mni_flt >> >> > rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt >> >> rh.unc_AS_avg33_mni_flt >> >> > fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt >> >> lh.atr_PP_avg33_mni_flt >> >> > rh.atr_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt >> >> rh.ccg_PP_avg33_mni_flt >> >> > lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt >> >> lh.slfp_PP_avg33_mni_flt >> >> > rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt >> >> rh.slft_PP_avg33_mni_flt >> >> > --slist /tmp/subj33.s1001.8627.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.ccg_PP.flt.trk >> >> > dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk >> >> > dlabel/mni/rh.cab_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.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.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.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 >> >> > >> >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/mni/lowb_brain_mask.flt.nii.gz >> >> > --fa >> >> > >> >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dmri/mni/dtifit_FA.flt.nii.gz >> >> > --ncpts 5 --debug >> >> > ERROR: fio_pushd: >> >> /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/mni >> >> > ERROR: must specify brain mask volume for output subject >> >> > _______________________________________________ >> >> > Freesurfer mailing list >> >> > Freesurfer@nmr.mgh.harvard.edu >> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> >> >> 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
