> 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 <
>
rspriti@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 <
>> >
rspriti@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
>> >> >
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>> >> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >>
>> >>
>> >>
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>> >> is
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>> >> HelpLine at
>> >>
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>