New subject: tracula ERROR: must specify brain mask volume for output subject

8 Dec 2011


      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 <
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
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Re: [Freesurfer] tracula ERROR: must specify brain mask volume for output subject