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
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#-------------------------------------
#@# 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