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Hello Freesurfer experts,
I am currently running into an issue that I can’t seem to resolve.
Is this due to incompatibilities with Mac OS Catalina ? I have the 6.0 version of Freesurfer.
Would it work better with the 7.0 beta version of Freesurfer ?
Please find below the output when the error occurs.
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Vinitas-MacBook-Pro:~ vinita$ export FREESURFER_HOME=/Applications/freesurfer
Vinitas-MacBook-Pro:~ vinita$
Vinitas-MacBook-Pro:~ vinita$ export SUBJECTS_DIR=/Users/vinita/Documents/FreeSurferDirs/subjects
Vinitas-MacBook-Pro:~ vinita$
Vinitas-MacBook-Pro:~ vinita$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-fsl-matlab-Darwin-OSX-stable-pub-v6.0.0-tutorial-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Users/vinita/Documents/FreeSurferDirs/subjects
MNI_DIR /Applications/freesurfer/mni
Vinitas-MacBook-Pro:~ vinita$
Vinitas-MacBook-Pro:~ vinita$ export FSL_DIR=$FREESURFER_HOME/fsl_507
Vinitas-MacBook-Pro:~ vinita$ export FSLDIR=$FSL_DIR
Vinitas-MacBook-Pro:~ vinita$ cd Desktop/
Vinitas-MacBook-Pro:Desktop vinita$ trac-all -prep -c Test01.txt
domainname: Command not found.
export: Command not found.
Too many )'s.
INFO: SUBJECTS_DIR is /Users/vinita/Documents/FreeSurferDirs/subjects
INFO: Diffusion root is /Users/vinita/Documents/FreeSurferDirs/subjects
Actual FREESURFER_HOME /Applications/freesurfer
trac-preproc -c /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/scripts/dmrirc.local -log /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/scripts/trac-all.log -cmd /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/scripts/trac-all.cmd
#-------------------------------------
/Applications/freesurfer/bin/trac-preproc
#-------------------------------------
#@# Image corrections Fri Apr 17 15:07:43 CDT 2020
mri_convert --bvec-voxel /Users/vinita/Documents/FreeSurferDirs/Data/Test01/DTI/IM-0001-0001.dcm /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel /Users/vinita/Documents/FreeSurferDirs/Data/Test01/DTI/IM-0001-0001.dcm /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Users/vinita/Documents/FreeSurferDirs/Data/Test01/DTI/IM-0001-0001.dcm...
Getting Series No
INFO: Found 105 files in /Users/vinita/Documents/FreeSurferDirs/Data/Test01/DTI
INFO: Scanning for Series Number 5
Scanning Directory
INFO: found 102 files in series
INFO: loading series header info.
RunNo = 4
WARNING: Run 1 appears to be truncated
Files Found: 102, Files Expected (lRep+1): 1
FileName /Users/vinita/Documents/FreeSurferDirs/Data/Test01/DTI/IM-0001-0001.dcm
Identification
NumarisVer syngo MR E11
ScannerModel Skyra
PatientName NELSON^JAMES
Date and time
StudyDate 20180331
StudyTime 113843
SeriesTime 115833.384000
AcqTime 115659.267500
Acquisition parameters
PulseSeq *ep_b0
Protocol ep2d_DTI PENRAD
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 95
InversionTime -1
RepetitionTime 4300
PhEncFOV 230
ReadoutFOV 230
Image information
RunNo 4
SeriesNo 5
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 102
SliceArraylSize 32
IsMosaic 1
ImgPos 658.2784 704.6226 66.6609
VolRes 1.7969 1.7969 4.0000
VolDim 128 128 32
Vc -0.9994 -0.0347 -0.0095
Vr 0.0349 -0.9991 -0.0241
Vs -0.0087 -0.0244 0.9997
VolCenter 0.0000 0.0000 0.0000
TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: sorting.
INFO: (128 128 32), nframes = 102, ismosaic=1
sdfi->UseSliceScaleFactor 0
datatype = 4, short=4, float=3
Could not parse NUMARIS version string syngo MR E11
found in dicom tag 18,1020 (len = 3 != 6)
Repetition Time = 4300, TR = 4300 ms
PE Dir COL COL
AutoAlign matrix detected
AutoAlign Matrix ---------------------
1.00000 0.00000 0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000;
0.00000 0.00000 1.00000 0.00000;
0.00000 0.00000 0.00000 1.00000;
FileName /Users/vinita/Documents/FreeSurferDirs/Data/Test01/DTI/IM-0001-0001.dcm
Identification
NumarisVer syngo MR E11
ScannerModel Skyra
PatientName NELSON^JAMES
Date and time
StudyDate 20180331
StudyTime 113843
SeriesTime 115833.384000
AcqTime 115659.267500
Acquisition parameters
PulseSeq *ep_b0
Protocol ep2d_DTI PENRAD
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 95
InversionTime -1
RepetitionTime 4300
PhEncFOV 230
ReadoutFOV 230
Image information
RunNo 4
SeriesNo 5
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 102
SliceArraylSize 32
IsMosaic 1
ImgPos 104.7923 113.2296 -102.6341
VolRes 1.7969 1.7969 4.0000
VolDim 128 128 32
Vc -0.9994 -0.0347 -0.0095
Vr 0.0349 -0.9991 -0.0241
Vs -0.0087 -0.0244 0.9997
VolCenter -6.6751 -7.2181 -42.5229
TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 1
sagrev = 0, correv =0, trarev = 1
Vs = -0.00867384 -0.0244271 0.999664
INFO: detected a Siemens slice order reversal in mosaic, so
I'm going to reverse them back to their 'original' order.
TR=4300.00, TE=95.00, TI=-1.00, flip angle=90.00
i_ras = (-0.999353, -0.0346773, -0.00951849)
j_ras = (0.0348982, -0.9991, -0.0241105)
k_ras = (-0.00867384, -0.0244271, 0.999664)
writing to /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz...
mri_probedicom --i /Users/vinita/Documents/FreeSurferDirs/Data/Test01/DTI/IM-0001-0001.dcm > /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dcminfo.dat
cp /Users/vinita/Documents/FreeSurferDirs/Data/Test01/DTI_bvec.txt /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.bvecs
cp /Users/vinita/Documents/FreeSurferDirs/Data/Test01/DTI_bval.txt /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.bvals
mv -f /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvecs.tmp /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.bvecs
mv -f /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvals.tmp /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.bvals
orientLAS /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig_las.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 12.915
mri_convert -oni 128 -onj 128 -onk 32 -oid -0.999353 -0.0346773 -0.00951849 -ojd -0.0348982 0.9991 0.0241105 -okd -0.00867384 -0.0244271 0.999664 -oc -6.73784 -5.42282 -42.4796 -rt nearest /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig_las.nii.gz
mri_convert.bin -oni 128 -onj 128 -onk 32 -oid -0.999353 -0.0346773 -0.00951849 -ojd -0.0348982 0.9991 0.0241105 -okd -0.00867384 -0.0244271 0.999664 -oc -6.73784 -5.42282 -42.4796 -rt nearest /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig_las.nii.gz
normalizing out_i_direction: (-0.999353, -0.0346773, -0.00951849) -> (-0.999353, -0.0346773, -0.00951849)
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz...
TR=4300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999353, -0.0346773, -0.00951849)
j_ras = (0.0348982, -0.9991, -0.0241105)
k_ras = (-0.00867384, -0.0244271, 0.999664)
Reslicing using nearest
writing to /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig_las.nii.gz...
INFO: found /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.bvals, copying
INFO: found /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.bvecs, converting to LAS
mv -f /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig_las.bvecs /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvecs
mv -f /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig_las.bvals /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvals
eddy_correct /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig_las.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi.nii.gz 0
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0000
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0001
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0002
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0003
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0004
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0005
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0006
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0007
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0008
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0009
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0010
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0011
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0012
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0013
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0014
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0015
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0016
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0017
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0018
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0019
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0020
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0021
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0022
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0023
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0024
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0025
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0026
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0027
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0028
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0029
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0030
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0031
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0032
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0033
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0034
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0035
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0036
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0037
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0038
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0039
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0040
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0041
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0042
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0043
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0044
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0045
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0046
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0047
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0048
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0049
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0050
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0051
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0052
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0053
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0054
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0055
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0056
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0057
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0058
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0059
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0060
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0061
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0062
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0063
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0064
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0065
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0066
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0067
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0068
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0069
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0070
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0071
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0072
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0073
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0074
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0075
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0076
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0077
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0078
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0079
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0080
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0081
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0082
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0083
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0084
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0085
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0086
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0087
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0088
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0089
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0090
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0091
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0092
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0093
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0094
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0095
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0096
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0097
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0098
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0099
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0100
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0101
mv -f /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvecs /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvecs.norot
xfmrot /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi.ecclog /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvecs.norot /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvecs
ln -sf /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/data.nii.gz
mri_convert --frame 0 31 62 93 94 95 96 97 98 99 100 101 /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/lowb.nii.gz
mri_convert.bin --frame 0 31 62 93 94 95 96 97 98 99 100 101 /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/lowb.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999353, -0.0346773, -0.00951849)
j_ras = (-0.0348982, 0.9991, 0.0241105)
k_ras = (-0.00867384, -0.0244271, 0.999664)
keeping frames 0 31 62 93 94 95 96 97 98 99 100 101
writing to /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/lowb.nii.gz...
mri_concat --i /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/lowb.nii.gz --mean --o /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/lowb.nii.gz
ninputs = 1
Checking inputs
nframestot = 12
Allocing output
Done allocing
nframes = 12
Computing mean across frames
Writing to /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/lowb.nii.gz
bet /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/lowb.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/lowb_brain.nii.gz -m -f 0.3
mv -f /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/lowb_brain_mask.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dlabel/diff
#-------------------------------------
#@# Image quality assessment Fri Apr 17 15:21:51 CDT 2020
/Applications/freesurfer/bin/dmri_motion --dwi /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz --mat /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi.ecclog --bval /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvals --T 229.416672 --out /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_motion.txt
cwd /Users/vinita/Desktop
cmdline /Applications/freesurfer/bin/dmri_motion --dwi /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz --mat /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi.ecclog --bval /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvals --T 229.416672 --out /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_motion.txt
sysname Darwin
hostname Vinitas-MacBook-Pro.local
machine x86_64
user vinita
Output motion measure file: /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_motion.txt
Input transform file: /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi.ecclog
Input DWI file: /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz
Input b-value table: /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvals
Low-b image intensity threshold: 229.417
Nominal diffusivity: 0.001
Loading volume-to-baseline affine transformations
Computing between-volume head motion measures
INFO: Processed transforms for 102 volumes
Loading DWI volume series from /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz
Loading b-value table from /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvals
Computing within-volume head motion measures
Done in 2.628 sec.
dmri_motion done
#-------------------------------------
#@# Intra-subject registration Fri Apr 17 15:21:54 CDT 2020
mri_convert /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/mri/brain.mgz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat_orig.nii.gz
mri_convert.bin /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/mri/brain.mgz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat_orig.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/mri/brain.mgz...
TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -8.29459e-10, 0)
j_ras = (9.31323e-10, 1.86265e-09, -1)
k_ras = (7.71252e-10, 1, 0)
writing to /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat_orig.nii.gz...
orientLAS /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat_orig.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 -8.29459e-10 0 -ojd 7.71252e-10 1 0 -okd -9.31323e-10 -1.86265e-09 1 -oc -6.2289 -6.71704 -17.0073 -rt nearest /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat_orig.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 -8.29459e-10 0 -ojd 7.71252e-10 1 0 -okd -9.31323e-10 -1.86265e-09 1 -oc -6.2289 -6.71704 -17.0073 -rt nearest /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat_orig.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat_orig.nii.gz...
TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -8.29459e-10, 0)
j_ras = (9.31323e-10, 1.86265e-09, -1)
k_ras = (7.71252e-10, 1, 0)
Reslicing using nearest
writing to /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat.nii.gz...
tkregister2 --mov /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat_orig.nii.gz --targ /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/xfms/anatorig2anat.mat --reg /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/xfms/anat2anatorig.dat
/Applications/freesurfer/tktools/tkregister2.bin: Bad CPU type in executable.
Darwin Vinitas-MacBook-Pro.local 19.4.0 Darwin Kernel Version 19.4.0: Wed Mar 4 22:28:40 PST 2020; root:xnu-6153.101.6~15/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Fri Apr 17 15:21:57 CDT 2020
Vinitas-MacBook-Pro:Desktop vinita$
It would be great if you could help me figure out a solution.
Thanks in advance,
Vinita Batra
Hi Vinita,
The tkregister visualizer is quite old and no longer supported. It was built as a 32bit executable, which unfortunately can’t be run on catalina, but we have a cmdl-only version that is built as a 64bit binary. Looks like this call is built into the trac-preproc script, so can you modify line #634 of $FREESURFER_HOME/bin/trac-preproc to read:
set cmd = tkregister2_cmdl
instead of:
set cmd = tkregister2
Let me know if that fixes things.
best, Andrew
From: "Batra, Vinita R." vbatra@lsuhsc.edu Date: Monday, April 20, 2020 at 10:48 AM To: FS Help freesurfer@nmr.mgh.harvard.edu, "Hoopes, Andrew" AHOOPES@mgh.harvard.edu Subject: Bad CPU type in executable
External Email - Use Caution Hello Freesurfer experts,
I am currently running into an issue that I can’t seem to resolve.
Is this due to incompatibilities with Mac OS Catalina ? I have the 6.0 version of Freesurfer.
Would it work better with the 7.0 beta version of Freesurfer ?
Please find below the output when the error occurs.
The default interactive shell is now zsh.
To update your account to use zsh, please run `chsh -s /bin/zsh`.
For more details, please visit https://support.apple.com/kb/HT208050.
Vinitas-MacBook-Pro:~ vinita$ export FREESURFER_HOME=/Applications/freesurfer
Vinitas-MacBook-Pro:~ vinita$
Vinitas-MacBook-Pro:~ vinita$ export SUBJECTS_DIR=/Users/vinita/Documents/FreeSurferDirs/subjects
Vinitas-MacBook-Pro:~ vinita$
Vinitas-MacBook-Pro:~ vinita$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-fsl-matlab-Darwin-OSX-stable-pub-v6.0.0-tutorial-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Users/vinita/Documents/FreeSurferDirs/subjects
MNI_DIR /Applications/freesurfer/mni
Vinitas-MacBook-Pro:~ vinita$
Vinitas-MacBook-Pro:~ vinita$ export FSL_DIR=$FREESURFER_HOME/fsl_507
Vinitas-MacBook-Pro:~ vinita$ export FSLDIR=$FSL_DIR
Vinitas-MacBook-Pro:~ vinita$ cd Desktop/
Vinitas-MacBook-Pro:Desktop vinita$ trac-all -prep -c Test01.txt
domainname: Command not found.
export: Command not found.
Too many )'s.
INFO: SUBJECTS_DIR is /Users/vinita/Documents/FreeSurferDirs/subjects
INFO: Diffusion root is /Users/vinita/Documents/FreeSurferDirs/subjects
Actual FREESURFER_HOME /Applications/freesurfer
trac-preproc -c /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/scripts/dmrirc.local -log /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/scripts/trac-all.log -cmd /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/scripts/trac-all.cmd
#-------------------------------------
/Applications/freesurfer/bin/trac-preproc
#-------------------------------------
#@# Image corrections Fri Apr 17 15:07:43 CDT 2020
mri_convert --bvec-voxel /Users/vinita/Documents/FreeSurferDirs/Data/Test01/DTI/IM-0001-0001.dcm /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel /Users/vinita/Documents/FreeSurferDirs/Data/Test01/DTI/IM-0001-0001.dcm /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Users/vinita/Documents/FreeSurferDirs/Data/Test01/DTI/IM-0001-0001.dcm...
Getting Series No
INFO: Found 105 files in /Users/vinita/Documents/FreeSurferDirs/Data/Test01/DTI
INFO: Scanning for Series Number 5
Scanning Directory
INFO: found 102 files in series
INFO: loading series header info.
RunNo = 4
WARNING: Run 1 appears to be truncated
Files Found: 102, Files Expected (lRep+1): 1
FileName /Users/vinita/Documents/FreeSurferDirs/Data/Test01/DTI/IM-0001-0001.dcm
Identification
NumarisVer syngo MR E11
ScannerModel Skyra
PatientName NELSON^JAMES
Date and time
StudyDate 20180331
StudyTime 113843
SeriesTime 115833.384000
AcqTime 115659.267500
Acquisition parameters
PulseSeq *ep_b0
Protocol ep2d_DTI PENRAD
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 95
InversionTime -1
RepetitionTime 4300
PhEncFOV 230
ReadoutFOV 230
Image information
RunNo 4
SeriesNo 5
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 102
SliceArraylSize 32
IsMosaic 1
ImgPos 658.2784 704.6226 66.6609
VolRes 1.7969 1.7969 4.0000
VolDim 128 128 32
Vc -0.9994 -0.0347 -0.0095
Vr 0.0349 -0.9991 -0.0241
Vs -0.0087 -0.0244 0.9997
VolCenter 0.0000 0.0000 0.0000
TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: sorting.
INFO: (128 128 32), nframes = 102, ismosaic=1
sdfi->UseSliceScaleFactor 0
datatype = 4, short=4, float=3
Could not parse NUMARIS version string syngo MR E11
found in dicom tag 18,1020 (len = 3 != 6)
Repetition Time = 4300, TR = 4300 ms
PE Dir COL COL
AutoAlign matrix detected
AutoAlign Matrix ---------------------
1.00000 0.00000 0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000;
0.00000 0.00000 1.00000 0.00000;
0.00000 0.00000 0.00000 1.00000;
FileName /Users/vinita/Documents/FreeSurferDirs/Data/Test01/DTI/IM-0001-0001.dcm
Identification
NumarisVer syngo MR E11
ScannerModel Skyra
PatientName NELSON^JAMES
Date and time
StudyDate 20180331
StudyTime 113843
SeriesTime 115833.384000
AcqTime 115659.267500
Acquisition parameters
PulseSeq *ep_b0
Protocol ep2d_DTI PENRAD
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 95
InversionTime -1
RepetitionTime 4300
PhEncFOV 230
ReadoutFOV 230
Image information
RunNo 4
SeriesNo 5
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 102
SliceArraylSize 32
IsMosaic 1
ImgPos 104.7923 113.2296 -102.6341
VolRes 1.7969 1.7969 4.0000
VolDim 128 128 32
Vc -0.9994 -0.0347 -0.0095
Vr 0.0349 -0.9991 -0.0241
Vs -0.0087 -0.0244 0.9997
VolCenter -6.6751 -7.2181 -42.5229
TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 1
sagrev = 0, correv =0, trarev = 1
Vs = -0.00867384 -0.0244271 0.999664
INFO: detected a Siemens slice order reversal in mosaic, so
I'm going to reverse them back to their 'original' order.
TR=4300.00, TE=95.00, TI=-1.00, flip angle=90.00
i_ras = (-0.999353, -0.0346773, -0.00951849)
j_ras = (0.0348982, -0.9991, -0.0241105)
k_ras = (-0.00867384, -0.0244271, 0.999664)
writing to /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz...
mri_probedicom --i /Users/vinita/Documents/FreeSurferDirs/Data/Test01/DTI/IM-0001-0001.dcm > /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dcminfo.dat
cp /Users/vinita/Documents/FreeSurferDirs/Data/Test01/DTI_bvec.txt /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.bvecs
cp /Users/vinita/Documents/FreeSurferDirs/Data/Test01/DTI_bval.txt /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.bvals
mv -f /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvecs.tmp /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.bvecs
mv -f /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvals.tmp /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.bvals
orientLAS /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig_las.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 12.915
mri_convert -oni 128 -onj 128 -onk 32 -oid -0.999353 -0.0346773 -0.00951849 -ojd -0.0348982 0.9991 0.0241105 -okd -0.00867384 -0.0244271 0.999664 -oc -6.73784 -5.42282 -42.4796 -rt nearest /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig_las.nii.gz
mri_convert.bin -oni 128 -onj 128 -onk 32 -oid -0.999353 -0.0346773 -0.00951849 -ojd -0.0348982 0.9991 0.0241105 -okd -0.00867384 -0.0244271 0.999664 -oc -6.73784 -5.42282 -42.4796 -rt nearest /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig_las.nii.gz
normalizing out_i_direction: (-0.999353, -0.0346773, -0.00951849) -> (-0.999353, -0.0346773, -0.00951849)
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz...
TR=4300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999353, -0.0346773, -0.00951849)
j_ras = (0.0348982, -0.9991, -0.0241105)
k_ras = (-0.00867384, -0.0244271, 0.999664)
Reslicing using nearest
writing to /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig_las.nii.gz...
INFO: found /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.bvals, copying
INFO: found /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.bvecs, converting to LAS
mv -f /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig_las.bvecs /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvecs
mv -f /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig_las.bvals /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvals
eddy_correct /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig_las.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi.nii.gz 0
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0000
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0001
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0002
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0003
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0004
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0005
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0006
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0007
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0008
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0009
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0010
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0011
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0012
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0013
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0014
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0015
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0016
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0017
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0018
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0019
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0020
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0021
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0022
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0023
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0024
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0025
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0026
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0027
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0028
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0029
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0030
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0031
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0032
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0033
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0034
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0035
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0036
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0037
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0038
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0039
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0040
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0041
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0042
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0043
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0044
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0045
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0046
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0047
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0048
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0049
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0050
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0051
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0052
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0053
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0054
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0055
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0056
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0057
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0058
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0059
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0060
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0061
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0062
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0063
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0064
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0065
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0066
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0067
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0068
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0069
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0070
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0071
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0072
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0073
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0074
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0075
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0076
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0077
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0078
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0079
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0080
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0081
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0082
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0083
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0084
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0085
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0086
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0087
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0088
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0089
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0090
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0091
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0092
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0093
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0094
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0095
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0096
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0097
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0098
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0099
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0100
processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0101
mv -f /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvecs /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvecs.norot
xfmrot /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi.ecclog /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvecs.norot /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvecs
ln -sf /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/data.nii.gz
mri_convert --frame 0 31 62 93 94 95 96 97 98 99 100 101 /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/lowb.nii.gz
mri_convert.bin --frame 0 31 62 93 94 95 96 97 98 99 100 101 /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/lowb.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999353, -0.0346773, -0.00951849)
j_ras = (-0.0348982, 0.9991, 0.0241105)
k_ras = (-0.00867384, -0.0244271, 0.999664)
keeping frames 0 31 62 93 94 95 96 97 98 99 100 101
writing to /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/lowb.nii.gz...
mri_concat --i /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/lowb.nii.gz --mean --o /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/lowb.nii.gz
ninputs = 1
Checking inputs
nframestot = 12
Allocing output
Done allocing
nframes = 12
Computing mean across frames
Writing to /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/lowb.nii.gz
bet /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/lowb.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/lowb_brain.nii.gz -m -f 0.3
mv -f /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/lowb_brain_mask.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dlabel/diff
#-------------------------------------
#@# Image quality assessment Fri Apr 17 15:21:51 CDT 2020
/Applications/freesurfer/bin/dmri_motion --dwi /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz --mat /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi.ecclog --bval /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvals --T 229.416672 --out /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_motion.txt
cwd /Users/vinita/Desktop
cmdline /Applications/freesurfer/bin/dmri_motion --dwi /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz --mat /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi.ecclog --bval /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvals --T 229.416672 --out /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_motion.txt
sysname Darwin
hostname Vinitas-MacBook-Pro.local
machine x86_64
user vinita
Output motion measure file: /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_motion.txt
Input transform file: /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi.ecclog
Input DWI file: /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz
Input b-value table: /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvals
Low-b image intensity threshold: 229.417
Nominal diffusivity: 0.001
Loading volume-to-baseline affine transformations
Computing between-volume head motion measures
INFO: Processed transforms for 102 volumes
Loading DWI volume series from /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz
Loading b-value table from /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvals
Computing within-volume head motion measures
Done in 2.628 sec.
dmri_motion done
#-------------------------------------
#@# Intra-subject registration Fri Apr 17 15:21:54 CDT 2020
mri_convert /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/mri/brain.mgz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat_orig.nii.gz
mri_convert.bin /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/mri/brain.mgz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat_orig.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/mri/brain.mgz...
TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -8.29459e-10, 0)
j_ras = (9.31323e-10, 1.86265e-09, -1)
k_ras = (7.71252e-10, 1, 0)
writing to /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat_orig.nii.gz...
orientLAS /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat_orig.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 -8.29459e-10 0 -ojd 7.71252e-10 1 0 -okd -9.31323e-10 -1.86265e-09 1 -oc -6.2289 -6.71704 -17.0073 -rt nearest /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat_orig.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 -8.29459e-10 0 -ojd 7.71252e-10 1 0 -okd -9.31323e-10 -1.86265e-09 1 -oc -6.2289 -6.71704 -17.0073 -rt nearest /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat_orig.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat_orig.nii.gz...
TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -8.29459e-10, 0)
j_ras = (9.31323e-10, 1.86265e-09, -1)
k_ras = (7.71252e-10, 1, 0)
Reslicing using nearest
writing to /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat.nii.gz...
tkregister2 --mov /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat_orig.nii.gz --targ /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/xfms/anatorig2anat.mat --reg /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/xfms/anat2anatorig.dat
/Applications/freesurfer/tktools/tkregister2.bin: Bad CPU type in executable.
Darwin Vinitas-MacBook-Pro.local 19.4.0 Darwin Kernel Version 19.4.0: Wed Mar 4 22:28:40 PST 2020; root:xnu-6153.101.6~15/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Fri Apr 17 15:21:57 CDT 2020
Vinitas-MacBook-Pro:Desktop vinita$
It would be great if you could help me figure out a solution.
Thanks in advance,
Vinita Batra
freesurfer@nmr.mgh.harvard.edu
-
Batra, Vinita R. -
Hoopes, Andrew