Hi Doug,
I thought I figured this out, but I was wrong...
my b-values are 700, and number of directions is 64.
Number of images with b=0 is 1.
Text file for bvals has 65 rows, first row has 0, followed by 64 of 700.
0
700
700
700
...
Text file for bvecs has 65 rows and three columns. The first row is 0 0 0, and
the rest was provided by Siemens.
With these files, I did:
dt_recon --i
/Users/yuko/Documents/FreeSurfer/raw/AGY11ADTI/DTIs/IM-0011-0001.dcm --b
bvals.txt bvecs.txt --s AGY11 --o
/Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A
And got the following error (dt_recon.log pasted in the end of this email):
-----------------------------------------------------------------------------------------------------------------
sysname Darwin
hostname Yukos-iMac.local
machine i386
user yuko
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii
logyflag 1
usedti 1
glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A
IllCondOK 0
DoFFx 0
Creating output directory /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A
Loading y from /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii
Using DTI
Loading BValues from
/Users/yuko/Documents/FreeSurfer/sessions/YDTI//bvalsbvecs/bvals.txt
Found 64 bvalues
Loading BVectors from
/Users/yuko/Documents/FreeSurfer/sessions/YDTI//bvalsbvecs/bvecs.txt
Found 64 bvectorss
Detected BVec file as MGH formatted
Saving design matrix to
/Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/Xg.dat
Matrix condition is 272.452
Pruning voxels by thr: 0.000000
Found 1025121 voxels in mask
Saving mask to /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/mask.nii
search space = 8.20097e+06
ERROR: dimension mismatch between y and X.
y has 65 inputs, X has 64 rows.
--------------------------------------------------------------------------------------------------------------------
What should I do from here? Am I still using wrong bvals and bvecs?
Thank you in advance.
Yuko
% ---------------------------------------------
dt_recon.log starts here
% --------------------------------------------
dt_recon logfile
Wed Dec 14 12:52:34 JST 2011
VERSION $Id: dt_recon,v 1.6.2.5 2009/05/20 17:59:50 greve Exp $
setenv SUBJECTS_DIR /Users/yuko/Documents/freesurfer/subjects
cd /Users/yuko/Documents/FreeSurfer/sessions
/Applications/freesurfer/bin/dt_recon --i
/Users/yuko/Documents/FreeSurfer/raw/AGY11ADTI/DTIs/IM-0011-0001.dcm --b
/Users/yuko/Documents/FreeSurfer/sessions/YDTI//bvalsbvecs/bvals.txt
/Users/yuko/Documents/FreeSurfer/sessions/YDTI//bvalsbvecs/bvecs.txt --s AGY11
--o /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A
Yukos-iMac.local
yuko
/usr/local/fsl/bin/eddy_correct
ECRefTP 0
#@#-------------------------------
Converting input
Wed Dec 14 12:52:34 JST 2011
cd /Users/yuko/Documents/FreeSurfer/sessions
mri_convert
/Users/yuko/Documents/FreeSurfer/raw/AGY11ADTI/DTIs/IM-0011-0001.dcm
/Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi.nii
mri_convert
/Users/yuko/Documents/FreeSurfer/raw/AGY11ADTI/DTIs/IM-0011-0001.dcm
/Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi.nii
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
reading from
/Users/yuko/Documents/FreeSurfer/raw/AGY11ADTI/DTIs/IM-0011-0001.dcm...
Getting Series No
INFO: Found 323 files in /Users/yuko/Documents/FreeSurfer/raw/AGY11ADTI/DTIs
INFO: Scanning for Series Number 12
Scanning Directory
INFO: found 65 files in series
INFO: loading series header info.
RunNo = 11
WARNING: Run 1 appears to be truncated
Files Found: 65, Files Expected (lRep+1): 1
FileName
/Users/yuko/Documents/FreeSurfer/raw/AGY11ADTI/DTIs/IM-0011-0001.dcm
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName AGY11
Date and time
StudyDate 20111019
StudyTime 112632.765000
SeriesTime 122206.687000
AcqTime 121908.682500
Acquisition parameters
PulseSeq *ep_b0
Protocol ep2d_diff_highRes
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 84
InversionTime -1
RepetitionTime 8100
PhEncFOV 256
ReadoutFOV 256
Image information
RunNo 11
SeriesNo 12
ImageNo 1
NImageRows 1024
NImageCols 1024
NFrames 65
SliceArraylSize 64
IsMosaic 1
ImgPos 1021.2289 1019.0401 204.2930
VolRes 2.0000 2.0000 2.0000
VolDim 128 128 64
Vc -1.0000 -0.0000 0.0000
Vr 0.0000 -0.9715 -0.2368
Vs -0.0000 -0.2368 0.9715
VolCenter 0.0000 0.0000 0.0000
TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: sorting.
INFO: (128 128 64), nframes = 65, ismosaic=1
Could not parse NUMARIS version string syngo MR B17
found in dicom tag 18,1020 (len = 3 != 6)
Repetition Time = 8100, TR = 8100 ms
PE Dir COL COL
AutoAlign matrix detected
AutoAlign Matrix ---------------------
1.000 0.000 0.000 0.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
FileName
/Users/yuko/Documents/FreeSurfer/raw/AGY11ADTI/DTIs/IM-0011-0001.dcm
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName AGY11
Date and time
StudyDate 20111019
StudyTime 112632.765000
SeriesTime 122206.687000
AcqTime 121908.682500
Acquisition parameters
PulseSeq *ep_b0
Protocol ep2d_diff_highRes
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 84
InversionTime -1
RepetitionTime 8100
PhEncFOV 256
ReadoutFOV 256
Image information
RunNo 11
SeriesNo 12
ImageNo 1
NImageRows 1024
NImageCols 1024
NFrames 65
SliceArraylSize 64
IsMosaic 1
ImgPos 125.2289 148.5321 -7.9140
VolRes 2.0000 2.0000 2.0000
VolDim 128 128 64
Vc -1.0000 -0.0000 0.0000
Vr 0.0000 -0.9715 -0.2368
Vs -0.0000 -0.2368 0.9715
VolCenter -2.7711 9.0162 23.9499
TransferSyntaxUID 1.2.840.10008.1.2.1
sagrev = 0, correv =0, trarev = 0
Vs = -0 -0.236838 0.971549
INFO: no Siemens slice order reversal detected (good!).
TR=8100.00, TE=84.00, TI=-1.00, flip angle=90.00
i_ras = (-1, -2e-16, 0)
j_ras = (2e-16, -0.971549, -0.236838)
k_ras = (-0, -0.236838, 0.971549)
writing to /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi.nii...
#@#-------------------------------
Eddy/Motion Correct
Wed Dec 14 12:52:48 JST 2011
cd /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/ectmp
eddy_correct /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi.nii
/Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii 0
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0000
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0001
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0002
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0003
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0004
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0005
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0006
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0007
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0008
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0009
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0010
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0011
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0012
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0013
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0014
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0015
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0016
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0017
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0018
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0019
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0020
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0021
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0022
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0023
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0024
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0025
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0026
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0027
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0028
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0029
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0030
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0031
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0032
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0033
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0034
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0035
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0036
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0037
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0038
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0039
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0040
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0041
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0042
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0043
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0044
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0045
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0046
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0047
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0048
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0049
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0050
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0051
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0052
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0053
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0054
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0055
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0056
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0057
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0058
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0059
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0060
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0061
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0062
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0063
processing /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec_tmp0064
#@#-------------------------------
Fitting Tensors
Wed Dec 14 13:09:34 JST 2011
cd /Users/yuko/Documents/FreeSurfer/sessions
mri_glmfit --y /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii
--glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A --dti
/Users/yuko/Documents/FreeSurfer/sessions/YDTI//bvalsbvecs/bvals.txt
/Users/yuko/Documents/FreeSurfer/sessions/YDTI//bvalsbvecs/bvecs.txt
$Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $
cwd /Users/yuko/Documents/FreeSurfer/sessions
cmdline mri_glmfit --y
/Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii --glmdir
/Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A --dti
/Users/yuko/Documents/FreeSurfer/sessions/YDTI//bvalsbvecs/bvals.txt
/Users/yuko/Documents/FreeSurfer/sessions/YDTI//bvalsbvecs/bvecs.txt
sysname Darwin
hostname Yukos-iMac.local
machine i386
user yuko
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii
logyflag 1
usedti 1
glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A
IllCondOK 0
DoFFx 0
Creating output directory /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A
Loading y from /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii
Using DTI
Loading BValues from
/Users/yuko/Documents/FreeSurfer/sessions/YDTI//bvalsbvecs/bvals.txt
Found 64 bvalues
Loading BVectors from
/Users/yuko/Documents/FreeSurfer/sessions/YDTI//bvalsbvecs/bvecs.txt
Found 64 bvectorss
Detected BVec file as MGH formatted
Saving design matrix to
/Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/Xg.dat
Matrix condition is 272.452
Pruning voxels by thr: 0.000000
Found 1025121 voxels in mask
Saving mask to /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/mask.nii
search space = 8.20097e+06
ERROR: dimension mismatch between y and X.
y has 65 inputs, X has 64 rows.
On Dec 10, 2011, at 1:42 PM, Douglas Greve wrote:
> Hi Yuko, it will get the bvals and bvecs from a set of tables
> distributed with FS. But the dicom has to have some information in it
> that tells it which table to use. It looks like your dicom did not have
> this information (it is not in the info dump created from the dicom). So
> you'll have to create text files of the bval/bvecs. The expected format
> is given in the help. You'll have to ask someone who knows about your
> sequences as to what the actual values you should use.
> doug
>
> On 12/9/11 10:09 PM, Yuko Yotsumoto wrote:
>> Hi Doug,
>>
>> Thank you for your reply.
>>> If so, then it cannot extract the bvecs and bvals. If you supply them in a
>>> file on the command line
>> I don't quite understand how --b works with dt_recon.
>>
>> I did:
>> dt_recon --i
>> /Users/yuko/Documents/FreeSurfer/raw/AGY11ADTI/DTIs/IM-0011-0001.dcm --s
>> AGY11 --o /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A
>>
>> and it stopped after creating dwi.nii and dwi-ec.nii.
>> I thought dt_recon is the command to compute bvals and bvecs. How do I
>> supply bvecs and bvals on the command line?
>>
>> Yuko
>>
>>
>> On Dec 10, 2011, at 2:24 AM, Douglas N Greve wrote:
>>
>>> Hi Yuko, your dicom file might be from a different versioned scanner than
>>> dt_recon is used to seeing. If so, then it cannot extract the bvecs and
>>> bvals. If you supply them in a file on the command line, it should run
>>> properly.
>>> doug
>>>
>>> Yuko Yotsumoto wrote:
>>>> Hello,
>>>>
>>>> I'm having a problem with dt_recon on data scanned by Siemens TrioTim.
>>>> I'm using v4.5.0, with Mac OS 10.6.8.
>>>>
>>>> dt_recon ran for a while, and stopped with an error "ERROR: cannot extract
>>>> sWiPMemBlock.alFree[8] from
>>>> /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat"
>>>>
>>>> I found the same errors reported to this mailing list, but found no
>>>> solution.
>>>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019755.html
>>>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07935.html
>>>>
>>>> In YDTI/YD11A/ folder, I have the following files
>>>> dt_recon.log
>>>> dwi-ec.ecclog
>>>> dwi-ec.nii
>>>> dwi-infodump.dat
>>>> dwi.nii
>>>> mri_glmfit.log
>>>>
>>>> In dwi-infodump.dat, I see bunch of lines, but I don't see
>>>> "sWiPMemBlock.alFree".
>>>>
>>>> Please help!
>>>> Thanks,
>>>> Yuko Yotsumoto
>>>>
>>>>
>>>>
>>>>
>>>> #@#-------------------------------
>>>> Fitting Tensors
>>>> Wed Dec 7 10:15:52 JST 2011
>>>> cd /Users/yuko/Documents/FreeSurfer/subjects
>>>> mri_glmfit --y
>>>> /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii --glmdir
>>>> /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A --dti
>>>> /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat
>>>>
>>>> $Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $
>>>> cwd /Users/yuko/Documents/FreeSurfer/subjects
>>>> cmdline mri_glmfit --y
>>>> /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii --glmdir
>>>> /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A --dti
>>>> /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat
>>>> sysname Darwin
>>>> hostname Yukos-iMac.local
>>>> machine i386
>>>> user yuko
>>>> FixVertexAreaFlag = 1
>>>> UseMaskWithSmoothing 1
>>>> OneSampleGroupMean 0
>>>> y /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii
>>>> logyflag 1
>>>> X /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat
>>>> usedti 1
>>>> glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A
>>>> IllCondOK 0
>>>> DoFFx 0
>>>> Creating output directory
>>>> /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A
>>>> Loading y from
>>>> /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii
>>>> Using DTI
>>>> bValue = 700
>>>> ERROR: cannot extract sWiPMemBlock.alFree[8] from
>>>> /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat
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