Hi Doug,

I used text edit, and the file looks OK on xterm window (more bvals.txt).
I just tried it with one more row with b=0, and it worked.

0
0
700
...

and

0 0 0
0 0 0
...

Siemens told me that the number of images with b=0 is 1, so I should be still worried, right?

Yuko

On Dec 14, 2011, at 1:55 PM, Douglas Greve wrote:

Hi Yuko, i'm guessing that something is fishy with your bval and bvec files. Make sure that there is a new line after the last entry. How did you make the files?
doug


On 12/13/11 11:22 PM, Yuko Yotsumoto wrote:
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






The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


-----------------------------------
Yuko Yotsumoto, Ph. D.
Associate Professor (research)
The Global Centers of Excellence Program, Keio University

TEL:011-81-3-5427-1156 x 23851
e-mail: yukoyy@a7.keio.jp
HP  : http://web.keio.jp/~yukoyy/
------------------------------------