So you now have 66 rows in your bval/bvec file? What do you get if you run wc -l on them? wc -l bval.txt wc -l bvec.txt doug
On 12/13/11 11:59 PM, Yuko Yotsumoto wrote:
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.ht... > 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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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 mailto:yukoyy@a7.keio.jp HP : http://web.keio.jp/~yukoyy/ http://web.keio.jp/%7Eyukoyy/