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/[email protected]/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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