Thanks Doug,

In the dt_recon help, 

The bvalues are in a simple text file, one for each direction

(including b=0). The bvectors (gradient directions) are also in a

simple text file with three components on each row. These also include

the b=0 values. There must be as many rows in the bvals/bvecs

as there are frames in the input.

I got the bvectors from Siemens tech. The file looks similar to one in $FREESURFER_HOME/diffusion/mgh-dti-seqpack

However, I am still not sure about bvalues.

The bvalues are in a simple text file, one for each direction

(including b=0).

I think I'm using b-value=700, and I have 64 directions.

Should I have b-values for each of the 64 directions? Then the text file should have 64 rows and each row has the same value?

Thank you for your help!

Yuko

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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