Dear, Dr. Greve:
 
 I have rerun dt_recon as you suggested, but it still does not work.
 Attachment is the new dt_recon.log file, please check it.

Thanks.

Zonglei Zhen



2008/3/13, Doug Greve <greve@nmr.mgh.harvard.edu>:

This is a problem with the dicom reader mistaking the .IMA file as an old siemens format file (before they started using dicom). I've fixed it in our distribution. You  can get around it by converting the input to nifti, so:

mri_convert 20080202_JL_CHENGUANNAN.MR.BNU_CST_LIU_JIA.5.1.2008.02.02.13.51.44.78125.51418224.IMA dwi.nii -it siemens_dicom

dt_recon --i dwi.nii  --s chenGN1995 --o dti_analysis


doug


Zhen Zonglei wrote:

Dear, Dr. Greve:

  Thanks for your help. Today, when we tried to run the new function of FS in DTI analysis, we got stuck again. The dt_recon command cannot run successfully, and always report us 'MRIresample(): error inverting matrix'.

The data is from Siemens Trio 3T system, and has 64 diffusion directions. Before running dt_recon, we have unpacked the DTI dicom data to a specific directory with unpacksdcmdir command.

To provide more details, I attach the dt_recon.log file and a DTI image (one direction) to this mail.

Please help us again.

 
Thanks again!

 

Zonglei Zhen



2008/3/12, Doug Greve <greve@nmr.mgh.harvard.edu>:

If you are using the 4-column par file, then just code them as separate, overlapping events, ie. If condition 1 is the block (lasting 10 sec) and condition 2 is the event (lasting 2 sec), then

0  1  10  1  ---> starts at t=0, lasts 10 sec
0  2    2   1 ----> starts att=0, lasts 2 sec
5  2    2   1 ----> starts at t=5, lasts 2 sec
7  2     2  1  ---> starts at t=7, lasts 2 sec

The last col of 1s just means that the event weight is one (probably what you want).

doug



Zhen Zonglei wrote:

Dear, Dr. Greve:

I hope I don't bother you too much. But I'm wondering about how to analyze mixed blocked/event related design with FSFAST. In our experiment, we have two blocked conditions and three event-related conditions in every block. We are not sure how to write the parfiles and construct the model to analyze these data in FSFAST.

Please give us some suggestions on this issue.

 

Thanks in advance.

 

Zonglei Zhen


-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

    


-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting