Hello All,
I’m working with some data that I would like to compare inter-site, and would like to correct the gradient distortion from the different scanners (Siemens Allegra and Trio). That being said, I have looked online at the documentation to do this and have not been able to get the correction working properly. I have gotten the .grad files from Siemens and tried to use them with the two solutions online (the NITRC files and the grad_unwarp command in FreeSurfer) to no avail. I appreciate any advice from those experienced in correcting distortions.
The two problems that I am having now is:
1. While I have done all the steps listed online for the NITRC and do get an output, the files come out in what looks to be more distortion than before the correction. (The heads look very blocky after the correction and the surrounding box, which I believe should turn out square, now looks like Pacman went crazy and ate bites out of the sides.)
2. To use the grad_unwarp from freesurfer, I used the NITRC files to make the converted .gwv file for the distortion correction, but get this error (below). I assume this means I don’t have a table.mat file. Where do I get this? Also, grad_unwarp -help doesn’t really say much about how we’re supposed to setup the files/make the correction tables, any advice?
Thanks for any help you have to offer!
Matthew Russell
Error Log:
FreeSurfer/INDIV-2/grainab13530_WF_WNA/mri/orig 11% grad_unwarp -i 001.mgh -o allegra_uw.mgh -unwarp allegra -mydev
….
convert_unwarp_resample(infile,seriesno,outfile,corfovflag,unwarpflag,jacflag,interp_method,unwarptype,QuitOnError); % 1 = run from script, for qoe
INFO: using matlab installation matlab
Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen.
< M A T L A B (R) >
Copyright 1984-2009 The MathWorks, Inc.
Version 7.8.0.347 (R2009a) 64-bit (glnxa64)
February 12, 2009
>> >> >> >> >> >> >> >> >> >> >> >> >> >>
GRADWARPPATH=/labs/deyounglab/FreeSurfer/grad_unwarp_tables
TABLE=/labs/deyounglab/FreeSurfer/grad_unwarp_tables/table.mat
QuitOnError=1
Interp method is cubic
INFO: loading mgh-format infile 001.mgh
INFO: loading mgh volume 001.mgh
??? Error using ==> load
Unable to read file /labs/deyounglab/FreeSurfer/grad_unwarp_tables/table.mat:
No such file or directory.
Error in ==> convert_unwarp_resample>type2map at 331
load(TABLE);
Error in ==> convert_unwarp_resample at 141
gradwarpfile = type2map(user_gradwarpfile);
ERROR: output file not created