Hello,
I'm trying to use mri_convert to convert old (~1999) functional data
that was acquired on a GE LX scanner. However, nothing seems to work.
I'm running version 4.4.0 on RHEL4 x86_64. Here's my command line:
(results are similar if I omit the -in_type flag)
[matl...@occipital functional]$
I renamed them all to I.1, I.2, ..., I.8000 (there are 8000 images
total), and I got the same error messages. (With the -it ge option, it
is still looking for the old filename, it seems)
[matl...@occipital new_func]$ mri_convert I.1 -it lx -ot spm image
mri_convert I.1 -it lx -ot spm image
$Id:
sorry, it's a little finicky, I think it is looking for a %03d format,
meaning I.001 for slices numbers less than 1000, and I.1001 for greater
Chris Watson wrote:
I renamed them all to I.1, I.2, ..., I.8000 (there are 8000 images
total), and I got the same error messages. (With the -it ge
It got a little further (with -it ge and without any --in_type flag),
but I get this error:
[matl...@occipital new_func]$ mri_convert I.001 -it ge -ot spm image
mri_convert I.001 -it ge -ot spm image
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
reading from I.001...
You can try specifying the input geometry with something like -iis 1
-ijs 1 -iks 1 -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1
this is undoubtedly wrong, but should allow the command to finish
Chris Watson wrote:
It got a little further (with -it ge and without any --in_type
flag), but I get this
Still get an error:
[matl...@occipital new_func]$ mri_convert I.001 -it ge -ot spm -iis 1
-ijs 1 -iks 1 -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1 image
mri_convert I.001 -it ge -ot spm -iis 1 -ijs 1 -iks 1 -iid 1 0 0 -ijd 0
1 0 -ikd 0 0 1 image
$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks
sorry, also add -ic 0 0 0
Chris Watson wrote:
Still get an error:
[matl...@occipital new_func]$ mri_convert I.001 -it ge -ot spm -iis 1
-ijs 1 -iks 1 -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1 image
mri_convert I.001 -it ge -ot spm -iis 1 -ijs 1 -iks 1 -iid 1 0 0 -ijd
0 1 0 -ikd 0 0 1 image
$Id:
It completed but it's only giving me 1 .img file, and when I loaded it
into mricro, it thinks the z dimension is 8000 (the number of slices
total). It should give me 400 volumes (20 slices each). So I want
image001.img, 002.img, and so on. How can I do this? Do I have to rename
the files
Sorry, I don't know how to make our tools do this. It's a one-off on an
old data set on a file format that we don't really support anymore, so
I'm afraid that you're on your own on this one.
doug
Chris Watson wrote:
It completed but it's only giving me 1 .img file, and when I loaded it
