Hi Mark

When I just type imglob *, it gives me a list of my structurals, tab-separated:
F02_d1   F02_d5 ...

Not sure what version of FSL, I guess the most recent one since I'm running it through jalapeno. If I type fsl, the main window says version 5.0.4 - I guess that version also applies to the components of FSLVBM.

Anyway, the slicesdir created after "fslvbm_1_bet -b" was created normally, and I was able to visually inspect all structurals there.

As a side note, I have a pre&post-treatment scan of each of my subjects, all acquired on the same 3T scanner. For some subjects, their pre and the post structurals look completely different from each other, even though it is or course the same person. The way in which they are different suggests to me a non-linear warping, in the sense that dimension ratios do not appear to be maintained across pre&post. Is this normal, and is it something that is corrected for to a sufficient degree during the registration phase of an analysis (e.g., FSLVBM) pipe-line?

Thanks!
Tudor


On 27 May 2013 10:17, Mark Jenkinson <[log in to unmask]> wrote:
Hi,

What happens when you just type:
   imglob *
in the terminal (in the right directory)?

Also, what version of FSL are you using, because there was at least one old version that had a problem with imglob.

All the best,
Mark



On 25 May 2013, at 23:15, Tudor Popescu <[log in to unmask]> wrote:

Hi Mark,

I was in the right directory, as I did a dir prior to typing the command, and it showed all the files. If by backquotes you mean the character that is to the left of the '1' key, then this is what I typed. I'll check again tomorrow but I'm pretty sure that that's the case with both issues. In that case, is there anything else I can try?

Many thanks

Tudor

On 25 May 2013 23:01, Mark Jenkinson <[log in to unmask]> wrote:
Hi,

You must use the backquotes.
If, when you use backquotes, you are only getting the usage message from slicesdir then you are probably in the wrong directory, as this is what happens when there are no images in the directory.
So I would check on what directory you are in.

All the best,
Mark




On 25 May 2013, at 21:03, Tudor Popescu <[log in to unmask]> wrote:

Hi everyone,

I was following the FSLVBM tutorial, but the command slicesdir `imglob *`, to check if all structurals look as expected, results in the following errors:
Image Exception : #22 :: ERROR: Could not open image imglob
Error in slicer input, exiting...

 Cannot open slicesdir/grota.png for reading
/usr/local/fsl/bin/slicesdir: line 141: 11987 Segmentation fault      ${FSLDIR}/bin/pngappend $convertopts slicesdir/${Q}.png

/usr/local/fsl/bin/slicesdir: line 141: 11993 Segmentation fault      ${FSLDIR}/bin/slicer $A $pairimage -s 1 $sliceropts

 Cannot open slicesdir/grota.png for reading
/usr/local/fsl/bin/slicesdir: line 141: 11997 Segmentation fault      ${FSLDIR}/bin/pngappend $convertopts slicesdir/${Q}.png>
 
This happens when I use single quotes (') around the imglob * command. If I use backticks (`), as appears in the tutorial, I just get the slicesdir syntax help.

Thanks in advance for any help!

Tudor