Dear Emily,
I have not experienced this myself but this does sound a little like a memory issue, especially given the FreeSurfer error.
How much memory do you have on your Mac?
And what version of FSL are you using?
Are there any errors or warnings from fslmerge or does it just silently give this poor output?
It might be worth working out whether the 70th-80th image corresponds to the 2GB point.
To do this just calculate xsize * ysize * zsize * 70 * 4 (the 4 is if the output image is in float, but should be 8 if it is in double)
If the image was 128*128*128 voxels then this would only be 560MB at 70 images (or 936MB for 117 images) by my calculations.
So unless your images are much bigger than this then I don't think it is to do with the 2GB limit.
Even if it is over 2GB I'm not sure why this would happen, but let us know the answer to the above questions and we'll try and help get to the bottom of it.
All the best,
Mark
On 9 Aug 2012, at 20:21, Emily Lindemer wrote:
> Hi All,
> I am working with a somewhat large set of FA data, and I have come across a problem when using fslmerge and fslsplit with my data. I have 117 subjects, and when I try to concatenate them into a 4D image using fslmerge, the first 70ish images of the 4D output file are in the correct order, but then the last chunk of them are in a seemingly-random order. I have checked and re-checked this many times to make sure that I wasn't mistaking the order of my input subjects, and I am sure that I am not doing anything wrong with labelling. I have used both imglob and an input list that I created, and I am having the problem both ways. I'm running FSL with a MAC OS, and I'm starting to think that it is a memory issue, for a couple of reasons.
>
> 1. When I try to loop through all of the images in the 4D file with fslview, the video crashes around the 80th subject.
> 2. For anyone who uses FreeSurfer: I also attempted to create the 4D image with mri_concat and I get a "cannot allocate memory" error.
>
> The most puzzling part is that the first chunk of subjects appear in the correct order in the 4D image, and this disorganization does not start at an obvious point (such as subject ID number switching to the 100's.)
>
> Furthermore, when I then go to use fslsplit on the 4D image, the splits come out in the same order as I input them (i.e. the last output split does not match up with the last frame of the 4D image, but rather, with the last subject that I input to fslmerge.)
>
> If anyone has an answer or has come across a similar problem, please let me know.
> Best,
> Emily
>
|