Hi,

It sounds like you might just have a problem with the display range of the images that you are looking at.  Try changing the min/max values in FSLView to 0 and 1, and see if that fixes the problems.

All the best,
Mark




On 27 Jun 2014, at 16:59, "Garlinghouse, Matthew Aaron,Ph.D." <[log in to unmask]> wrote:

Hello listmates,

I am running the latest update of FSL FIRST (for the first time), on a 64-bit Linux cluster, and going through some QA.  Everything from run_first_all, to the creation of the slicesdir/index.html, to the concatenation of the .bvar files in the proper group order for the two groups I am interested in seems to have gone very well.  

However, I think I am running into difficulty when I run the script below - I have adjusted for my own file names and paths….
________________

first_utils --vertexAnalysis --usebvars -i con_to_dis_L_Hipp.bvars -d con1_dis2.mat -o shape_analysis/con1_dis2_L_Hipp --useReconNative --useRigidAlign -v >& shape_analysis/con1_dis2_L_Hipp_output.txt

_________________

After running this command I get a .txt file, a .nii.gz file for the specific structure I am interested in and a mask.nii.gz file for that structure.  When I view the text file I read that the model has been processed with 732 vertices and 336 modes of variation were retained and etc….……..  

However when I try to view the resulting image files in fslview, both the image file and the mask file are empty - and no changes in intensity are noted when I scroll through the blank display.  I also don't see any structures appear when I change the color of the image display.  

However when I load the structural image in FreeView I see what looks like a very faint outline of a hippocampus. When I load the mask, I see these outlines in white - although the space inside the lines is not masked.  Is this to be expected?  

I was thinking I had made a processing error at some point, but I can't seem to pinpoint it in the few steps I've done - and I can't seem to find a potential solution to my concern in the listserv archives.


Any tips or thoughts would be most appreciated.

Kind Regards,

Matthew

 

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