Dear Dr. Webster,
Thank you for your response. The randomise call was:
randomise -i ..//all_MD_skeletonised.nii -o MDAnx -d MDAnx.mat -t MDAnx.con -m ..//all_MD.nii -n 500 -T
When run like that, it returned the “no data voxels present” error.
I omitted the -m ..//all_MD.nii and it ran fine, so I suspect I’m using something inappropriate as a mask. I am guessing right? If so, what would be a correct mask, if one is necessary?
Thanks again for your time,
Dawn
On Jun 12, 2018, at 11:17 AM, Matthew Webster <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Hello,
Can you let me know your randomise command line call?
Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
On 11 Jun 2018, at 13:56, Dawn Jensen <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Hi everyone,
I've been trying to run some analysis on the Mean Diffusivity and have been getting stuck in a couple places.
I've followed the FSL-Wiki instructions, creating the new directory, renaming the files to match the origdata image names and then ran the tbss_non_FA MD.
That produced the all_MD.nii image.
But I kept getting an error when it was supposed to create the all_MD_skeletonised that the thresh.txt file couldn't be found. I couldn't find it anywhere either and noticed that the tbss_4 had a set threshold of .2, rather than reading a thresh.txt file. So I ran the tbss_skeleton script by hand -
tbss_skeleton -i mean_FA -p .2 mean_FA_skeleton_mask_dst ${FSLDIR}/data/standard/LowerCingulum_1mm all_FA all_MD_skeletonised -a all_MD
which created an image that had all the appropriate volumes and when viewed in fslview_deprecated and mricron seemed to be correct.
The problem is when I run the MD images through randomise (after creating the .mat and .con files through Glm) it kicks back an error stating "No data voxels present".
I've searched the web and the archives, and while I've seen people post similar issues with the tbss_non_FA, I can't seem to dig up an answer to the above. I'd be grateful for any clues regarding where I've gone wrong or where to look next.
Thanks in advance,
Dawn Jensen
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