Hello,
You can either use mean_FA_skeleton_mask, or if that file is not available/suitable you can threshold your mean skeletonised MD data to create a suitable mask, eg..
fslmaths all_MD_skeletonised -Tmean -thr <myThreshlold> -bin mean_MD_skeleton_mask
Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
> On 13 Jun 2018, at 14:34, Dawn Marie Jensen <[log in to unmask]> wrote:
>
> 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]> 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]> 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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