Hi Sam,
Sorry my delay (I promised Matt I was going to reply next day but forgot to say
I was at an airport and since then I wasn't able to keep up with emails and
other stuff!).
May I ask you to upload your files (data, design, and contrasts) to some file
sharing service and send the link off-list? I'll try to have a look then.
Thanks.
All the best,
Anderson
On 4/29/19, 08:16, "Samuel Berry" <berr...@cardiff.ac.uk> wrote:
Hello,
I have been having some issues when running one-sample PALM analysis on a
4d nifti image that contains 3T zmaps from a seed-based correlation analysis.
The error I get is:
Error using palm_competitive
Data cannot be sorted. Check for NaNs that might be present, or precision
issues that may cause over/underflow. If you are using “-approx tail”, consider
adding “nouncorrected”.
Having read some other posts on this error I have taken the following steps.
1) Changed the seed to be ‘twist’
2) Run fslmaths -nan on my data before running the analysis
3) Converted the 4d file to ‘double’ using fslmaths <4dimg> <output> -odt
double
4) Run with and without tail approximation, always with the -nouncorrected
option.
5) Tried without the EB blocks
6) Used up to 10,000 permutations
Unfortunately I always get the same error. I went into the palm_competitive
script and saved the variables created and it shows that I do indeed have NaNs
(from the gg variable). I tried, just to see what happens, to bypass the error
by replacing any NaNs with the mean of the ’S’ variable which did let me
progress past the error. However my output is then a fwep image that is all ‘1’
and a tstat image that is just NaN. Do you have any idea what I am doing wrong?
I have been stuck on this for a while now and can’t figure it out!
My PALM input is the following (with the variations I have mentioned above,
and -n 5 being just for testing).
palm -i <4d_img>, -T, -eb <EB_file>, -save1-p, -n 5, -seed twist, -m
<mask_file>, -o <output_file>
Many thanks,
Sam
_______________________________________________
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
_______________________________________________
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
