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Hi Sam, It worked for me with up to 1000 permutations. Also, this message, regarding coordinates, don't seem to be coming from PALM... maybe there's another program running that has been wrapped around it? All the best, Anderson On Mon, 24 Jun 2019 at 05:42, Samuel Berry <[log in to unmask]> wrote: > Hi Anderson, > > thank you for doing this its much appreciated. It also runs okay for me if > I use 10 permutations, the problem is when I use more (say 100) the error I > get is: > > ’The coordinates of the input points must be finite values: Inf and NaN > are not permitted’ > > I think this might be due to the fact I get extremely low p-values. I have > tried to remove the seed-region, which was very highly correlated with > itself, but I am still having the same problem. Do you have any > recommendations for how to proceed? > > Best wishes, > Sam > > On 23 Jun 2019, at 21:45, Anderson M. Winkler <[log in to unmask]> > wrote: > > Hi Sam, > > Thanks for sending. I wasn't able to replicate, though. It run fine for me > -- that is, a one-sample t-test in a file that has 1071 maps. I run with 10 > permutations using Octave 4.4.1 and the code run through completion with no > error... unsure what may be going on... perhaps if you try in a different > computer that has different software versions/configurations? > > All the best, > > Anderson > > > On Wed, 29 May 2019 at 08:27, Samuel Berry <[log in to unmask]> wrote: > >> Thank you Anderson, I have sent you an email with a link to share a >> dropbox folder. >> >> Best wishes, >> Sam >> ------------------------------ >> *From:* FSL - FMRIB's Software Library <[log in to unmask]> on behalf of >> Anderson M. Winkler <[log in to unmask]> >> *Sent:* 14 May 2019 00:39 >> *To:* [log in to unmask] >> *Subject:* Re: [FSL] PALM analysis errors with HCP data - data cannot be >> sorted >> >> Hi Sam, >> >> Would you mind sending your input files so I could have a look? You could >> use any file sharing service of your preference, just let me know the link >> then. >> >> Thanks! >> >> All the best, >> >> Anderson >> >> On Mon, 29 Apr 2019 at 10:33, Samuel Berry <[log in to unmask]> 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 >> >> ######################################################################## >> >> To unsubscribe from the FSL list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >> <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DFSL%26A%3D1&data=01%7C01%7Cberrysc%40CARDIFF.AC.UK%7C6d840cc04ea44ff7ecbd08d6f81bfcac%7Cbdb74b3095684856bdbf06759778fcbc%7C1&sdata=a4C%2F5PoGADADjJcA45W7DJSDn8EzcZKPnYV2CSG%2FeZI%3D&reserved=0> >> >> >> ------------------------------ >> >> To unsubscribe from the FSL list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >> <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DFSL%26A%3D1&data=01%7C01%7Cberrysc%40CARDIFF.AC.UK%7C6d840cc04ea44ff7ecbd08d6f81bfcac%7Cbdb74b3095684856bdbf06759778fcbc%7C1&sdata=a4C%2F5PoGADADjJcA45W7DJSDn8EzcZKPnYV2CSG%2FeZI%3D&reserved=0> >> >> ------------------------------ >> >> To unsubscribe from the FSL list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >> <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DFSL%26A%3D1&data=01%7C01%7Cberrysc%40CARDIFF.AC.UK%7C6d840cc04ea44ff7ecbd08d6f81bfcac%7Cbdb74b3095684856bdbf06759778fcbc%7C1&sdata=a4C%2F5PoGADADjJcA45W7DJSDn8EzcZKPnYV2CSG%2FeZI%3D&reserved=0> >> > > ------------------------------ > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 > <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DFSL%26A%3D1&data=01%7C01%7Cberrysc%40CARDIFF.AC.UK%7C6d840cc04ea44ff7ecbd08d6f81bfcac%7Cbdb74b3095684856bdbf06759778fcbc%7C1&sdata=a4C%2F5PoGADADjJcA45W7DJSDn8EzcZKPnYV2CSG%2FeZI%3D&reserved=0> > > > ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1