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Hi Laura,

The call that would be equivalent to that of randomise is very similar to what you did in your first run, except that you also need the option "-save1-p".

The error message about L/R orientation seems to be coming from FSL, but that isn't compatible with reading via the NIFTI class as implied by the lack of "-noniiclass" in the first run. In any case, this is likely due to something not being right with the header of the NIFTI files.

The error about LAPACK seems to be coming from Matlab. If you could post the full error, I could tell what is the offending situation in which rank is invoked. If the error then persists outside PALM, you could reach out to Mathworks support. It could be a linking problem, or incompatibility between library versions in your system.

All the best,

Anderson


On 16 May 2018 at 10:43, Laura E <[log in to unmask]> wrote:
Hi all,

To familiarize myself with palm before conducting more advanced analyses, I would like to confirm that the result of applying palm commands to group-level FSL output (specifically, filtered_func_data.nii.gz) matches what I get after applying comparable randomise commands to the same group-level FSL output. The simplified randomise command that I have successfully executed in the past is: randomise -i filtered_func_data.nii.gz -d design.mat -t design.con -n 10000 -T

When I attempted to recapture this with a palm command applied to the unzipped nifti image (palm -i filtered_func_data.nii -d design.mat -t design.con -n 10000 -T), palm finished running, but I got this error: "Inconsistent left-right order stored in sform and qform in file...Using sform instead of qform values." Additionally, the intensity of the palm output file I'm interested in, palm_tfce_tstat_fwep_c1.nii.gz, was uniformly 1.

Thinking that this may reflect an (un)zipping problem, I ran the palm command on the zipped file as follows: palm -i filtered_func_data.nii.gz -d design.mat -t design.con -n 10000 -T -noniiclass. Palm did not finish running, and I received the following errors: "Error using rank (/opt/apps/matlab/2018a/toolbox/matlab/matfun/rank.m:14)
LAPACK loading error: /opt/apps/intel/16.0.1.150/compilers_and_libraries_2016.1.150/linux/mkl/lib/intel64/libmkl_rt.so: undefined symbol: cgejsv_"

Any suggestions or points of clarification from veteran palm users would be welcome!