This is the purpose of fsplam. fspalm is just a frontend for palm meant to produce the output your would have gotten if you had run mri_glmfit-sim. If you don't want to run fspalm, then look inside it for the commands that do this.

On 2/11/19 9:05 AM, C.P.E. Rollins wrote:

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Hi Douglas, I'm using FSL PALM, but am wondering if there is a way to produce a file like the something.y.ocn.dat file from fspalm. That is, I would like to calculate the mean thickness for each subject and cluster from FSL PALM outputs. Thanks again Colleen

On 2019-02-08 11:16, C.P.E. Rollins wrote:

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Dear Freesurfer Developers, I'm using PALM to run permutation analyses to correct for multiple comparisons on Freesurfer cortical thickness and LGI data. fspalm from a command like "mri_glmfit-sim --glmdir lh.lgi.glmdir --perm 1000 2 pos --cwp .05 --2spaces" produces output files including *.cluster.mgh

• map of signifcant clusters, *.cluster.summary - text file of of

cluster table (incl. sizes, cluster annotation, MNI coordinates, and significance), and *.y.ocn.dat – text file containing LGI or cortical thickness values for each subject from significant clusters. I was wondering if PALM produces similar output? From my understanding the *clustere_tstat_fwep.mgz file from PALM would be equivalent to the *.cluster.mgh from fspalm, but is there any way to get a text file of the cluster table or of the LGI/CT values for each subject from significant clusters?I would like to report significant clusters (ie. coordinates or parcellation, cluster size, pvalue) in a table and also to extract the average lgi/thickness from significant clusters for each subject.

Thanks very much Colleen

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