Hi Ajay, The mask is a file of the "curvature" type, that is, it contains vertexwise data, and should mask out the "unknown" region (that region in the medial aspect that is not cortex and is there to ensure the topology is the same as that of a sphere). The mask can alternatively be a .mgz file as a pseudo-volume, still with the same number of vertices as the input data and surface.
Although I'm not seeing your input files, I believe your mask is fine, otherwise PALM would have failed even before starting the permutations. I'd think there is something else going on. Could you show the full design, contrasts, and command line used? All the best, Anderson On 18 September 2016 at 04:03, Ajay Kurani <dr.ajay.kur...@gmail.com> wrote: > Hi Anderson, > Thanks for the help. When viewing my results they looked very > strange. Upon further investigation it looks as though the mask I supplied > to PALM was a white matter mask (mask.mgh from running qdec initially) > created when I ran qdec. I assumed this would be the whole cortex but I > was wrong. Therefore it seems to only run permutation testing on the > surface of the white matter. Due to the fact that it is unsmoothed white > matter, I think this is why we see some speckling bleeding through near the > boundaries > > In order to do permutation testing accurately for surface based cortical > thickness, would the mask need to be a volume file which is between the > pial and white matter surfaces or would it just need to be the pial surface > (lh.pial / rh.pial), or something else? Any suggestions on the best way to > create this? > > Thanks, > Ajay > > On Sat, Sep 17, 2016 at 1:03 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> > wrote: > >> Hi Anderson, >> Thanks for the help. When viewing my results they looked very >> strange. Upon further investigation it looks as though the mask I supplied >> to PALM was a white matter mask (mask.mgh from running qdec initially) >> created when I ran qdec. I assumed this would be the whole cortex but I >> was wrong. Therefore it seems to only run permutation testing on the >> surface of the white matter as seen in the attached photo. Due to the fact >> that it is unsmoothed white matter, I think this is why we see some >> speckling bleeding through near the boundaries >> >> In order to do permutation testing accurately for surface based cortical >> thickness, would the mask need to be a volume file which is between the >> pial and white matter surfaces or would it just need to be the pial surface >> (lh.pial / rh.pial), or something else? Any suggestions on the best way to >> create this? >> >> Thanks, >> Ajay >> >> >> >> >> On Thu, Sep 15, 2016 at 1:46 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> >> wrote: >> >>> Hello Freesurfer Experts, >>> I was running permutation simulations on cortical thickness data and >>> I had an issue with non-orthogonal covariates with mri_glmfit-sim -perm. I >>> then tried FSL's PALM which is an extension of randomize to calculate >>> threshold free stats. I saved the output as logp(which is similar to qdec >>> I believe), however I have not been able to load the stats files >>> correctly. The output of palm is lh.thickness_tfce.mgz for my various >>> contrasts. >>> >>> 1) Is .mgz the proper format for the stats files or do I need to convert >>> this to another type like .mgh etc? >>> >>> 2) Can I display this in freeview or is another program needed? I also >>> tried tksurfer but when I loaded the stats file as an overlay nothing >>> displayed. I want to make sure that the stats is loaded as an overlay in >>> freeview/tksurfer and if so, do I need to select anything special so that >>> it scales the logp values correctly? >>> >>> Thanks, >>> Ajay >>> >> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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