Re: [Freesurfer] fspalm error

[Stefano Delli Pizzi]

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I have the same error that doesn't resolve with --mgh or mgz. 

warning: excluding contrast file 
/Volumes/mnu/MRI/XXX/NIFTI/FreeSurfer/rs-fMRI_AROMA/G3V0_Comparison/fc.MDseed.surf.rh/MD/G3V0_PALM.glmdir/group.effect/C.dat
 since it has multiple rows
ERROR: for surface based analysis, input cannot be nii or nii.gz

Thanks

Stefano

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Re: [Freesurfer] fspalm error : --sig2p-max unknown

[Greve, Douglas N.,Ph.D.]

You need the patch. See the docs here 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm under Setting Up

On 12/16/2020 2:02 PM, Marina Fernández wrote:

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Dear experts,

When I was running permutations with fspalm an error appeared because it 
couldn't find the --sig2p-max option when using mri_surfcluster internally.  
You can find below the terminal output.

How can I fix this error?

Thank you in advance
Marina.

 *Terminal output:
...
>> >> palm processing complete - running the surface cluster analysis...
/usr/local/freesurfer/subjects/merchi182_thickness_stats/stats/thickness/permutation/lctx/across/across_age_cov_none_0.05/pos/lh.fsgd_subj_gauss003/palm
mri_surfcluster --in fsp_clustere_tstat_fwep.mgz --thmin 1.301030 --subject 
merchi182_thickness_average --hemi lh --annot aparc --sum 
contrast.clustertable.summary --no-fixmni --surf white --ocn contrast.ocn.mgz 
--oannot ./contrast.ocn.annot --sig2p-max
ERROR: Option --sig2p-max unknown
error: mri_surfcluster failed
fspalm --glmdir 
/usr/local/freesurfer/subjects/merchi182_thickness_stats//stats/thickness/permutation/lctx/across//across_age_cov_none_0.05/pos//lh.fsgd_subj_gauss003
 --cft 1.301 --name palm --iters 100 --cwp .05 --onetail: Signal 127
ans =
   255



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Re: [Freesurfer] fspalm error

[Greve, Douglas N.,Ph.D.]

I think palm itself requires mgh or mgz files. I can't remember why we don't 
convert it. You can run mri_glmfit with --mgz or --mgh (or just without 
--nii.gz) and it should work.


On 9/9/2019 9:24 AM, Barbour, Tracy,M.D. wrote:
Hello Freesurfer community!

I am trying to run fspalm on surface based data. I have installed PALM, fspalm, 
mri_surfcluster, and mri_volcluster.

This is my fspalm command:
fspalm --glmdir TEPSC.glmdir --cft 1.3 --twotail --name palm-twotail-1.3 
--iters 1000 --2spaces --cwp .05

When I run the fspalm command I get the error: "for surface based analysis, 
input cannot be nii or nii.gz"

I thought that fspalm was supposed to convert ces.nii.gz files into something 
that PALM could use.

Please let me know if there is another step I need to run or if I need to 
change the script.

Best,

Tracy



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