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Hi Douglas,
Thank you for your response. I followed your suggestions and
additionally tried using Matlab instead of Octave for FsPalm
analysis, but I still failed to get the results. Adding
$FREESURFER_HOME/fsfast/toolbox to my matlab path removed
the first error output <error: 'fast_p2z' undefined near
line 1 column 11>, but I still get the other error output
<error: cannot find expected palm output
"fsp_clustere_tstat_fwep.mgz" - check for run_palm.m failures'>.
Do you have any suggestions for this problem?
Thanks,
Hyunwoo
2020년 8월 13일 (목) 오후 10:37, Douglas N. Greve
<dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>>님이
작성:
On 8/12/2020 2:44 AM, 정현우 wrote:
External Email - Use Caution
Hello Freesurfer Developers,
I'm trying to do permutation simulation on 50 subjects
to find brain region clusters of which cortical
thicknesses have significant association with clinical
parameters while controlling for age and sex. I tried
this via 'mri_glmfit-sim' but it seems that permutation
analysis could not be done with non-orthogonal
variables in Freesurfer. I copied the command I used
and the error output below.
mri_glmfit-sim --glmdir
NK_IES_avoidance_correlation.rh.glmdir --perm 1000 1.3
abs --cwp 0.05 --2spaces
ERROR: design matrix is not orthogonal, cannot be used
with permutation.
If this something you really want to do, run with
--perm-force
What version of FS are you using? If Version 6, then
make sure you download the patch. See "If You're Not in
an organized course" from
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
So I tried using PALM, which allows permutation
analysis with non-orthogonal variables according to a
post in the Freesurfer Archive. I installed PALM,
FsPalm and Octave on my computer and ran the command
below, but I ran into another error output (copied
below) that I do not quite understand.
You need to add $FREESURFER_HOME/fsfast/toolbox to your
matlab path
fspalm --glmdir NK_IES_avoidance_correlation.rh.glmdir
--cft 1.3 --twotail --name
perm.NK_IES_avoidance_correlation.rh --iters 1000
--2spaces --cwp .05 --octave
preparing a palm subdirectory in
/media/sjkim/hd2/subject_data/glm/NK_IES_avoidance_correlation.rh.glmdir/perm.NK_IES_avoidance_correlation.rh
found NK_IES_avoidance_correlation.rh.glmdir/surface
file - this is a surface-based analysis
using the glmfit input file
/media/sjkim/hd2/subject_data/glm/NK_IES_avoidance_correlation.rh.10.mgh
using area file
/media/sjkim/hd2/subject_data/fsaverage/surf/rh.white.avg.area.mgh
palm prep complete - running the generated matlab script...
error: 'fast_p2z' undefined near line 1 column 11
error: cannot find expected palm output
"fsp_clustere_tstat_fwep.mgz" - check for run_palm.m
failures
I copied the matlab script 'run_palm.m' below.
hemi = 'rh';
input =
'/media/sjkim/hd2/subject_data/glm/NK_IES_avoidance_correlation.rh.10.mgh';
maskfile =
'/media/sjkim/hd2/subject_data/glm/NK_IES_avoidance_correlation.rh.glmdir/mask.mgh';
surffile =
'/media/sjkim/hd2/subject_data/fsaverage/surf/rh.white';
areafile =
'/media/sjkim/hd2/subject_data/fsaverage/surf/rh.white.avg.area.mgh';
%% Changing threshold for two-tailed test
cft = 1.3 + 0.301;
pthresh = 10^-cft;
zthresh = fast_p2z(pthresh);
iters = 1000;
zthreshstr = sprintf('%f',zthresh);
itersstr = sprintf('%d',iters);
palm('-i',input,'-m',maskfile,'-d','design.mat','-t','design.con','-logp',...
'-n',itersstr,'-C',zthreshstr,'-o','fsp','-twotail','-s',surffile,
areafile);
return;
Do you have any suggestions on how I could figure out
this problem? Of note, I am using Freesurfer v6.0 and
Ubuntu 18.04.4 LTS platform.
Thanks in advance,
Hyunwoo Jeong
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