what version of fs are you using?
On 8/19/2020 9:03 AM, 정현우 wrote:
External Email - Use Caution
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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