External Email - Use Caution
Sorry for the different approach - but I just propensity matched people for now
so I don't have to deal with so many confounding variables. Now I am trying to
do multiple correction, with mriglmfit-sim not working because of high FWHM
(you can ignore my other email about that...). So therefore, I am trying palm,
and come up with this error:
Running PALM alpha119 using MATLAB 8.3.0.532 (R2014a) with the following
options:
-i
/mnt/V/Datasets/BSNIP2/Processing/Finished_q2/0analysisMGH/Replication/rh.pial_lgi.NCBT1_.10.mgh
-m
/mnt/V/Datasets/BSNIP2/Processing/Finished_q2/0analysisGLM/Replication/rh.pial_lgi.NCBT1_.10.glmdir/mask.mgh
-d design.mat
-t design.con
-logp
-n 1000
-C 1.958920
-o fsp
-twotail
-s /mnt/V/Datasets/BSNIP2/Processing/Finished_q2/fsaverage/surf/rh.white
/mnt/V/Datasets/BSNIP2/Processing/Finished_q2/fsaverage/surf/rh.white.avg.area.mgh
Found FSL in /usr/share/fsl/5.0
Found FreeSurfer in /usr/local/freesurfer/dev7
Found SPM in /home/gamma/spm8
Loading surface 1/1:
/mnt/V/Datasets/BSNIP2/Processing/Finished_q2/fsaverage/surf/rh.white
Reading input 1/1:
/mnt/V/Datasets/BSNIP2/Processing/Finished_q2/0analysisMGH/Replication/rh.pial_lgi.NCBT1_.10.mgh
Reading design matrix and contrasts.
Elapsed time parsing inputs: ~ 7.22525 seconds.
Number of possible permutations is 9.7768e+204.
Generating 1000 shufflings (permutations only).
Building null distribution.
0.1% [Design 1/1, Contrast 1/1, Shuffling 1/1000, Modality 1/1]
/bin/sh: line 1: 14553 Illegal instruction matlab -display iconic <
run_palm.m
error: cannot find expected palm output "fsp_clustere_tstat_fwep.mgz"
This is with Freesurfer dev 20211206. Thanks and sorry for so many questions
lately
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
Sent: Wednesday, March 16, 2022 6:09 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [External] Re: [Freesurfer] [External] Re: classes for GLM analysis
Can't tell without the fsgd file
On 3/7/2022 8:30 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
Just to double check the numbers - I seem to have been getting into an error in
how many columns in the FSGD it is expecting.
I have 9 different sites, 4 different patient groups, and M/F -> 72 classes.
I also am covarying for four different factors, so the contrast matrix I am
making is 72*(4+1) long. Since I want to regress out the four factors
completely, only the first 72 numbers in 360 contrast matters. My FSGD file has
4 columns e.g like
Input GP0001 NCBostonM 60 12000 -0.01 -0.02
It says ERROR: gdfReadV1: Input line 1, subjid = GP0001
Found 4 variables, expected. 10
Where is this 10 coming from?
Get Outlook for
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________________________________
From: Zeng,Victor (BIDMC - Keshavan - Psychiatry)
<vz...@bidmc.harvard.edu><mailto:vz...@bidmc.harvard.edu>
Sent: Monday, February 21, 2022 5:50:46 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [External] Re: [Freesurfer] classes for GLM analysis
Do you have a Freesurfer page I can read up on those hybrid ways just to see
whether that could be an option?
Also, although its a binary, you would recommend against have sex be a
continuous measurement like age, due to the design of how the contrasts are
determined? I.e continuous measurements aren't treated like integers
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Sent: Sunday, February 13, 2022 12:24 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [External] Re: [Freesurfer] classes for GLM analysis
It is probably not going to work very well if you have some classes that only
have one member. You can eliminate members of classes that only have a few
members. If you really need to have those cases, there are hybrid ways to
analyze the data (but you can't use an FSGD at that point)
On 2/6/2022 10:41 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
Hi all,
I am doing an analysis and generating the FSGD. I understand sex and race are
classes in this context, but something I was also hoping to regress out is the
effects of scanner/sequences. We have a large participant size, so we have
around 10+ scanner/sequences, which makes for a large amount of classes
combinations, with some having just 1 (if not zero) fitting into a class.
Would you proceed with this nonetheless? If not, should scanner/sequence be
something that we consider? Should we find some other way to adjust site (I
don't think we can z-score...). Or can we consider site/scanner as a continuous
variable
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
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