it does not suprise me that 2014 is not working as that is pretty old.
I've been using 2018 and that seems to work.
On 3/24/2022 9:31 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
It is seemingly working in matlab R2021b rather than matlab R2014a.
Can you confirm this? Otherwise that should be noted in the wiki
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------------------------------------------------------------------------
*From:* Zeng,Victor (BIDMC - Keshavan - Psychiatry)
<vz...@bidmc.harvard.edu>
*Sent:* Wednesday, March 16, 2022 5:52:54 PM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [External] Re: [Freesurfer] [External] Re: classes for
GLM analysis
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?
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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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