On 10/4/2021 7:09 PM, Giuseppe Miranda wrote:
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Hello,
I have been looking through tutorials on the website and referencing
the freesurfer mail archives, but I am a bit unsure if I am following
the correct procedures for my analysis. The main source of confusion
on my end stems from trying to apply tutorials (and in some cases the
tutorials they reference) to my longitudinal data. I appreciate your
help in advance.
I have longitudinal data with scans from two time points. My variables
were all collected at time point 1 (TP1). I am interested in change in
cortical thickness in relation to these variables as well as
interacting effects on cortical thickness; some of these variables are
continuous (e.g. suvr) and some are categorical (e.g. alleles). My
initial goal was to use QDEC, but I quickly learned that should use
glmfit. For the purpose of understanding, I am writing in focusing on
age and suvr as my variables. I started with the longitudinal tutorial.
1.) The first point of confusion came near the end of the tutorial at
"long_stats_slopes". The command runs for me, but I'd appreciate a
second look on whether this is correct:
long_stats_slopes --qdec $SUBJECTS_DIR/long.qdec.table.dat --stats
lh.aparc.stats --meas thickness --sd $SUBJECTS_DIR --do-avg --do-rate
--do-pc1 --do-spc --do-stack --time years --stack-avg [desired
path]/stack-avg --stack-rate[desired path]/stack-rate
--stack-pc1[desired path]/stack-pc1 --stack-spc[desired path]/stack-spc
I'm not sure about this; it is not necessary for your other steps. I'll
CC Martin R and Kersten in case they want to weigh in.
>From there, the tutorial says to run my data through the glm tutorial. I
have several points of confusion here - the first being that I'm
concerned that I may not have my data set up correctly.
2.) I looked at the FSGD examples and built my file from them, and I
also referenced the mail archives for similar projects to mine. I am
unsure as to whether I should be using the [LONG] files created or the
[BASE] files created with the longitudinal tutorial in my FSGD file.
For example, if I am just looking at age and another factor (suvr)
should my FSGD look like this...
It has to be the long because that is what you want to analyze
GroupDescriptorFile 1
MeasurementName thickness
Class subject
Variables age suvr
Input Subject1_TP1 subject 57 0.93
Input Subject1_TP2 subject 57 0.93
Input Subject2_TP1 subject 64 1.22
Input Subject2_TP2 subject 57 1.22
Or should it point to the directories made during the [BASE] step of
the longitudinal tutorial like this?
GroupDescriptorFile 1
MeasurementName thickness
Class subject
Variables age suvr
Input Subject1_base subject 57 0.93
Input Subject2_base subject 56 1.06
3.) From there, I understand that I need an individual contrast matrix
for each contrast that I'd like to run. Here is what I have been using:
Age: 0 1 0
Suvr: 0 0 1
Age x Suvr: 0 1 -1
The first two are ok, but the 3rd one will not work. If you want an
interaction between two continuous variables, you need to create a 3rd
variable where you multiply them together. I would normalize them
(subtract the mean, divide by the stddev)
4.) Next, I ran through the rest of the GLM tutorial to assemble the
data and run glmfit, followed by a clusterwise comparison for multiple
comparisons
mris_preproc --fsgd file_name.fsgd \
--target fsaverage \
--hemi lh \
--meas thickness \
--out lh.file_name.thickness.00.mgh
mri_surf2surf --hemi lh \
--s fsaverage \
--sval lh.file_name.thickness.00.mgh \
--fwhm 10 \
--cortex \
--tval lh.file_name.thickness.10.mgh
Add --prune to this
mri_glmfit \
--y lh.file_name.10.mgh \
--fsgd file_name.fsgd dods\
--C age.mtx \
--C suvr.mtx \
--C age_suvr.mtx \
--surf fsaverage lh \
--cortex \
--glmdir lh.directory_name.glmdir
mri_glmfit-sim \
--glmdir lh.gender_age.glmdir \
--cache 4 neg \
--cwp 0.05\
--2spaces
You will probably need to change the vertex-wise threshold to something
lower (currently at 4). The "neg" means you are only looking for
negative correlations (probably use abs to make it unsigned).
5.) My last question is, if I want to run glmfit to analyze my data
with other variables, is there anything that I have to delete or
re-run on my end? From what I understand, I would only have to run
glmfit and its' corrections again.
Correct
I appreciate your help - I just want to make sure that I am, and that
I am following these tutorials properly.
Vince
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