On 6/20/2025 3:19 PM, Isabella Rossellini wrote:
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Dear Douglas,
Thank you for your kind help and advice!
Good to know that a two-stage model is not needed for one subject. So
I should not run the longitudinal preprocessing either, right?
Actually, you can run it on a single subject as this will impose similar
processing (eg, interpolation) that the longitudinal stream would have
imposed.
Following your advice, I created this FSGD file below for subjid1 with
5 timepoints (0, 3, 6, 9, 12).
Name of the imaging files: subjid1_base, subjid1_3mo, subjid1_6mo,
subjid1_9mo, subjid1_12mo
GroupDescriptorFile 1
Title Onesubject
Class Class1
Variables TimePoint
Input subjid1_base Class1 0
Input subjid1_3mo Class1 3
#Input subjid1_6mo Class1 6
Input subjid1_9mo Class1 9
Input subjid1_12mo Class1 12
Does this look okay to you?
You also wrote that I should "remove the mean of the time points from the time
point number number". (The mean is 6 in our case) I wonder why?
Does this mean that the TimePoint variables should be -6 -3 0 3 6
instead? (and not 0 3 6 9 12)
Yes, this is correct. Removing the mean can make the design matrix
better conditioned. It will also influence the offset; but if you're
only interested in the slope, that part won't make a difference.
GroupDescriptorFile 1
Title Onesubject
Class Class1
Variables TimePoint
Input subjid1_base Class1 -6
Input subjid1_3mo Class1 -3
#Input subjid1_6mo Class1 0
Input subjid1_9mo Class1 3
Input subjid1_12mo Class1 6
Sincerely,
Isa Rosselini
On Thu, Apr 17, 2025 at 5:37 PM Isabella Rossellini
<[email protected]> wrote:
Dear Douglas,
I am sorry for the late response. I did not see your message up until now.
I would like to see how the brain changes for a patient with anxiety
who got better gradually (again, we have 5-time points (0, 3, 6, 9,
12). And then do the same for another participant who did not get
better up until 12 months.
That is the reason I would like to look at patients one by one.
I ran the mri_glmfit analysis but I received an error message:
ERROR: DOF=0
Is this because I tried to run it on one participant?
Sincerely,
Isa Rosselini
Date: Mon, 3 Feb 2025 09:20:40 -0500
From: "Douglas N. Greve" <[email protected]>
Subject: Re: [Freesurfer] longitudinal analysis on one subject
To: [email protected]
Message-ID: <[email protected]>
Content-Type: text/plain; charset="utf-8"
The glm can be run on this data in theory. With only 5 time points, you
probably won't have much power though. What are you trying to test?
On Sat, Feb 1, 2025 at 11:56 PM Isabella Rossellini
<[email protected]> wrote:
Hello Freesurfer users/experts,
I am working with Freesurfer 7.4.1 on a MacStudio (macOS 15.2) and I would like
to ask your opinion about the following.
Basically, we had an anxiety treatment study and I would like to analyze one
subject who has 5-time points (0, 3, 6, 9, 12) with a longitudinal pipeline,
two-stage model.
Is it possible to run this on one person only and see the changes between these
time points?
I have never done this before on one subject so I am not sure what the best
approach would be to look at the changes.
After running the longitudinal preprocessing (base, long), should I generate
the tables of freesurfer parcellation/segmentation stats data
(aparcstats2table, asegstats2table)?
Or can I just follow the two stage model steps? Maybe glm only works on a group
of subjects.
https://secure-web.cisco.com/1PBrCxPtnV_cyA4wjTbApPKLTn7-VE-boLvlA7ZOq8U2_gMV3mVfwQW400P-AE4blknStdaEUX25IhFSt8AiV9yKnPhcMfMsvDVhYBDCWINUX4zFR9AFCp1Nji_lfI_mAeWZRm2W83Uw_qjKJGBEXYTF9O2jJ7oVZLqWa7nrfPGfIZ-Smi4A52OI_0-Ug7qyllBjyrVvncJf0ytOeKlGbgX4LTbfpae9BzVf4ZD-yNFUdSGTJVdehj4I6Tq9OQLYN0ETVRr7-z_K8Z0UEJM1jZnkWLYTRmUX6PPXhAAgTbotdvGBvMC4nJYm2UG4qVLMmfsH2VuMVHFRqAPc_S6p9Yw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLongitudinalTwoStageModel
(We have 9 more subjects - 10 in total - so I was hoping to visualize the
pattern of changes one by one, in each subject, since these patients showed
different changes in anxiety based on self-reported
questionnaires)
Sincerely,
Isa Rosselini
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