[Freesurfer] Specifying contrasts for an unbalanced design

2022-09-19 Thread Trolle, Carl 
Dear FreeSurfer team,

We are investigating if there is a difference in cortical thicknesses between 
persons with a condition and controls, regressing out the effect of site, sex, 
age, but have some concerns on how to specify our contrasts. We don’t think 
that the age-slopes will be different between the patients and the controls but 
would like to check that formally using DODS before trying DOSS. Currently, we 
have only one female control from two of the sites and are left with 10 instead 
of 12 classes. Would be very grateful if you have time to check that we’ve got 
this right.

Also, when we want to check for interactions between class and age to see if we 
can use DOSS instead, is the attached “interactionmatrix” correct? I’ve looked 
at the tutorials and this 
example,
 but tried to adapt it to our situation. If we do find an interaction, would 
that cluster then show up on the cluster summary in the glmdir-folder?

Thank you and sorry for all the questions, just wanting to make sure we are 
doing this correctly.

Kind regards,

Carl Trolle
Research Fellow
Spaulding Neuroimaging Lab

FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551
Platform: CentOS Stream 8



GroupDescriptorFile 1
Title MyStudy
#Class HC_female_site1
Class P_female_site1
Class HC_male_site1
Class P_male_site1
#Class HC_female_site2
Class P_female_site2
Class HC_male_site2
Class P_male_site2
Class HC_female_site3
Class P_female_site3
Class HC_male_site3
Class P_male_site3
Variables Age
Input subject1 HC_female_site1 21
Input subject2 P_female_site1 34
Input subject3 P_female_site2 55
Input subject4 P_male_site3 89
... -0.167 0.25 -0.167 -0.167 0.25 -0.167 0.25 -0.167 0.25 -0.167 0 0 0 0 0 0 0 0 
0 0  0 0 0 0 0 0 0 0 0 0 -0.167 0.25 -0.167 -0.167 0.25 -0.167 0.25 -0.167 0.25 
-0.167___
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Re: [Freesurfer] Help - segmentHA_T1_long.sh "list of time points not found"

2022-09-19 Thread Iglesias Gonzalez, Juan E.,PHD 
Dear Kimi,

When you process the scans longitudinally with FreeSurfer, the file base-tps 
should be created in the subject directory of the template. Isn’t this the case?

Cheers,

/Eugenio

Juan Eugenio Iglesias
http://www.jeiglesias.com





On 19 Sep 2022, at 01:02, Raikkonen Kimi 
mailto:akdaus2...@gmail.com>> wrote:


External Email - Use Caution

Dear FreeSurfer,

Hi, I was trying to run longitudinal analysis of the hippocampus and amygdala 
segmentation pipeline after running the main FreeSurfer longitudinal pipeline.

I ran
segmentHA_T1_long.sh 101_MRI1.long.101_template
segmentHA_T1_long.sh 101_MRI2.long.101_template
segmentHA_T1_long.sh 101_MRI3.long.101_template   etc.

but I got the following error message:
List of time points:
   /study/101_MRI1.long.101_template/base-tps
does not exist




I think I’ve headed the wrong direction, I was wondering how to do the list of 
time points for a subject.
Thanks so much for your help in advance.

Best regards,
Alex
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[Freesurfer] Zip folder passcode

2022-09-19 Thread Chi-Wen Jao 
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Dear freesurf developer
 
I was trying to install FreeSurfer on a virtual machine and was asked for the 
password to open the archive in the zip folder FS_7_2_0_Ubuntu_18_04_06.ova.7z 
 I just wanted to ask for that password.
 
Thank you for your help!
 
Kind regards,
Chi-Wen___
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[Freesurfer] Zip folder passcode

2022-09-19 Thread Enya Weidner 
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Hi everyone,

I was trying to install FreeSurfer on a virtual machine and was asked for the 
password to open the archive in the zip folder FS_7_2_0_Ubuntu_18_04_06.ova.7z 
– I just wanted to ask for that password.

Thank you for your help!

Kind regards, 
Enya

--
M.Sc. Enya Weidner
Universität Bielefeld
Fakultät für Psychologie und Sportwissenschaft
AE02 Affektive Neuropsychologie
Raum: T5-220
Telefon: 0521-106 4533
Email: enya.weid...@uni-bielefeld.de

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