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Hi Kersten

I am really confused about creating a contrast matrix. Could you please help out with this?

To give you a brief introduction to my study hypothesis. We are analyzing the effects of yoga on schizophrenia patients. So we have 2 scans for each patient, one before starting yoga and the second scan will be after undergoing 3 months of rigorous yoga therapy. So we are considering age, gender, ICV, and education as covariates in this longitudinal study.

I have gone through the longitudinal pipeline and I find it very difficult to create CM.C matrix as per my study requirements. Hoping for your guidance!

With regards Vittal

On Tue, Nov 24, 2020 at 10:30 PM vittal korann vittalkorann@gmail.com wrote:

Thanks, Kersten!

The design matrix X has a dimension of 47x6 and the contrast matrix CM.C has a dimension of 3x17. I wish to know the steps to correct this error?

Thanks again for your kind help!

With regards Korann

On Mon, Nov 23, 2020 at 10:31 PM freesurfer-request@nmr.mgh.harvard.edu wrote:

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Today's Topics:

1. Re: License error on Windows Subsystem for Linux (Shen Lunhao)
2. smooth longitudinal analysis {Disarmed} (Agurne Sampedro Calvete)
3. Re: Error in longitudinal pipeline {Disarmed} (Diers, Kersten /DZNE)
4. Smoothing GWC mgh data (Valentina Meregalli)

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Message: 1 Date: Mon, 23 Nov 2020 06:26:28 +0000 From: Shen Lunhao lunhao0104@hotmail.com Subject: Re: [Freesurfer] License error on Windows Subsystem for Linux To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: < DM6PR02MB6493EB25230B280B7DCFF288DBFC0@DM6PR02MB6493.namprd02.prod.outlook.com

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Hi Andrew,

The following is the information of four systems. System #3 and #4 are same configuration where license error occurred.

#1 #2 #3 #4 Core Intel(R) Xeon(R) CPU E5-2620 Intel i7 AMD R9 5900X AMD R9 5900X Mem 32GB 16GB 32GB 32GB Platform Linux version 4.15.0-112-generic (buildd@lcy01-amd64-027) (gcc version 7.5.0 (Ubuntu 7.5.0-3ubuntu1~18.04)) Window subsystem for linux(WSL2) + Ubuntu20.04 Window subsystem for linux(WSL2) + Ubuntu20.04 Window subsystem for linux(WSL2) + Ubuntu20.04

Worked Worked Didn?t work Didn?t work The freesurfer package I used is freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0which downloaded from freesurfer website. The license file was four lines type. Hope this information is helpful.

Thanks, Lunhao

From: freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> ?? Hoopes, Andrew < AHOOPES@mgh.harvard.edu> Date: 2020?11?21? 1:19 Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] License error on Windows Subsystem for Linux

Hi Lunhao,

Interesting. Can you provide some details on the configurations where this worked? Were you using the same linux subsystem and windows versions?

thanks

Andrew

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Shen Lunhao < lunhao0104@hotmail.com> Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Friday, November 20, 2020 at 2:44 AM To: FS Help freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] License error on Windows Subsystem for Linux

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Hello FreeSurfer Developers,

I'm attempting to use freesurfer 5.3.0 on Windows Subsystem for Linux (Ubuntu 20.04), but I got license error message as described below:

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ERROR: Invalid FreeSurfer license key found in license file /space/tools/freesurfer/5.3.0/license.txt

If you are outside the NMR-Martinos Center,

go to http://secure-web.cisco.com/1gwoaE20Y7b27ULq16GgvwkvDuYOzRdARFYzw1XJCoskz3-o... to

get a valid license file (it's free).

If you are inside the NMR-Martinos Center,

make sure to source the standard environment.

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I tried with the same 5.3.0 packages and same license file on four different computers, and two of them work well with the other two got similar license error. Does anyone have any thoughts on how to trouble-shoot this one?

1. FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

2. Platform: Windows Subsystem for Linux (Ubuntu 20.04)

3. uname -a: Linux DESKTOP-SJ2K1B2 4.4.0-19041-Microsoft #488-Microsoft

Mon Sep 01 13:43:00 PST 2020 x86_64 x86_64 x86_64 GNU/Linux

Best, Lunhao