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Hello FS experts
Thank you for your kind response. This is regarding my previous mail.
I think we need to talk about the design matrix X first (sorry, I did not look at your xlsx file; I think it's probably better to send simple csv files if at all). I attached longitudinal data in csv format.
Besides the covariates that you mention, the matrix needs to contain an intercept, a variable for ?time?, a variable for ?group? (assuming you have a control group also), and a group-by-time interaction term in order to asses differential change over time (again, if you have a control group). I do not have a control group. Right now I have only schizophrenia patients who underwent 2 scans: the first is the baseline and the second one is after 3 months of yoga therapy. Wish to know how can I proceed with my available data.
Just to make sure: ?age? should be ?age at baseline? (i.e. constant across time per subject), otherwise, it will be confounded with time. Yes, I used the same across the study.
Could you review (and possibly adapt) your design matrix X with respect to which columns it contains, and write it in the reply? I tried but couldn't get there.
Looking forward to your response.
Thanks, Vittal
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Hello VIttal,
thanks for the info about the design.
You wrote before that the Matlab variable X (i.e., the design matrix) has a dimension of 47x6. X is a translation of the study design into a numerical matrix, which is part of the statistical model. In your case, I assume that he first column is a vector of ones (i.e. the intercept/constant of the statistical model), and that the other columns reflect the numerical data in the table that you sent, in the same order. Correct me if I am wrong.
Now, the contrast "matrix“ specifies the questions that you want to ask to the data, i.e. the effect of a certain variable (or sometimes combinations of variables) onto the outcome variable Y. I put "matrix" in quotes, because in many cases a simple vector is sufficient; contrasts need not necessarily be specified as a matrix, and contrasts specified as a matrix are typically more complex than those specified by a vector.
In any case, the contrast vector/matrix needs to have as many elements/columns as there are columns in X, because the elements/columns oft the contrast vector/matrix will be matched with (and therefore need to correspond to) the columns of X. I.e. the nth element/column in your contrast vector/matrix refers to the nth predictor variable in the statistical model, i.e. the nth column of X. There are 6 columns in X in your case.
The entries in the contrast vector/matrix represent weights that you assign to each variable in order to test for its effect. One often (but not always or necessarily) uses +1 to test for a positive relation of the chosen variable on Y, -1 for a negative effect, and zero for not considering a variable for a given contrast. Therefore, the simplest contrast is a vector with a single non-zero entry, and this already allows for the testing of effects. In other cases, contrasts can have more than one non-zero entry, or can be formulated as a matrix, but we don’t need this at the moment.
The major issue with your design in its current form is that you will not be able to distinguish effects of time from effects of treatment, due to the absence of a control group. This precludes, as far as I can see, a clear interpretation of any changes in Y that you might observe. If you still want to go ahead and test the time/treatment effect, just set the corresponding element of the contrast vector to +1 or -1.
Best,
Kersten
Am 30.11.2020 um 12:44 schrieb vittal korann <vittalkorann@gmail.commailto:vittalkorann@gmail.com>:
Hello FS experts
Thank you for your kind response. This is regarding my previous mail.
I think we need to talk about the design matrix X first (sorry, I did not look at your xlsx file; I think it's probably better to send simple csv files if at all). I attached longitudinal data in csv format.
Besides the covariates that you mention, the matrix needs to contain an intercept, a variable for ?time?, a variable for ?group? (assuming you have a control group also), and a group-by-time interaction term in order to asses differential change over time (again, if you have a control group). I do not have a control group. Right now I have only schizophrenia patients who underwent 2 scans: the first is the baseline and the second one is after 3 months of yoga therapy. Wish to know how can I proceed with my available data.
Just to make sure: ?age? should be ?age at baseline? (i.e. constant across time per subject), otherwise, it will be confounded with time. Yes, I used the same across the study.
Could you review (and possibly adapt) your design matrix X with respect to which columns it contains, and write it in the reply? I tried but couldn't get there.
Looking forward to your response.
Thanks, Vittal <longitudinal_data.csv>
-- Kersten Diers Image Analysis Group (AG Reuter) German Center for Neurodegenerative Diseases (DZNE) B.1.114 | Building 99 | Venusberg-Campus 1 | 53127 Bonn | Germany https://secure-web.cisco.com/1-2DMCqsEAxXMrF8CjX08W54lPnfE5EsDPiGxF4zYoYh78i... Phone: +49 / 228 / 43302 - 381
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Dear FreeSurfer experts
This is just a gentle reminder of my previous mail. Diers Kersten has replied to my query. He asked me to send a few details pertaining to my issue. I shared all the necessary details with you people and waiting for your response.
Below is the link where I wrote about my query regarding the longitudinal analysis. Looking forward to your assistance!
Thanks, Vittal
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Today's Topics:
- Re: License error on Windows Subsystem for Linux (Shen Lunhao)
- smooth longitudinal analysis {Disarmed} (Agurne Sampedro Calvete)
- Re: Error in longitudinal pipeline {Disarmed} (Diers, Kersten /DZNE)
- Smoothing GWC mgh data (Valentina Meregalli)
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
Content-Type: text/plain; charset="gb2312" External Email - Use Caution 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
External Email - Use CautionHello 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:
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.
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?
- FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
- Platform: Windows Subsystem for Linux (Ubuntu 20.04)
- 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
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Hi Vittal,
please see my response from Nov 30th on this list.
Best,
Kersten.
Am 04.12.2020 um 08:16 schrieb vittal korann <vittalkorann@gmail.commailto:vittalkorann@gmail.com>:
External Email - Use Caution
Dear FreeSurfer experts
This is just a gentle reminder of my previous mail. Diers Kersten has replied to my query. He asked me to send a few details pertaining to my issue. I shared all the necessary details with you people and waiting for your response.
Below is the link where I wrote about my query regarding the longitudinal analysis. Looking forward to your assistance!
Thanks, Vittal
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/16nsuCaPAPrx2m31D9mbk_ELYa52InflARFMeKmzMEvVSZH... https://secure-web.cisco.com/1VpKxsiVae3KbaNGm2RndFtO0tJs8ENmwclbckfVGAawWhozAPFA6tYE8LvMYv4CUlLbYwavNETA2pqMs7H9QIXuFNSjl53NfoX5o_G-eW_9rRAAiZ_ORvHEASeioG2pM_K_wm4a6PQtLIHnnVhT5GOCJY6LoiG2RykLKWUQf3IYBu-QrsKjeGXpS8GKMVYj0SJm4rX9SBjwtlKMXfmIapW5mD1wVRoeN24Kkv-elzNnNp1rE84YHmnk22fG84O460011LTdUWfhp5-7k3ZuFzQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurferor, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edumailto:freesurfer-request@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edumailto:freesurfer-owner@nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
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)
---------------------------------------------------------------------- Message: 1 Date: Mon, 23 Nov 2020 06:26:28 +0000 From: Shen Lunhao <lunhao0104@hotmail.commailto:lunhao0104@hotmail.com> Subject: Re: [Freesurfer] License error on Windows Subsystem for Linux To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <DM6PR02MB6493EB25230B280B7DCFF288DBFC0@DM6PR02MB6493.namprd02.prod.outlook.commailto:DM6PR02MB6493EB25230B280B7DCFF288DBFC0@DM6PR02MB6493.namprd02.prod.outlook.com> Content-Type: text/plain; charset="gb2312" External Email - Use Caution 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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> ?? Hoopes, Andrew <AHOOPES@mgh.harvard.edumailto:AHOOPES@mgh.harvard.edu> Date: 2020?11?21? 1:19 Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Shen Lunhao <lunhao0104@hotmail.commailto:lunhao0104@hotmail.com> Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, November 20, 2020 at 2:44 AM To: FS Help <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] License error on Windows Subsystem for Linux
External Email - Use Caution 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:
-------------------------------------------------------------------------- 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. --------------------------------------------------------------------------
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
freesurfer@nmr.mgh.harvard.edu
-
Diers, Kersten /DZNE -
vittal korann