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:
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
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-oj6huJndWIuxVbk0yVCvgdNi0Oj7GVdtZArfy5iumc2YeEOL6EISaDDZGWxaxL72Jxeq5-rM4PosrAs61L--DGrGQ-qb6mJmz6fxO60OjBUnCaZo11TNmUIUXHBpMTl4hR5bCGLuyCBsEOIcsOAMKVpo5pMFchOkNgp8Uz33jMejFvHUvBttqS1GYSr4rTD6rFCPd5-FxiOBOmu03bHcOZxB8Piql-cfJGw_9i9Q/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu 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
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Message: 2
Date: Mon, 23 Nov 2020 11:55:04 +0100
From: Agurne Sampedro Calvete <a.sampedro@deusto.es>
Subject: [Freesurfer] smooth longitudinal analysis {Disarmed}
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAJsj2xjccF30E-RvcB9bsL8sXUqUznKrni8xNR-G0=JwN+b_-g@mail.gmail.com>
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Dear Freesurfer experts,
I am doing a longitudinal repeated measures analysis and I would like to
know which smooth is better to use (with the mri_surf2surf command).
In the repeated measures guide (
https://secure-web.cisco.com/1VH4PbpfczyEHmEvf-DmwaQIY3QzK6JXAwbehilCfVS00wb0ePGRglRaMqLwBTNWmPTEbH_5iOxVF9p2fPeZdEF-ZcQX3Sxq_n9oFK0y-PgqiQ_xpmDSa5jfGCgCmHJH5R1IxtK3UEqx3_lgRiHE_yyY49B_kiAOmx8osmc7sC1P5polu2Lu7XOkzEJz7KnSNbvzeF9QKcUWBNhYBMQv3J_TJkZ7RocVkzjt6RuPiLEJtrOH7ToOkEAUCCzK6BcJ0wTlatY1akMFB2aNgWEnHwg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FRepeatedMeasuresAnova), the
example includes an spatial smooth of 5mm FWHM, but in the group analysis
guide (
https://secure-web.cisco.com/1oS1UIb6CdjIYlaVy9MrNL5Jmb_OznCDVVe5aIhhhjuuRFV-QXM2WugfLnnmeB915cxZ3y2DfoEjF3QKUSDTP-NQi6oXweZ-lLHs0FQdj2jjEv2KAjOdzYqcVaHsRMEWemo31ieC2y48EG-ehOW4EHnZ_j35ObPUXa1k5G11BLAqilaYamlHwTGZea2Sc-htTi4KjPqBI_v2UD7S5U1AZ2NZ9A4ZAd3CXSAyf5VUc84kUub0Oc97khN5or57qLRRUbgyZRN9O6WSiWZNMa0mUBw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysisV6.0),
the example includes a smooth of 10mm.
Which one would be more appropriate? And, does it depend on the kind of
analysis I am doing (e.g., longitudinal analysis VS a simple group
analysis)?
Thank you very much in advance.
Kind regards,
Agurne Sampedro
Neuropsychology of Severe Medical Conditions Research Team
Dpt of Methods and Experimental Psychology
Faculty of Psychology and Education
University of Deusto
neurolab.deusto.es
Avda. de las Universidades 24,
48007, Bilbao (Spain)
Phone: +34 944139000 (ext. 3015)
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Message: 3
Date: Mon, 23 Nov 2020 13:13:30 +0000
From: "Diers, Kersten /DZNE" <Kersten.Diers@dzne.de>
Subject: Re: [Freesurfer] Error in longitudinal pipeline {Disarmed}
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <4EF5FD94-3172-41E1-8D88-2DF439D71D33@dzne.de>
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Hello,
could you check if the contrast matrix CM.C has the same number of columns as the design matrix X that was supplied to the lme_mass_fit_Rgw() (or possibly lme_mass_fit_vw()) function?
The number of columns (and their respective meaning) need to match between CM.C and X.
Best regards,
Kersten
Am 21.11.2020 um 18:12 schrieb vittal korann <vittalkorann@gmail.com<mailto:vittalkorann@gmail.com>>:
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---------- Forwarded message ---------
From: vittal korann <vittalkorann@gmail.com<mailto:vittalkorann@gmail.com>>
Date: Tue, Nov 17, 2020 at 1:16 PM
Subject: Error in longitudinal pipeline
To: <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Hi FreeSurfer experts
Recently I started working on the longitudinal data.
I followed the pipeline described in the below link.
Also, I attached my longitudinal table along with freesurfer data.
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I got the error while executing the following commands:
CM.C = [zeros(3,5) [1 0 0 0 0 0 0;-1 0 0 1 0 0 0;0 0 0 -1 0 0 1] zeros(3,5)];
F_lhstats = lme_mass_F(lhstats,CM);
And the Matlab threw an error shown below
>> CM.C = [zeros(3,5) [1 0 0 0 0 0 0;-1 0 0 1 0 0 0;0 0 0 -1 0 0 1] zeros(3,5)];
>> F_lhstats = lme_mass_F(lhstats,CM);
Error using lme_mass_F (line 50)
The number of colums in the contrast matrix CM(1).C is different from the corresponding number of fixed effects in stats(1).Bhat
Any help would be appreciated!
With regards
Korann
<long.qdec.table.dat.xlsx>_______________________________________________
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--
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/1EIwxbCqb50DAKOEZ0hpbclTx3XLYzRzIG3Ohk8bKj_dvT2CkYfgZbZbRl7qCwnTJOB42Ij82U3lVYS8lXd2gDPm94Pw_v4yLvdSGyhvlDskeO5hYK0faXvS8ruwHjZfYQvu1fZFPRI2lXs3lWS6sYVztftf66zvod49iYoun9VvCTVcUeKXNk1EhVMQEJc360sFjt5plQP2vkDh_-n9A-QpNK8MAF0GNl4vrqRZC7kM48ttLd2-0XgBLAE95YTEt_gHARME4RM9NVhuP2bDLgw/https%3A%2F%2Fwww.dzne.de%2Fen%2Fsites%2Fbonn%2Fresearch-groups%2Freuter.html
Phone: +49 / 228 / 43302 - 381
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Message: 4
Date: Mon, 23 Nov 2020 15:51:57 +0100
From: Valentina Meregalli <valentina.meregalli@studenti.unipd.it>
Subject: [Freesurfer] Smoothing GWC mgh data
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
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Dear all,
I computed the gray/white matter contrast using the function 'pctsurfcon'
for an individual subject. The output is a .mgh file containing the GWC
values for each vertex. It is possible to smooth these data using
freesurfer? If it's not, there is another way in which I could do that?
Thanks for the help,
Valentina Meregalli
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End of Freesurfer Digest, Vol 201, Issue 34
*******************************************
vittal korann Tue, Nov 24, 10:30 PM (10 days ago)
vittal korann Tue, Nov 24, 10:30 PM (10 days ago)
vittal korann
Tue, Nov 24, 10:30 PM (10 days ago)
Tue, Nov 24, 10:30 PM (10 days ago)
Tue, Nov 24, 10:30 PM (10 days ago)
| Tue, Nov 24, 10:51 PM (10 days ago) |  | ||
| ||||
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!