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
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> 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 <lunhao0...@hotmail.com>
> Subject: Re: [Freesurfer] License error on Windows Subsystem for Linux
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
>         <
> dm6pr02mb6493eb25230b280b7dcff288db...@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-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> ?? Hoopes, Andrew <
> ahoo...@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-boun...@nmr.mgh.harvard.edu> on behalf of Shen Lunhao <
> lunhao0...@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.sampe...@deusto.es>
> Subject: [Freesurfer] smooth longitudinal analysis {Disarmed}
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
>         <CAJsj2xjccF30E-RvcB9bsL8sXUqUznKrni8xNR-G0=
> jwn+b...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>         External Email - Use Caution
> 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.di...@dzne.de>
> Subject: Re: [Freesurfer] Error in longitudinal pipeline {Disarmed}
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <4ef5fd94-3172-41e1-8d88-2df439d71...@dzne.de>
> Content-Type: text/plain; charset="us-ascii"
>         External Email - Use Caution
> 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 <vittalkor...@gmail.com
> <mailto:vittalkor...@gmail.com>>:
>
>         External Email - Use Caution
>
>
>
>
> ---------- Forwarded message ---------
> From: vittal korann <vittalkor...@gmail.com<mailto:vittalkor...@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.
> MailScanner has detected a possible fraud attempt from "
> secure-web.cisco.com" claiming to be
> https://secure-web.cisco.com/17EO_HpDRleA41mq0u2vD_q-nCifTXkGxnG_DHzaQDvSbQjalGwSuVlbmre2LfT_pL2eIXqCjAmNruALD7WQuCa8OeOAaMa2j--azwKUJdrFasq1GedfwpvlrjJDknPzkBsxdbnIPEtX_UZIWN1fNsj7C8T4e8n-UlCZYJWWzxV93DC3P-iExjeRmyJnz2DfPiRPZlqpOZjye7FOsaRjO4dTT0rtDf3vKFq6fJjn9ZVH9TvZOeR5aFxAcsVMJPxWaoqNKPK3iT92NZCF8iM9bMg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLinearMixedEffectsModels
> <
> https://secure-web.cisco.com/1tkYny6yViIok4HHSJ4fdMQL186SjX1A72s5pbjDlpttjtAFE-0v8RFBy_Lk2cKKs4MGT9RFKv5HsAu_7F8jM2TtWaxqsyoMQW-CTzq3bhcMd-7Wo2S3eNWwTudolPJ-_WhLmM5DVNO_0ULMkb1h-pHwkm8fwNvCyLDEyh7IHl2De94ETqs1YrtsWn7VrIdDRrcbsCTnG4tUkpn5RdBwzkgouQ6YY06qwKUlG7AaN5jsrJRE5-yYMXoqWijHvYICv-yhXkkpuox_SkoU4u-4lcA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLinearMixedEffectsModels
> >
> 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>_______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>
> https://secure-web.cisco.com/17DDwngHuPUUpXEKbYvaDeyi1HrDN_BiFqzoUOaLJ96yqi6blJUsToB0rhLScsc2gJUajK8WfuHftfTP81B0eGu324D9AYkLMHlBlzIEUvXsXi70cpppWUIENX9Mc2IpJXpExaOtUgZTlaL9CCoPSJuKAHpVr1qQUQnOervJuKbrK2D8oobK4Lkkl7AtcwoCp0Uxe7lyuae1d6K-ZKzQL8nDKxE1DfEpUFVoWP0dUpzqHFwnmU_7Zva2QrXfzrjqF_mrQK0LyhLYiT14Yph6xYQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> --
> 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.merega...@studenti.unipd.it>
> Subject: [Freesurfer] Smoothing GWC mgh data
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID:
>         <
> cafr2n_ypusho5kuc3mh1tj6xj3n_trbz0z_hqip067dhrun...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>         External Email - Use Caution
> 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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> Freesurfer mailing list
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> End of Freesurfer Digest, Vol 201, Issue 34
> *******************************************
> vittal korann Tue, Nov 24, 10:30 PM (10 days ago)
> 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
> vittal korann Tue, Nov 24, 10:30 PM (10 days ago)
> 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
> vittal korann
> Tue, Nov 24, 10:30 PM (10 days ago)
> 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
> Tue, Nov 24, 10:30 PM (10 days ago)
> 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
> Tue, Nov 24, 10:30 PM (10 days ago)
>
> 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, 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
>
vittal korann <vittalkor...@gmail.com>
Tue, Nov 24, 10:51 PM (10 days ago)
to freesurfer, Kersten.Diers
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!


On Mon, Nov 30, 2020 at 5:14 PM vittal korann <vittalkor...@gmail.com>
wrote:

> 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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