External Email - Use Caution 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 <vittalkor...@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-requ...@nmr.mgh.harvard.edu> > wrote: > >> Send Freesurfer mailing list submissions to >> freesurfer@nmr.mgh.harvard.edu >> >> To subscribe or unsubscribe via the World Wide Web, visit >> >> https://secure-web.cisco.com/1udknGNk55PcCtTOL76wjb4oQNyRE-TSJqn5m27R-IJvwNhK97p6Q9riaJGb36IXvp3B0GujWnO_hy96RUj44HgV5AC9F8adlGbyURtpzxgxSMqwaL1s9dgPTf2S0f4lYSZ20_aUJ1I1UkGL_iAbc_HsDHNAF7VzrGiOm6gJMq8MhgsYMJtoXBshKa_vbUX9uy0nX2t0JFfeo2a4N3pVnjdd8Sn3--7I7j7yntgPw3BXFaRDp5P1caApZzfeVllRMXtBlA7mu_k5-46VcWtf-1A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> or, via email, send a message with subject or body 'help' to >> freesurfer-requ...@nmr.mgh.harvard.edu >> >> You can reach the person managing the list at >> freesurfer-ow...@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 <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 >> >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://secure-web.cisco.com/1ouMToKda1uE-gV2mRBTgaEVRNj39h2E8ylPcyQoCMDrCgVr3_MOkGA-IPQ7e9_mSYCXL7aldwl-cerJzBQ4YGm_Wry2GL35kmxat6Mcp9nTOekvMWTive_STApjVyg_vvoGOO0UsOKd7URIQZUJDyXXqSKLbD6hp8AWu-8bZl6lvrFf4Jm4xCwHog5O102UxDGBfY7lf0SBB9auZbJ1Nbm6dckC5XN2eKxlJ__R07g9cfXxZ9tGaa79at2u9zsZZDoNe7lvEzONSdsMr4YzkkQ/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20201123%2Fc77e7dd5%2Fattachment-0001.html >> >> ------------------------------ >> >> 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) >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://secure-web.cisco.com/1uqs91C60CJAwTEgXZh7v9ZBmg45VhPTbfhmmtpyQDFqnf_XKSo9uA7JthaCLuHk3bkAAag1sm7ejJD8qP3N8feP9AWT9n8TRSoA2K3ViCs-RJcH01Vs39gZn8thVX-63HfoxHRVmtWHUAvsnORu7jeaENPYRQVX3Uy3ckxQgL7soCj0xwRD4kc9Reg0ICJTPrsBpDyi75j0yEFGcbrJcN_YbdLSmH-AzjeYDs1m8lr932Gwgvc0qDDlnPOmx4uIwWP_QG5hACf2jXNT2055j_w/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20201123%2F7dc628cf%2Fattachment-0001.html >> >> ------------------------------ >> >> 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 >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://secure-web.cisco.com/1jRsr28H7iTDwB7UccZXakuxWTZZ4gfN5dghykjJwV23f0FxrBxmktSFgjz2qBPPbTXjZXyFfwQlKrbSaxvWqLDd6BQhuJKCCYOpxjJza9YvRBbBFve3TYcukZhDLwaCWy84cl2pvk8n_8H6wiU54ijSHaPrvN0dZ8oUadb6hXuiZJQ5PNr8f15G88luuumLYSBD0ps6iVpflpKFpy5b5F9Apb94rQyLXLMYB7at1nEq8DxdS42welgtmS7WHCDzEJzqXkFaCTvlN8jcV-oZDcA/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20201123%2Fa5989a87%2Fattachment-0001.html >> >> ------------------------------ >> >> 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 >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://secure-web.cisco.com/1IlcZWaGRtLmZJ6ITkCIU7QmVmq7QZbJHIS0S9_Bfw7MgYHdF5_Q6_-YbvwaaohIkJZ91dc-utZZM8TizLnum9OzBRxm66It_aVSqV8ISwEVyUKNA9G2SEo0h7wusVgim7-tme2NLB8ZJ_Dm-WrJ4YWCDWZQLGezk1yWkth70OE8JFB3xqfQbcWEqqagbHAU73qvD3yZDcGXxgYz0JQFxnXK_GQxJE_VM18aWorDlug7JGj9uYH8TpnVe4HZoWmjlvzIYtTjg142brzlgpVyDMA/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20201123%2F7b6893fd%2Fattachment-0001.html >> >> ------------------------------ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://secure-web.cisco.com/1udknGNk55PcCtTOL76wjb4oQNyRE-TSJqn5m27R-IJvwNhK97p6Q9riaJGb36IXvp3B0GujWnO_hy96RUj44HgV5AC9F8adlGbyURtpzxgxSMqwaL1s9dgPTf2S0f4lYSZ20_aUJ1I1UkGL_iAbc_HsDHNAF7VzrGiOm6gJMq8MhgsYMJtoXBshKa_vbUX9uy0nX2t0JFfeo2a4N3pVnjdd8Sn3--7I7j7yntgPw3BXFaRDp5P1caApZzfeVllRMXtBlA7mu_k5-46VcWtf-1A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> >> End of Freesurfer Digest, Vol 201, Issue 34 >> ******************************************* >> >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
