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.edu > To subscribe or unsubscribe via the World Wide Web, visit > > 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%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/1PqKJoMkN3arnPDEmxXDpfZjMP037UotngnBsWT8PfaLoXvL4HE-zqjuZmhtmneyRopUz1MwKCrhYOuUCO672R7ol57UaCa3XBpO0ewDSM5eay3m0BkVce_hBhM5DIzrdWbQO_FgYAp_0n-G7Z_cJBRODv252c5h60Q8ufVCpF3OsFfxlVAtDspAmwSewTeY3pKjNeW_Mrhyh0-ZVbP0zFMWaKfR-o8K2mY9GZm70tCjOL2l5TltWr49zOnfPBVWxhKmHeyXA6d1bWhmA6uy8NQ/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/1zp1t-9W8dkfwy4PQA0vRheHOcscTlGKBhCGffdDSWYC1KR6vqx6rRFARsYv8MENjTSJN96fCtPxi797JPKSl99aaFwHteT50Q_3tpwAqZ7Ag9FQ2y3_kxFAllLv5KcoWoK7AIj7qHNk9SiSq3wA19jrIfTnFCmm6zbfwqfMBZqQ42GQP_hR42geDW27w3t8V33x3mUI4weDq183i7YkzkC6MXn-yI-_iojMwlrurozIwcp-_OU-zUcsh3Wc-MY7egl9EWO5ULPJdVev2hJ70cw/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/14DJO2pZGh-_5sbOhIUFWdCJx2_VJhrJzdu2P2yP5N8jUgE-hO4gCtyRRaJBDxIak47HUhcYOao4abciUFeiEKqmjGw_OZ8WPUTOH71-aPo4TplKkZUVNJq2tFv835TFcfmkA27ZJkgsyhLyvGB96CU762U3gTQ43kMcjThGc_bTxQH_Nofq11a5iurJx_QQwbG9CwrAybUtOMtjkTYHt-3ruZEi-ReXgc5iUOt8cWWDEGZtOARhWyve5BJrOywm9Kkr0Pkj-MqQh3qtqNk0WWw/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/1a_4fwuQAJROjAsm7_ZToKZUneS9YS7aP60bWepuFmxnlYSij0jBVAXt-zYaJCM2nqnOKbbUfU8CWBJ30Bsr_0h-UEBOS6_bPgMCm0TEhCHn53dUowZE8R0YxDf6G5bP52gy76sCpoXmA49I7PCJKYby4g3QODJCPjjSe_vZTnPGnUGnCy83cNV3RE19RqC2wZkLhRBtT1tUrhgnyjMU3U4qwCb6WXiSU1S4kSWpgkR9pjMuJXlZjcbuYgWKQh_jAectoDOzTfUgwlgbzYcUidw/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/1VpKxsiVae3KbaNGm2RndFtO0tJs8ENmwclbckfVGAawWhozAPFA6tYE8LvMYv4CUlLbYwavNETA2pqMs7H9QIXuFNSjl53NfoX5o_G-eW_9rRAAiZ_ORvHEASeioG2pM_K_wm4a6PQtLIHnnVhT5GOCJY6LoiG2RykLKWUQf3IYBu-QrsKjeGXpS8GKMVYj0SJm4rX9SBjwtlKMXfmIapW5mD1wVRoeN24Kkv-elzNnNp1rE84YHmnk22fG84O460011LTdUWfhp5-7k3ZuFzQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > 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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