External Email - Use Caution 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/1Yf2I0SaCp4AVxLwAORs81BeTMH0g33xRhY1CDT68ohUBJ0L7VDu3kuGy0wd8m2d65w6mHDNoRLHypTfm5ZB-5FNGf9tQ5YyJeinEQ9bivUF8KQHGKl32tSRylkdJ5_pzK-MEp0qTxrrXNojhMGOtv_yVDpUJnPOz8G4chfwogaJy9t0g4Uo8rqN3rF3cfn5-f-6-Zqma1smRBsMm0UKzr4vzQlcvQo2hO2VZF7TWoXJSlP64wNOD4pq29dIMFHlluG_uASK8I8OStLa6NT_nwQ/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/1SGhiESKjBcNwBTDQxwwcvlB7obnY6vH3xv4pmeNlrPYeap_2uTtZRcxbsVDmYFxxsQJ3OfXovxxvWq5eD2eQejhGVxiTh51NJY524AwF00Uce1XUJK_XtT79SSkaEXC4FyQK9nKwrERYhl8pJ9yiM-Joo8BhxP82eDuV14To3igG5hrkco0G1wlCZSUCc2twDF7AMy3E0Lbc8Y48sPkWEgRkaunE5pIapRFMnxbUgsoHh7iRhcYQsjBU5oulgCCMfbBZZYl1bi2UDbhvEmszbA/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/1zfG5z6P2jyfC71PewDgYY-AVp9n5GIF77rQdkEi6X3yr8K_8UwgKO7HP3tzcwD5OSpXAvJelmVSECRE5jJ_LcJV4gFNMyPhOWiGsZ_wVkN0BujP19lILLCmjm4s7CujMylU7qx8XoW8knUh8JT4LIENd5hzx1TjNWfXUndlLjDE0mMEMEnm31nhUvKLueVvbtnEH9_8yqsyOiO5UyVQbwzqaD1pIIx5fysVGpg4RtvwrL607Pih1qLP1T4vZqNQE-D0rl9-4jHxg3_azdbkkMQ/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/1LS8O_oaJLev7ia9_aEtL3LzSaC-1fLXf3GvDSQwmj18n00LtBEj_a3xjB81sFgxJgNZwY0PFYJbIkIYJa2I2MTHu2b6vnsmNDnAVj8GLQlixyRN7FAo7z0k_2wxkZABbWO6y9fwRsTXrDYMoFCa82KesPT32BNLb-uKS6mZFVMc6WW8LyAQnVtJjA0f7TSa4AEdG9hRaTRumXFgBNC9zmDc2_Taj9p2gNpCTMNGedcw0PbPT_VfZK7l0XEkR2ge1-kZiByM7bdWR3K6j07A2HA/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/1oM31CBIFsyH57-AvSStdjXFipCnqyou0NH12dHWroJxum06Evdx5GpKRYkuzn8ZrvL9dWvpZiIPn3lQQBKWNbQvfOBZYbycmKl8YVKY_C9hUOvwH-KL4shuOhSaM-Yyf7NQ5HvQz4JA2Wjd5-e4pCNlTKHsWdhyvSkewBmq0rrF1P4fMQ8Sg6wVty_9RG7Dq8aQGnnqvEYvn_dzoUjGw-UxUR2NtoCdiJnTQWKJkI8FCvUcKQH8YlhIGvxRYRmYwYM5ETOQozgQ3GkpGpP_aqw/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/1Yf2I0SaCp4AVxLwAORs81BeTMH0g33xRhY1CDT68ohUBJ0L7VDu3kuGy0wd8m2d65w6mHDNoRLHypTfm5ZB-5FNGf9tQ5YyJeinEQ9bivUF8KQHGKl32tSRylkdJ5_pzK-MEp0qTxrrXNojhMGOtv_yVDpUJnPOz8G4chfwogaJy9t0g4Uo8rqN3rF3cfn5-f-6-Zqma1smRBsMm0UKzr4vzQlcvQo2hO2VZF7TWoXJSlP64wNOD4pq29dIMFHlluG_uASK8I8OStLa6NT_nwQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > End of Freesurfer Digest, Vol 201, Issue 34 > ******************************************* >
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