External Email - Use Caution Hello Vittal,
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). 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). A similar, but slightly more complex example (with three groups) is given in the lme tutorial. Just to make sure: ‚age‘ should be ‚age at baseline‘ (i.e. constant across time per subject), otherwise it will be confounded with time. Could you review (and possibly adapt) your design matrix X with respect to which columns it contains, and write it in the reply? Best, Kersten PS Let’s reply to this mail (and not the 'Freesurfer Digest‘ thread) to keep the email thread clean ;) Am 24.11.2020 um 18:21 schrieb vittal korann <vittalkor...@gmail.com<mailto:vittalkor...@gmail.com>>: 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<mailto: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 Am 23.11.2020 um 14:13 schrieb Diers, Kersten /DZNE <kersten.di...@dzne.de<mailto:kersten.di...@dzne.de>>: 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/1Gcilx44D2-9AtsxmNg75t5eWUyQxgwoSPIJOgtlr_F4ptwYnWgz1wPfoEO2UUEbpdB3rTd2Tndqm9eUARYiFKM8gqV4MyIfR3PqAJBMB7MJBRtJCVF4stiwGHujPJkWmozX2JTUTPmXFH71xikPaf7d6fqOES8x9yNrfTH2ZH0JQc8gf3OWGEn57GVQqspCW6dU_NU2KB62dn3sVPps7IlLiPywOvEwKYr9oZbCBhRUtx_a9-Va55DMue9SwoHBbv4-q3mMtEw5MmcV67o_alA/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/1tLtQcL1EHXFJ8H9KSxX60yo817UOWRczy6zoCmXXohpchSf6-rj4Q_mRadoxmhZ_V052xHfuDL9N_BtQw8MbZTpwkTYdcf9a0vPyECNUIkMamVn6ZT_UnoFr0dYjpTu30Rhvoo0y_JOq7_X60puNBaDX8mUl4tZXAqpc_4RXN5vEdTLOWj-ELp6g0B8m2tHCe53rTHva99hH08NqEUhop4hj-ukXkF8slxoFuHMyiJuaNq3t4iVlYNYkcmpFh2WtwlC7mt1uPyOUsXbrZdK6ow/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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Kk_dgKWPS3W0XKFChZFK-tmszpPv9BNIplSvdqQ6vISnm9G0AjlJO1Do9XImJGTxHch5l-MvFYXzQvCnIKOx2zovh13LzOYBzRMEaJx7oIBi_t-6b46Hah3yqFyohcUOpxi7kaDWlgWebf1tH4Fh6AF1CqvTeitXKL7N-w6_0SjUHkg7y7sANKJ7brXiC4QtJZbbGKbDPZMekXz81e7F8cFjDaJiCyk2A9D6RdOidCaKO-3a3DEXSpJqyzxHEy6iDaDW6XIdkbWqZAFK90-c0A/https%3A%2F%2Fwww.dzne.de%2Fen%2Fsites%2Fbonn%2Fresearch-groups%2Freuter.html<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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1tLtQcL1EHXFJ8H9KSxX60yo817UOWRczy6zoCmXXohpchSf6-rj4Q_mRadoxmhZ_V052xHfuDL9N_BtQw8MbZTpwkTYdcf9a0vPyECNUIkMamVn6ZT_UnoFr0dYjpTu30Rhvoo0y_JOq7_X60puNBaDX8mUl4tZXAqpc_4RXN5vEdTLOWj-ELp6g0B8m2tHCe53rTHva99hH08NqEUhop4hj-ukXkF8slxoFuHMyiJuaNq3t4iVlYNYkcmpFh2WtwlC7mt1uPyOUsXbrZdK6ow/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/1Kk_dgKWPS3W0XKFChZFK-tmszpPv9BNIplSvdqQ6vISnm9G0AjlJO1Do9XImJGTxHch5l-MvFYXzQvCnIKOx2zovh13LzOYBzRMEaJx7oIBi_t-6b46Hah3yqFyohcUOpxi7kaDWlgWebf1tH4Fh6AF1CqvTeitXKL7N-w6_0SjUHkg7y7sANKJ7brXiC4QtJZbbGKbDPZMekXz81e7F8cFjDaJiCyk2A9D6RdOidCaKO-3a3DEXSpJqyzxHEy6iDaDW6XIdkbWqZAFK90-c0A/https%3A%2F%2Fwww.dzne.de%2Fen%2Fsites%2Fbonn%2Fresearch-groups%2Freuter.html Phone: +49 / 228 / 43302 - 381
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