My guess is that the variable (G_cingul vol) should be normalized (remove the mean and divide by the stddev).
On 9/6/2022 5:44 PM, Piot, Alex wrote:
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Hello Freesurfer experts,
I am trying to perform a GLM, using the volume of a brain region as a covariate. I am doing a two-group, one covariate design. I originally tried to use QDEC to facilitate the process and received an error message that the mri_glmfit command had failed. I then saw that QDEC was deprecated and followed the instructions set out on the freesurfer wiki for doing it manually (*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0 https://secure-web.cisco.com/1W0gEAYXZeH6XMYzikihrf4Ct-vcV_3e-WmTr1eqTVlVGWz8ZAzr0ToHAdQVWw6seyPj2yu31w7pqzGFZrFu7wQ5so3ZFfYQjKCTQ_ExMc1qL3caPs38GvVhvpKQ2NXDmLYaNxgZkGAilAmdd8JnWqAEkh_EBy23scDzimQ4p5fuMO002JYf6Si2hgy5xDHl5Yf748DEHIe1u3vA-E3BtAxiCGBB67Hm4Dc6xHuUk_Na_DLM_uYMDcy3z8UttfwM1TTMP0_JLn_rmvpcqSqGN2rtaA3UGOE5aOOm0GnQgDXQWm5MIgG9_A0PeUuBfAxRgunRr7ZxcVBapNEIOwCUPdg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysisV6.0).
I received the same error message as I had with QDEC on the command line:
ERROR: MatrixResidualForming(): X is not invertable RD is not invertable n = 1
This only occurs for certain of the brain regions used as covariates; for others, the QDEC and command-line streams work perfectly. Additionally, I've noticed that if I input different numbers for the covariate values in the fsgd file, the command runs smoothly.
I haven't been able to find a similar error on the mailing list, does anyone have an idea of how to work around this? I would greatly appreciate it.
Please find attached my fsgd file, and the full log of what happens after I run the mri_glmfit command (when it works and when it doesn't) The hands.fsgd file doesn't work, whereas the hands_works.fsgd file does.
Freesurfer version: 7.2.0, Ubuntu 20.04, Windows WSL
Best wishes, Alex
--
Alexandre Piot, MSc. Queen Square Institute of Neurology President of the Application of Psychedelics Society https://secure-web.cisco.com/1txv4iCOx4-mObxXkQBwlHnKAPMdNbmkUOMySvRIxTq9ls1uXZ8Kl62y3I49HdkLsX6y7u-cbb0hhFAgyYtQiLyvLqmJHRpVile95hsJIW_BkEPsZYU7xlCSImzrBqWQ04vGC-z5o197phurtwnpjWg9swrt2VVrxiiXYGg9bY0RbMOrknb9AaoPwF5FSDuMc0WVXrwnhjXQY6v4i38hVb6sLx6MLR2rCdDLI8W_lEtTFtoddcERVMfMlp1QPST7zgdW1ISSG1NIw0Y7AGPrRMAOgyDEDDbcO5Bw5ZAdy0JZpVjRnYzg9UIT_Svi--kUWS1MEmI_sDO3lstJ-3GIgMQ/https%3A%2F%2Fwww.uclsap.com%2F-- UCL UNITy Project https://secure-web.cisco.com/11-VCBFrldtskQk64mTlGciM29YjbhiPBFq0qJNEn4t16fq2dpqPk8MULNrPk_hdW3xFgDWoez2dpX7V5EsWwjhjv5xLowcqQlWm8H8z1bfrLct3k0RqTnpX1n8ctYdYTBN4YZweUcivxmxcuvMem-Gc6V7-VqRYMBpF6H6kHTK_UcUi5UnP5yWRqhIkMLWkdPffFie-WcMxkLkdKIpTISAHztKFwrtv1Z0KJlrr03qryskIQu6LNxCa5spVh0LxIs6qkUPD7pRD2E8dl-jERSFNiw0WJygtI9HdMjxfWc8x9C2KVtbdX5UmF1A-hcqoRaqNXrfS42WsaQI_sTTEKdA/https%3A%2F%2Fwww.psychedelicunit.com%2F
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