External Email - Use Caution
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 (https://secure-web.cisco.com/1W0gEAYXZeH6XMYzikihrf4Ct-vcV_3e-WmTr1eqTVlVGWz...).
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 Projecthttps://secure-web.cisco.com/11-VCBFrldtskQk64mTlGciM29YjbhiPBFq0qJNEn4t16fq2dpqPk8MULNrPk_hdW3xFgDWoez2dpX7V5EsWwjhjv5xLowcqQlWm8H8z1bfrLct3k0RqTnpX1n8ctYdYTBN4YZweUcivxmxcuvMem-Gc6V7-VqRYMBpF6H6kHTK_UcUi5UnP5yWRqhIkMLWkdPffFie-WcMxkLkdKIpTISAHztKFwrtv1Z0KJlrr03qryskIQu6LNxCa5spVh0LxIs6qkUPD7pRD2E8dl-jERSFNiw0WJygtI9HdMjxfWc8x9C2KVtbdX5UmF1A-hcqoRaqNXrfS42WsaQI_sTTEKdA/https%3A%2F%2Fwww.psychedelicunit.com%2F
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:
External Email - Use Caution
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thanks so much, Doug that worked!
--
Alexandre Piot Clinical Neuroscience MSc. -- Queen Square Institute of Neurology President of the Application of Psychedelics Society https://secure-web.cisco.com/14QCtn-rMuCXkiml5_4I5IXFKX66Ncu_AGQ8fvExAsL8gWmxqQcHvd2kGWlDCWvSUOfbLDIjXuX3fuQKO-5eyxhZtT30_7hevE8ltwjNXtghqCjtxi2goS8fo38AME_JY9Fqvuif0tSqY4AZuGkRPYPkLdalnLLMU_q3HNsXjk5z6GClTBOx70-LsoFWh--kA6Y3E1Em-ctQJMV9H_D6MbP6NLDJh03ORTTAVtQxMFxpN1GKFRQ6syUz1sOwHXX7d5Bj9mJeTbtKUuCJCER7oBDA_w6czmo1uikYUgjiqoTmcrevVlIcDiHMZEKkfvqxE/https%3A%2F%2Fwww.uclsap.com%2F -- UCL UNITy Projecthttps://secure-web.cisco.com/1NtBKC7uL_DuYiDb5y-hj20dZDvYr9ijFl1uMQerXX8XxG6cgyVrXGkykk6AzP-78-d8I12EmGuFwqaRB-JakskN_fsg1PtgtbsB6D7xicxnvYXom36ocXwx1hCTyBPioBd66_J-C7FFSSrIxlSpytGrr7PBQXtBGl9FkNuiTgGrFFgiBeX9LGov1zV6MVOrR3M2jSPnd5u-d13ucPwNneHlLWVfMtQdOnutlBO_1tkJ3G23_Hg_cICSTgxSN0wWJkuT-RxhGjxlnzwcr2vM2cEeoy_ubgepgY09Dg8whkWQDwyvc2fpfyUWH2kVZjDEk/https%3A%2F%2Fwww.psychedelicunit.com%2F
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU Sent: Wednesday, September 7, 2022 3:50 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_glmfit error: MatrixResidualForming(): X is not invertable
⚠ Caution: External sender
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:
External Email - Use Caution
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://secure-web.cisco.com/1AVbn8ayTwZ1pIMwfAGmvXnOUKpv-ZxIzALR0W6MmXrotHq...https://secure-web.cisco.com/1L6dm2yjf87UmfZNslR1O80hp2NRnPaRHt2XfHNiM9VKLumGdZWe18tsgJY8NM4r2MF8Ab3UK0ehExtk3fp4BlaA4mUnGZ8HkHXv_n1swN689JVdxqODicn5lWi-KNJKXxB2aj7Uv4nz3rlbRHc040ZmE3BGrEGUnjPna0nWEd6vqpl-P85nWzaKRkVDp3Xo4jKJeTeCgPcHODDlSokdIXAx68bHm1VZoRZLlR9cOFtwsHBTlw8YvSGuuTl2o1M-X1c9lwhTWMQIL0Omc7ePvtQgHWIiZlga_IUB3SBZYeIPe41s38UiXHUTomPdG0uiU1ZsltbSFnbs2DflkU01YtQ/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1W0gEAYXZeH6XMYzikihrf4Ct-vcV_3e-WmTr1eqTVlVGWz8ZAzr0ToHAdQVWw6seyPj2yu31w7pqzGFZrFu7wQ5so3ZFfYQjKCTQ_ExMc1qL3caPs38GvVhvpKQ2NXDmLYaNxgZkGAilAmdd8JnWqAEkh_EBy23scDzimQ4p5fuMO002JYf6Si2hgy5xDHl5Yf748DEHIe1u3vA-E3BtAxiCGBB67Hm4Dc6xHuUk_Na_DLM_uYMDcy3z8UttfwM1TTMP0_JLn_rmvpcqSqGN2rtaA3UGOE5aOOm0GnQgDXQWm5MIgG9_A0PeUuBfAxRgunRr7ZxcVBapNEIOwCUPdg%252Fhttps%25253A%25252F%25252Fsurfer.nmr.mgh.harvard.edu%25252Ffswiki%25252FFsTutorial%25252FGroupAnalysisV6.0%26data%3D05%257C01%257Calexandre.piot.20%2540ucl.ac.uk%257C73c035e9e6cf487d2e5108da907c2a21%257C1faf88fea9984c5b93c9210a11d9a5c2%257C0%257C0%257C637981160222235295%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DLh6n24JxgAem7SrBwdAYGJdgM594SN2DrIfBZNPVDSc%253D%26reserved%3D0).
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/14kGvsxe2BqKznYjgaUiDT9atpsHB4dq_ptXv0ziaM8FphgMzWDgOY98Z1tD_0xz2c1cjD4POxN1urE_pW2tIVN9jA6YFxi3itYB5gGUCExiftfzcbLNLbcJFtAq31NqdT7OflBKfVUyS92EfHwsnUnMZUBUBe5BYHcmQIdJgGNTDB3A2QYzLuB7xekByUUp5S1IwbanINJlNNnrCJm6O5AMbjxNqTjslN2kDBhNg3n09MZGKiUdYIdOxg_a8Hgh7WxjjviftaOT-3dnDpuBUEbXTpeJPFtBhobwBR5Ww7Pzrd4rUjPiCJGZc0xXwTel5npgLvCrI7gVzgTOhcag6UQ/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1txv4iCOx4-mObxXkQBwlHnKAPMdNbmkUOMySvRIxTq9ls1uXZ8Kl62y3I49HdkLsX6y7u-cbb0hhFAgyYtQiLyvLqmJHRpVile95hsJIW_BkEPsZYU7xlCSImzrBqWQ04vGC-z5o197phurtwnpjWg9swrt2VVrxiiXYGg9bY0RbMOrknb9AaoPwF5FSDuMc0WVXrwnhjXQY6v4i38hVb6sLx6MLR2rCdDLI8W_lEtTFtoddcERVMfMlp1QPST7zgdW1ISSG1NIw0Y7AGPrRMAOgyDEDDbcO5Bw5ZAdy0JZpVjRnYzg9UIT_Svi--kUWS1MEmI_sDO3lstJ-3GIgMQ%252Fhttps%25253A%25252F%25252Fwww.uclsap.com%25252F%26data%3D05%257C01%257Calexandre.piot.20%2540ucl.ac.uk%257C73c035e9e6cf487d2e5108da907c2a21%257C1faf88fea9984c5b93c9210a11d9a5c2%257C0%257C0%257C637981160222235295%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DxeKB0bgJ0VcOKRFKztTmP1Gn3SNPmu3oeElW7E6T6A8%253D%26reserved%3D0 -- UCL UNITy Projecthttps://secure-web.cisco.com/1g27k1tBBY-gVk8X3dC3Y1PGD3eL7u6CiYZnMcfAqPNikC-VGo-nW4FH7CvfazJ4XBmL6L1bwZZPCtzMILBG0KjqDi1AowGriJij7LclWbQLH3QU1W4JDtMHGX66ovXvYkM44VUpQlU_5ZLkZpbhsFky0yKJ-SR9mwaGCmgjnDlqXB720KYn9yaUJJUdqfUVWTFKfztXlDwqgDRLPdpeXYTTpMMg_IogZteiJ-iD65UW66b5NiU1Zqoxz0OzjX_Cxvc_g2zdu9Mm5RyhdIl1fB6fLSln8hbPvBsbakCe1Qkh1xN2pR1V8yKfQz6BcsiiH-9IAOADjm6bS5SbqIG3tkQ/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F11-VCBFrldtskQk64mTlGciM29YjbhiPBFq0qJNEn4t16fq2dpqPk8MULNrPk_hdW3xFgDWoez2dpX7V5EsWwjhjv5xLowcqQlWm8H8z1bfrLct3k0RqTnpX1n8ctYdYTBN4YZweUcivxmxcuvMem-Gc6V7-VqRYMBpF6H6kHTK_UcUi5UnP5yWRqhIkMLWkdPffFie-WcMxkLkdKIpTISAHztKFwrtv1Z0KJlrr03qryskIQu6LNxCa5spVh0LxIs6qkUPD7pRD2E8dl-jERSFNiw0WJygtI9HdMjxfWc8x9C2KVtbdX5UmF1A-hcqoRaqNXrfS42WsaQI_sTTEKdA%252Fhttps%25253A%25252F%25252Fwww.psychedelicunit.com%25252F%26data%3D05%257C01%257Calexandre.piot.20%2540ucl.ac.uk%257C73c035e9e6cf487d2e5108da907c2a21%257C1faf88fea9984c5b93c9210a11d9a5c2%257C0%257C0%257C637981160222392089%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DVTSD2E8nuwyHQW3c3r4RvtEKYzUbVYbDVFnIEQXP03E%253D%26reserved%3D0
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Douglas N. Greve -
Piot, Alex