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I thought that I could not remove the class since this would mean that the contrast positive and negative values would no longer add up to 0. For instance if I remove only class "patient_centre2_female", then my contrast would have 11 (-1) and 12 (1) as opposed to 12 and 12. Could you please clarify?
Thanks again, Colleen
-------- Original Message -------- Subject: Re: [Freesurfer] FSGD design for multi-centre study Date: 2018-04-20 11:19 From: "C.P.E. Rollins" cper2@cam.ac.uk To: Freesurfer freesurfer@nmr.mgh.harvard.edu
Thanks a lot for the explanation. The issue is that I don't think Freesurfer will run a design for which there are no subjects for a given class. So if I keep the classes (24 classes since 6 centres x 2 gender x 2 groups (patient vs. control), and have the contrast with 12 (-1) and 12 (1), -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 1 1 1 1 1 1 1 1 1 1 1 0 I get the error: -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class.
I'm assuming this is because there are no participants in, for example, patient_centre2_female Is there any way to get around this issue, or should I remove those centres from my analysis (since I can't only remove "patient_centre2_female", as this would make the contrast unbalanced (positives and negatives would not add to the same number). I hope this was clear but please let me know if it was not.
Thanks again, Colleen
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Hi,
Sorry for coming back to this, but I'm still confused about the issue of having unbalanced classes. I thought that I could not remove the class as you suggested since this would mean that the contrast positive and negative values would no longer add up to 0. For instance if I remove only class "patient_centre2_female", then my contrast would have 11 (-1) and 12 (1) as opposed to 12 and 12. Could you please clarify?
Thanks again, Colleen
On 2018-04-30 14:43, C.P.E. Rollins wrote:
I thought that I could not remove the class since this would mean that the contrast positive and negative values would no longer add up to 0. For instance if I remove only class "patient_centre2_female", then my contrast would have 11 (-1) and 12 (1) as opposed to 12 and 12. Could you please clarify?
Thanks again, Colleen
-------- Original Message -------- Subject: Re: [Freesurfer] FSGD design for multi-centre study Date: 2018-04-20 11:19 From: "C.P.E. Rollins" cper2@cam.ac.uk To: Freesurfer freesurfer@nmr.mgh.harvard.edu
Thanks a lot for the explanation. The issue is that I don't think Freesurfer will run a design for which there are no subjects for a given class. So if I keep the classes (24 classes since 6 centres x 2 gender x 2 groups (patient vs. control), and have the contrast with 12 (-1) and 12 (1), -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 1 1 1 1 1 1 1 1 1 1 1 0 I get the error:
ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class.
I'm assuming this is because there are no participants in, for example, patient_centre2_female Is there any way to get around this issue, or should I remove those centres from my analysis (since I can't only remove "patient_centre2_female", as this would make the contrast unbalanced (positives and negatives would not add to the same number). I hope this was clear but please let me know if it was not.
Thanks again, Colleen
You cannot have empty classes. You should adjust the weights so that all the positives add up to 1 and all the negatives add up to -1
On 05/04/2018 04:49 AM, C.P.E. Rollins wrote:
External Email - Use CautionHi,
Sorry for coming back to this, but I'm still confused about the issue of having unbalanced classes. I thought that I could not remove the class as you suggested since this would mean that the contrast positive and negative values would no longer add up to 0. For instance if I remove only class "patient_centre2_female", then my contrast would have 11 (-1) and 12 (1) as opposed to 12 and 12. Could you please clarify?
Thanks again, Colleen
On 2018-04-30 14:43, C.P.E. Rollins wrote:
I thought that I could not remove the class since this would mean that the contrast positive and negative values would no longer add up to 0. For instance if I remove only class "patient_centre2_female", then my contrast would have 11 (-1) and 12 (1) as opposed to 12 and 12. Could you please clarify?
Thanks again, Colleen
-------- Original Message -------- Subject: Re: [Freesurfer] FSGD design for multi-centre study Date: 2018-04-20 11:19 From: "C.P.E. Rollins" cper2@cam.ac.uk To: Freesurfer freesurfer@nmr.mgh.harvard.edu
Thanks a lot for the explanation. The issue is that I don't think Freesurfer will run a design for which there are no subjects for a given class. So if I keep the classes (24 classes since 6 centres x 2 gender x 2 groups (patient vs. control), and have the contrast with 12 (-1) and 12 (1), -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 1 1 1 1 1 1 1 1 1 1 1 0 I get the error:
ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class.
I'm assuming this is because there are no participants in, for example, patient_centre2_female Is there any way to get around this issue, or should I remove those centres from my analysis (since I can't only remove "patient_centre2_female", as this would make the contrast unbalanced (positives and negatives would not add to the same number). I hope this was clear but please let me know if it was not.
Thanks again, Colleen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Ah, I think I understand now, thanks. I've attached my contrast and FSGD file to confirm. In the FSGD file, the format for the classes are <group>_<sex>_<centre>. Please let me know.
Thanks again, Colleen
On 2018-05-04 09:49, C.P.E. Rollins wrote:
Hi,
Sorry for coming back to this, but I'm still confused about the issue of having unbalanced classes. I thought that I could not remove the class as you suggested since this would mean that the contrast positive and negative values would no longer add up to 0. For instance if I remove only class "patient_centre2_female", then my contrast would have 11 (-1) and 12 (1) as opposed to 12 and 12. Could you please clarify?
Thanks again, Colleen
On 2018-04-30 14:43, C.P.E. Rollins wrote:
I thought that I could not remove the class since this would mean that the contrast positive and negative values would no longer add up to 0. For instance if I remove only class "patient_centre2_female", then my contrast would have 11 (-1) and 12 (1) as opposed to 12 and 12. Could you please clarify?
Thanks again, Colleen
-------- Original Message -------- Subject: Re: [Freesurfer] FSGD design for multi-centre study Date: 2018-04-20 11:19 From: "C.P.E. Rollins" cper2@cam.ac.uk To: Freesurfer freesurfer@nmr.mgh.harvard.edu
Thanks a lot for the explanation. The issue is that I don't think Freesurfer will run a design for which there are no subjects for a given class. So if I keep the classes (24 classes since 6 centres x 2 gender x 2 groups (patient vs. control), and have the contrast with 12 (-1) and 12 (1), -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 1 1 1 1 1 1 1 1 1 1 1 0 I get the error:
ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class.
I'm assuming this is because there are no participants in, for example, patient_centre2_female Is there any way to get around this issue, or should I remove those centres from my analysis (since I can't only remove "patient_centre2_female", as this would make the contrast unbalanced (positives and negatives would not add to the same number). I hope this was clear but please let me know if it was not.
Thanks again, Colleen
That looks right for DOSS
On 05/08/2018 11:56 AM, C.P.E. Rollins wrote:
External Email - Use Caution Ah, I think I understand now, thanks. I've attached my contrast and FSGD file to confirm. In the FSGD file, the format for the classes are <group>_<sex>_<centre>. Please let me know.
Thanks again, Colleen
On 2018-05-04 09:49, C.P.E. Rollins wrote:
Hi,
Sorry for coming back to this, but I'm still confused about the issue of having unbalanced classes. I thought that I could not remove the class as you suggested since this would mean that the contrast positive and negative values would no longer add up to 0. For instance if I remove only class "patient_centre2_female", then my contrast would have 11 (-1) and 12 (1) as opposed to 12 and 12. Could you please clarify?
Thanks again, Colleen
On 2018-04-30 14:43, C.P.E. Rollins wrote:
I thought that I could not remove the class since this would mean that the contrast positive and negative values would no longer add up to 0. For instance if I remove only class "patient_centre2_female", then my contrast would have 11 (-1) and 12 (1) as opposed to 12 and 12. Could you please clarify?
Thanks again, Colleen
-------- Original Message -------- Subject: Re: [Freesurfer] FSGD design for multi-centre study Date: 2018-04-20 11:19 From: "C.P.E. Rollins" cper2@cam.ac.uk To: Freesurfer freesurfer@nmr.mgh.harvard.edu
Thanks a lot for the explanation. The issue is that I don't think Freesurfer will run a design for which there are no subjects for a given class. So if I keep the classes (24 classes since 6 centres x 2 gender x 2 groups (patient vs. control), and have the contrast with 12 (-1) and 12 (1), -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 1 1 1 1 1 1 1 1 1 1 1 0 I get the error:
ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class.
I'm assuming this is because there are no participants in, for example, patient_centre2_female Is there any way to get around this issue, or should I remove those centres from my analysis (since I can't only remove "patient_centre2_female", as this would make the contrast unbalanced (positives and negatives would not add to the same number). I hope this was clear but please let me know if it was not.
Thanks again, Colleen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi again,
What about for DODS? I tried to create the contrast for this but got the following error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit.bin --y rh.5.lgi.centre.mgh --fsgd FSGD_centre.txt dods --glmdir rh.5.lgi.centre.glmdir --surf fsaverage rh --C H-NH_centre.dods.txt 2. The FSGD file (if using one) 3. And the design matrix above Attempting to diagnose further SumSq: Min=1.000000 (col 4), Max=183.117447 (col 31) The scale is much different between columns 4 and 31, you may want to normalize by subtracting the mean and dividing by the standard deviation.
My contrast was 1 -1 -1 -1 -1 -1 -1 -1 -1 0.75 0.75 0.75 0.75 0.75 0.75 0.75 0.75 0.75 0.75 0.75 0.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 and FSGD attached (does not include full list of subjects).
Thanks again, Colleen
On 2018-05-08 16:56, C.P.E. Rollins wrote:
Ah, I think I understand now, thanks. I've attached my contrast and FSGD file to confirm. In the FSGD file, the format for the classes are <group>_<sex>_<centre>. Please let me know.
Thanks again, Colleen
On 2018-05-04 09:49, C.P.E. Rollins wrote:
Hi,
Sorry for coming back to this, but I'm still confused about the issue of having unbalanced classes. I thought that I could not remove the class as you suggested since this would mean that the contrast positive and negative values would no longer add up to 0. For instance if I remove only class "patient_centre2_female", then my contrast would have 11 (-1) and 12 (1) as opposed to 12 and 12. Could you please clarify?
Thanks again, Colleen
On 2018-04-30 14:43, C.P.E. Rollins wrote:
I thought that I could not remove the class since this would mean that the contrast positive and negative values would no longer add up to 0. For instance if I remove only class "patient_centre2_female", then my contrast would have 11 (-1) and 12 (1) as opposed to 12 and 12. Could you please clarify?
Thanks again, Colleen
-------- Original Message -------- Subject: Re: [Freesurfer] FSGD design for multi-centre study Date: 2018-04-20 11:19 From: "C.P.E. Rollins" cper2@cam.ac.uk To: Freesurfer freesurfer@nmr.mgh.harvard.edu
Thanks a lot for the explanation. The issue is that I don't think Freesurfer will run a design for which there are no subjects for a given class. So if I keep the classes (24 classes since 6 centres x 2 gender x 2 groups (patient vs. control), and have the contrast with 12 (-1) and 12 (1), -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 1 1 1 1 1 1 1 1 1 1 1 0 I get the error:
ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class.
I'm assuming this is because there are no participants in, for example, patient_centre2_female Is there any way to get around this issue, or should I remove those centres from my analysis (since I can't only remove "patient_centre2_female", as this would make the contrast unbalanced (positives and negatives would not add to the same number). I hope this was clear but please let me know if it was not.
Thanks again, Colleen
freesurfer@nmr.mgh.harvard.edu
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C.P.E. Rollins -
Douglas N. Greve