The problem is that all of your class=0 subjects have a 0 duration meaning that you cannot compute a duration slope for this class. In this special case, you can run a different-offset, same-slope analysis with --fsgd dur.fsgd doss Change your contrast matrix to 1 -1 0

On 11/14/19 9:47 AM, Ferraro, Pilar wrote:

External Email - Use Caution

Hi,

I'm trying to run a surface based group analysis comparing patients and HC, correcting for disease duration. I enclose here the fsgd file and the design matrix. I've followed all the steps of the tutorial (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0)%C2%A0... no errors. However, when I try to run the glm analysis with the following command:

mri_glmfit.bin --y lh.dur.thickness.10.mgh --fsgd dur.fsgd dods --C lh-Avg-thickness-dur-Cor.mtx --surf fsaverage lh --cortex --glmdir lh.dur.glmdir

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.

Of course there is no range for the continuous variable (disease duration) in the control group, so I'm wondering how to overcome this limit and proceed correctly with the glm analysis.

Many thanks in advance for any help you will provide,

Pilar

---

*From:* Ferraro, Pilar *Sent:* Monday, November 11, 2019 7:07 AM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* surface group analysis with qdec Hi!

I've previously run a comparison between patients and HC using qdec, but now I'd like to correct the analysis for disease duration. I've therefore generated a second qdec.table.dat file inserting the disease duration column with the following structure: fsid group duration Input subj1 1 13 Input subj2 0

(For healthy controls group (group 0) I've tried both options, leaving the duration column blank or inserting 0 as a value). I've also left the group.level file the same of the previous analysis. However, when i open the new qdec.table.dat file with qdec I get problems in correctly uploading the data. In particular, I get 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:  This is the command line:  mri_glmfit.bin --y /home/ospite/Pilar/freesurfer/qdec/Untitled/y.mgh --fsgd /home/ospite/Pilar/freesurfer/qdec/Untitled/qdec.fsgd dods --glmdir /home/ospite/Pilar/freesurfer/qdec/Untitled --surf fsaverage lh --label /home/ospite/Pilar/freesurfer/fsaverage/label/lh.aparc.label --C /home/ospite/Pilar/freesurfer/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /home/ospite/Pilar/freesurfer/qdec/Untitled/contrasts/lh-Diff-1-0-Intercept-thickness.mat

Of course there is no range for the continuous variable (disease duration) in the control group, so I'm wondering how to overcome this and generate a correct qdec.table.dat file.

Thanks in advance for any help!

Pilar

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

I responded to this a few days ago. Below is what I said

The problem is that all of your class=0 subjects have a 0 duration meaning that you cannot compute a duration slope for this class. In this special case, you can run a different-offset, same-slope analysis with --fsgd dur.fsgd doss Change your contrast matrix to 1 -1 0

On 11/19/19 5:00 AM, Ferraro, Pilar wrote:

External Email - Use Caution

Hi,

I’ve never got a response to my last email (you can find it below).

Would you be able to let me know so I can proceed with the analyses?

Many thanks,

Pilar

...

Inizio messaggio inoltrato:

*Da: *"Ferraro, Pilar" <FerraroP@pennmedicine.upenn.edu mailto:FerraroP@pennmedicine.upenn.edu> *Oggetto: **Fw: surface group analysis with qdec* *Data: *14 novembre 2019 3:47:42 PM CET *A: *"freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>

Hi,

I'm trying to run a surface based group analysis comparing patients and HC, correcting for disease duration. I enclose here the fsgd file and the design matrix. I've followed all the steps of the tutorial (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0)%C2%A0... no errors. However, when I try to run the glm analysis with the following command:

mri_glmfit.bin --y lh.dur.thickness.10.mgh --fsgd dur.fsgd dods --C lh-Avg-thickness-dur-Cor.mtx --surf fsaverage lh --cortex --glmdir lh.dur.glmdir

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.

Of course there is no range for the continuous variable (disease duration) in the control group, so I'm wondering how to overcome this limit and proceed correctly with the glm analysis.

Many thanks in advance for any help you will provide,

Pilar

---

*From:*Ferraro, Pilar *Sent:*Monday, November 11, 2019 7:07 AM *To:*freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> *Subject:*surface group analysis with qdec Hi!

I've previously run a comparison between patients and HC using qdec, but now I'd like to correct the analysis for disease duration. I've therefore generated a second qdec.table.dat file inserting the disease duration column with the following structure: fsid group duration Input subj1 1 13 Input subj2 0

(For healthy controls group (group 0) I've tried both options, leaving the duration column blank or inserting 0 as a value). I've also left the group.level file the same of the previous analysis. However, when i open the new qdec.table.dat file with qdec I get problems in correctly uploading the data. In particular, I get 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:  This is the command line:  mri_glmfit.bin --y /home/ospite/Pilar/freesurfer/qdec/Untitled/y.mgh --fsgd /home/ospite/Pilar/freesurfer/qdec/Untitled/qdec.fsgd dods --glmdir /home/ospite/Pilar/freesurfer/qdec/Untitled --surf fsaverage lh --label /home/ospite/Pilar/freesurfer/fsaverage/label/lh.aparc.label --C /home/ospite/Pilar/freesurfer/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /home/ospite/Pilar/freesurfer/qdec/Untitled/contrasts/lh-Diff-1-0-Intercept-thickness.mat

Of course there is no range for the continuous variable (disease duration) in the control group, so I'm wondering how to overcome this and generate a correct qdec.table.dat file.

Thanks in advance for any help!

Pilar

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer