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Hello Freesurfer friends!
I'm going through the "paired analysis" tutorial and am running into an issue with the mri_glmfit. I am running on just one subject pair. https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis#Runmriglmfit
I ran mris_preproc on my 2 timepoints and am getting an error at mri_glmfit
mris_preproc --target fsaverage --hemi lh \ --meas thickness --out lh.paired-diff.thickness.mgh \ --fsgd pairs.fsgd --paired-diff
mri_glmfit \ --glmdir lh.paired-diff \ --y lh.paired-diff.thickness.sm05.mgh \ --fsgd paired-diff.fsgd \
--osgm \
--surf fsaverage lh
I am getting an ERROR: DOF = 0.
MRI's have been put through recon-all and are in there own directories within SUBJECTS_DIR.
What is the cause of the error?
Thanks,
Ken
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as one of the nation’s top hospitals by U.S. News & World Report (2019-2020). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
how many subjects are there in your fsgd? How many groups in your fsgd file? Also, you should not use --osgm and --fsgd
On 4/30/2020 1:09 PM, KennethSPrice wrote:
External Email - Use Caution
Hello Freesurfer friends!
I'm going through the "paired analysis" tutorial and am running into an issue with the mri_glmfit. I am running on just one subject pair. https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis#Runmriglmfit
I ran mris_preproc on my 2 timepoints and am getting an error at mri_glmfit mris_preproc --target fsaverage --hemi lh \ --meas thickness --out lh.paired-diff.thickness.mgh \ --fsgd pairs.fsgd --paired-diff
mri_glmfit \ --glmdir lh.paired-diff \ --y lh.paired-diff.thickness.sm05.mgh \ --fsgd paired-diff.fsgd \ --osgm \ --surf fsaverage lh I am getting an ERROR: DOF = 0. MRI's have been put through recon-all and are in there own directories within SUBJECTS_DIR. What is the cause of the error? Thanks, Ken
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as one of the nation’s top hospitals by /U.S. News & World Report/ (2019-2020). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
In the FSGD file I have one subject pair (timepoint 1 and timepoint 2), and it is the only group. However, I removed --fsgd and replaced it with --osgm upon your reccomendation, and am still getting the error.
I am also having an issue visualizing the output of mri_preproc in freeview - isnt this mgh file supposed to be a volume? Is there a way to center the freeview cursor to the middle of the current volume?
Thanks, Ken
‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On Thursday, April 30, 2020 2:16 PM, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
how many subjects are there in your fsgd? How many groups in your fsgd file? Also, you should not use --osgm and --fsgd
On 4/30/2020 1:09 PM, KennethSPrice wrote:
External Email - Use CautionHello Freesurfer friends!
I'm going through the "paired analysis" tutorial and am running into an issue with the mri_glmfit. I am running on just one subject pair. https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis#Runmriglmfit
I ran mris_preproc on my 2 timepoints and am getting an error at mri_glmfit
mris_preproc --target fsaverage --hemi lh \ --meas thickness --out lh.paired-diff.thickness.mgh \ --fsgd pairs.fsgd --paired-diff
mri_glmfit \ --glmdir lh.paired-diff \ --y lh.paired-diff.thickness.sm05.mgh \ --fsgd paired-diff.fsgd \
--osgm \
--surf fsaverage lh
I am getting an ERROR: DOF = 0.
MRI's have been put through recon-all and are in there own directories within SUBJECTS_DIR.
What is the cause of the error?
Thanks,
Ken
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as one of the nation’s top hospitals by U.S. News & World Report (2019-2020). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Oh, right. You only have one data point (the difference) and you are computing one parameter (the mean), so you have 0 DOF. If you only have one data point, there are not statistical tests you can do
On 5/1/2020 3:34 AM, KennethSPrice wrote:
External Email - Use Caution
In the FSGD file I have one subject pair (timepoint 1 and timepoint 2), and it is the only group. However, I removed --fsgd and replaced it with --osgm upon your reccomendation, and am still getting the error.
I am also having an issue visualizing the output of mri_preproc in freeview - isnt this mgh file supposed to be a volume? Is there a way to center the freeview cursor to the middle of the current volume?
Thanks, Ken
‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On Thursday, April 30, 2020 2:16 PM, Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
how many subjects are there in your fsgd? How many groups in your fsgd file? Also, you should not use --osgm and --fsgd
On 4/30/2020 1:09 PM, KennethSPrice wrote:
* External Email - Use Caution *
Hello Freesurfer friends!
I'm going through the "paired analysis" tutorial and am running into an issue with the mri_glmfit. I am running on just one subject pair. https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis#Runmriglmfit
I ran mris_preproc on my 2 timepoints and am getting an error at mri_glmfit mris_preproc --target fsaverage --hemi lh \ --meas thickness --out lh.paired-diff.thickness.mgh \ --fsgd pairs.fsgd --paired-diff
mri_glmfit \ --glmdir lh.paired-diff \ --y lh.paired-diff.thickness.sm05.mgh \ --fsgd paired-diff.fsgd \
--osgm \
--surf fsaverage lh
I am getting an ERROR: DOF = 0.
MRI's have been put through recon-all and are in there own directories within SUBJECTS_DIR.
What is the cause of the error?
Thanks,
Ken
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as one of the nation’s top hospitals by /U.S. News & World Report/ (2019-2020). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
is there a way to visualize the changes in thickness, area, and volume between the 2 timepoints (cortical and subcortical)? I was under the impression that running mri_preproc would aloow me to visualize change in cortical thickness bt the 2 timepoints (lh.paired.thickness.mgh).
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‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On Friday, May 1, 2020 12:14 PM, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Oh, right. You only have one data point (the difference) and you are computing one parameter (the mean), so you have 0 DOF. If you only have one data point, there are not statistical tests you can do
On 5/1/2020 3:34 AM, KennethSPrice wrote:
External Email - Use CautionIn the FSGD file I have one subject pair (timepoint 1 and timepoint 2), and it is the only group. However, I removed --fsgd and replaced it with --osgm upon your reccomendation, and am still getting the error.
I am also having an issue visualizing the output of mri_preproc in freeview - isnt this mgh file supposed to be a volume? Is there a way to center the freeview cursor to the middle of the current volume?
Thanks, Ken
‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On Thursday, April 30, 2020 2:16 PM, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
how many subjects are there in your fsgd? How many groups in your fsgd file? Also, you should not use --osgm and --fsgd
On 4/30/2020 1:09 PM, KennethSPrice wrote:
External Email - Use CautionHello Freesurfer friends!
I'm going through the "paired analysis" tutorial and am running into an issue with the mri_glmfit. I am running on just one subject pair. https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis#Runmriglmfit
I ran mris_preproc on my 2 timepoints and am getting an error at mri_glmfit
mris_preproc --target fsaverage --hemi lh \ --meas thickness --out lh.paired-diff.thickness.mgh \ --fsgd pairs.fsgd --paired-diff
mri_glmfit \ --glmdir lh.paired-diff \ --y lh.paired-diff.thickness.sm05.mgh \ --fsgd paired-diff.fsgd \
--osgm \
--surf fsaverage lh
I am getting an ERROR: DOF = 0.
MRI's have been put through recon-all and are in there own directories within SUBJECTS_DIR.
What is the cause of the error?
Thanks,
Ken
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as one of the nation’s top hospitals by U.S. News & World Report (2019-2020). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
For thickness, you can look at the difference (or percent difference). You would use freeview (or tksurferfv, which is a frontend for freeview). When you run mris_preproc, you can specify that you want it to compute the (percent) difference, or you can do it with the multi-frame output of mris_preproc. For subcortical, it is more difficult since you don't get a map out of it (just a single value like total volume of hippocampus).
On 5/11/2020 3:52 PM, KennethSPrice wrote:
External Email - Use Caution
is there a way to visualize the changes in thickness, area, and volume between the 2 timepoints (cortical and subcortical)? I was under the impression that running mri_preproc would aloow me to visualize change in cortical thickness bt the 2 timepoints (lh.paired.thickness.mgh).
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‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On Friday, May 1, 2020 12:14 PM, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Oh, right. You only have one data point (the difference) and you are computing one parameter (the mean), so you have 0 DOF. If you only have one data point, there are not statistical tests you can do
On 5/1/2020 3:34 AM, KennethSPrice wrote:
* External Email - Use Caution *
In the FSGD file I have one subject pair (timepoint 1 and timepoint 2), and it is the only group. However, I removed --fsgd and replaced it with --osgm upon your reccomendation, and am still getting the error.
I am also having an issue visualizing the output of mri_preproc in freeview - isnt this mgh file supposed to be a volume? Is there a way to center the freeview cursor to the middle of the current volume?
Thanks, Ken
‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On Thursday, April 30, 2020 2:16 PM, Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
how many subjects are there in your fsgd? How many groups in your fsgd file? Also, you should not use --osgm and --fsgd
On 4/30/2020 1:09 PM, KennethSPrice wrote:
* External Email - Use Caution *
Hello Freesurfer friends!
I'm going through the "paired analysis" tutorial and am running into an issue with the mri_glmfit. I am running on just one subject pair. https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis#Runmriglmfit
I ran mris_preproc on my 2 timepoints and am getting an error at mri_glmfit mris_preproc --target fsaverage --hemi lh \ --meas thickness --out lh.paired-diff.thickness.mgh \ --fsgd pairs.fsgd --paired-diff
mri_glmfit \ --glmdir lh.paired-diff \ --y lh.paired-diff.thickness.sm05.mgh \ --fsgd paired-diff.fsgd \
--osgm \
--surf fsaverage lh
I am getting an ERROR: DOF = 0.
MRI's have been put through recon-all and are in there own directories within SUBJECTS_DIR.
What is the cause of the error?
Thanks,
Ken
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as one of the nation’s top hospitals by /U.S. News & World Report/ (2019-2020). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
KennethSPrice