Dear all,
I am interested in looking at developmental changes in the brain during adolescence period in normal subjects and also comparing our controls to our clinical patients. Examples in the longitudinal processing stream tutorial have only mentioned volume and thickness, so I was wondering if area is also something we could look at and analyze. I successfully generated rate of change, spc, pc2 etc .mgz files in the post processing stage using 'long_mris_slopes' using '--meas area', but I just wanted to make sure if rate of change in surface area using freesurfer longitudinal stream is something we can report in our ms. I haven't found any papers reporting changes in the surface area using fs long stream so I was wondering if this measure is good to go or if it is something that is still work in progress
Cheers, Yoon
Dear Freesurfers,
Is there a way to visualize average absolute symmetrized percent thickness/volume/area change (not significance map) using qdec or tksurfer or other freesurfer tools? I successfully generated correlation significance map using qdec for the longitudinal data we processed, but I am also interested in looking at just simple average across all subjects. Thanks so much!
Cheers, Yoon
Hi Yoon,
I usually run mri_glmfit directly and then look at the gamma map (that is the average if you ran a one sample group mean analysis, which is what you did, I think).
qdec is just a wrapper around glmfit so the file should be there, I am not sure if qdec can visualize it directly? (am not too familiar with that tool). Maybe someone else knows as this is the same for any analysis run via qdec (I cc'ed Nick who probably knows more).
If qdec cannot do it, you can probably find the gamma.mgh file in the glm/constrast subdirectory and then open it with tksurfer.
Best, Martin
On 08/30/2013 02:16 PM, Chung, Yoonho wrote:
Dear Freesurfers,
Is there a way to visualize average absolute symmetrized percent thickness/volume/area change (not significance map) using qdec or tksurfer or other freesurfer tools? I successfully generated correlation significance map using qdec for the longitudinal data we processed, but I am also interested in looking at just simple average across all subjects. Thanks so much!
Cheers, Yoon _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Martin!. I have another quick question.
I am also interested in looking at developmental changes in the brain during adolescence period in normal subjects and also comparing our controls to our clinical cohort. Examples in the longitudinal processing stream tutorial have only mentioned volume and thickness, so I was wondering if area is also something we could include in our analyses. I successfully generated rate of change, spc, pc1 etc .mgz files in the post processing stage using 'long_mris_slopes' using '--meas area', but I just wanted to make sure if rate of change in surface area using freesurfer longitudinal stream and also the corresponding significance maps using tksurfer is something we can report in our manuscript. I haven't found any papers reporting changes in the surface area using fs long stream so I was wondering if this measure is good to go or if it is something that is still work in progress. Thanks for your help!
Cheers, Yoon
On Aug 30, 2013, at 4:14 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edumailto:mreuter@nmr.mgh.harvard.edu> wrote:
Hi Yoon,
I usually run mri_glmfit directly and then look at the gamma map (that is the average if you ran a one sample group mean analysis, which is what you did, I think).
qdec is just a wrapper around glmfit so the file should be there, I am not sure if qdec can visualize it directly? (am not too familiar with that tool). Maybe someone else knows as this is the same for any analysis run via qdec (I cc'ed Nick who probably knows more).
If qdec cannot do it, you can probably find the gamma.mgh file in the glm/constrast subdirectory and then open it with tksurfer.
Best, Martin
On 08/30/2013 02:16 PM, Chung, Yoonho wrote: Dear Freesurfers,
Is there a way to visualize average absolute symmetrized percent thickness/volume/area change (not significance map) using qdec or tksurfer or other freesurfer tools? I successfully generated correlation significance map using qdec for the longitudinal data we processed, but I am also interested in looking at just simple average across all subjects. Thanks so much!
Cheers, Yoon _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edumailto:mreuter@nmr.mgh.harvard.edu reuter@mit.edumailto:reuter@mit.edu Web : http://reuter.mit.edu
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Yoon Yes, you can also analyze area that way.
Best, Martin
On 08/30/2013 04:47 PM, Chung, Yoonho wrote:
Thanks Martin!. I have another quick question. I am also interested in looking at developmental changes in the brain during adolescence period in normal subjects and also comparing our controls to our clinical cohort. Examples in the longitudinal processing stream tutorial have only mentioned volume and thickness, so I was wondering if area is also something we could include in our analyses. I successfully generated rate of change, spc, pc1 etc .mgz files in the post processing stage using 'long_mris_slopes' using '--meas area', but I just wanted to make sure if rate of change in surface area using freesurfer longitudinal stream and also the corresponding significance maps using tksurfer is something we can report in our manuscript. I haven't found any papers reporting changes in the surface area using fs long stream so I was wondering if this measure is good to go or if it is something that is still work in progress. Thanks for your help! Cheers, Yoon
On Aug 30, 2013, at 4:14 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edu mailto:mreuter@nmr.mgh.harvard.edu> wrote:
Hi Yoon,
I usually run mri_glmfit directly and then look at the gamma map (that is the average if you ran a one sample group mean analysis, which is what you did, I think).
qdec is just a wrapper around glmfit so the file should be there, I am not sure if qdec can visualize it directly? (am not too familiar with that tool). Maybe someone else knows as this is the same for any analysis run via qdec (I cc'ed Nick who probably knows more).
If qdec cannot do it, you can probably find the gamma.mgh file in the glm/constrast subdirectory and then open it with tksurfer.
Best, Martin
On 08/30/2013 02:16 PM, Chung, Yoonho wrote:
Dear Freesurfers,
Is there a way to visualize average absolute symmetrized percent thickness/volume/area change (not significance map) using qdec or tksurfer or other freesurfer tools? I successfully generated correlation significance map using qdec for the longitudinal data we processed, but I am also interested in looking at just simple average across all subjects. Thanks so much!
Cheers, Yoon _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu mailto:mreuter@nmr.mgh.harvard.edu reuter@mit.edu mailto:reuter@mit.edu Web : http://reuter.mit.edu
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Chung, Yoonho -
Martin Reuter