Dear Freesurfers,
I'm doing a longitudinal analysis of cortical thickness using the newest version of Freesurfer and there is something i would like to ask you all.
I have two time points and only one group of patients.
I've finished the pre-processing and am now searching for differences between the two time points using Qdec.
Since i only have one group my cross.qdec.table.dat file looks pretty much like this:
fsid years template_M_b01 0.665 template_M_b02 0.665 template_b03 0.71 template_b04 0.79 template_b05 0.915 template_b07 0.665 template_b09 0.625 template_b10 0.625 template_b11 0.71 template_b13 1.04 template_b14 0.71 template_b15 0.665 template_b16 0.835 template_b17 0.665 template_b18 0.625 template_M_b19 0.71 template_M_b20 0.625 template_b21 0.71 template_b22 0.585
I selected the long.thickness.rate in Qdec interface and years as continuous covariate since it is the only variable that i have in my cross.qdec.table.dat (no groups or other covariates of interest).
My question is: Is this the analysis i should be doing given that i want to know the differences between time point 1 - time point 2?
Many thanks,
Joana
This is actually something that you cannot currently do in QDEC. Try doing a search for "paired" on our wiki for instructions on how to do this type of analysis. doug
Joana Braga Pereira wrote:
Dear Freesurfers,
I'm doing a longitudinal analysis of cortical thickness using the newest version of Freesurfer and there is something i would like to ask you all.
I have two time points and only one group of patients.
I've finished the pre-processing and am now searching for differences between the two time points using Qdec.
Since i only have one group my cross.qdec.table.dat file looks pretty much like this:
fsid years template_M_b01 0.665 template_M_b02 0.665 template_b03 0.71 template_b04 0.79 template_b05 0.915 template_b07 0.665 template_b09 0.625 template_b10 0.625 template_b11 0.71 template_b13 1.04 template_b14 0.71 template_b15 0.665 template_b16 0.835 template_b17 0.665 template_b18 0.625 template_M_b19 0.71 template_M_b20 0.625 template_b21 0.71 template_b22 0.585
I selected the long.thickness.rate in Qdec interface and years as continuous covariate since it is the only variable that i have in my cross.qdec.table.dat (no groups or other covariates of interest).
My question is: Is this the analysis i should be doing given that i want to know the differences between time point 1 - time point 2?
Many thanks,
Joana
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Joana,
actually it is possible, when using long_mris_slopes after running your longitudinal data (I think that is what you did).
I cannot judge if your table is correct. You did create that table from the longitudinal qdec table as described on the wiki (longitudinal tutorial) right? So each line should be a template/base name and in the longitudinal table there should be two entries for each of these templates.
I notice that the years (here the average, so probably the distance in time between your two time points) differs a lot (half a year to a year) between subjects, that is of course not optimal.
You can look at different things:
difference per year (rate) percent change per year with respect to baseline (pc1) or percent change per year with respect to average thickness (spc, called symmetrized percent change as it is symmetric).
If you are interested in the change per year, long_thickness_rate is correct. It accounts for the different time intervals. You can then (in qdec) check if this is measure is different from zero.
So everything you describe looks good.
Best, Martin
On Fri, 2011-09-23 at 11:25 -0400, Douglas N Greve wrote:
This is actually something that you cannot currently do in QDEC. Try doing a search for "paired" on our wiki for instructions on how to do this type of analysis. doug
Joana Braga Pereira wrote:
Dear Freesurfers,
I'm doing a longitudinal analysis of cortical thickness using the newest version of Freesurfer and there is something i would like to ask you all.
I have two time points and only one group of patients.
I've finished the pre-processing and am now searching for differences between the two time points using Qdec.
Since i only have one group my cross.qdec.table.dat file looks pretty much like this:
fsid years template_M_b01 0.665 template_M_b02 0.665 template_b03 0.71 template_b04 0.79 template_b05 0.915 template_b07 0.665 template_b09 0.625 template_b10 0.625 template_b11 0.71 template_b13 1.04 template_b14 0.71 template_b15 0.665 template_b16 0.835 template_b17 0.665 template_b18 0.625 template_M_b19 0.71 template_M_b20 0.625 template_b21 0.71 template_b22 0.585
I selected the long.thickness.rate in Qdec interface and years as continuous covariate since it is the only variable that i have in my cross.qdec.table.dat (no groups or other covariates of interest).
My question is: Is this the analysis i should be doing given that i want to know the differences between time point 1 - time point 2?
Many thanks,
Joana
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Martin,
Many thanks for your reply!
I did follow all the steps as described in the wiki.
I'm not sure i understand your suggestion though..
Are you proposing that, instead of using the cross.qdec.table, i should use the longitudinal table to see the difference between two time points?
My long.qdec.table looks like this:
fsid fsid-base years M_b01_pre template_M_b01 0 M_b01_post template_M_b01 1.33 M_b02_pre template_M_b02 0 M_b02_post template_M_b02 1.33 M_b03_pre template_b03 0 M_b03_post template_b03 1.42 M_b04_pre template_b04 0 M_b04_post template_b04 1.58 M_b05_pre template_b05 0 M_b05_post template_b05 1.83 M_b07_pre template_b07 0 M_b07_post template_b07 1.33 M_b09_pre template_b09 0 M_b09_post template_b09 1.25 M_b10_pre template_b10 0 M_b10_post template_b10 1.25 M_b11_pre template_b11 0 M_b11_post template_b11 1.42 M_b13_pre template_b13 0 M_b13_post template_b13 2.08 M_b14_pre template_b14 0 M_b14_post template_b14 1.42 M_b15_pre template_b15 0 M_b15_post template_b15 1.33 M_b16_pre template_b16 0 M_b16_post template_b16 1.67 M_b17_pre template_b17 0 M_b17_post template_b17 1.33 M_b18_pre template_b18 0 M_b18_post template_b18 1.25 M_b19_pre template_M_b19 0 M_b19_post template_M_b19 1.42 M_b20_pre template_M_b20 0 M_b20_post template_M_b20 1.25 M_b21_pre template_b21 0 M_b21_post template_b21 1.42 M_b22_pre template_b22 0 M_b22_post template_b22 1.17
If i did that, qdec won't find long.thickness-rate...This measure as well as the other longitudinal measures (pc1, spc, etc) can only be found in the surf subfolders of the templates (fsid-base).
What did i miss?
Thanks for your patience,
Joana
2011/9/23 Martin Reuter mreuter@nmr.mgh.harvard.edu
Hi Joana,
actually it is possible, when using long_mris_slopes after running your longitudinal data (I think that is what you did).
I cannot judge if your table is correct. You did create that table from the longitudinal qdec table as described on the wiki (longitudinal tutorial) right? So each line should be a template/base name and in the longitudinal table there should be two entries for each of these templates.
I notice that the years (here the average, so probably the distance in time between your two time points) differs a lot (half a year to a year) between subjects, that is of course not optimal.
You can look at different things:
difference per year (rate) percent change per year with respect to baseline (pc1) or percent change per year with respect to average thickness (spc, called symmetrized percent change as it is symmetric).
If you are interested in the change per year, long_thickness_rate is correct. It accounts for the different time intervals. You can then (in qdec) check if this is measure is different from zero.
So everything you describe looks good.
Best, Martin
On Fri, 2011-09-23 at 11:25 -0400, Douglas N Greve wrote:
This is actually something that you cannot currently do in QDEC. Try doing a search for "paired" on our wiki for instructions on how to do this type of analysis. doug
Joana Braga Pereira wrote:
Dear Freesurfers,
I'm doing a longitudinal analysis of cortical thickness using the newest version of Freesurfer and there is something i would like to ask you all.
I have two time points and only one group of patients.
I've finished the pre-processing and am now searching for differences between the two time points using Qdec.
Since i only have one group my cross.qdec.table.dat file looks pretty much like this:
fsid years template_M_b01 0.665 template_M_b02 0.665 template_b03 0.71 template_b04 0.79 template_b05 0.915 template_b07 0.665 template_b09 0.625 template_b10 0.625 template_b11 0.71 template_b13 1.04 template_b14 0.71 template_b15 0.665 template_b16 0.835 template_b17 0.665 template_b18 0.625 template_M_b19 0.71 template_M_b20 0.625 template_b21 0.71 template_b22 0.585
I selected the long.thickness.rate in Qdec interface and years as continuous covariate since it is the only variable that i have in my cross.qdec.table.dat (no groups or other covariates of interest).
My question is: Is this the analysis i should be doing given that i want to know the differences between time point 1 - time point 2?
Many thanks,
Joana
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Joana,
no, what you did is fine. I just wanted to make sure that you are using the cross table created from the long table (so that there is only a single entry for each subject). It looks like that is the case.
Best, Martin
On Tue, 2011-09-27 at 12:11 +0200, Joana Braga Pereira wrote:
Hi Martin,
Many thanks for your reply!
I did follow all the steps as described in the wiki.
I'm not sure i understand your suggestion though..
Are you proposing that, instead of using the cross.qdec.table, i should use the longitudinal table to see the difference between two time points?
My long.qdec.table looks like this:
fsid fsid-base years M_b01_pre template_M_b01 0 M_b01_post template_M_b01 1.33 M_b02_pre template_M_b02 0 M_b02_post template_M_b02 1.33 M_b03_pre template_b03 0 M_b03_post template_b03 1.42 M_b04_pre template_b04 0 M_b04_post template_b04 1.58 M_b05_pre template_b05 0 M_b05_post template_b05 1.83 M_b07_pre template_b07 0 M_b07_post template_b07 1.33 M_b09_pre template_b09 0 M_b09_post template_b09 1.25 M_b10_pre template_b10 0 M_b10_post template_b10 1.25 M_b11_pre template_b11 0 M_b11_post template_b11 1.42 M_b13_pre template_b13 0 M_b13_post template_b13 2.08 M_b14_pre template_b14 0 M_b14_post template_b14 1.42 M_b15_pre template_b15 0 M_b15_post template_b15 1.33 M_b16_pre template_b16 0 M_b16_post template_b16 1.67 M_b17_pre template_b17 0 M_b17_post template_b17 1.33 M_b18_pre template_b18 0 M_b18_post template_b18 1.25 M_b19_pre template_M_b19 0 M_b19_post template_M_b19 1.42 M_b20_pre template_M_b20 0 M_b20_post template_M_b20 1.25 M_b21_pre template_b21 0 M_b21_post template_b21 1.42 M_b22_pre template_b22 0 M_b22_post template_b22 1.17
If i did that, qdec won't find long.thickness-rate...This measure as well as the other longitudinal measures (pc1, spc, etc) can only be found in the surf subfolders of the templates (fsid-base).
What did i miss?
Thanks for your patience,
Joana
2011/9/23 Martin Reuter mreuter@nmr.mgh.harvard.edu Hi Joana,
actually it is possible, when using long_mris_slopes after running your longitudinal data (I think that is what you did). I cannot judge if your table is correct. You did create that table from the longitudinal qdec table as described on the wiki (longitudinal tutorial) right? So each line should be a template/base name and in the longitudinal table there should be two entries for each of these templates. I notice that the years (here the average, so probably the distance in time between your two time points) differs a lot (half a year to a year) between subjects, that is of course not optimal. You can look at different things: difference per year (rate) percent change per year with respect to baseline (pc1) or percent change per year with respect to average thickness (spc, called symmetrized percent change as it is symmetric). If you are interested in the change per year, long_thickness_rate is correct. It accounts for the different time intervals. You can then (in qdec) check if this is measure is different from zero. So everything you describe looks good. Best, Martin On Fri, 2011-09-23 at 11:25 -0400, Douglas N Greve wrote: > This is actually something that you cannot currently do in QDEC. Try > doing a search for "paired" on our wiki for instructions on how to do > this type of analysis. > doug > > Joana Braga Pereira wrote: > > Dear Freesurfers, > > > > I'm doing a longitudinal analysis of cortical thickness using the > > newest version of Freesurfer and there is something i would like to > > ask you all. > > > > I have two time points and only one group of patients. > > > > I've finished the pre-processing and am now searching for differences > > between the two time points using Qdec. > > > > Since i only have one group my cross.qdec.table.dat file looks pretty > > much like this: > > > > fsid years > > template_M_b01 0.665 > > template_M_b02 0.665 > > template_b03 0.71 > > template_b04 0.79 > > template_b05 0.915 > > template_b07 0.665 > > template_b09 0.625 > > template_b10 0.625 > > template_b11 0.71 > > template_b13 1.04 > > template_b14 0.71 > > template_b15 0.665 > > template_b16 0.835 > > template_b17 0.665 > > template_b18 0.625 > > template_M_b19 0.71 > > template_M_b20 0.625 > > template_b21 0.71 > > template_b22 0.585 > > > > I selected the long.thickness.rate in Qdec interface and years as > > continuous covariate since it is the only variable that i have in > > my cross.qdec.table.dat (no groups or other covariates of interest). > > > > My question is: Is this the analysis i should be doing given that i > > want to know the differences between time point 1 - time point 2? > > > > Many thanks, > > > > Joana > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > 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
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Douglas N Greve -
Joana Braga Pereira -
Martin Reuter