Pedro Rosa
Hi, I have a couple of questions about the mris_preproc: 1) Can I include all subjects in the qdec.table, but afterwards exclude some of them (based on a determined categorial variable) during the statistical analysis? I understood that the script assembles thickness / area data into a single file, but individual data is not changed depending of other subjects’ data (it assembles individual data independently of other subjects into common-space fsaverage). Am I mistaken?
2) In a longitudinal study, should I include the .base. folders in the qdec-long.table (variable 2), or is it the same to include only the .long. folders in the qdec.table (below fsid)?
Thanks a lot, Pedro.
On 01/27/2014 06:03 PM, Pedro Rosa wrote:
Pedro Rosa
Hi, I have a couple of questions about the mris_preproc:
- Can I include all subjects in the qdec.table, but afterwards exclude some of them (based on a determined categorial variable) during the statistical analysis?
I don't think so. This was originally part of the plan but we never got around to implementing it.
I understood that the script assembles thickness / area data into a single file, but individual data is not changed depending of other subjects’ data (it assembles individual data independently of other subjects into common-space fsaverage). Am I mistaken?
No, you are correct
- In a longitudinal study, should I include the .base. folders in the qdec-long.table (variable 2), or is it the same to include only the .long. folders in the qdec.table (below fsid)?
QDEC is not the right tool for doing longitudinal analysis. Use mri_glmfit from the command line instead. doug
Thanks a lot, Pedro. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, 1) So I should generate a .mgh file, which will be the input for the mri_surf2surf script, for each comparison I wish to do? I have three 3 groups (schizophrenia, bipolar disorder and controls), and both schizophrenia and bipolar disorder can be further divided into remission / non-remission subgroups. If I want to compare schizophrenia subgroups to controls, not including bipolar disorder, should I run mris_preproc separately including only schizophrenia subjects and controls?
2) I intent to use de Mass-univariate model from the Linear Mixed Effects (LME) Models Wiki page. I just used the qdec.table to input the subjects list, as suggested in the Wiki. Should I necessarily include -qdec-long (table also with the .base. templates folders) in the mris_preproc or may I use the -qdec instead (including only .long. processing)?
Thanks a lot!
-- Pedro Rosa
On Monday, January 27, 2014 at 9:07 PM, Douglas N Greve wrote:
On 01/27/2014 06:03 PM, Pedro Rosa wrote:
Pedro Rosa
Hi, I have a couple of questions about the mris_preproc:
- Can I include all subjects in the qdec.table, but afterwards exclude some of them (based on a determined categorial variable) during the statistical analysis?
I don't think so. This was originally part of the plan but we never got around to implementing it.
I understood that the script assembles thickness / area data into a single file, but individual data is not changed depending of other subjects’ data (it assembles individual data independently of other subjects into common-space fsaverage). Am I mistaken?
No, you are correct
- In a longitudinal study, should I include the .base. folders in the qdec-long.table (variable 2), or is it the same to include only the .long. folders in the qdec.table (below fsid)?
QDEC is not the right tool for doing longitudinal analysis. Use mri_glmfit from the command line instead. doug
Thanks a lot, Pedro. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu (mailto:greve@nmr.mgh.harvard.edu) Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html (http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html) Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu (mailto: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.
On 01/27/2014 06:28 PM, Pedro Rosa wrote:
Hi,
- So I should generate a .mgh file, which will be the input for the
mri_surf2surf script, for each comparison I wish to do? I have three 3 groups (schizophrenia, bipolar disorder and controls), and both schizophrenia and bipolar disorder can be further divided into remission / non-remission subgroups. If I want to compare schizophrenia subgroups to controls, not including bipolar disorder, should I run mris_preproc separately including only schizophrenia subjects and controls?
Yes
- I intent to use de Mass-univariate model from the Linear Mixed
Effects (LME) Models Wiki page. I just used the qdec.table to input the subjects list, as suggested in the Wiki. Should I necessarily include -qdec-long (table also with the .base. templates folders) in the mris_preproc or may I use the -qdec instead (including only .long. processing)?
I'll leave this one for Martin (or Jorge if he is still tracking this list)
Thanks a lot!
Pedro Rosa
On Monday, January 27, 2014 at 9:07 PM, Douglas N Greve wrote:
On 01/27/2014 06:03 PM, Pedro Rosa wrote:
Pedro Rosa
Hi, I have a couple of questions about the mris_preproc:
- Can I include all subjects in the qdec.table, but afterwards
exclude some of them (based on a determined categorial variable) during the statistical analysis?
I don't think so. This was originally part of the plan but we never got around to implementing it.
I understood that the script assembles thickness / area data into a single file, but individual data is not changed depending of other subjects’ data (it assembles individual data independently of other subjects into common-space fsaverage). Am I mistaken?
No, you are correct
- In a longitudinal study, should I include the .base. folders in
the qdec-long.table (variable 2), or is it the same to include only the .long. folders in the qdec.table (below fsid)?
QDEC is not the right tool for doing longitudinal analysis. Use mri_glmfit from the command line instead. doug
Thanks a lot, Pedro. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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
-
Douglas N Greve -
Pedro Rosa