Re: [Freesurfer] PCA on PET / Thickness in Freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Centergr...@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/filedrop2www.nmr.mgh.harvard.edu/facility/f... Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Re: [Freesurfer] PCA on PET / Thickness in Freesurfer http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50407.html 2016-12-01 http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=date:20161201&o=newest&f=1 Thread http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+PCA+on+PET+%5C%2F+Thickness+in+Freesurfer%22&o=newest&f=1 Foo Keat Mak http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=from:%22Foo+Keat+Mak%22&o=newest&f=1 Hi Doug, I have pasted the correspondences below. My question is, if I want to identify the PCs in a group for a single modality (PET), how should I run the mri_glmfit? A single group design with A contrast of 1 0 (for a nuisance covariate)? Thanks ! Elijah Doug: For within modality, you can add --pca to mri_glmfit (run it with --help to get more info). We do not have ICA tools in FS. On 12/01/2016 02:04 PM, Foo Keat Mak wrote: > Hi Freesurfer Team, > > For a given group, I want to look at the covariance patterns between > thickness and PET. Within Freesurfer, what are some general workflow > tips on how I could go about performing PCA (within modality) or joint > ICA analyses looking at the covariance patterns across modalities? Is > the -pca flag a good starting point? > > Any feedback is appreciated! > > Thanks a lot. > > Best Wishes, > Elijah > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Centergr...@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/filedrop2www.nmr.mgh.harvard.edu/facility/f... Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://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. Sent from my iPad On 1 Dec 2016, at 23:30, Foo Keat Mak > wrote: Thanks Doug. Does that mean that a one group design? With a contrast of 1 0 (adjusting for one variable)? ___ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://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. Re: [Freesurfer] PCA on PET / Thickness in Freesurfer http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50406.html 2016-12-01 http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=date:20161201&o=newest&f=1 Thread http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+PCA+on+PET+%5C%2F+Thickness+in+Freesurfer%22&o=newest&f=1 Douglas N Greve http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=from:%22Douglas+N+Greve%22&o=newest&f=1 sorry, can you repost with previous correspondence? On 12/01/2016 06:30 PM, Foo Keat Mak wrote: > Thanks Doug. Does that mean that a one group design? With a contrast > of 1 0 (adjusting for one variable)? > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Centergr...@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/filedrop2www.nmr.mgh.harvard.edu/facility/f... Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://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. Re: [Freesurfer] PCA on PET / Thickness in Freesurfer http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50405.html 2016-12-01 http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=date:20161201&o=newest&f=1 Thread http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+PCA+on+PET+%5C%2F+Thickness+in+Freesurfer%22&o=newest&f=1 Foo Keat Mak http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=from:%22Foo+Keat+Mak%22&o=newest&f=1 Thanks Doug. Does that mean that a one group design? With a contrast of 1 0 (adjusting for one variable)? ___ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://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. Re: [Freesurfer] PCA on PET / Thickness in Freesurfer http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50396.html 2016-12-01 http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=date:20161201&o=newest&f=1 Thread http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+PCA+on+PET+%5C%2F+Thickness+in+Freesurfer%22&o=newest&f=1 Douglas N Greve http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=from:%22Douglas+N+Greve%22&o=newest&f=1 For within modality, you can add --pca to mri_glmfit (run it with --help to get more info). We do not have ICA tools in FS. On 12/01/2016 02:04 PM, Foo Keat Mak wrote: > Hi Freesurfer Team, > > For a given group, I want to look at the covariance patterns between > thickness and PET. Within Freesurfer, what are some general workflow > tips on how I could go about performing PCA (within modality) or joint > ICA analyses looking at the covariance patterns across modalities? Is > the -pca flag a good starting point? > > Any feedback is appreciated! > > Thanks a lot. > > Best Wishes, > Elijah > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Centergr...@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/filedrop2www.nmr.mgh.harvard.edu/facility/f... Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://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.