Hi Doug, Thanks. It works! What does each vertex represent in V.mgh? http://imgur.com/W1RZdKn
Here are the results from the stats. Then, I would like to extract the 1st component and convert it into label for mri_segstats. How may I do that? 1 105131.57 105131.57 73.79 73.79 2 9130.61 114262.18 6.41 80.20 3 8052.58 122314.77 5.65 85.85 4 5480.79 127795.56 3.85 89.69 5 4398.33 132193.89 3.09 92.78 6 3504.02 135697.91 2.46 95.24 7 2386.62 138084.53 1.68 96.92 8 2055.74 140140.27 1.44 98.36 9 1603.79 141744.06 1.13 99.48 10 734.89 142478.95 0.52 100.00 11 0.00 142478.95 0.00 100.00 Thanks. Best Wishes, Elijah Re: [Freesurfer] PCA on PET / Thickness in Freesurfer <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50417.html> 2016-12-02 <http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=date:20161202&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> You can run it like that or with --osgm (instead of --fsgd and --C), osgm = one sample group mean. On 12/01/2016 07:13 PM, Foo Keat Mak wrote: > 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 Center gr...@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 > > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > ___ 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. > > > 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 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/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing listfreesur...@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/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing listfreesur...@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 listfreesur...@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/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing listfreesur...@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 listfreesur...@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/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing listfreesur...@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.
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