[Freesurfer] Multimodality analysis in FreeSurfer
Dear Freesurfer team, I've scanned a group of subjects and gained structural and myelination data. Then, I've used mris_preproc to map the data onto the surface of fsaverage (and concatenating the data). I would like to investigate the correlation between cortical thickness and myelination by mapping this correlation onto the fsaverage (an one sample group mean analysis) - is this possible? Do you have an existing guide approaching this problem? Thank you! Best, Silas ___ 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.
Re: [Freesurfer] Multimodality analysis in FreeSurfer
I'm not sure what you mean. You say that you have mapped the thickness and myelin data into fsaverage space but then need to map the correlation into fsaverage. Isn't it already there? On 11/17/2015 10:33 AM, Silas wrote: > > Dear Freesurfer team, > > > I've scanned a group of subjects and gained structural and myelination > data. Then, I've used mris_preproc to map the data onto the surface of > fsaverage (and concatenating the data). I would like to investigate > the correlation between cortical thickness and myelination by mapping > this correlation onto the fsaverage (an one sample group mean > analysis) - is this possible? Do you have an existing guide > approaching this problem? > > > Thank you! > > > Best, Silas > > > > ___ > 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.
Re: [Freesurfer] Multimodality analysis in FreeSurfer
I've mapped cortical thickness and the myelination data onto the fsaverage, and also used general linear modelling to investigate the one sample group mean of myelination data og cortical thickness (not very useful since the mean thickness or myelination should never be 0) data separately. I would like to map the correlation between cortical thickness and myelination onto the fsaverage. I've investigated this statistical correlation by a vertex wise correlation study in matlab, and it should be possible to map this onto the fsaverage. Though, I would like to perform this correlation study entirely in FreeSurfer - in this way I would easily be able to correlate for multiple comparisons using the standardized pipeline for FreeSurfer group analysis. Best, Silas From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve Sent: Tuesday, November 17, 2015 7:10 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Multimodality analysis in FreeSurfer I'm not sure what you mean. You say that you have mapped the thickness and myelin data into fsaverage space but then need to map the correlation into fsaverage. Isn't it already there? On 11/17/2015 10:33 AM, Silas wrote: > > Dear Freesurfer team, > > > I've scanned a group of subjects and gained structural and myelination > data. Then, I've used mris_preproc to map the data onto the surface of > fsaverage (and concatenating the data). I would like to investigate > the correlation between cortical thickness and myelination by mapping > this correlation onto the fsaverage (an one sample group mean > analysis) - is this possible? Do you have an existing guide > approaching this problem? > > > Thank you! > > > Best, Silas > > > > ___ > 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Multimodality analysis in FreeSurfer
If I understand you, you want to do a vertex-wise correlation between thickness and myelin. You can do this with a "per vertex regressor", --pvr input to mri_glmfit, something like mri_glmfit --y thickness.mgh --pvr myelin.mgh --surf fsaverage lh --C contrats.mtx --o glmdir with contrast.mtx being 0 1 This will set up a model thickness = offset + beta*myelin and then test whether beta=0 doug On 11/18/2015 02:48 AM, Silas wrote: > I've mapped cortical thickness and the myelination data onto the fsaverage, > and also used general linear modelling to investigate the one sample group > mean of myelination data og cortical thickness (not very useful since the > mean thickness or myelination should never be 0) data separately. > I would like to map the correlation between cortical thickness and > myelination onto the fsaverage. I've investigated this statistical > correlation by a vertex wise correlation study in matlab, and it should be > possible to map this onto the fsaverage. Though, I would like to perform this > correlation study entirely in FreeSurfer - in this way I would easily be able > to correlate for multiple comparisons using the standardized pipeline for > FreeSurfer group analysis. > > Best, Silas > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Douglas N Greve > > Sent: Tuesday, November 17, 2015 7:10 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Multimodality analysis in FreeSurfer > > I'm not sure what you mean. You say that you have mapped the thickness > and myelin data into fsaverage space but then need to map the > correlation into fsaverage. Isn't it already there? > > On 11/17/2015 10:33 AM, Silas wrote: >> Dear Freesurfer team, >> >> >> I've scanned a group of subjects and gained structural and myelination >> data. Then, I've used mris_preproc to map the data onto the surface of >> fsaverage (and concatenating the data). I would like to investigate >> the correlation between cortical thickness and myelination by mapping >> this correlation onto the fsaverage (an one sample group mean >> analysis) - is this possible? Do you have an existing guide >> approaching this problem? >> >> >> Thank you! >> >> >> Best, Silas >> >> >> >> ___ >> 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. > > > ___ > 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
