Dear FreeSurfer experts
I have come across with this issue as I don't know how visualize the result after mri_glmfit done using --table aparc flag instead of --y. Do I use Matlab to do it? Please give me the instructions briefly as I've just started doing this?
Any help is appreciated! Warmest regards, *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme@gmail.com duy.nguyenbme@gmail.com*
Dear FreeSurfer Experts
One more question I would like to add is how to interpret the output data after running mri_glmfit like beta.mgh, rstd.mgh on Matlab.
Thanks so much for your help Regards,
*--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme@gmail.com duy.nguyenbme@gmail.com*
On Sat, May 13, 2017 at 12:00 AM, Duy Nguyen duy.nguyenbme@gmail.com wrote:
Dear FreeSurfer experts
I have come across with this issue as I don't know how visualize the result after mri_glmfit done using --table aparc flag instead of --y. Do I use Matlab to do it? Please give me the instructions briefly as I've just started doing this?
Any help is appreciated! Warmest regards, *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme@gmail.com duy.nguyenbme@gmail.com*
run mri_glmfit --help for more info
On 5/13/17 2:28 AM, Duy Nguyen wrote:
Dear FreeSurfer Experts
One more question I would like to add is how to interpret the output data after running mri_glmfit like beta.mgh, rstd.mgh on Matlab.
Thanks so much for your help Regards,
*--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme@gmail.com mailto:duy.nguyenbme@gmail.com*
On Sat, May 13, 2017 at 12:00 AM, Duy Nguyen <duy.nguyenbme@gmail.com mailto:duy.nguyenbme@gmail.com> wrote:
Dear FreeSurfer experts I have come across with this issue as I don't know how visualize the result after mri_glmfit done using --table aparc flag instead of --y. Do I use Matlab to do it? Please give me the instructions briefly as I've just started doing this? Any help is appreciated! Warmest regards, *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme@gmail.com <mailto:duy.nguyenbme@gmail.com>*
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you for you quick response Doug
Please instruct me how I can read out the output file beta.mgh to get the values from the mri_glmfit output on FreeSurfer. Thank you for your help and warmest regards,
Duy Nguyen
*--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme@gmail.com duy.nguyenbme@gmail.com*
On Sat, May 13, 2017 at 11:41 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
run mri_glmfit --help for more info
On 5/13/17 2:28 AM, Duy Nguyen wrote:
Dear FreeSurfer Experts
One more question I would like to add is how to interpret the output data after running mri_glmfit like beta.mgh, rstd.mgh on Matlab.
Thanks so much for your help Regards,
*--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme@gmail.com duy.nguyenbme@gmail.com*
On Sat, May 13, 2017 at 12:00 AM, Duy Nguyen duy.nguyenbme@gmail.com wrote:
Dear FreeSurfer experts
I have come across with this issue as I don't know how visualize the result after mri_glmfit done using --table aparc flag instead of --y. Do I use Matlab to do it? Please give me the instructions briefly as I've just started doing this?
Any help is appreciated! Warmest regards, *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme@gmail.com duy.nguyenbme@gmail.com*
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
beta = MRIread('beta.mgh');
beta.vol will have the pixel data
On 05/19/2017 11:04 PM, Duy Nguyen wrote:
Thank you for you quick response Doug
Please instruct me how I can read out the output file beta.mgh to get the values from the mri_glmfit output on FreeSurfer. Thank you for your help and warmest regards,
Duy Nguyen
*--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme@gmail.com mailto:duy.nguyenbme@gmail.com*
On Sat, May 13, 2017 at 11:41 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
run mri_glmfit --help for more info On 5/13/17 2:28 AM, Duy Nguyen wrote:Dear FreeSurfer Experts One more question I would like to add is how to interpret the output data after running mri_glmfit like beta.mgh, rstd.mgh on Matlab. Thanks so much for your help Regards, *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme@gmail.com <mailto:duy.nguyenbme@gmail.com>* On Sat, May 13, 2017 at 12:00 AM, Duy Nguyen <duy.nguyenbme@gmail.com <mailto:duy.nguyenbme@gmail.com>> wrote: Dear FreeSurfer experts I have come across with this issue as I don't know how visualize the result after mri_glmfit done using --table aparc flag instead of --y. Do I use Matlab to do it? Please give me the instructions briefly as I've just started doing this? Any help is appreciated! Warmest regards, *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme@gmail.com <mailto:duy.nguyenbme@gmail.com>* _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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
Dear Doug
From what you instructed me is the data of its voxels on the whole brain?
Because I analyze on the whole brain. I would like to interpret the result by know the result like beta 1's value, beta 2's value and beta N's value from the file beta.mgh for the formula Y = X*b so I can write out the result on my thesis report like one guy got the beta values from the thread: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg17519.html.
"I use the command
mri_glmfit --table lh.volume.txt --fsgd volume.gender.fsgddoss --C gender.diff.mtx --glmdir lh.vol.glmdir to finish regression analysis. and got the beta value ( beta1 = 1.9781e+03, beta2 = 2.0639e+03, beta3 = 110.9220, beta4 = 5.1964e-04 ) from beta.mgh file."
The same question as I want to interpret the sig.mgh which means to know the values.
Please sort me out this issue. I am totally confusing.
Warmest regards, Duy Nguyen
*--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme@gmail.com duy.nguyenbme@gmail.com*
On Mon, May 22, 2017 at 9:56 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
beta = MRIread('beta.mgh');
beta.vol will have the pixel data
On 05/19/2017 11:04 PM, Duy Nguyen wrote:
Thank you for you quick response Doug
Please instruct me how I can read out the output file beta.mgh to get the values from the mri_glmfit output on FreeSurfer. Thank you for your help and warmest regards,
Duy Nguyen
*--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme@gmail.com mailto:duy.nguyenbme@gmail.com*
On Sat, May 13, 2017 at 11:41 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
run mri_glmfit --help for more info On 5/13/17 2:28 AM, Duy Nguyen wrote:Dear FreeSurfer Experts One more question I would like to add is how to interpret the output data after running mri_glmfit like beta.mgh, rstd.mgh on Matlab. Thanks so much for your help Regards, *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme@gmail.com <mailto:duy.nguyenbme@gmail.com>* On Sat, May 13, 2017 at 12:00 AM, Duy Nguyen <duy.nguyenbme@gmail.com <mailto:duy.nguyenbme@gmail.com>> wrote: Dear FreeSurfer experts I have come across with this issue as I don't know how visualize the result after mri_glmfit done using --table aparc flag instead of --y. Do I use Matlab to do it? Please give me the instructions briefly as I've just started doingthis?
Any help is appreciated! Warmest regards, *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme@gmail.com <mailto:duy.nguyenbme@gmail.com
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 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 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
I don't know how he extracted those exact numbers. If I were doing it I would load it into matlab as I said before.
beta = MRIread('beta.mgh'); betamat = fast_vol2mat(beta); Then betamat will be a matrix of Nbetas by Nvoxels. Decide which beta and which voxel you want and print out the volume. (note that FS voxels are 0-based whereas they will be 1-based in matlab)
On 5/26/17 3:18 AM, Duy Nguyen wrote:
Dear Doug
From what you instructed me is the data of its voxels on the whole brain? Because I analyze on the whole brain. I would like to interpret the result by know the result like beta 1's value, beta 2's value and beta N's value from the file beta.mgh for the formula Y = X*b so I can write out the result on my thesis report like one guy got the beta values from the thread: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg17519.html.
"I use the command mri_glmfit --table lh.volume.txt --fsgd volume.gender.fsgd doss --C gender.diff.mtx --glmdir lh.vol.glmdir to finish regression analysis. and got the beta value ( beta1 = 1.9781e+03, beta2 = 2.0639e+03, beta3 = 110.9220, beta4 = 5.1964e-04 ) from beta.mgh file."
The same question as I want to interpret the sig.mgh which means to know the values.
Please sort me out this issue. I am totally confusing.
Warmest regards, Duy Nguyen
*--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme@gmail.com mailto:duy.nguyenbme@gmail.com*
On Mon, May 22, 2017 at 9:56 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
beta = MRIread('beta.mgh'); beta.vol will have the pixel data On 05/19/2017 11:04 PM, Duy Nguyen wrote: > Thank you for you quick response Doug > > Please instruct me how I can read out the output file beta.mgh to get > the values from the mri_glmfit output on FreeSurfer. > Thank you for your help and warmest regards, > > Duy Nguyen > > *--v-- Peace --v--* > *Duy Nguyễn * > *Biomedical Engineering Department- IU HCMC* > *Cell: (+84)909999056* > *Email: duy.nguyenbme@gmail.com <mailto:duy.nguyenbme@gmail.com> <mailto:duy.nguyenbme@gmail.com <mailto:duy.nguyenbme@gmail.com>>* > > On Sat, May 13, 2017 at 11:41 PM, Douglas Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > run mri_glmfit --help for more info > > > On 5/13/17 2:28 AM, Duy Nguyen wrote: >> Dear FreeSurfer Experts >> >> One more question I would like to add is how to interpret the >> output data after running mri_glmfit like beta.mgh, rstd.mgh on >> Matlab. >> >> Thanks so much for your help >> Regards, >> >> >> *--v-- Peace --v--* >> *Duy Nguyễn * >> *Biomedical Engineering Department- IU HCMC* >> *Cell: (+84)909999056* >> *Email: duy.nguyenbme@gmail.com <mailto:duy.nguyenbme@gmail.com> <mailto:duy.nguyenbme@gmail.com <mailto:duy.nguyenbme@gmail.com>>* >> >> On Sat, May 13, 2017 at 12:00 AM, Duy Nguyen >> <duy.nguyenbme@gmail.com <mailto:duy.nguyenbme@gmail.com> <mailto:duy.nguyenbme@gmail.com <mailto:duy.nguyenbme@gmail.com>>> wrote: >> >> Dear FreeSurfer experts >> >> I have come across with this issue as I don't know how >> visualize the result after mri_glmfit done using --table >> aparc flag instead of --y. Do I use Matlab to do it? Please >> give me the instructions briefly as I've just started doing this? >> >> Any help is appreciated! >> Warmest regards, >> *--v-- Peace --v--* >> *Duy Nguyễn * >> *Biomedical Engineering Department- IU HCMC* >> *Cell: (+84)909999056* >> *Email: duy.nguyenbme@gmail.com <mailto:duy.nguyenbme@gmail.com> <mailto:duy.nguyenbme@gmail.com <mailto:duy.nguyenbme@gmail.com>>* >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > _______________________________________________ Freesurfer mailing > list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <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/ <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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
There is a text output table in the glmdir that has the values for each roi
On 5/12/17 1:00 PM, Duy Nguyen wrote:
Dear FreeSurfer experts
I have come across with this issue as I don't know how visualize the result after mri_glmfit done using --table aparc flag instead of --y. Do I use Matlab to do it? Please give me the instructions briefly as I've just started doing this?
Any help is appreciated! Warmest regards, *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme@gmail.com mailto:duy.nguyenbme@gmail.com*
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Douglas N Greve
-
Duy Nguyen