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mri_glmfit --y lh.t1t2ratio_12CMT_fmed_3sm_decurv.fsavg.mgh --fsgd age_dexterity.fsgd --surf fsaverage lh --C contrast.mtx --o lh_NHPT_T1T2_12CMT_allbrain
Il giorno gio 11 apr 2019 alle ore 21:58 Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> ha scritto:
what is your command line?
On 4/11/19 3:53 PM, TMS lab wrote:
External Email - Use CautionUnfortunately I get such error message with the matrix 0 0 0 1 ERROR: dimension mismatch between X and contrast contrast.mtx X has 3 cols, C has 4 cols
Instead if I use 0 0 1, it works
Best, RAFAEL That should have failed because it only has 3 values (should have 4). I think it should be 0 0 0 1
On 4/11/19 3:20 AM, TMS lab wrote:
External Email - Use CautionYou are right. I want simply to correlate myelin and nhpt regressing out age. I did it with the following matrix: 0 0 1 And it seems to work. Is it ok this matrix?
Thanks a lot Rafael
Il giorno gio 11 apr 2019 alle 00:22 Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu>> ha scritto:
That will compute the average of the Age slope and the NHPT slope.Probably not what you want to do
On 4/6/19 12:24 PM, TMS lab wrote: > > External Email - Use Caution > > Dear Freesurfer team, > > I'm running a correlation analysis where I'd like to corelate > myelination and a clinical parameter (NHPT) regressing out theeffect > of age. > > My contrast.mtx: 0 0 0.5 0.5 > > This is my FSGD FILE: > GroupDescriptorFile 1 > Title Myelin > Class Main > Variables Age NHPT > Inputfs_CGaMain 19 18.2 > ....... > > Is the matrix ok? > > Thanks > Rafael > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu
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Il giorno gio 11 apr 2019 alle ore 09:20 TMS lab <tmslabna@gmail.com mailto:tmslabna@gmail.com> ha scritto:
You are right. I want simply to correlate myelin and nhpt regressing out age. I did it with the following matrix: 0 0 1 And it seems to work. Is it ok this matrix? Thanks a lot Rafael Il giorno gio 11 apr 2019 alle 00:22 Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> ha scritto: That will compute the average of the Age slope and the NHPT slope. Probably not what you want to do On 4/6/19 12:24 PM, TMS lab wrote: > > External Email - Use Caution > > Dear Freesurfer team, > > I'm running a correlation analysis where I'd like to corelate > myelination and a clinical parameter (NHPT) regressing out the effect > of age. > > My contrast.mtx: 0 0 0.5 0.5 > > This is my FSGD FILE: > GroupDescriptorFile 1 > Title Myelin > Class Main > Variables Age NHPT > Inputfs_CGaMain 19 18.2 > ....... > > Is the matrix ok? > > Thanks > Rafael > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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
can you send your fsgd file and your contrast.mtx file?
On 4/17/19 4:12 PM, TMS lab wrote:
External Email - Use Caution
mri_glmfit --y lh.t1t2ratio_12CMT_fmed_3sm_decurv.fsavg.mgh --fsgd age_dexterity.fsgd --surf fsaverage lh --C contrast.mtx --o lh_NHPT_T1T2_12CMT_allbrain
Il giorno gio 11 apr 2019 alle ore 21:58 Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> ha scritto:
what is your command line? On 4/11/19 3:53 PM, TMS lab wrote: > > External Email - Use Caution > > Unfortunately I get such error message with the matrix 0 0 0 1 > ERROR: dimension mismatch between X and contrast contrast.mtx X has > 3 cols, C has 4 cols > > Instead if I use 0 0 1, it works > > Best, > RAFAEL > That should have failed because it only has 3 values (should have 4). I > think it should be 0 0 0 1 > > > On 4/11/19 3:20 AM, TMS lab wrote: > > > > External Email - Use Caution > > > > You are right. I want simply to correlate myelin and nhpt regressing > > out age. > > I did it with the following matrix: > > 0 0 1 > > And it seems to work. Is it ok this matrix? > > > > Thanks a lot > > Rafael > > > > Il giorno gio 11 apr 2019 alle 00:22 Greve, Douglas N.,Ph.D. > > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> ha scritto: > > > > That will compute the average of the Age slope and the NHPT slope. > > Probably not what you want to do > > > > On 4/6/19 12:24 PM, TMS lab wrote: > > > > > > External Email - Use Caution > > > > > > Dear Freesurfer team, > > > > > > I'm running a correlation analysis where I'd like to corelate > > > myelination and a clinical parameter (NHPT) regressing out the > > effect > > > of age. > > > > > > My contrast.mtx: 0 0 0.5 0.5 > > > > > > This is my FSGD FILE: > > > GroupDescriptorFile 1 > > > Title Myelin > > > Class Main > > > Variables Age NHPT > > > Inputfs_CGaMain 19 18.2 > > > ....... > > > > > > Is the matrix ok? > > > > > > Thanks > > > Rafael > > > > > > _______________________________________________ > > > 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>> > > <mailto: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 > > > > > > _______________________________________________ > > 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>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > RispondiRispondi a tuttiInoltra > > > > > > > Il giorno gio 11 apr 2019 alle ore 09:20 TMS lab <tmslabna@gmail.com <mailto:tmslabna@gmail.com> > <mailto:tmslabna@gmail.com <mailto:tmslabna@gmail.com>>> ha scritto: > > You are right. I want simply to correlate myelin and nhpt > regressing out age. > I did it with the following matrix: > 0 0 1 > And it seems to work. Is it ok this matrix? > > Thanks a lot > Rafael > > Il giorno gio 11 apr 2019 alle 00:22 Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> ha scritto: > > That will compute the average of the Age slope and the NHPT > slope. > Probably not what you want to do > > On 4/6/19 12:24 PM, TMS lab wrote: > > > > External Email - Use Caution > > > > Dear Freesurfer team, > > > > I'm running a correlation analysis where I'd like to corelate > > myelination and a clinical parameter (NHPT) regressing out > the effect > > of age. > > > > My contrast.mtx: 0 0 0.5 0.5 > > > > This is my FSGD FILE: > > GroupDescriptorFile 1 > > Title Myelin > > Class Main > > Variables Age NHPT > > Inputfs_CGaMain 19 18.2 > > ....... > > > > Is the matrix ok? > > > > Thanks > > Rafael > > > > _______________________________________________ > > 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 > > > _______________________________________________ > 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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > 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
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External Email - Use Caution
There you go. The contrast.mtx gives me the error ERROR: dimension mismatch between X and contrast contrast.mtx X has 3 cols, C has 4 cols
Il giorno mer 17 apr 2019 alle ore 22:12 TMS lab tmslabna@gmail.com ha scritto:
mri_glmfit --y lh.t1t2ratio_12CMT_fmed_3sm_decurv.fsavg.mgh --fsgd age_dexterity.fsgd --surf fsaverage lh --C contrast.mtx --o lh_NHPT_T1T2_12CMT_allbrain
Il giorno gio 11 apr 2019 alle ore 21:58 Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> ha scritto:
what is your command line?
On 4/11/19 3:53 PM, TMS lab wrote:
External Email - Use CautionUnfortunately I get such error message with the matrix 0 0 0 1 ERROR: dimension mismatch between X and contrast contrast.mtx X has 3 cols, C has 4 cols
Instead if I use 0 0 1, it works
Best, RAFAEL That should have failed because it only has 3 values (should have 4). I think it should be 0 0 0 1
On 4/11/19 3:20 AM, TMS lab wrote:
External Email - Use CautionYou are right. I want simply to correlate myelin and nhpt regressing out age. I did it with the following matrix: 0 0 1 And it seems to work. Is it ok this matrix?
Thanks a lot Rafael
Il giorno gio 11 apr 2019 alle 00:22 Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu>> ha scritto:
That will compute the average of the Age slope and the NHPT slope.Probably not what you want to do
On 4/6/19 12:24 PM, TMS lab wrote: > > External Email - Use Caution > > Dear Freesurfer team, > > I'm running a correlation analysis where I'd like to corelate > myelination and a clinical parameter (NHPT) regressing out theeffect > of age. > > My contrast.mtx: 0 0 0.5 0.5 > > This is my FSGD FILE: > GroupDescriptorFile 1 > Title Myelin > Class Main > Variables Age NHPT > Inputfs_CGaMain 19 18.2 > ....... > > Is the matrix ok? > > Thanks > Rafael > > _______________________________________________ > 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu>
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Il giorno gio 11 apr 2019 alle ore 09:20 TMS lab <tmslabna@gmail.com mailto:tmslabna@gmail.com> ha scritto:
You are right. I want simply to correlate myelin and nhpt regressing out age. I did it with the following matrix: 0 0 1 And it seems to work. Is it ok this matrix? Thanks a lot Rafael Il giorno gio 11 apr 2019 alle 00:22 Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> hascritto:
That will compute the average of the Age slope and the NHPT slope. Probably not what you want to do On 4/6/19 12:24 PM, TMS lab wrote: > > External Email - Use Caution > > Dear Freesurfer team, > > I'm running a correlation analysis where I'd like to corelate > myelination and a clinical parameter (NHPT) regressing out the effect > of age. > > My contrast.mtx: 0 0 0.5 0.5 > > This is my FSGD FILE: > GroupDescriptorFile 1 > Title Myelin > Class Main > Variables Age NHPT > Inputfs_CGaMain 19 18.2 > ....... > > Is the matrix ok? > > Thanks > Rafael > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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
In this case, there is only one class and two continuous variables, so there will be only 3 regressors, so your contrast matrix should only have 3 items. try 0 0 1
On 4/17/19 5:17 PM, TMS lab wrote:
External Email - Use Caution
There you go. The contrast.mtx gives me the error ERROR: dimension mismatch between X and contrast contrast.mtx X has 3 cols, C has 4 cols
Il giorno mer 17 apr 2019 alle ore 22:12 TMS lab <tmslabna@gmail.com mailto:tmslabna@gmail.com> ha scritto:
mri_glmfit --y lh.t1t2ratio_12CMT_fmed_3sm_decurv.fsavg.mgh --fsgd age_dexterity.fsgd --surf fsaverage lh --C contrast.mtx --o lh_NHPT_T1T2_12CMT_allbrain Il giorno gio 11 apr 2019 alle ore 21:58 Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> ha scritto: what is your command line? On 4/11/19 3:53 PM, TMS lab wrote: > > External Email - Use Caution > > Unfortunately I get such error message with the matrix 0 0 0 1 > ERROR: dimension mismatch between X and contrast contrast.mtx X has > 3 cols, C has 4 cols > > Instead if I use 0 0 1, it works > > Best, > RAFAEL > That should have failed because it only has 3 values (should have 4). I > think it should be 0 0 0 1 > > > On 4/11/19 3:20 AM, TMS lab wrote: > > > > External Email - Use Caution > > > > You are right. I want simply to correlate myelin and nhpt regressing > > out age. > > I did it with the following matrix: > > 0 0 1 > > And it seems to work. Is it ok this matrix? > > > > Thanks a lot > > Rafael > > > > Il giorno gio 11 apr 2019 alle 00:22 Greve, Douglas N.,Ph.D. > > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> ha scritto: > > > > That will compute the average of the Age slope and the NHPT slope. > > Probably not what you want to do > > > > On 4/6/19 12:24 PM, TMS lab wrote: > > > > > > External Email - Use Caution > > > > > > Dear Freesurfer team, > > > > > > I'm running a correlation analysis where I'd like to corelate > > > myelination and a clinical parameter (NHPT) regressing out the > > effect > > > of age. > > > > > > My contrast.mtx: 0 0 0.5 0.5 > > > > > > This is my FSGD FILE: > > > GroupDescriptorFile 1 > > > Title Myelin > > > Class Main > > > Variables Age NHPT > > > Inputfs_CGaMain 19 18.2 > > > ....... > > > > > > Is the matrix ok? > > > > > > Thanks > > > Rafael > > > > > > _______________________________________________ > > > 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>> > > <mailto: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 > > > > > > _______________________________________________ > > 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>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > RispondiRispondi a tuttiInoltra > > > > > > > Il giorno gio 11 apr 2019 alle ore 09:20 TMS lab <tmslabna@gmail.com <mailto:tmslabna@gmail.com> > <mailto:tmslabna@gmail.com <mailto:tmslabna@gmail.com>>> ha scritto: > > You are right. I want simply to correlate myelin and nhpt > regressing out age. > I did it with the following matrix: > 0 0 1 > And it seems to work. Is it ok this matrix? > > Thanks a lot > Rafael > > Il giorno gio 11 apr 2019 alle 00:22 Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> ha scritto: > > That will compute the average of the Age slope and the NHPT > slope. > Probably not what you want to do > > On 4/6/19 12:24 PM, TMS lab wrote: > > > > External Email - Use Caution > > > > Dear Freesurfer team, > > > > I'm running a correlation analysis where I'd like to corelate > > myelination and a clinical parameter (NHPT) regressing out > the effect > > of age. > > > > My contrast.mtx: 0 0 0.5 0.5 > > > > This is my FSGD FILE: > > GroupDescriptorFile 1 > > Title Myelin > > Class Main > > Variables Age NHPT > > Inputfs_CGaMain 19 18.2 > > ....... > > > > Is the matrix ok? > > > > Thanks > > Rafael > > > > _______________________________________________ > > 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 > > > _______________________________________________ > 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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > 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
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Greve, Douglas N.,Ph.D. -
TMS lab