[Freesurfer] correlation analysis
External Email - Use Caution Dear FS team, in my analysis I'd like to correlate two variables such as cortical myelination and neurophysiological metrics, regressing-out thickness and age of the subjects. I have only one group. My FSGD file should be: GroupDescriptorFile 1 Title NF_Myelin Class Main Variables NF age Input fs_VF Main 1.57 46 Input fs_RF Main 1.522 Input fs_SE Main 1.09 30 . My intercet2.mtx should be: 1 0 0 0 My slope2.mtx should be: 0 1 0 0 This is my line command: mri_glmfit --y rh.t1t2ratio_20_fmed_3sm_decurv.fsavg.mgh --fsgd T1T2_NF_AGE_HS.fsgd --pvr lh.thickness_20.fsavg.mgh --C intercept2.mtx --C slope2.mtx --surf fsaverage lh --o lh_NF_AGE_T1T2_thickness Is everything ok? Thanks a lot Raf ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] question about curv.mgh
External Email - Use Caution Hello FS team, can you please tell me what is the measurement scale of the curv.mg file? Is it a mean curvature (mm-1) or a gaussian curvature (mm-2)? I got values between 0.02 and -0.08 and it seems they are gaussian curvature. Thanks a lot for your help Best regards Rafael ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] correlation analysis
> 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 -- ___ Raffaele Dubbioso, MD, PhD University Federico II of Naples Department of Neurosciences, Reproductive Sciences and Odontostomatology. Via Sergio Pansini, 5 80131 Napoli, ITALY phone: +39-0817464579 fax: +39-0817462667 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FSGD file
External Email - Use Caution Thanks, but I got the following error message: RROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit.bin --y rh.t1t2ratio_30_fmed_3sm_decurv.fsavg.mgh --fsgd age_gender.fsgd --pvr rh.thickness_30.fsavg.mgh --C group.diff.mtx --surf fsaverage rh --cortex --glmdir rh_allbrain_t1t2_group_thickness_age_gender.glmdir 2. The FSGD file (if using one) 3. And the design matrix above Attempting to diagnose further SumSq: Min=0.00 (col 5), Max=146.140350 (col 3) The scale is much different between columns 5 and 3, you may want to normalize by subtracting the mean and dividing by the standard deviation. Column 5, all values are 0 Column 6, all values are 0 Columns 5 and 6 are the same Il giorno dom 6 gen 2019 alle ore 20:18 Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> ha scritto: > yes, that is the right contrast > > On 1/5/19 7:30 AM, Raffaele Dubbioso wrote: > > External Email - Use Caution > Thanks a lot. > Sorry if I bother you again: > If I want to remove thickness, age and gender as nuisance variables; > My FSGD file should be: > > GroupDescriptorFile 1 > Title Func > Class HC > Class CMT > Variables Age gender > Input fs_VF HC 46 Female > Input fs_RF HC 24 Female > ... > > My group.diff.mtx should be: > 1 -1 0 0 0 0 0 > > Is it ok? > > Thanks a lot > Raffaele > > Il giorno gio 3 gen 2019 alle ore 20:11 Greve, Douglas N.,Ph.D. < > dgr...@mgh.harvard.edu> ha scritto: > >> The contrast is not correct for your design. Your design matrix will >> have 3 columns, one for HC, one for CMT, and one for >> rh.thickness_30.fsavg.mgh. Ie, it automatcailly interprets PVRs in a >> DOSS kind of way. If you want to test for a difference in >> thickness-meylin slopes between the two groups, you will need to have >> two PVRs, one where the value is the thickness for HC subjects and 0 for >> CMT subjects, the other the reverse, then set your contrast to 0 0 1 -1. >> If you just want to remove thickness as a nuisance, then you can stick >> with what you have and just use a contrast of 1 -1 0 >> >> On 12/25/18 5:05 AM, Raffaele Dubbioso wrote: >> > >> > External Email - Use Caution >> > >> > Dear Freesurfer team, >> > >> > I'm running a group analysis where I'd like to compare myelination >> > between two groups regressing out cortical thickness. >> > Unfortunately I get always the same error message: >> > dimension mismatch between X and contrast group.diff.mtx X has 3 >> > cols, C has 4 cols. Is my group.mtx correct? >> > >> > My command line is: >> > mri_glmfit --y rh.t1t2ratio_30_fmed_3sm_decurv.fsavg.mgh --fsgd >> > thickness.fsgd --pvr rh.thickness_30.fsavg.mgh --C group.diff.mtx --C >> > group-x-thick --Cg1g2.intercept.mts --C g1g2.thick.mtx --surf >> > fsaverage rh --cortex --glmdir rh_allbrain_t1t2_group_thickness.glmdir >> > >> > My group_diff.mtx: 1 -1 0 0 >> > >> > This is my FSGD FILE: >> > GroupDescriptorFile 1 >> > Title Myelin >> > Class HC >> > Class CMT >> > Inputfs_VFHC >> > >> > >> > >> > Thank you very much for your help >> > >> > Best regards, >> > Raffaele >> > >> > ___ >> > 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 > > > > -- > > ___ > Raffaele Dubbioso, MD, PhD > University Federico II of Naples > Department of Neurosciences, Reproductive Sciences > and Odontostomatology. > Via Sergio Pansini, 5 > 80131 Napoli, ITALY > phone: +39-0817464579 > fax: +39-0817462667 > > ___ > Freesurfer mailing > listfreesur...@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 -- ___ Raffaele Dubbioso, MD, PhD University Federico II of Naples Department of Neurosciences, Reproductive Sciences and Odontostomatology. Via Sergio Pansini, 5 80131 Napoli, ITALY phone: +39-0817464579 fax: +39-0817462667 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FSGD file
External Email - Use Caution Thanks a lot. Sorry if I bother you again: If I want to remove thickness, age and gender as nuisance variables; My FSGD file should be: GroupDescriptorFile 1 Title Func Class HC Class CMT Variables Age gender Input fs_VF HC 46 Female Input fs_RF HC 24 Female ... My group.diff.mtx should be: 1 -1 0 0 0 0 0 Is it ok? Thanks a lot Raffaele Il giorno gio 3 gen 2019 alle ore 20:11 Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> ha scritto: > The contrast is not correct for your design. Your design matrix will > have 3 columns, one for HC, one for CMT, and one for > rh.thickness_30.fsavg.mgh. Ie, it automatcailly interprets PVRs in a > DOSS kind of way. If you want to test for a difference in > thickness-meylin slopes between the two groups, you will need to have > two PVRs, one where the value is the thickness for HC subjects and 0 for > CMT subjects, the other the reverse, then set your contrast to 0 0 1 -1. > If you just want to remove thickness as a nuisance, then you can stick > with what you have and just use a contrast of 1 -1 0 > > On 12/25/18 5:05 AM, Raffaele Dubbioso wrote: > > > > External Email - Use Caution > > > > Dear Freesurfer team, > > > > I'm running a group analysis where I'd like to compare myelination > > between two groups regressing out cortical thickness. > > Unfortunately I get always the same error message: > > dimension mismatch between X and contrast group.diff.mtx X has 3 > > cols, C has 4 cols. Is my group.mtx correct? > > > > My command line is: > > mri_glmfit --y rh.t1t2ratio_30_fmed_3sm_decurv.fsavg.mgh --fsgd > > thickness.fsgd --pvr rh.thickness_30.fsavg.mgh --C group.diff.mtx --C > > group-x-thick --Cg1g2.intercept.mts --C g1g2.thick.mtx --surf > > fsaverage rh --cortex --glmdir rh_allbrain_t1t2_group_thickness.glmdir > > > > My group_diff.mtx: 1 -1 0 0 > > > > This is my FSGD FILE: > > GroupDescriptorFile 1 > > Title Myelin > > Class HC > > Class CMT > > Inputfs_VFHC > > > > > > > > Thank you very much for your help > > > > Best regards, > > Raffaele > > > > ___ > > 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 -- ___ Raffaele Dubbioso, MD, PhD University Federico II of Naples Department of Neurosciences, Reproductive Sciences and Odontostomatology. Via Sergio Pansini, 5 80131 Napoli, ITALY phone: +39-0817464579 fax: +39-0817462667 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Fwd: FSGD file
External Email - Use Caution Dear Freesurfer team, I'm running a group analysis where I'd like to compare myelination between two groups regressing out cortical thickness. Unfortunately I get always the same error message: dimension mismatch between X and contrast group.diff.mtx X has 3 cols, C has 4 cols. Is my group.mtx correct? My command line is: mri_glmfit --y rh.t1t2ratio_30_fmed_3sm_decurv.fsavg.mgh --fsgd thickness.fsgd --pvr rh.thickness_30.fsavg.mgh --C group.diff.mtx --C group-x-thick.mtx --Cg1g2.intercept.mtx --C g1g2.thick.mtx --surf fsaverage rh --cortex --glmdir rh_allbrain_t1t2_group_thickness.glmdir My group_diff.mtx: 1 -1 0 0 This is my FSGD FILE: GroupDescriptorFile 1 Title Myelin Class HC Class CMT Input fs_VF HC Thank you very much for your help Best regards, Raffaele ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FSGD file
External Email - Use Caution Dear Freesurfer team, I'm running a group analysis where I'd like to compare myelination between two groups regressing out cortical thickness. Unfortunately I get always the same error message: dimension mismatch between X and contrast group.diff.mtx X has 3 cols, C has 4 cols. Is my group.mtx correct? My command line is: mri_glmfit --y rh.t1t2ratio_30_fmed_3sm_decurv.fsavg.mgh --fsgd thickness.fsgd --pvr rh.thickness_30.fsavg.mgh --C group.diff.mtx --C group-x-thick --Cg1g2.intercept.mts --C g1g2.thick.mtx --surf fsaverage rh --cortex --glmdir rh_allbrain_t1t2_group_thickness.glmdir My group_diff.mtx: 1 -1 0 0 This is my FSGD FILE: GroupDescriptorFile 1 Title Myelin Class HC Class CMT Input fs_VF HC Thank you very much for your help Best regards, Raffaele ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] correlation analysis
External Email - Use Caution Dear Freesurfer team, I'm working on correlation between fMRI data and a clinical score. Since such fMRI data correlate also with cortical thickness, I'd like to regress out this variable (cortical thickness). How can I write my fsgd file and command line mri_glmfit ? Thank you very much for your help Best regards Raffaele Dubbioso -- ___ Raffaele Dubbioso, MD, PhD University Federico II of Naples Department of Neurosciences, Reproductive Sciences and Odontostomatology. Via Sergio Pansini, 5 80131 Napoli, ITALY phone: +39-0817464579 fax: +39-0817462667 ___ 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] label analysis
Dear Freesurfer team, I'm working on structural data analysis using Fressurfer. I have drawn my own labels and now I'd like to get data like thickness, curvature, folding index in the same way that I usually get when I run the aparc.stat function. Can you please help me how to solve this problem? Thanks a lot and looking forward to hearing from you Best regards, Raffaele ___ 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.
