Hi list,
Is there a way to obtain a map that report the "vertex by vertex" correlation between the FC (obtained by FS-FAST) and cortical thickness?
Thanks
Stefano
Yes, use the --pvr option to mri_glmfit (per-voxel regressor). Search through the mail archives for an example on how to use it
On 2/3/18 12:10 PM, stdp82@virgilio.it wrote:
Hi list,
Is there a way to obtain a map that report the "vertex by vertex" correlation between the FC (obtained by FS-FAST) and cortical thickness?
Thanks
Stefano
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I have run:
1)
mris_preproc --fsgd GROUP1.fsgd --target fsaverage --hemi rh --meas thickness --out rh.GROUP1.thickness.00.mgh mri_surf2surf --hemi rh --s fsaverage --sval rh.GROUP1.thickness.00.mgh --fwhm 10 --cortex --tval rh.GROUP1.thickness.10B.mgh
2)
mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --glmdir Age.wls --nii.gz --fsgd g1v1_Age.fsgd --C intercept.mtx --C slope.mtx --pvr rh.GROUP1.thickness.10B.mgh
The command line is correct?
My concern is on the fsgd file.
I have
GroupDescriptorFile 1 Title All Class Main Variables thickness Input ADNI0XX_GROUP1 Main ???? Input ADNI0XY_GROUP1 Main ???? Input ADNI0YX.GROUP1 Main ???? ...
What I should add after Main if I would like to assess the vertex by vertex correlation between FC (between seed and target vertex) and thickness (in the target vertex)?
Should I add the path where is contained rh.thickness.mgh of each subject?
Please give me an help because I did not find these information using --help or mail list.
Thanks
Stefano
Il 3 febbraio 2018 alle 19.55 Douglas Greve greve@nmr.mgh.harvard.edu ha scritto:
Yes, use the --pvr option to mri_glmfit (per-voxel regressor). Search through the mail archives for an example on how to use it
On 2/3/18 12:10 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote:
Hi list, Is there a way to obtain a map that report the "vertex by vertex" correlation between the FC (obtained by FS-FAST) and cortical thickness? Thanks Stefano _______________________________________________ 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 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.
On 2/4/18 10:06 AM, stdp82@virgilio.it wrote:
I have run:
mris_preproc --fsgd GROUP1.fsgd --target fsaverage --hemi rh --meas thickness --out rh.GROUP1.thickness.00.mgh mri_surf2surf --hemi rh --s fsaverage --sval rh.GROUP1.thickness.00.mgh --fwhm 10 --cortex --tval rh.GROUP1.thickness.10B.mgh
looks good
mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --glmdir Age.wls --nii.gz --fsgd g1v1_Age.fsgd --C intercept.mtx --C slope.mtx --pvr rh.GROUP1.thickness.10B.mgh
The command line is correct?
Yes, though I'm not sure about the effect of using --wls and --pvr. I guess it will be ok, I just have not used it.
My concern is on the fsgd file.
I have
GroupDescriptorFile 1 Title All Class Main Variables thickness Input ADNI0XX_GROUP1 Main ???? Input ADNI0XY_GROUP1 Main ???? Input ADNI0YX.GROUP1 Main ???? ...
What I should add after Main if I would like to assess the vertex by vertex correlation between FC (between seed and target vertex) and thickness (in the target vertex)?
Don't represent the PVR in the FSGD file. You only need to include items in the contrast matrix. Eg, for intercept use [1 0] and for slope use [0 1] eventhough you only have a single class.
Should I add the path where is contained rh.thickness.mgh of each subject?
No
Please give me an help because I did not find these information using --help or mail list.
Thanks
Stefano
Il 3 febbraio 2018 alle 19.55 Douglas Greve greve@nmr.mgh.harvard.edu ha scritto:
Yes, use the --pvr option to mri_glmfit (per-voxel regressor). Search through the mail archives for an example on how to use it
On 2/3/18 12:10 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote:
Hi list,
Is there a way to obtain a map that report the "vertex by vertex" correlation between the FC (obtained by FS-FAST) and cortical thickness?
Thanks
Stefano
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
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.
I obtain this error:
mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --glmdir Thickness.wls --nii.gz --fsgd g1v1_thickness.fsgd --C intercept.mtx --C slope.mtx --pvr $SUBJECTS_DIR/rh.MCI.thickness.10B.mgh
Reading source surface /Applications/freesurfer/subjects/fsaverage/surf/rh.white
gdfRead(): reading g1v1_thickness.fsgd
ERROR: fio_FileHasCarriageReturn(): cannot open g1v1_thickness.fsgd
Il 5 febbraio 2018 alle 18.26 Douglas Greve greve@nmr.mgh.harvard.edu ha scritto:
On 2/4/18 10:06 AM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > >I have run: 1) mris_preproc --fsgd GROUP1.fsgd --target fsaverage --hemi rh --meas thickness --out rh.GROUP1.thickness.00.mgh mri_surf2surf --hemi rh --s fsaverage --sval rh.GROUP1.thickness.00.mgh --fwhm 10 --cortex --tval rh.GROUP1.thickness.10B.mgh > looks good> >2) mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --glmdir Age.wls --nii.gz --fsgd g1v1_Age.fsgd --C intercept.mtx --C slope.mtx --pvr rh.GROUP1.thickness.10B.mgh The command line is correct? > Yes, though I'm not sure about the effect of using --wls and --pvr. I guess it will be ok, I just have not used it.> >My concern is on the fsgd file. I have GroupDescriptorFile 1 Title All Class Main Variables thickness Input ADNI0XX_GROUP1 Main ???? Input ADNI0XY_GROUP1 Main ???? Input ADNI0YX.GROUP1 Main ???? ... What I should add after Main if I would like to assess the vertex by vertex correlation between FC (between seed and target vertex) and thickness (in the target vertex)? > Don't represent the PVR in the FSGD file. You only need to include items in the contrast matrix. Eg, for intercept use [1 0] and for slope use [0 1] eventhough you only have a single class.> >Should I add the path where is contained rh.thickness.mgh of each subject? > No> >Please give me an help because I did not find these information using --help or mail list. Thanks Stefano Il 3 febbraio 2018 alle 19.55 Douglas Greve <greve@nmr.mgh.harvard.edu> mailto:greve@nmr.mgh.harvard.edu ha scritto: Yes, use the --pvr option to mri_glmfit (per-voxel regressor). Search through the mail archives for an example on how to use it On 2/3/18 12:10 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > >Hi list, Is there a way to obtain a map that report the "vertex by vertex" correlation between the FC (obtained by FS-FAST) and cortical thickness? Thanks Stefano _______________________________________________ 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 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. > >>
I have resolve the previous error (there was a typo in the fsdg file) but re-running I obtain this error:
Normalized matrix condition is 1
Matrix condition is 1
mghRead(/Applications/freesurfer/subjects/rh.GROUP.thickness.10B.mgh, -1): could not open file
fsgd file is:
GroupDescriptorFile 1 Title All Class Main Input 032_XX Main Input 047_XX Main Input 049_XX Main Input 060_XX Main
and I have two contrast (intercept 1 0; slope 0 1)
command line that runs:
mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --glmdir Thickness.wls --nii.gz --fsgd g1v1_thickness.fsgd --C intercept.mtx --C slope.mtx --pvr $SUBJECTS_DIR/rh.GROUP1.thickness.10B.mgh
Il 5 febbraio 2018 alle 19.36 stdp82@virgilio.it ha scritto:
I obtain this error: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --glmdir Thickness.wls --nii.gz --fsgd g1v1_thickness.fsgd --C intercept.mtx --C slope.mtx --pvr $SUBJECTS_DIR/rh.MCI.thickness.10B.mgh Reading source surface /Applications/freesurfer/subjects/fsaverage/surf/rh.white gdfRead(): reading g1v1_thickness.fsgd ERROR: fio_FileHasCarriageReturn(): cannot open g1v1_thickness.fsgd > > Il 5 febbraio 2018 alle 18.26 Douglas Greve <greve@nmr.mgh.harvard.edu> ha scritto:On 2/4/18 10:06 AM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > >I have run: 1) mris_preproc --fsgd GROUP1.fsgd --target fsaverage --hemi rh --meas thickness --out rh.GROUP1.thickness.00.mgh mri_surf2surf --hemi rh --s fsaverage --sval rh.GROUP1.thickness.00.mgh --fwhm 10 --cortex --tval rh.GROUP1.thickness.10B.mgh > > looks good> > >2) mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --glmdir Age.wls --nii.gz --fsgd g1v1_Age.fsgd --C intercept.mtx --C slope.mtx --pvr rh.GROUP1.thickness.10B.mgh The command line is correct? > > Yes, though I'm not sure about the effect of using --wls and --pvr. I guess it will be ok, I just have not used it.> > >My concern is on the fsgd file. I have GroupDescriptorFile 1 Title All Class Main Variables thickness Input ADNI0XX_GROUP1 Main ???? Input ADNI0XY_GROUP1 Main ???? Input ADNI0YX.GROUP1 Main ???? ... What I should add after Main if I would like to assess the vertex by vertex correlation between FC (between seed and target vertex) and thickness (in the target vertex)? > > Don't represent the PVR in the FSGD file. You only need to include items in the contrast matrix. Eg, for intercept use [1 0] and for slope use [0 1] eventhough you only have a single class.> > >Should I add the path where is contained rh.thickness.mgh of each subject? > > No> > >Please give me an help because I did not find these information using --help or mail list. Thanks Stefano Il 3 febbraio 2018 alle 19.55 Douglas Greve <greve@nmr.mgh.harvard.edu> mailto:greve@nmr.mgh.harvard.edu ha scritto: Yes, use the --pvr option to mri_glmfit (per-voxel regressor). Search through the mail archives for an example on how to use it On 2/3/18 12:10 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > > >Hi list, Is there a way to obtain a map that report the "vertex by vertex" correlation between the FC (obtained by FS-FAST) and cortical thickness? Thanks Stefano _______________________________________________ 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 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 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@nmr.mgh.harvard.edu
-
Douglas Greve -
stdp82＠virgilio.it