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Dear Freesurfer experts,
I would like to transform the task-based surface data to volume. May I know if it is applicable? I tried "mri_surf2vol --o test.nii.gz --subject sub002 --so fs/sub002/surf/lh.white fMRI/sub002/task/001/fmcpr.odd.sm5.fsaverage.lh.nii.gz", but my system frozen. Any suggestions would be appreciated.
Another problem is that in some individuals I found the RAS information of preprocessed surface data of different sessions are not identical, that means the "voxel to ras transform" and "ras to voxel transform" in fmcpr.odd.sm5.fsaverage.lh.nii.gz are different between seesion1 (folder 001) and session2 (folder 002). May I know how this happened and will it influence the final result? Should I keep them the same?
Thanks,
LIzhi
On 4/2/19 4:23 PM, Zhi Li wrote:
External Email - Use Caution
Dear Freesurfer experts,
I would like to transform the task-based surface data to volume. May I know if it is applicable? I tried "mri_surf2vol --o test.nii.gz --subject sub002 --so fs/sub002/surf/lh.white fMRI/sub002/task/001/fmcpr.odd.sm5.fsaverage.lh.nii.gz", but my system frozen. Any suggestions would be appreciated.
You are trying to convert the raw time series data into the anatomical space. The anat space is 256*256*256. If you have many time points, the functional volume in the anatomical space is going to be huge. This would explain why your computer is frozen. Also, the surface fmri data is on subject fsaverage, not on sub002.
Another problem is that in some individuals I found the RAS information of preprocessed surface data of different sessions are not identical, that means the "voxel to ras transform" and "ras to voxel transform" in fmcpr.odd.sm5.fsaverage.lh.nii.gz are different between seesion1 (folder 001) and session2 (folder 002). May I know how this happened and will it influence the final result? Should I keep them the same?
The vox2ras for surface overlay data is not valid, so ignore it.
Thanks,
LIzhi
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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I see and thank you very much. May I know If I could transform the surface-based time series data to volume space, like the space of subcortical data 'fmcpr.odd.sm5.mni305.2mm.nii.gz'? I know I could get the whole brain 3D volume fmri data by changing the subcortical mask in folder 'mri.2mm' to the whole brain mask, but I do not need the part of white matter. See if it is applicable?
Thanks,
Lizhi
On Tue, 2 Apr 2019 at 17:32, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote:
On 4/2/19 4:23 PM, Zhi Li wrote:
External Email - Use CautionDear Freesurfer experts,
I would like to transform the task-based surface data to volume. May I know if it is applicable? I tried "mri_surf2vol --o test.nii.gz --subject sub002 --so fs/sub002/surf/lh.white fMRI/sub002/task/001/fmcpr.odd.sm5.fsaverage.lh.nii.gz", but my system frozen. Any suggestions would be appreciated.
You are trying to convert the raw time series data into the anatomical space. The anat space is 256*256*256. If you have many time points, the functional volume in the anatomical space is going to be huge. This would explain why your computer is frozen. Also, the surface fmri data is on subject fsaverage, not on sub002.
Another problem is that in some individuals I found the RAS information of preprocessed surface data of different sessions are not identical, that means the "voxel to ras transform" and "ras to voxel transform" in fmcpr.odd.sm5.fsaverage.lh.nii.gz are different between seesion1 (folder 001) and session2 (folder 002). May I know how this happened and will it influence the final result? Should I keep them the same?
The vox2ras for surface overlay data is not valid, so ignore it.
Thanks,
LIzhi
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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you mean just subcortical gray matter? You could map the aseg into the functional space with mri_label2vol (run with --help to get docs and examples). Then mri_binarize --i aseg.func.nii.gz --subcort-gm --o subcortgm.mgz, then mask the fmri time series (fmcpr.nii.gz) using mri_mask.
On 4/3/19 10:23 AM, Zhi Li wrote:
External Email - Use Caution
I see and thank you very much. May I know If I could transform the surface-based time series data to volume space, like the space of subcortical data 'fmcpr.odd.sm5.mni305.2mm.nii.gz'? I know I could get the whole brain 3D volume fmri data by changing the subcortical mask in folder 'mri.2mm' to the whole brain mask, but I do not need the part of white matter. See if it is applicable?
Thanks,
Lizhi
On Tue, 2 Apr 2019 at 17:32, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
On 4/2/19 4:23 PM, Zhi Li wrote: > > External Email - Use Caution > > Dear Freesurfer experts, > > I would like to transform the task-based surface data to volume. May I > know if it is applicable? I tried "mri_surf2vol --o test.nii.gz > --subject sub002 --so fs/sub002/surf/lh.white > fMRI/sub002/task/001/fmcpr.odd.sm5.fsaverage.lh.nii.gz", but my system > frozen. Any suggestions would be appreciated. You are trying to convert the raw time series data into the anatomical space. The anat space is 256*256*256. If you have many time points, the functional volume in the anatomical space is going to be huge. This would explain why your computer is frozen. Also, the surface fmri data is on subject fsaverage, not on sub002. > > Another problem is that in some individuals I found the RAS > information of preprocessed surface data of different sessions are not > identical, that means the "voxel to ras transform" and "ras to voxel > transform" in fmcpr.odd.sm5.fsaverage.lh.nii.gz are different between > seesion1 (folder 001) and session2 (folder 002). May I know how this > happened and will it influence the final result? Should I keep them > the same? The vox2ras for surface overlay data is not valid, so ignore it. > > Thanks, > > LIzhi > > > _______________________________________________ > 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
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Sorry for my confusing explanation. I mean cortical grey matter. How could I map the left and right surface fmri data to volume? For example, how to transform the preprocessed left surface data 'fmcpr.odd.sm5.fsaverage.lh.nii.gz' to 3D volume?
Thanks,
Lizhi
On Wed, 3 Apr 2019 at 12:13, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote:
you mean just subcortical gray matter? You could map the aseg into the functional space with mri_label2vol (run with --help to get docs and examples). Then mri_binarize --i aseg.func.nii.gz --subcort-gm --o subcortgm.mgz, then mask the fmri time series (fmcpr.nii.gz) using mri_mask.
On 4/3/19 10:23 AM, Zhi Li wrote:
External Email - Use CautionI see and thank you very much. May I know If I could transform the surface-based time series data to volume space, like the space of subcortical data 'fmcpr.odd.sm5.mni305.2mm.nii.gz'? I know I could get the whole brain 3D volume fmri data by changing the subcortical mask in folder 'mri.2mm' to the whole brain mask, but I do not need the part of white matter. See if it is applicable?
Thanks,
Lizhi
On Tue, 2 Apr 2019 at 17:32, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
On 4/2/19 4:23 PM, Zhi Li wrote: > > External Email - Use Caution > > Dear Freesurfer experts, > > I would like to transform the task-based surface data to volume. May I > know if it is applicable? I tried "mri_surf2vol --o test.nii.gz > --subject sub002 --so fs/sub002/surf/lh.white > fMRI/sub002/task/001/fmcpr.odd.sm5.fsaverage.lh.nii.gz", but my system > frozen. Any suggestions would be appreciated. You are trying to convert the raw time series data into the anatomical space. The anat space is 256*256*256. If you have many time points, the functional volume in the anatomical space is going to be huge. This would explain why your computer is frozen. Also, the surface fmri data is on subject fsaverage, not on sub002. > > Another problem is that in some individuals I found the RAS > information of preprocessed surface data of different sessions are not > identical, that means the "voxel to ras transform" and "ras to voxel > transform" in fmcpr.odd.sm5.fsaverage.lh.nii.gz are different between > seesion1 (folder 001) and session2 (folder 002). May I know how this > happened and will it influence the final result? Should I keep them > the same? The vox2ras for surface overlay data is not valid, so ignore it. > > Thanks, > > LIzhi > > > _______________________________________________ > 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
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Refer to my previous question. I found that 'vlrmerge' could be used to visualize the whole brain activation through mapping the left and right surface to the volume. But the data generated by vlrmerge cannot be used for analyzing. Hence I am wandering if there is a way to sample/map the 2D raw fmri time series to 3D volume?
On Wed, 3 Apr 2019 at 12:26, Zhi Li lizhi.psych@gmail.com wrote:
Sorry for my confusing explanation. I mean cortical grey matter. How could I map the left and right surface fmri data to volume? For example, how to transform the preprocessed left surface data 'fmcpr.odd.sm5.fsaverage.lh.nii.gz' to 3D volume?
Thanks,
Lizhi
On Wed, 3 Apr 2019 at 12:13, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
you mean just subcortical gray matter? You could map the aseg into the functional space with mri_label2vol (run with --help to get docs and examples). Then mri_binarize --i aseg.func.nii.gz --subcort-gm --o subcortgm.mgz, then mask the fmri time series (fmcpr.nii.gz) using mri_mask.
On 4/3/19 10:23 AM, Zhi Li wrote:
External Email - Use CautionI see and thank you very much. May I know If I could transform the surface-based time series data to volume space, like the space of subcortical data 'fmcpr.odd.sm5.mni305.2mm.nii.gz'? I know I could get the whole brain 3D volume fmri data by changing the subcortical mask in folder 'mri.2mm' to the whole brain mask, but I do not need the part of white matter. See if it is applicable?
Thanks,
Lizhi
On Tue, 2 Apr 2019 at 17:32, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
On 4/2/19 4:23 PM, Zhi Li wrote: > > External Email - Use Caution > > Dear Freesurfer experts, > > I would like to transform the task-based surface data to volume. May I > know if it is applicable? I tried "mri_surf2vol --o test.nii.gz > --subject sub002 --so fs/sub002/surf/lh.white > fMRI/sub002/task/001/fmcpr.odd.sm5.fsaverage.lh.nii.gz", but my system > frozen. Any suggestions would be appreciated. You are trying to convert the raw time series data into the anatomical space. The anat space is 256*256*256. If you have many time points, the functional volume in the anatomical space is going to be huge. This would explain why your computer is frozen. Also, the surface fmri data is on subject fsaverage, not on sub002. > > Another problem is that in some individuals I found the RAS > information of preprocessed surface data of different sessions are not > identical, that means the "voxel to ras transform" and "ras to voxel > transform" in fmcpr.odd.sm5.fsaverage.lh.nii.gz are different between > seesion1 (folder 001) and session2 (folder 002). May I know how this > happened and will it influence the final result? Should I keepthem
> the same? The vox2ras for surface overlay data is not valid, so ignore it. > > Thanks, > > LIzhi > > > _______________________________________________ > 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
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why not just map the fmri volume into the anatomical volume (mri_vol2vol)? Why go through the surface at all?
On 4/3/19 12:34 PM, Zhi Li wrote:
External Email - Use Caution
Refer to my previous question. I found that 'vlrmerge' could be used to visualize the whole brain activation through mapping the left and right surface to the volume. But the data generated by vlrmerge cannot be used for analyzing. Hence I am wandering if there is a way to sample/map the 2D raw fmri time series to 3D volume?
On Wed, 3 Apr 2019 at 12:26, Zhi Li <lizhi.psych@gmail.com mailto:lizhi.psych@gmail.com> wrote:
Sorry for my confusing explanation. I mean cortical grey matter. How could I map the left and right surface fmri data to volume? For example, how to transform the preprocessed left surface data 'fmcpr.odd.sm5.fsaverage.lh.nii.gz' to 3D volume? Thanks, Lizhi On Wed, 3 Apr 2019 at 12:13, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote: you mean just subcortical gray matter? You could map the aseg into the functional space with mri_label2vol (run with --help to get docs and examples). Then mri_binarize --i aseg.func.nii.gz --subcort-gm --o subcortgm.mgz, then mask the fmri time series (fmcpr.nii.gz) using mri_mask. On 4/3/19 10:23 AM, Zhi Li wrote: > > External Email - Use Caution > > I see and thank you very much. May I know If I could transform the > surface-based time series data to volume space, like the space of > subcortical data 'fmcpr.odd.sm5.mni305.2mm.nii.gz'? I know I could get > the whole brain 3D volume fmri data by changing the subcortical mask > in folder 'mri.2mm' to the whole brain mask, but I do not need the > part of white matter. See if it is applicable? > > Thanks, > > Lizhi > > On Tue, 2 Apr 2019 at 17:32, Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > > > On 4/2/19 4:23 PM, Zhi Li wrote: > > > > External Email - Use Caution > > > > Dear Freesurfer experts, > > > > I would like to transform the task-based surface data to volume. > May I > > know if it is applicable? I tried "mri_surf2vol --o test.nii.gz > > --subject sub002 --so fs/sub002/surf/lh.white > > fMRI/sub002/task/001/fmcpr.odd.sm5.fsaverage.lh.nii.gz", but my > system > > frozen. Any suggestions would be appreciated. > You are trying to convert the raw time series data into the > anatomical > space. The anat space is 256*256*256. If you have many time > points, the > functional volume in the anatomical space is going to be huge. This > would explain why your computer is frozen. Also, the surface fmri > data > is on subject fsaverage, not on sub002. > > > > Another problem is that in some individuals I found the RAS > > information of preprocessed surface data of different sessions > are not > > identical, that means the "voxel to ras transform" and "ras to > voxel > > transform" in fmcpr.odd.sm5.fsaverage.lh.nii.gz are different > between > > seesion1 (folder 001) and session2 (folder 002). May I know how > this > > happened and will it influence the final result? Should I keep them > > the same? > The vox2ras for surface overlay data is not valid, so ignore it. > > > > Thanks, > > > > LIzhi > > > > > > _______________________________________________ > > 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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I would like to apply dynamic causal modelling analysis to surface based data, and I posted other several related questions before. I am a newbie to FreeSurfer. According to my understanding, the normalization in FSFAST should take the advantages of structural surface normalization when sample the volume fmri data to surface based data. The ROIs for DCM are taken from the HCP parcellation. Hence the data from the surface should be conceptually more accurate than volume in space, right? Given to that the SPM12 cannot analyze the surface fmri data appropriately (although these data could be loaded), I need to calculate the 1st eigenvariate in each ROI by myself. So far I have figured out how to extracted the raw time series, design matrix and beta value from the FSFAST-preprocessed surface data, the only remaining question is how to acquire the whitening matrix. It seems that FSFAST don't save the whitening matrix, hence I want to calculated it with the codes in SPM. That's why I would like to transform the surface data to volume space. Also, it would be better if I know how to derive the whitening matrix from the FSFAST directly. Any suggestions would be much appreciated.
Thanks,
Lizhi
On Wed, 3 Apr 2019 at 12:39, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote:
why not just map the fmri volume into the anatomical volume (mri_vol2vol)? Why go through the surface at all?
On 4/3/19 12:34 PM, Zhi Li wrote:
External Email - Use CautionRefer to my previous question. I found that 'vlrmerge' could be used to visualize the whole brain activation through mapping the left and right surface to the volume. But the data generated by vlrmerge cannot be used for analyzing. Hence I am wandering if there is a way to sample/map the 2D raw fmri time series to 3D volume?
On Wed, 3 Apr 2019 at 12:26, Zhi Li <lizhi.psych@gmail.com mailto:lizhi.psych@gmail.com> wrote:
Sorry for my confusing explanation. I mean cortical grey matter. How could I map the left and right surface fmri data to volume? For example, how to transform the preprocessed left surface data 'fmcpr.odd.sm5.fsaverage.lh.nii.gz' to 3D volume? Thanks, Lizhi On Wed, 3 Apr 2019 at 12:13, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote: you mean just subcortical gray matter? You could map the aseg into the functional space with mri_label2vol (run with --help to get docs and examples). Then mri_binarize --i aseg.func.nii.gz --subcort-gm --o subcortgm.mgz, then mask the fmri time series (fmcpr.nii.gz) using mri_mask. On 4/3/19 10:23 AM, Zhi Li wrote: > > External Email - Use Caution > > I see and thank you very much. May I know If I could transform the > surface-based time series data to volume space, like the space of > subcortical data 'fmcpr.odd.sm5.mni305.2mm.nii.gz'? I know I could get > the whole brain 3D volume fmri data by changing the subcortical mask > in folder 'mri.2mm' to the whole brain mask, but I do not need the > part of white matter. See if it is applicable? > > Thanks, > > Lizhi > > On Tue, 2 Apr 2019 at 17:32, Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > > > On 4/2/19 4:23 PM, Zhi Li wrote: > > > > External Email - Use Caution > > > > Dear Freesurfer experts, > > > > I would like to transform the task-based surface data to volume. > May I > > know if it is applicable? I tried "mri_surf2vol --o test.nii.gz > > --subject sub002 --so fs/sub002/surf/lh.white > > fMRI/sub002/task/001/fmcpr.odd.sm5.fsaverage.lh.nii.gz", but my > system > > frozen. Any suggestions would be appreciated. > You are trying to convert the raw time series data into the > anatomical > space. The anat space is 256*256*256. If you have many time > points, the > functional volume in the anatomical space is going to be huge. This > would explain why your computer is frozen. Also, the surface fmri > data > is on subject fsaverage, not on sub002. > > > > Another problem is that in some individuals I found the RAS > > information of preprocessed surface data of different sessions > are not > > identical, that means the "voxel to ras transform" and "ras to > voxel > > transform" in fmcpr.odd.sm5.fsaverage.lh.nii.gz are different > between > > seesion1 (folder 001) and session2 (folder 002). May I know how > this > > happened and will it influence the final result? Should I keep them > > the same? > The vox2ras for surface overlay data is not valid, so ignore it. > > > > Thanks, > > > > LIzhi > > > > > > _______________________________________________ > > 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. -
Zhi Li