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Dear Freesurfer experts.
Now I am using preproc-sess to preprocess functional MRI data. I would like to smooth the data first and then resample them into the standard space. Hence I run 'preproc-sess -s sub001 -fsd func -stc odd -fwhm 0 -per-run' first, and then 'spatialsmooth-sess -s sub001 -fsd func -i fmcpr.odd -o fmcpr.odd.sm5 -fwhm 5', finally 'preproc-sess -s sub001 -fsd func -stc odd -surface fsaverage lhrh -mni305 -fwhm 0 -per-run' (I have already renamed the stem of smoothed file from fmcpr.odd.sm5 to fmcpr.odd). However, the preprocessed data 'fmcpr.odd.sm0.mni305.2mm.nii.gz' contains both cortical and subcortical data. If I use '-fwhm 1' this file only contains the subcortical area. May I know why and how to fix it?
About each stage embedded in 'preproc-sess', if I would like replace one stage with other software/algorithms, can I just change the name of the generated file by other software/algorithms to the name of file in this stage of 'prepoc-sess', and them rerun 'preproc-sess' while keep the flag '-update' on? For example, if I would like to use FSL/SPM to register the functional image to structural data, can I just rename the mat-file which describes the affine registration generated by FSL/SPM to 'register.dof6.mat'?
Looking forward to your kind suggestions.
Thanks and best wishes,
Lizhi
sorry, I'm not sure what you are trying to do. When you say you would like to smooth the data then resample, do you mean smooth on the surface? and do you mean resample to the standard surface or volume space?
On 5/13/2019 11:26 AM, Zhi Li wrote:
External Email - Use Caution
Dear Freesurfer experts.
Now I am using preproc-sess to preprocess functional MRI data. I would like to smooth the data first and then resample them into the standard space. Hence I run 'preproc-sess -s sub001 -fsd func -stc odd -fwhm 0 -per-run' first, and then 'spatialsmooth-sess -s sub001 -fsd func -i fmcpr.odd -o fmcpr.odd.sm5 -fwhm 5', finally 'preproc-sess -s sub001 -fsd func -stc odd -surface fsaverage lhrh -mni305 -fwhm 0 -per-run' (I have already renamed the stem of smoothed file from fmcpr.odd.sm5 to fmcpr.odd). However, the preprocessed data 'fmcpr.odd.sm0.mni305.2mm.nii.gz' contains both cortical and subcortical data. If I use '-fwhm 1' this file only contains the subcortical area. May I know why and how to fix it?
About each stage embedded in 'preproc-sess', if I would like replace one stage with other software/algorithms, can I just change the name of the generated file by other software/algorithms to the name of file in this stage of 'prepoc-sess', and them rerun 'preproc-sess' while keep the flag '-update' on? For example, if I would like to use FSL/SPM to register the functional image to structural data, can I just rename the mat-file which describes the affine registration generated by FSL/SPM to 'register.dof6.mat'?
Looking forward to your kind suggestions.
Thanks and best wishes,
Lizhi
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Sorry for the confusing expression. I mean smooth on the volume before resampling volume to the three standard spaces (left and right surface and subcortical space). Anyway, I think I have figured it out. In the last two steps of 'preproc-sess', the volume data is first resampled to the standard surface with 'mri_vol2surf' and volume space with 'mri_vol2vol', and then smoothed on each space with 'mri_fwhm'. The masks of surface and volume are applied in 'mri_fwhm', not 'mri_vol2surf' nor 'mri_vol2vol'. So if the flag '-fwhm' is set as 0, 'mri_fwhm' will not be initiated and the data will not be masked, that's why I got the whole brain data in the file 'fmcpr.odd.sm0.mni305.2mm.nii.gz', is that correct? If so, may I know the command to mask the volume and surface fMRI data?
Besides, is that correct about the second question? Thank you very much.
Best wishes,
Lizhi
On Tue, 14 May 2019 at 11:29, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
sorry, I'm not sure what you are trying to do. When you say you would like to smooth the data then resample, do you mean smooth on the surface? and do you mean resample to the standard surface or volume space?
On 5/13/2019 11:26 AM, Zhi Li wrote:
External Email - Use CautionDear Freesurfer experts.
Now I am using preproc-sess to preprocess functional MRI data. I would like to smooth the data first and then resample them into the standard space. Hence I run 'preproc-sess -s sub001 -fsd func -stc odd -fwhm 0 -per-run' first, and then 'spatialsmooth-sess -s sub001 -fsd func -i fmcpr.odd -o fmcpr.odd.sm5 -fwhm 5', finally 'preproc-sess -s sub001 -fsd func -stc odd -surface fsaverage lhrh -mni305 -fwhm 0 -per-run' (I have already renamed the stem of smoothed file from fmcpr.odd.sm5 to fmcpr.odd). However, the preprocessed data 'fmcpr.odd.sm0.mni305.2mm.nii.gz' contains both cortical and subcortical data. If I use '-fwhm 1' this file only contains the subcortical area. May I know why and how to fix it?
About each stage embedded in 'preproc-sess', if I would like replace one stage with other software/algorithms, can I just change the name of the generated file by other software/algorithms to the name of file in this stage of 'prepoc-sess', and them rerun 'preproc-sess' while keep the flag '-update' on? For example, if I would like to use FSL/SPM to register the functional image to structural data, can I just rename the mat-file which describes the affine registration generated by FSL/SPM to 'register.dof6.mat'?
Looking forward to your kind suggestions.
Thanks and best wishes,
Lizhi
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Why do you want to smooth in the volume before sampling onto the surface? That would defeat one of the main reasons to sample on the surface (ie, surface-based smoothing instead of volume-based). Volume-based smoothing in the subcortical regions is automatically done when you specify a FWHM in preproc-sess
On 5/14/19 1:02 PM, Zhi Li wrote:
External Email - Use Caution
Sorry for the confusing expression. I mean smooth on the volume before resampling volume to the three standard spaces (left and right surface and subcortical space). Anyway, I think I have figured it out. In the last two steps of 'preproc-sess', the volume data is first resampled to the standard surface with 'mri_vol2surf' and volume space with 'mri_vol2vol', and then smoothed on each space with 'mri_fwhm'. The masks of surface and volume are applied in 'mri_fwhm', not 'mri_vol2surf' nor 'mri_vol2vol'. So if the flag '-fwhm' is set as 0, 'mri_fwhm' will not be initiated and the data will not be masked, that's why I got the whole brain data in the file 'fmcpr.odd.sm0.mni305.2mm.nii.gz', is that correct? If so, may I know the command to mask the volume and surface fMRI data?
Besides, is that correct about the second question? Thank you very much.
Best wishes,
Lizhi
On Tue, 14 May 2019 at 11:29, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
sorry, I'm not sure what you are trying to do. When you say you would like to smooth the data then resample, do you mean smooth on the surface? and do you mean resample to the standard surface or volume space? On 5/13/2019 11:26 AM, Zhi Li wrote:External Email - Use Caution Dear Freesurfer experts. Now I am using preproc-sess to preprocess functional MRI data. I would like to smooth the data first and then resample them into the standard space. Hence I run 'preproc-sess -s sub001 -fsd func -stc odd -fwhm 0 -per-run' first, and then 'spatialsmooth-sess -s sub001 -fsd func -i fmcpr.odd -o fmcpr.odd.sm5 -fwhm 5', finally 'preproc-sess -s sub001 -fsd func -stc odd -surface fsaverage lhrh -mni305 -fwhm 0 -per-run' (I have already renamed the stem of smoothed file from fmcpr.odd.sm5 to fmcpr.odd). However, the preprocessed data 'fmcpr.odd.sm0.mni305.2mm.nii.gz' contains both cortical and subcortical data. If I use '-fwhm 1' this file only contains the subcortical area. May I know why and how to fix it? About each stage embedded in 'preproc-sess', if I would like replace one stage with other software/algorithms, can I just change the name of the generated file by other software/algorithms to the name of file in this stage of 'prepoc-sess', and them rerun 'preproc-sess' while keep the flag '-update' on? For example, if I would like to use FSL/SPM to register the functional image to structural data, can I just rename the mat-file which describes the affine registration generated by FSL/SPM to 'register.dof6.mat'? Looking forward to your kind suggestions. Thanks and best wishes, 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
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Yes. Smoothing in the volume may smooth across sulci and other tissue types. I would like to use ICA-AROMA to denoise the data, especially remove the head motion component. However, this toolbox do not support surface-based data, and according to the suggestions in their study( https://www.ncbi.nlm.nih.gov/pubmed/25770991 ), ICA denoising should be applied after spatial smoothing and prior to temporal filtering. That's why I want to smooth in the volume before resampling, I set the flag '-fwhm' in preproc-sess as 0, hence it should not smooth the data, right?
Best wishes,
Lizhi
On Tue, 14 May 2019 at 13:40, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
Why do you want to smooth in the volume before sampling onto the surface? That would defeat one of the main reasons to sample on the surface (ie, surface-based smoothing instead of volume-based). Volume-based smoothing in the subcortical regions is automatically done when you specify a FWHM in preproc-sess
On 5/14/19 1:02 PM, Zhi Li wrote:
External Email - Use CautionSorry for the confusing expression. I mean smooth on the volume before resampling volume to the three standard spaces (left and right surface and subcortical space). Anyway, I think I have figured it out. In the last two steps of 'preproc-sess', the volume data is first resampled to the standard surface with 'mri_vol2surf' and volume space with 'mri_vol2vol', and then smoothed on each space with 'mri_fwhm'. The masks of surface and volume are applied in 'mri_fwhm', not 'mri_vol2surf' nor 'mri_vol2vol'. So if the flag '-fwhm' is set as 0, 'mri_fwhm' will not be initiated and the data will not be masked, that's why I got the whole brain data in the file 'fmcpr.odd.sm0.mni305.2mm.nii.gz', is that correct? If so, may I know the command to mask the volume and surface fMRI data?
Besides, is that correct about the second question? Thank you very much.
Best wishes,
Lizhi
On Tue, 14 May 2019 at 11:29, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
sorry, I'm not sure what you are trying to do. When you say you would like to smooth the data then resample, do you mean smooth on the surface? and do you mean resample to the standard surface or volume space? On 5/13/2019 11:26 AM, Zhi Li wrote:External Email - Use Caution Dear Freesurfer experts. Now I am using preproc-sess to preprocess functional MRI data. I would like to smooth the data first and then resample them into the standard space. Hence I run 'preproc-sess -s sub001 -fsd func -stc odd -fwhm 0 -per-run' first, and then 'spatialsmooth-sess -s sub001 -fsd func -i fmcpr.odd -o fmcpr.odd.sm5 -fwhm 5', finally 'preproc-sess -s sub001 -fsd func -stc odd -surface fsaverage lhrh -mni305 -fwhm 0 -per-run' (I have already renamed the stem of smoothed file from fmcpr.odd.sm5 to fmcpr.odd). However, the preprocessed data 'fmcpr.odd.sm0.mni305.2mm.nii.gz' contains both cortical and subcortical data. If I use '-fwhm 1' this file only contains the subcortical area. May I know why and how to fix it? About each stage embedded in 'preproc-sess', if I would like replace one stage with other software/algorithms, can I just change the name of the generated file by other software/algorithms to the name of file in this stage of 'prepoc-sess', and them rerun 'preproc-sess' while keep the flag '-update' on? For example, if I would like to use FSL/SPM to register the functional image to structural data, can I just rename the mat-file which describes the affine registration generated by FSL/SPM to 'register.dof6.mat'? Looking forward to your kind suggestions. Thanks and best wishes, Lizhi _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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Right, with -fwhm 0, it will not smooth the data.
On 5/14/19 2:21 PM, Zhi Li wrote:
External Email - Use Caution
Yes. Smoothing in the volume may smooth across sulci and other tissue types. I would like to use ICA-AROMA to denoise the data, especially remove the head motion component. However, this toolbox do not support surface-based data, and according to the suggestions in their study( https://www.ncbi.nlm.nih.gov/pubmed/25770991 ), ICA denoising should be applied after spatial smoothing and prior to temporal filtering. That's why I want to smooth in the volume before resampling, I set the flag '-fwhm' in preproc-sess as 0, hence it should not smooth the data, right?
Best wishes,
Lizhi
On Tue, 14 May 2019 at 13:40, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
Why do you want to smooth in the volume before sampling onto the surface? That would defeat one of the main reasons to sample on the surface (ie, surface-based smoothing instead of volume-based). Volume-based smoothing in the subcortical regions is automatically done when you specify a FWHM in preproc-sess On 5/14/19 1:02 PM, Zhi Li wrote: > > External Email - Use Caution > > Sorry for the confusing expression. I mean smooth on the volume before > resampling volume to the three standard spaces (left and right surface > and subcortical space). Anyway, I think I have figured it out. In the > last two steps of 'preproc-sess', the volume data is first resampled > to the standard surface with 'mri_vol2surf' and volume space with > 'mri_vol2vol', and then smoothed on each space with 'mri_fwhm'. The > masks of surface and volume are applied in 'mri_fwhm', not > 'mri_vol2surf' nor 'mri_vol2vol'. So if the flag '-fwhm' is set as 0, > 'mri_fwhm' will not be initiated and the data will not be masked, > that's why I got the whole brain data in the file > 'fmcpr.odd.sm0.mni305.2mm.nii.gz', is that correct? If so, may I know > the command to mask the volume and surface fMRI data? > > Besides, is that correct about the second question? Thank you very much. > > Best wishes, > > Lizhi > > > On Tue, 14 May 2019 at 11:29, 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: > > sorry, I'm not sure what you are trying to do. When you say you > would like to smooth the data then resample, do you mean smooth on > the surface? and do you mean resample to the standard surface or > volume space? > > On 5/13/2019 11:26 AM, Zhi Li wrote: >> >> External Email - Use Caution >> >> Dear Freesurfer experts. >> >> Now I am using preproc-sess to preprocess functional MRI data. I >> would like to smooth the data first and then resample them into >> the standard space. Hence I run 'preproc-sess -s sub001 -fsd func >> -stc odd -fwhm 0 -per-run' first, and then 'spatialsmooth-sess -s >> sub001 -fsd func -i fmcpr.odd -o fmcpr.odd.sm5 -fwhm 5', finally >> 'preproc-sess -s sub001 -fsd func -stc odd -surface fsaverage >> lhrh -mni305 -fwhm 0 -per-run' (I have already renamed the stem >> of smoothed file from fmcpr.odd.sm5 to fmcpr.odd). However, the >> preprocessed data 'fmcpr.odd.sm0.mni305.2mm.nii.gz' contains both >> cortical and subcortical data. If I use '-fwhm 1' this file only >> contains the subcortical area. May I know why and how to fix it? >> >> About each stage embedded in 'preproc-sess', if I would like >> replace one stage with other software/algorithms, can I just >> change the name of the generated file by other >> software/algorithms to the name of file in this stage of >> 'prepoc-sess', and them rerun 'preproc-sess' while keep the flag >> '-update' on? For example, if I would like to use FSL/SPM to >> register the functional image to structural data, can I just >> rename the mat-file which describes the affine registration >> generated by FSL/SPM to 'register.dof6.mat'? >> >> Looking forward to your kind suggestions. >> >> Thanks and best wishes, >> >> 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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Thanks.
On Wed, 15 May 2019 at 16:42, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
Right, with -fwhm 0, it will not smooth the data.
On 5/14/19 2:21 PM, Zhi Li wrote:
External Email - Use CautionYes. Smoothing in the volume may smooth across sulci and other tissue types. I would like to use ICA-AROMA to denoise the data, especially remove the head motion component. However, this toolbox do not support surface-based data, and according to the suggestions in their study( https://www.ncbi.nlm.nih.gov/pubmed/25770991 ), ICA denoising should be applied after spatial smoothing and prior to temporal filtering. That's why I want to smooth in the volume before resampling, I set the flag '-fwhm' in preproc-sess as 0, hence it should not smooth the data, right?
Best wishes,
Lizhi
On Tue, 14 May 2019 at 13:40, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
Why do you want to smooth in the volume before sampling onto the surface? That would defeat one of the main reasons to sample on the surface (ie, surface-based smoothing instead of volume-based). Volume-based smoothing in the subcortical regions is automatically done when you specify a FWHM in preproc-sess On 5/14/19 1:02 PM, Zhi Li wrote: > > External Email - Use Caution > > Sorry for the confusing expression. I mean smooth on the volume before > resampling volume to the three standard spaces (left and right surface > and subcortical space). Anyway, I think I have figured it out. In the > last two steps of 'preproc-sess', the volume data is first resampled > to the standard surface with 'mri_vol2surf' and volume space with > 'mri_vol2vol', and then smoothed on each space with 'mri_fwhm'. The > masks of surface and volume are applied in 'mri_fwhm', not > 'mri_vol2surf' nor 'mri_vol2vol'. So if the flag '-fwhm' is set as 0, > 'mri_fwhm' will not be initiated and the data will not be masked, > that's why I got the whole brain data in the file > 'fmcpr.odd.sm0.mni305.2mm.nii.gz', is that correct? If so, may I know > the command to mask the volume and surface fMRI data? > > Besides, is that correct about the second question? Thank you very much. > > Best wishes, > > Lizhi > > > On Tue, 14 May 2019 at 11:29, 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: > > sorry, I'm not sure what you are trying to do. When you say you > would like to smooth the data then resample, do you mean smooth on > the surface? and do you mean resample to the standard surfaceor
> volume space? > > On 5/13/2019 11:26 AM, Zhi Li wrote: >> >> External Email - Use Caution >> >> Dear Freesurfer experts. >> >> Now I am using preproc-sess to preprocess functional MRI data. I >> would like to smooth the data first and then resample theminto
>> the standard space. Hence I run 'preproc-sess -s sub001 -fsd func >> -stc odd -fwhm 0 -per-run' first, and then 'spatialsmooth-sess -s >> sub001 -fsd func -i fmcpr.odd -o fmcpr.odd.sm5 -fwhm 5', finally >> 'preproc-sess -s sub001 -fsd func -stc odd -surface fsaverage >> lhrh -mni305 -fwhm 0 -per-run' (I have already renamed thestem
>> of smoothed file from fmcpr.odd.sm5 to fmcpr.odd). However,the
>> preprocessed data 'fmcpr.odd.sm0.mni305.2mm.nii.gz' contains both >> cortical and subcortical data. If I use '-fwhm 1' this file only >> contains the subcortical area. May I know why and how to fix it? >> >> About each stage embedded in 'preproc-sess', if I would like >> replace one stage with other software/algorithms, can I just >> change the name of the generated file by other >> software/algorithms to the name of file in this stage of >> 'prepoc-sess', and them rerun 'preproc-sess' while keep the flag >> '-update' on? For example, if I would like to use FSL/SPM to >> register the functional image to structural data, can I just >> rename the mat-file which describes the affine registration >> generated by FSL/SPM to 'register.dof6.mat'? >> >> Looking forward to your kind suggestions. >> >> Thanks and best wishes, >> >> 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>
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Greve, Douglas N.,Ph.D. -
Zhi Li