External Email - Use Caution
Hi FreeSurfer Experts,
I am trying surface-based analysis of task-fMRI with FS-FAST. However, I would like to apply ICA-based denoising and wavelet-despiking which can be not done with the 'preproc-sess'. I wonder if I can do the preprocessing with other tools before registration with FS anatomical and normalization? If it is available, how can I do it with command line?
Another question is if can I use other template for parcellation during using 'recon-all', such as the template of Human Connectome Project?
Looking forward to your kind reply.
Thank you and best wishes,
Zhi
If you do all the preprocessing yourself, then store the output in the run folder with a certain name, fmri-denoised.nii.gz, then when you run mkanalysis-sess specify -funcstem fmri-denoised and proceed as norm.
On 10/22/2018 04:08 PM, Zhi Li wrote:
External Email - Use Caution
Hi FreeSurfer Experts,
I am trying surface-based analysis of task-fMRI with FS-FAST. However, I would like to apply ICA-based denoising and wavelet-despiking which can be not done with the 'preproc-sess'. I wonder if I can do the preprocessing with other tools before registration with FS anatomical and normalization? If it is available, how can I do it with command line?
Another question is if can I use other template for parcellation during using 'recon-all', such as the template of Human Connectome Project?
Looking forward to your kind reply.
Thank you and best wishes,
Zhi
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thank you. But the fmri-denoised.nii.gz will be a volume-based data, how can I register and normalize it to the surface-based space, as 'preproc-sess' do that will generate the bilateral cortex in surface and subcortical area in volume?
On Mon, 22 Oct 2018 at 17:12, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
If you do all the preprocessing yourself, then store the output in the run folder with a certain name, fmri-denoised.nii.gz, then when you run mkanalysis-sess specify -funcstem fmri-denoised and proceed as norm.
On 10/22/2018 04:08 PM, Zhi Li wrote:
External Email - Use CautionHi FreeSurfer Experts,
I am trying surface-based analysis of task-fMRI with FS-FAST. However, I would like to apply ICA-based denoising and wavelet-despiking which can be not done with the 'preproc-sess'. I wonder if I can do the preprocessing with other tools before registration with FS anatomical and normalization? If it is available, how can I do it with command line?
Another question is if can I use other template for parcellation during using 'recon-all', such as the template of Human Connectome Project?
Looking forward to your kind reply.
Thank you and best wishes,
Zhi
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
Actually, if you just store the denoised data as f.nii.gz, then run preproc-sess it should do ok. It will do motion correction, but it should not really do any thing if MC is already done. Just make sure that the image has a proper baseline so that the registration will work.
On 10/22/18 11:14 PM, Zhi Li wrote:
External Email - Use Caution
Thank you. But the fmri-denoised.nii.gz will be a volume-based data, how can I register and normalize it to the surface-based space, as 'preproc-sess' do that will generate the bilateral cortex in surface and subcortical area in volume?
On Mon, 22 Oct 2018 at 17:12, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: If you do all the preprocessing yourself, then store the output in the run folder with a certain name, fmri-denoised.nii.gz, then when you run mkanalysis-sess specify -funcstem fmri-denoised and proceed as norm.
On 10/22/2018 04:08 PM, Zhi Li wrote:
External Email - Use CautionHi FreeSurfer Experts,
I am trying surface-based analysis of task-fMRI with FS-FAST. However, I would like to apply ICA-based denoising and wavelet-despiking which can be not done with the 'preproc-sess'. I wonder if I can do the preprocessing with other tools before registration with FS anatomical and normalization? If it is available, how can I do it with command line?
Another question is if can I use other template for parcellation during using 'recon-all', such as the template of Human Connectome Project?
Looking forward to your kind reply.
Thank you and best wishes,
Zhi
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
I see. Can I add the flag -nomc to skip motion correction? If I have done the slice timing, realignment and denoising, can I use the following command to do registration, normalization and smoothing?
*preproc-sess -s sess01 -fsd bold -nomc -nostc -surface fsaverage lhrh -mni305 -fwhm 5 -per-run* If I have modified the functional data before I run preproc-sess, will it influence the registration and normalization?
On Tue, 23 Oct 2018 at 00:08, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
Actually, if you just store the denoised data as f.nii.gz, then run preproc-sess it should do ok. It will do motion correction, but it should not really do any thing if MC is already done. Just make sure that the image has a proper baseline so that the registration will work.
On 10/22/18 11:14 PM, Zhi Li wrote:
External Email - Use CautionThank you. But the fmri-denoised.nii.gz will be a volume-based data, how can I register and normalize it to the surface-based space, as 'preproc-sess' do that will generate the bilateral cortex in surface and subcortical area in volume?
On Mon, 22 Oct 2018 at 17:12, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
If you do all the preprocessing yourself, then store the output in the run folder with a certain name, fmri-denoised.nii.gz, then when you run mkanalysis-sess specify -funcstem fmri-denoised and proceed as norm.
On 10/22/2018 04:08 PM, Zhi Li wrote:
External Email - Use CautionHi FreeSurfer Experts,
I am trying surface-based analysis of task-fMRI with FS-FAST. However, I would like to apply ICA-based denoising and wavelet-despiking which can be not done with the 'preproc-sess'. I wonder if I can do the preprocessing with other tools before registration with FS anatomical and normalization? If it is available, how can I do it with command
line?
Another question is if can I use other template for parcellation during using 'recon-all', such as the template of Human Connectome Project?
Looking forward to your kind reply.
Thank you and best wishes,
Zhi
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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Yes. When you run mkanalysis-sess, you may still have to use the -funcstem
On 10/23/18 10:06 AM, Zhi Li wrote:
External Email - Use Caution
I see. Can I add the flag -nomc to skip motion correction? If I have done the slice timing, realignment and denoising, can I use the following command to do registration, normalization and smoothing?
preproc-sess -s sess01 -fsd bold -nomc -nostc -surface fsaverage lhrh -mni305 -fwhm 5 -per-run
If I have modified the functional data before I run preproc-sess, will it influence the registration and normalization?
On Tue, 23 Oct 2018 at 00:08, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: Actually, if you just store the denoised data as f.nii.gz, then run preproc-sess it should do ok. It will do motion correction, but it should not really do any thing if MC is already done. Just make sure that the image has a proper baseline so that the registration will work.
On 10/22/18 11:14 PM, Zhi Li wrote:
External Email - Use Caution
Thank you. But the fmri-denoised.nii.gz will be a volume-based data, how can I register and normalize it to the surface-based space, as 'preproc-sess' do that will generate the bilateral cortex in surface and subcortical area in volume?
On Mon, 22 Oct 2018 at 17:12, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: If you do all the preprocessing yourself, then store the output in the run folder with a certain name, fmri-denoised.nii.gz, then when you run mkanalysis-sess specify -funcstem fmri-denoised and proceed as norm.
On 10/22/2018 04:08 PM, Zhi Li wrote:
External Email - Use CautionHi FreeSurfer Experts,
I am trying surface-based analysis of task-fMRI with FS-FAST. However, I would like to apply ICA-based denoising and wavelet-despiking which can be not done with the 'preproc-sess'. I wonder if I can do the preprocessing with other tools before registration with FS anatomical and normalization? If it is available, how can I do it with command line?
Another question is if can I use other template for parcellation during using 'recon-all', such as the template of Human Connectome Project?
Looking forward to your kind reply.
Thank you and best wishes,
Zhi
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ 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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External Email - Use Caution
Thank you. May I ask what do we use the flag -funcstem for? I found that there are similar flags in preproc-sess, -mcin, -stcin, etc. Sorry I am a beginner of FreeSufer and not clear about some terms such as 'stem' in both preproc-sess and mkanalysis-sess.
On Tue, 23 Oct 2018 at 11:09, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
Yes. When you run mkanalysis-sess, you may still have to use the -funcstem
On 10/23/18 10:06 AM, Zhi Li wrote:
External Email - Use CautionI see. Can I add the flag -nomc to skip motion correction? If I have done the slice timing, realignment and denoising, can I use the following command to do registration, normalization and smoothing?
*preproc-sess -s sess01 -fsd bold -nomc -nostc -surface fsaverage lhrh -mni305 -fwhm 5 -per-run * If I have modified the functional data before I run preproc-sess, will it influence the registration and normalization?
On Tue, 23 Oct 2018 at 00:08, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
Actually, if you just store the denoised data as f.nii.gz, then run preproc-sess it should do ok. It will do motion correction, but it should not really do any thing if MC is already done. Just make sure that the image has a proper baseline so that the registration will work.
On 10/22/18 11:14 PM, Zhi Li wrote:
External Email - Use CautionThank you. But the fmri-denoised.nii.gz will be a volume-based data, how can I register and normalize it to the surface-based space, as 'preproc-sess' do that will generate the bilateral cortex in surface and subcortical area in volume?
On Mon, 22 Oct 2018 at 17:12, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
If you do all the preprocessing yourself, then store the output in the run folder with a certain name, fmri-denoised.nii.gz, then when you run mkanalysis-sess specify -funcstem fmri-denoised and proceed as norm.
On 10/22/2018 04:08 PM, Zhi Li wrote:
External Email - Use CautionHi FreeSurfer Experts,
I am trying surface-based analysis of task-fMRI with FS-FAST. However, I would like to apply ICA-based denoising and wavelet-despiking which can be not done with the 'preproc-sess'. I wonder if I can do the preprocessing with other tools before registration with FS anatomical and normalization? If it is available, how can I do it with command
line?
Another question is if can I use other template for parcellation during using 'recon-all', such as the template of Human Connectome Project?
Looking forward to your kind reply.
Thank you and best wishes,
Zhi
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
Freesurfer mailing listFreesurfer@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
Freesurfer mailing listFreesurfer@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
You specify the input you want selxavg3-sess to use. Otherwise, it will try to look for things that have been preprocessed.
On 10/23/18 12:17 PM, Zhi Li wrote:
External Email - Use Caution
Thank you. May I ask what do we use the flag -funcstem for? I found that there are similar flags in preproc-sess, -mcin, -stcin, etc. Sorry I am a beginner of FreeSufer and not clear about some terms such as 'stem' in both preproc-sess and mkanalysis-sess.
On Tue, 23 Oct 2018 at 11:09, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: Yes. When you run mkanalysis-sess, you may still have to use the -funcstem
On 10/23/18 10:06 AM, Zhi Li wrote:
External Email - Use Caution
I see. Can I add the flag -nomc to skip motion correction? If I have done the slice timing, realignment and denoising, can I use the following command to do registration, normalization and smoothing?
preproc-sess -s sess01 -fsd bold -nomc -nostc -surface fsaverage lhrh -mni305 -fwhm 5 -per-run
If I have modified the functional data before I run preproc-sess, will it influence the registration and normalization?
On Tue, 23 Oct 2018 at 00:08, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: Actually, if you just store the denoised data as f.nii.gz, then run preproc-sess it should do ok. It will do motion correction, but it should not really do any thing if MC is already done. Just make sure that the image has a proper baseline so that the registration will work.
On 10/22/18 11:14 PM, Zhi Li wrote:
External Email - Use Caution
Thank you. But the fmri-denoised.nii.gz will be a volume-based data, how can I register and normalize it to the surface-based space, as 'preproc-sess' do that will generate the bilateral cortex in surface and subcortical area in volume?
On Mon, 22 Oct 2018 at 17:12, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: If you do all the preprocessing yourself, then store the output in the run folder with a certain name, fmri-denoised.nii.gz, then when you run mkanalysis-sess specify -funcstem fmri-denoised and proceed as norm.
On 10/22/2018 04:08 PM, Zhi Li wrote:
External Email - Use CautionHi FreeSurfer Experts,
I am trying surface-based analysis of task-fMRI with FS-FAST. However, I would like to apply ICA-based denoising and wavelet-despiking which can be not done with the 'preproc-sess'. I wonder if I can do the preprocessing with other tools before registration with FS anatomical and normalization? If it is available, how can I do it with command line?
Another question is if can I use other template for parcellation during using 'recon-all', such as the template of Human Connectome Project?
Looking forward to your kind reply.
Thank you and best wishes,
Zhi
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ 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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External Email - Use Caution
I see. Thank you very much. Another question is if I can use other template for parcellation when I use recon-all?
On Tue, 23 Oct 2018 at 13:42, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
You specify the input you want selxavg3-sess to use. Otherwise, it will try to look for things that have been preprocessed.
On 10/23/18 12:17 PM, Zhi Li wrote:
External Email - Use CautionThank you. May I ask what do we use the flag -funcstem for? I found that there are similar flags in preproc-sess, -mcin, -stcin, etc. Sorry I am a beginner of FreeSufer and not clear about some terms such as 'stem' in both preproc-sess and mkanalysis-sess.
On Tue, 23 Oct 2018 at 11:09, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
Yes. When you run mkanalysis-sess, you may still have to use the -funcstem
On 10/23/18 10:06 AM, Zhi Li wrote:
External Email - Use CautionI see. Can I add the flag -nomc to skip motion correction? If I have done the slice timing, realignment and denoising, can I use the following command to do registration, normalization and smoothing?
*preproc-sess -s sess01 -fsd bold -nomc -nostc -surface fsaverage lhrh -mni305 -fwhm 5 -per-run * If I have modified the functional data before I run preproc-sess, will it influence the registration and normalization?
On Tue, 23 Oct 2018 at 00:08, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
Actually, if you just store the denoised data as f.nii.gz, then run preproc-sess it should do ok. It will do motion correction, but it should not really do any thing if MC is already done. Just make sure that the image has a proper baseline so that the registration will work.
On 10/22/18 11:14 PM, Zhi Li wrote:
External Email - Use CautionThank you. But the fmri-denoised.nii.gz will be a volume-based data, how can I register and normalize it to the surface-based space, as 'preproc-sess' do that will generate the bilateral cortex in surface and subcortical area in volume?
On Mon, 22 Oct 2018 at 17:12, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
If you do all the preprocessing yourself, then store the output in the run folder with a certain name, fmri-denoised.nii.gz, then when you run mkanalysis-sess specify -funcstem fmri-denoised and proceed as norm.
On 10/22/2018 04:08 PM, Zhi Li wrote:
External Email - Use CautionHi FreeSurfer Experts,
I am trying surface-based analysis of task-fMRI with FS-FAST.
However,
I would like to apply ICA-based denoising and wavelet-despiking which can be not done with the 'preproc-sess'. I wonder if I can do the preprocessing with other tools before registration with FS anatomical and normalization? If it is available, how can I do it with command
line?
Another question is if can I use other template for parcellation during using 'recon-all', such as the template of Human Connectome Project?
Looking forward to your kind reply.
Thank you and best wishes,
Zhi
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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can you clarify what you mean? We produce two cortical parcellations by default (one from Christophe Destrieux and one from Rahul Desikan). What kind of parcellation would you want? Note that the parcellation is not done by propagating a template to the individual. Rather we extract an array of statistics from a manually labeled training set and use them to parcellate new subjects
cheers Bruce
On Tue, 23 Oct 2018, Zhi Li wrote:
External Email - Use Caution
I see. Thank you very much. Another question is if I can use other template for parcellation when I use recon-all?
On Tue, 23 Oct 2018 at 13:42, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote: You specify the input you want selxavg3-sess to use. Otherwise, it will try to look for things that have been preprocessed.
On 10/23/18 12:17 PM, Zhi Li wrote: External Email - Use Caution Thank you. May I ask what do we use the flag -funcstem for? I found that there are similar flags in preproc-sess, -mcin, -stcin, etc. Sorry I am a beginner of FreeSufer and not clear about some terms such as 'stem' in both preproc-sess and mkanalysis-sess.On Tue, 23 Oct 2018 at 11:09, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote: Yes. When you run mkanalysis-sess, you may still have to use the -funcstem
On 10/23/18 10:06 AM, Zhi Li wrote: External Email - Use Caution I see. Can I add the flag -nomc to skip motion correction? If I have done the slice timing, realignment and denoising, can I use the following command to do registration, normalization and smoothing? preproc-sess -s sess01 -fsd bold -nomc -nostc -surface fsaverage lhrh -mni305 -fwhm 5 -per-run If I have modified the functional data before I run preproc-sess, will it influence the registration and normalization?On Tue, 23 Oct 2018 at 00:08, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote: Actually, if you just store the denoised data as f.nii.gz, then run preproc-sess it should do ok. It will do motion correction, but it should not really do any thing if MC is already done. Just make sure that the image has a proper baseline so that the registration will work.
On 10/22/18 11:14 PM, Zhi Li wrote: External Email - Use Caution Thank you. But the fmri-denoised.nii.gz will be a volume-based data, how can I register and normalize it to the surface-based space, as 'preproc-sess' do that will generate the bilateral cortex in surface and subcortical area in volume?On Mon, 22 Oct 2018 at 17:12, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote: If you do all the preprocessing yourself, then store the output in the run folder with a certain name, fmri-denoised.nii.gz, then when you run mkanalysis-sess specify -funcstem fmri-denoised and proceed as norm.
On 10/22/2018 04:08 PM, Zhi Li wrote: > > External Email - Use Caution > > Hi FreeSurfer Experts, > > I am trying surface-based analysis of task-fMRI with FS-FAST. However, > I would like to apply ICA-based denoising and wavelet-despiking which > can be not done with the 'preproc-sess'. I wonder if I can do the > preprocessing with other tools before registration with FS anatomical > and normalization? If it is available, how can I do it with command line? > > Another question is if can I use other template for parcellation > during using 'recon-all', such as the template of Human Connectome > Project? > > Looking forward to your kind reply. > > Thank you and best wishes, > > Zhi > > > _______________________________________________ > 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
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Got it. Thank you very much for your patient reply.
Best wishes
On Tue, 23 Oct 2018 at 18:59, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
can you clarify what you mean? We produce two cortical parcellations by default (one from Christophe Destrieux and one from Rahul Desikan). What kind of parcellation would you want? Note that the parcellation is not done by propagating a template to the individual. Rather we extract an array of statistics from a manually labeled training set and use them to parcellate new subjects
cheers Bruce
On Tue, 23 Oct 2018, Zhi Li wrote:
External Email - Use CautionI see. Thank you very much. Another question is if I can use other
template for parcellation when I
use recon-all?
On Tue, 23 Oct 2018 at 13:42, Greve, Douglas N.,Ph.D. <
DGREVE@mgh.harvard.edu> wrote:
You specify the input you want selxavg3-sess to use. Otherwise, itwill try to look for
things that have been preprocessed. On 10/23/18 12:17 PM, Zhi Li wrote: External Email - Use Caution Thank you. May I ask what do we use the flag -funcstem for? Ifound that there are
similar flags in preproc-sess, -mcin, -stcin, etc. Sorry I am abeginner of
FreeSufer and not clear about some terms such as 'stem' in bothpreproc-sess and
mkanalysis-sess.On Tue, 23 Oct 2018 at 11:09, Greve, Douglas N.,Ph.D. <
DGREVE@mgh.harvard.edu> wrote:
Yes. When you run mkanalysis-sess, you may still have to use the-funcstem
On 10/23/18 10:06 AM, Zhi Li wrote: External Email - Use Caution I see. Can I add the flag -nomc to skip motion correction? If Ihave
done the slice timing, realignment and denoising, can I use the following command to do registration, normalization and smoothing? preproc-sess -s sess01 -fsd bold -nomc -nostc -surface fsaveragelhrh
-mni305 -fwhm 5 -per-run If I have modified the functional data before I run preproc-sess,will
it influence the registration and normalization?On Tue, 23 Oct 2018 at 00:08, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote: Actually, if you just store the denoised data as f.nii.gz, then run preproc-sess it should do ok. It will do motion correction, but it should not really do any thing if MC is already done. Just make sure that the image has a proper baseline so that the registration will work.
On 10/22/18 11:14 PM, Zhi Li wrote: External Email - Use Caution Thank you. But the fmri-denoised.nii.gz will be a volume-based data, how can I register and normalize it to the surface-based space, as 'preproc-sess' do that will generate the bilateral cortex in surface and subcortical area in volume?On Mon, 22 Oct 2018 at 17:12, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote: If you do all the preprocessing yourself, then store the output in the run folder with a certain name, fmri-denoised.nii.gz, then when you run mkanalysis-sess specify -funcstem fmri-denoised and proceed as norm.
On 10/22/2018 04:08 PM, Zhi Li wrote: > > External Email - Use Caution > > Hi FreeSurfer Experts, > > I am trying surface-based analysis of task-fMRI with FS-FAST. However, > I would like to apply ICA-based denoising and wavelet-despiking which > can be not done with the 'preproc-sess'. I wonder if I can do the > preprocessing with other tools before registration with FS anatomical > and normalization? If it is available, how can I do it with command line? > > Another question is if can I use other template for parcellation > during using 'recon-all', such as the template of Human Connectome > Project? > > Looking forward to your kind reply. > > Thank you and best wishes, > > Zhi > > > _______________________________________________ > 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
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Greve, Douglas N.,Ph.D. -
Zhi Li