Re: [Freesurfer] Surface-based analysis of tfMRI

2018-10-23 Thread Zhi Li 
External Email - Use Caution

Got it. Thank you very much for your patient reply.

Best wishes

On Tue, 23 Oct 2018 at 18:59, Bruce Fischl 
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 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. <
> dgr...@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. <
> dgr...@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.
> >  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.
> >  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
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fre

Re: [Freesurfer] Surface-based analysis of tfMRI

2018-10-23 Thread Bruce Fischl 
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.  
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.  
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.
 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.
 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


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Re: [Freesurfer] Surface-based analysis of tfMRI

2018-10-23 Thread Zhi Li 
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. <
dgr...@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. <
> dgr...@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. <
>> dgr...@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. <
>>> dgr...@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
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing 
>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>>>
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>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
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>>
>>
>>
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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>
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Re: [Freesurfer] Surface-based analysis of tfMRI

2018-10-23 Thread Greve, Douglas N.,Ph.D. 
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. 
mailto:dgr...@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. 
mailto:dgr...@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. 
mailto:dgr...@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


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Re: [Freesurfer] Surface-based analysis of tfMRI

2018-10-23 Thread Zhi Li 
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. <
dgr...@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. <
> dgr...@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. <
>> dgr...@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
>>
>>
>>
>> ___
>> 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
>
>
>
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Re: [Freesurfer] Surface-based analysis of tfMRI

2018-10-23 Thread Greve, Douglas N.,Ph.D. 
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. 
mailto:dgr...@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. 
mailto:dgr...@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


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Re: [Freesurfer] Surface-based analysis of tfMRI

2018-10-23 Thread Zhi Li 
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. <
dgr...@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. <
> dgr...@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
>
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] Surface-based analysis of tfMRI

2018-10-22 Thread Greve, Douglas N.,Ph.D. 
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. 
mailto:dgr...@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


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Re: [Freesurfer] Surface-based analysis of tfMRI

2018-10-22 Thread Zhi Li 
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. <
dgr...@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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Re: [Freesurfer] Surface-based analysis of tfMRI

2018-10-22 Thread Greve, Douglas N.,Ph.D. 
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


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[Freesurfer] Surface-based analysis of tfMRI

2018-10-22 Thread Zhi Li 
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
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