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:
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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:
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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:
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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:
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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
>
>
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