By default, mri_glmfit will "prune" voxels. Ie, if it finds any subject
that is zero at a given voxel, then that voxel is set to zero in the
output and in the mask. I suggest you load up your data
(lh.cbf.fsaverage.proj0.5sm00.nii.gz) as an overlay in freeview and
scroll through the subjects
I don't know much about the infant stream, but you can try running
mris_preproc. See here
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0
On 6/7/2022 11:09 AM, Steger Celine wrote:
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Dear FS experts,
We are currently exploring the
External Email - Use Caution
Dear FS experts,
We are currently exploring the Infant Freesurfer pipeline for surface based
analysis in our cohort. The generated surfaces seem reasonable, but now we are
wondering, how to proceed. To our understanding, by looking at the recon-all
External Email - Use Caution
Dear experts,
I have three groups:
- pre treatment (baseline)
- post treatment (follow-up after 6 month of the baseline visit)
- healthy controls.
The three groups have PET data. I ran surface based paired t test between pre
and post treatment. The
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
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
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
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
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
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
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
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
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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
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
>
>
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
Dear all,
Is there any approach that you recommend to quantify that changes in
cortical thickness in hippo campus sub fields , how could i perform
Surface based cortical thickness changes using freesurfer.
Thanks
Vasudev
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Freesurfer mailing list
Can I use mri_binarize for example and save the output as a label?
John
Sent: Thursday, January 26, 2017 at 1:15 PM
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface based analysis
FS does not come with correcti
FS does not come with correction tables for all labels. You'll have to
build your own. here are the instructions:
http://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo
On 01/26/2017 01:09 PM, John Anderson wrote:
> Hello Freesurfers,
> I am working on a PET surface based analysis
Hello Freesurfers,
I am working on a PET surface based analysis between two groups. I did the following:
1. I concatentaed the PET images using the command "mris_preproce" and I got the file (lh.mgh) for left hemisphere and (rh.mgh) for right hemisphere.
2. I smoothed "lh.mgh and rh.mgh) using
January 13, 2017 at 3:16 PM
> *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
> These differences are hard to track down because they are so subtle.
>
> Y
...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface based analysis (projfrac)
These differences are hard to track down because they are so subtle.
You may want to use our PET module, which includes PVC
http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer
On
cwp
> 0.01". How can I check that this differnce is a real differnce and
> not related to partial volume effect?
> Best,
> John
> *Sent:* Friday, January 13, 2017 at 2:46 PM
> *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> *To:* freesurfer@nmr.mgh.harvar
s ?
> Best,
> John
> *Sent:* Friday, January 13, 2017 at 12:21 PM
> *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
>
>
> On 01/12/2017 05:20 PM, Jo
t; *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
>
>
> On 01/12/2017 05:20 PM, John Anderson wrote:
> > Thank you very much Doug and thank you for
me effect be avoided by using larger
> numbers for "projfrac" ?
No, PVEs can't be avoided that way.
> Bests,
> John
> *Sent:* Thursday, January 12, 2017 at 5:08 PM
> *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> *To:* freesurfer@nmr.mgh.har
bers for "projfrac" ?
No, PVEs can't be avoided that way.
> Bests,
> John
> *Sent:* Thursday, January 12, 2017 at 5:08 PM
> *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] surface
PM
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface based analysis (projfrac)
yes, that is correct. However, understand that there might only be a
difference of 1mm between those two locations, so it could easily be
> John
> *Sent:* Tuesday, January 10, 2017 at 10:51 AM
> *From:* "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
>
> When you say in the corpus callosum, do y
Bests,
John
Sent: Tuesday, January 10, 2017 at 10:51 AM
From: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface based analysis (projfrac)
When you say in the corpus callosum, do you mean in WM? The
When you say in the corpus callosum, do you mean in WM? The
surface-based analysis is only for cortical GM. If you mean in GM near
the CC, then the analysis is appropriate. The projfrac parameter sets
the sampling location between the white and pial surfaces where 0.5
means half way.
On
Dear FS experts,
I am working on surface based analysis using freesurfer. I want to inquire about the flag "projfrac" in the command "mris_preproc"
I ran voxel wise analysis including the same subjects. I found differnce between the groups in areas close to the corpus callosum. I want to get
dvice
> Bests,
> John
> *Sent:* Thursday, October 20, 2016 at 12:16 PM
> *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] surface based analysis for subcortical
> structures
>
>
Sent: Thursday, October 20, 2016 at 12:16 PM
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface based analysis for subcortical structures
After spmregister, you can run
mri_vol2vol --mov pet.nii --reg reg.dat
After spmregister, you can run
mri_vol2vol --mov pet.nii --reg reg.dat --tal --talres 2 --talxfm
talairach.xfm --nearest --no-save-reg --o pet.tal2mm.nii
# mask out the cortical structures
mri_mask pet.tal2mm.nii
$FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz
Dear experts,
I ran surface based analysis using PET maps. As the following:
spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh
mris_preproc --target fsaverage --hemi lh --iv subj1/ubject1_pet.nii subject1/pet/pet_2_T1_register.dat . --projfrac 0.5 --out lh.mgh
urfer-boun...@nmr.mgh.harvard.edu] on behalf of Matt Glasser
>[m...@ma-tea.com]
>Sent: Wednesday, March 23, 2016 9:29 PM
>To: Freesurfer support list
>Subject: Re: [Freesurfer] Surface based analysis using FA maps
>
>FA or fractional anisotropy explains the fraction
...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Matt Glasser
[m...@ma-tea.com]
Sent: Wednesday, March 23, 2016 9:29 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Surface based analysis using FA maps
FA or fractional anisotropy explains the fraction of the diffusion
arch 23, 2016 8:49 PM
>To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>Subject: Re: [Freesurfer] Surface based analysis using FA maps
>
>Right but what do you think FA, MD, AD, RD, etc are telling you
>neurobiologically in the grey matter?
>
>Matt.
>
>On 3/23/16
urfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser
Sent: Wednesday, March 23, 2016 8:49 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Surface based analysis using FA maps
Right but what do you think FA, MD, AD, RD, etc are telling you
n
fer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser
>Sent: Wednesday, March 23, 2016 8:04 PM
>To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>Subject: Re: [Freesurfer] Surface based analysis using FA maps
>
>I too am puzzled as to why you would want to
23, 2016 8:04 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Surface based analysis using FA maps
I too am puzzled as to why you would want to do this. In terms of getting
improvement in the alignment across subjects TBSS is one way to ap
I too am puzzled as to why you would want to do this. In terms of getting
improvement in the alignment across subjects TBSS is one way to approach
this. Another would be to use the fiber orientations in the registration
like these folks have done:
I don't know of a reference where someone has done this (though I would
be surprised if it is not out there), so just be aware of this if you
try to publish. The commands look correct, however, you may or may not
want to sample in the middle of the cortical ribbon (--projfrac 0.5).
Since this
Dear FS experts,
I would like to run surface based analysis using FA maps. I am not exactly sure
that what I am doing is totally right specially step 2 . I used the following
commands:
1. I registered the FA maps to T1 using the command: bbregister --s bert
--mov dtifit_FA.nii --bold
Hi Doug,
I would like to run surface based analysis using FA maps. I am not exactly sure
that what I am doing is totally right specially step 2 . I used the following
commands:
1. I registered the FA maps to T1 using the command: bbregister --s bert
--mov dtifit_FA.nii --bold
Hi all!
Will surface-based fMRI analysis in FsFast show activation in
subcortical MTL structures (caudate, putamen, thalamus,
hippo/amygdala) or is it limited to the neocortical surface? If not,
is there a way to get such statistics without resorting to a volume
analysis?
Thanks!
David
Hi David,
not realiably, no. You'll need to analyze those in the volume (since they
are volumetric structures)
Bruce
On Mon, 3 Jul 2006, David Ziegler wrote:
Hi all!
Will surface-based fMRI analysis in FsFast show activation in subcortical
MTL structures (caudate, putamen, thalamus,
Just to clarify, fs-fast does functional analysis in the volume, then
samples the results to the surface for surface-based analysis, so you
can analyze subcortical structures. You can also do roi based
analysis, using either subcortical or cortical based rois.
doug
On Mon, 3 Jul 2006, Bruce
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