Have you looked at the individual subjects? This will sometimes happen
when there are strong global signals as the global signal (by
definition) gets into the regressor and is everywhere, so you end up
with these large swaths of positive activation. You're already doing the
things I would sugge
You can try following this tutorial
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalRegistration_freeview
Eg, run
tkregisterfv --s subject --mov template.nii.gz --regheader --reg
reg.manual.lta
Adjust the registration so that it is relatively close (does not need to
be exact)
Th
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Dear Douglas,
Yes, it happens with almost every subject I have (n=53). Is there a way to
apply the method to all the participants? If you could instruct me on
initializing by hand, I can manually do them on all subjects.
Thank you for your help!
Best
Does this happen on a lot of your subjects? I'm not entire sure why it
is happening to this one, but one reason may be that there is more torso
(eg, shoulders) than the usual scan. I was able to get it working if I
initialized it by hand. This would be ok for one subject, but you would
not have
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Dear Douglas,
I uploaded the file and the file name is wenzhen.tar.gz. the file has
freesurfer_results and template.nii.gz.
Thank you for looking into the problem. Please let me know if you need
anything.
Best,
Wenzhen
> On Sep 18, 2020, at 12
Both do both ways. I would recommend not using the --init-rr option for
BOLD images
On 9/15/2020 11:42 AM, Wenzhen Zhao wrote:
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Dear Douglas,
Thank you for your quick response. I just have one more question.
Does the “both-way” transformation only done th
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Dear Douglas,
Thank you for your quick response. I just have one more question.
Does the “both-way” transformation only done through mri_coreg command that is
embedded in preproc-sess command? Or does “bbregister —init-rr “ rigid
transformation al
On 9/15/2020 11:26 AM, Wenzhen Zhao wrote:
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Dear freesurfer developers,
I’m attempting to analyze my resting -state fMRI data, and I
followed procedures on your functional connectivity page. When I
tried to run preprocessing with my data,
can you send the command line and terminal output?
On 3/12/2020 3:07 PM, Renew Andrade wrote:
> External Email - Use Caution
>
> Dear FreeSurfer experts:
> I cannot fix the problem that I mention in the subject. I put the output of
> the terminal below. I was doing functional connectivit
Yes, see fcseedcor -help
On 11/11/18 4:40 AM, Maedeh Khalilian wrote:
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Dear FreeSurfer experts,
I have a general question, if i have a parcellation(an annotation file e.g
aparc.annot which is the output of FreeSurfer) is FreeSurfer able to calculate
the func
use mcprextreg (this is described in the wiki, isn't it?)
On 8/23/17 10:21 PM, Leathem, Logan Daniel wrote:
Hi Freesurfer list,
My group is switching to the fsfast functional connectivity pipeline.
We would like to continue regressing out the six-parameter rigid body
head motion as a nuisanc
I don't know that there will be a big difference. The surface-based fMRI
time course originally comes from the volume of course, so you're not
freeing yourself from the voxels. If you want to extract the time course
from the surface, you can do it with something like
cd session/bold/002
mri_se
Does the hippocampal subfields create a segmentation in the conformed
space? Ie, the 256^3, 1mm^3 volume, eg orig.mgz, aseg.mgz, etc. If so,
then you can specify that volume with the -seg option to fcseed-config
On 04/20/2016 06:12 AM, Julio Alberto González Torre wrote:
> Hi Freesurfers.
>
> As
un...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
> [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, March 27, 2015 3:15 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] functional connectivity maps (correlation and z
> maps)
>
> The statistic maps (z, t, corr
]
Sent: Friday, March 27, 2015 3:15 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] functional connectivity maps (correlation and z maps)
The statistic maps (z, t, correlation coefficient) depend on the noise
of the individual analysis, ie, two subjects could have identical
correlation
Friday, March 27, 2015 12:28 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] functional connectivity maps (correlation and z
> maps)
>
> I think that the ces is the better map to use, but there's not a
> consensus. For some reason that I don't understand, peo
...@nmr.mgh.harvard.edu]
Sent: Friday, March 27, 2015 12:28 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] functional connectivity maps (correlation and z maps)
I think that the ces is the better map to use, but there's not a
consensus. For some reason that I don't understand, peopl
?
>
> Thank you
>
> Tracy
>
>
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
> [gr...@nmr.mgh.harvard.edu]
> Sent: Wednesday, March 25, 2015 3:37 PM
du
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, March 25, 2015 3:37 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] functional connectivity maps (correlation and z maps)
cd glmdir/contrast
(could be sig.ni
cd glmdir/contrast
(could be sig.nii or sig.nii.gz)
matlab
sig = MRIread('sig.mgh');
p = (10.^-abs(sig.vol))/2;
z = sig;
z.vol = sign(sig.vol).*fast_p2z(p);
MRIwrite(z,'z.mgh')
On 03/25/2015 10:26 AM, Barbour, Tracy,M.D. wrote:
>
> Hello,
>
> I am doing a functional connectivity analysis. I
Mostly looks ok to me, except that you are using the left isthmus
cingulate (1010) instead of thalamus (10). If you want to use motion
correction parameters as nuisance regressors, use -mcextreg
Where did you see -mcreg ?
Step 7 is group level preprocessing
Step 8 is group analysis
Step 9 is co
You need to load it as an overlay onto a surface. If you mapped your FC
onto the native subject space, then use the subject's surface. If you
used fsaverage, then use the fsaverage surface.
doug
On 09/03/2014 11:58 AM, Martin Scherr wrote:
> Dear Freesurfer experts,
>
> We are trying to perform
yes, use isxconcat-sess (after you have done the 1st level analysis of
course). To use the r-rvalue, add "-m pcc" to the isxconcat-sess command
line
doug
On 7/25/13 1:54 PM, Mario Ortega wrote:
Hi Team,
I have a question on making a group average of subjects for functional
connectivity.
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