, but there is not a longitudinal functional analysis per
se.
On 11/5/2019 2:15 PM, Barbour, Tracy,M.D. wrote:
Hello Freesurfer experts!
I see that there is a longitudinal processing pipeline for volume/cortical
thickness. I was wondering if the same pipleline could be used for resting
state functional
Hello Freesurfer experts!
I see that there is a longitudinal processing pipeline for volume/cortical
thickness. I was wondering if the same pipleline could be used for resting
state functional connectivity based analysis?
Best,
Tracy
___
Freesurfer
Hello experts,
I am trying to convert insula ROIs that are in MNI 152 2 mm space to MNI305
space. I will eventually this ROI for connectivity analysis.
I ran mri_vol2vol:
mri_vol2vol --mov $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz --targ
Hello Freesurfer community!
I am trying to run fspalm on surface based data. I have installed PALM, fspalm,
mri_surfcluster, and mri_volcluster.
This is my fspalm command:
fspalm --glmdir TEPSC.glmdir --cft 1.3 --twotail --name palm-twotail-1.3
--iters 1000 --2spaces --cwp .05
When I run the
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] cluster info
Yes, the fraction of the ROI the cluster is covering, not the reverse, so sum >
1 is ok. Eg, if cluster covers all of hippo and amyg, then both would be 1 and
would sum to 2.
On 9/2/15 7:48 PM, Barbour, Tracy,M.D. wr
Hello,
I have a large cluster in my group volume map (sig.mgh). I would like to know
what percentage of this cluster is in amygdala, hippocampus, etc. Is there a
command I could run that would give me that information?
Thank you in advance.
Tracy
, --default-ctab, and your binarized
cluster as input. The "mean" column will then be the fraction of the cluster in
the ROI. Also, if the sig.mgh is 2mm in fsaverage space, then make sure to use
the aseg from the mri.2mm folder
On 9/2/15 6:06 PM, Barbour, Tracy,M.D. wrote:
Hello,
I ha
PM, Barbour, Tracy,M.D. wrote:
Thank you Doug
I tried the way you suggested and the registration actually looks worse. I
also tried:
mri_label2vol --subject fsaverage --label
/autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS53/fsaverage_copy/label/$label.label
--o
lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.mgz come from?
It must be in the space of $SUBJECTS_DIR/fsaverage/mri/orig.mgz for that
transform to work
On 07/17/2015 02:43 PM, Barbour, Tracy,M.D. wrote:
Hello,
I'm trying to convert an ROI mask I created in MNI305 space to MNI152.
After running
Hi Freesurfer listserve,
I hope you are well. I emailed the freesurfer listserve also but got no
response. I am trying to take an functional ROI that is anatomically constrined
that I created using tkmedit and transform it to MNI152 space. I saved it as
$label.label. Then did this command:
Hello,
I'm trying to convert an ROI mask I created in MNI305 space to MNI152. After
running MRI_vol2vol the registration looks off (too anterior).
Here are my commands:
mri_convert -ot nii lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.mgz
lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.nii
:21 AM, Barbour, Tracy,M.D. wrote:
Thanks Doug,
Hi,
I am wondering if you would give some input on this:
When we run the buckner scripts for functional connectivity analysis, those
scripts:
1. Obtain correlation maps of individual subjects, and convert them to
individual subject z-maps
).
doug
On 03/27/2015 01:53 PM, Barbour, Tracy,M.D. wrote:
Thanks! Would you please explain why you think ces is the better map (vs z or
correlation coefficient)?
Thank you
Tracy
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun
)
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 want to make
individual pearson correlation maps for each
When doing connectivity based within group analysis using mri_glmfit. If I
already smoothed the data in the first level analysis do I need to again smooth
using the --fwhm command? If so, why?
Tracy
___
Freesurfer mailing list
Hello,
I am doing a functional connectivity analysis. I want to make individual
pearson correlation maps for each subject (correlation between the seed region
and all other voxels in the brain) and then convert them to a map of z-scores
using a Fisher's z transformation. I want to then get an
Hello,
I am doing functional connectivity analysis using the FsFast functional
connectivity commands and would like to know how to do a group level whole
brain regression with questionnaire data (such as BDI score).
Are there any scripts available for this or do I add a covariate in at some
17 matches
Mail list logo
