Dear Freesurfer experts,
I am attaching a document showing the segmentation of a brain in version
5.1 and 5.3 with and without a 3-T flag. Image is from a 3-T camera.
What I am wondering about is that it seems that the cortex is too thin in
the later version of Freesurfer (both when using 3T
thanks Anastasia for taking the time
into this, once again!
the logs can be found here
https://dl.dropboxusercontent.com/u/8209026/p14ab.zip
cheers
ds
On Wed, Dec 11, 2013 at 8:11 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:
>
> Sorry, I can't tell what happened without looking
Hi Anastasia,
You were right ! I fixed ncpts = 5 for all 18 tracts and th preprocessing
step runs.
Thanks,
Matthieu
2013/12/11 Anastasia Yendiki
>
> Hi Matthieu - In 5.1 the number of control points (ncpts) was only one
> number, the same for all 18 tracts. Not sure if this is what's causing
Hi Doug and Bruce,
I have run "recon-all -autorecon-pial -s my_subject" after editing the pial by
tkmedit. I donot know wether "-autorecon-pial" option running the process
stages 24-31. So I want to know wether I need run "-autorecon3" option as I run
"-autorecon-pial" not "-autorecon2-pial" pr
Hi Freesurfers,
I would like to make sure I am using the funcroi commands correctly for
anatomical and functional ROI analyses (using the aseg to anatomically
constrain), and I have some questions about the commands.
If I want to extract the average percent signal change in the whole left
amyg
Dear experts,
To complete my error, I've got moreover another error in
"dmri.bedpostX/logs" for each slice :
*** ERROR (nifti_image_read): failed to find header file for
'/home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri/data_slice_'*
*** ERROR:
nifti_image_open(/home/matthieu/NAS/matthieu/DTI_A
On 12/12/2013 10:08 AM, Emily Boeke wrote:
> Hi Freesurfers,
>
> I would like to make sure I am using the funcroi commands correctly for
> anatomical and functional ROI analyses (using the aseg to anatomically
> constrain), and I have some questions about the commands.
>
> If I want to extract t
Dear FS experts,
I have the following questions that I am thinking probably got lost in the list
of emails. I would be grateful if you can help me out. Please find the
questions below.
Many thanks,
Pablo
From: pablon...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Date: Wed, 11 Dec 2013 15:12
Is it possible to get the individual subject data for the clusters, before the
monte carlo simulation has been run?
I click "find clusters and goto max" . then on the command line it shows me
the clusters stats and then when I click the "next" button under "Clusters".
it shows me the graph
Hi Doug,
Thanks for your response.
I have another question related to functional ROIs. The method below produces
ROIs based on individual subjects' activation for a contrast. I would also
like to make ROIs based on averaged group activation for a contrast and extract
individuals' percent sign
Hi Emily, there may be a simpler way to get at what you want. You can
use mri_label2vol to create a mask of the label in mni305 2mm space,
something like
mri_label2vol --label yourlabel --temp
$SUBJECTS_DIR/fsaverage/mri.2mm/orig.mgz --regheader
$SUBJECTS_DIR/fsaverage/mri.2mm/orig.mgz --o la
I'm not sure what is going on. Can you send a screen shot of the qdec
window when you see 40 clusters? It might be that it is showing clusters
regardless of the cluster significance. Do the 3 or 4 clusters created
when you run mri_glmfit-sim match clusters in qdec?
On 12/10/2013 05:32 PM, Jon
It is showing you scatter plots from individual vertices, not an average
over the cluster
doug
On 12/12/2013 12:27 PM, Jon Wieser wrote:
> Is it possible to get the individual subject data for the clusters, before
> the monte carlo simulation has been run?
> I click "find clusters and goto m
Dear Jorge and FreeSurfers,
Would you mind having a look at my set-up and advising on whether it is
correct or needs changing?
I have participants with one or two scans, who are divided into two groups.
I'm interested in the longitudinal effects of aging, and the difference in
the effect of age o
oh, so it's showing the thickness values for one vertex in the cluster, not
the average of all veretices in the cluster. we are interested in the average
of the cluster
Jon
- Original Message -
From: "Douglas N Greve"
To: "Jon Wieser"
Cc: "freesurfer"
Sent: Thursday, December 12, 20
Hi Jared
for the ones that run quickly and end, it's because you haven't told it
to do anything. The first couple of lines of the recon-all.log file give
the command line as:
Thu Dec 5 14:00:18 MST 2013
/mnt/NAS3/freesurfer/freesurfer//bin/recon-all
-i Time3_28908_s11038064-0005-1-01-0
Dear All,
Does anyone know how to run regression (with covariates of interest) in
freesurfer. I know people usually do group comparison but I need to do
regression with a continuous variable. Or do I have to use SPM?
Cheers,
Jacky
___
Freesurfer mailin
Hi Sean
An
important issue in the LME model concerns the centering of the times
of measurement. It changes the interpretation
of both the mean response and the variance of the random effects.
If tij represents time since baseline then the subject-specific intercept
coefficient ß1+b1i represen
Hi Bruce,
Thanks for your response. It's a bit of a pain to access the dicoms, but it's
possible. The bigger problem now is that I can't get freeview to work. I type
in freeview into the command line and receive the following error:
freeview.bin: error while loading shared libraries: libvtkverd
Hi Jacky, have you looked at the group analysis tutorial? It includes
instructions on how to include age as a continuous covariate.
doug
On 12/12/2013 06:28 PM, r...@nmr.mgh.harvard.edu wrote:
> Dear All,
>
> Does anyone know how to run regression (with covariates of interest) in
> freesurfer. I
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