/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz
And see how many voxels it has? Is it possible that that is a really
small segmentation?
doug
On 05/21/2015 10:30 AM, Alexandra Tanner wrote:
Hi Doug and Freesurfers,
I'm running fcseed-sess to compute the time course
Hi Doug and Freesurfers,
I'm running fcseed-sess to compute the time course in 12 different ROIs
(created with fcseed-config) across 27 subjects. I'm having an issue,
however, where fcseed-sess completes for a particular ROI in most subjects
but errors out for a few subjects (see log below). I
The voxel size for this functional sequence is 3x3x3mm
What is the voxel size of your functional? 54 is small, but I would
expect it to still work.
On 05/21/2015 11:20 AM, Alexandra Tanner wrote:
Hi Doug,
It is a pretty small segmentation. In subject NNC0931 (the example we're
looking
subjects, but see if it makes those two
work). For such a small seed, it may even be better to use .05.
On 05/21/2015 11:42 AM, Alexandra Tanner wrote:
The voxel size for this functional sequence is 3x3x3mm
What is the voxel size of your functional? 54 is small, but I would
expect
have
to
re-run fcseed-sess for all subjects, but see if it makes those two
work). For such a small seed, it may even be better to use .05. On
05/21/2015 11:42 AM, Alexandra Tanner wrote:
The voxel size for this functional sequence is 3x3x3mm
What is the voxel size of your functional? 54 is small
Hi Doug and Freesurfers,
I ran mri_surfcluster to generate coordinates for cluster maxima from a
functional surface analysis. The summary text file generated by
mri_surfcluster lists a bunch of information about the clusters, including
talairach coordinates for each cluster peak (see example
.,M.D. jroff...@partners.org
Date:Wed, December 10, 2014 11:52 am
To: Alexandra Tanner atan...@nmr.mgh.harvard.edu
--
Maybe...if we take this approach I guess we would want the cube root of
age, not age cubed
Hello Freesurfers,
Our group is wondering if any of you know whether it is possible to model
cortical thickness as a third order polynomial? The specific question is:
we are looking at whether there is a hyperbolic relationship between
cortical thickness and date of birth among a cohort of
for one subject). Is
-m cespct more accurate? Thanks!
Best,
Alex
Hi Alex, if you use -m cespct it will report the mean percent signal
change within the ROI. Does this work?
doug
On 10/31/2013 02:37 PM, Alexandra Tanner wrote:
Hi Doug and Freesurfers,
I would like to calculate percent signal
to computing 100*Sum(contrast_i)/Sum(baseline_i)
So they will be close but not exact. Which one is better? Hard to say. I
would tend toward -m cespect
doug
On 11/01/2013 01:43 PM, Alexandra Tanner wrote:
Hi Doug,
Thanks, this seems to work!
Quick question -- in the past we've done ROI
Hi Doug and Freesurfers,
I would like to calculate percent signal change within an anatomical ROI
for a group of subjects in Freesurfer 5.0. We are not functionally
constraining our ROI, however, we do want to calculate the percent signal
change across the entire region in each of our conditions
Hi Freesurfers,
Does anyone know how to make an average activation map of two subjects
without running a group analysis? I have 15 subjects that each have a pre
and a post scan (30 scans total) and we would like to combine the pre and
post bold runs for each subject to generate an averaged
be creating this
folder (bug). So, if you run it from the project folder, the log folder
will be there. Or can create a log folder in your current directory
(mkdir log)
doug
On 7/30/13 2:03 PM, Alexandra Tanner wrote:
Dear Doug and Freesurfers,
I am attempting to run funcroi-table-sess on a set
Dear Doug and Freesurfers,
I am attempting to run funcroi-table-sess on a set of subjects but keep
getting an error message I've never seen before:
funcroi-table-sess -roi
/cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/ctx.lh.insula.aparc+aseg_2vFix.roicfg
-sf
if not the slope between thickness and
age?
doug
On 04/05/2013 03:56 PM, Alexandra Tanner wrote:
Dear Doug and Freesurfers,
I'm running a group cortical thickness analysis covaried by age, and
we're
curious if there is a way to correlate thickness and age within groups
and
then look at whether
Dear Doug and Freesurfers,
I'm running a group cortical thickness analysis covaried by age, and we're
curious if there is a way to correlate thickness and age within groups and
then look at whether or not there is a difference in the strength of the
thickness/age relationship between groups.
with the CES.
That's the problem with trying to do group-wise multi-variate analysis.
Another thing you can do is to do a group analysis with each contrast
separately, then do a conjunction of the group sig maps.
doug
On 11/29/2012 03:39 PM, Alexandra Tanner wrote:
Thanks for the clarification! So I
, then mri_concat to stack all of the maps into one
file. At that point you can compute a mean (also with mri_concat).
Generally, one does not do group analysis on sig maps though.
doug
On 11/27/2012 05:08 PM, Alexandra Tanner wrote:
Hi Doug and Freesurfers,
I recently used mergecontrasts
image). Univariate maps are usually passed up to
the group level (the conjunction done with mergecontrasts is
multivariate).
doug
On 11/29/2012 01:05 PM, Alexandra Tanner wrote:
Hi Doug,
Thanks for the response! Just out of curiosity, what map is typically
used
for group analyses? Should I
Hi Doug and Freesurfers,
I recently used mergecontrasts-sess to merge two contrasts of an analysis
in 50 different subjects. The command ran on each subject individually and
created a sig.nii and sig.ovpl file within a merged contrast folder for
each subject. I'd now like to look at an average
Hi again,
This is a follow-up question to my previous email -- the method I used may
not be the most efficient or the correct way to extract cortical thickness
from manually created ROIs. I'm unfamiliar with how to obtain thickness
data from a label, so I'm not sure if what I did is correct or if
Hi Doug and Freesurfers,
I'm currently working on extracting thickness measurements from an ROI I
manually created. I created my ROI label in tksurfer and applied the label
to each subject I'd like to extract thickness data from using
mri_label2label. I then used the following command to generate
to replace the value with values of nearby voxels. Let me know if you
need some instructions on this.
doug
On 08/22/2012 02:08 PM, Alexandra Tanner wrote:
Hi Doug,
I'm currently working with 4-6 year old clinical pediatric non-Siemens
DICOM files that I'm unpacking and preprocessing
target -run last MEMPRAGE scan MPRAGE COR blah -- for this scan
should I be converting to mgh/mgz instead?
Thanks,
Alex
dcmunpack will convert them to whatever file format you want (don't use
COR though).
doug
On 08/20/2012 09:51 AM, Alexandra Tanner wrote:
Thanks Bruce. I see that because
Dear Doug,
As I mentioned in a previous email, I'm currently working with T1 DICOM
files from the Clinical PACS System that I'd like to pull into the
freesurfer stream to get cortical thickness. I've unpacked the data,
converting the DICOM files to mgz format, and successfully ran the first
Dear Doug,
We're getting T1 DICOM files from the Clinical PACS System (via mi2b2) and
would like to pull them info the freesurfer stream to get cortical
thickness. In order to run the standard unpacking commands, do we need any
other files besides the DICOM files themselves? Of note, these scans
Hi Doug,
I'm currently looking into doing surface edits on past data and I heard
someone mention that one should never scale the brain when editing the
talairach registration. I was wondering if this was true, or if it's okay
to scale the brain so long as you check the scaling in all 3 dimensions
careful with
scaling.
doug
On 08/10/2012 08:51 AM, Alexandra Tanner wrote:
Hi Doug,
I'm currently looking into doing surface edits on past data and I heard
someone mention that one should never scale the brain when editing the
talairach registration. I was wondering if this was true, or if it's
time
points, then import this table into SPSS. Or you can run the table
through mri_glmfit to do the paired-t analysis.
doug
On 07/24/2012 01:56 PM, Alexandra Tanner wrote:
Hi Doug,
Yes, sorry about that! I realized after I'd sent the email to you that
I
should've sent the email
the opportunity to answer and to learn. thanks!
On 07/23/2012 12:03 PM, Alexandra Tanner wrote:
Hi Mr. Greve,
My name is Alex Tanner, I'm the new CRC for Dr. Roffman in the Brain
Genomics Lab. I had a question regarding conducting volume analyses. On
the freesurfer wiki there are commands that show how
can run the table
through mri_glmfit to do the paired-t analysis.
doug
On 07/24/2012 01:56 PM, Alexandra Tanner wrote:
Hi Doug,
Yes, sorry about that! I realized after I'd sent the email to you that I
should've sent the email to the freesurfer list as well.
We were hoping to look at volume
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