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 below
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 saw
able5_PerRun/NNC0931/mri/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 Fre
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 subj
ss 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
seed-config (means you 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
>>>&
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 (
ex. 0.0159 vs 0.01444 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:
>
in the ROI
> Your method is equivalent 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 Do
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. Origi
ckness/age relationship 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
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
/cluster/roffman/users/Stab
irectory. It should 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 Fre
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 AllvFix
> it gives others 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 con
en 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
>
; On 07/24/2012 03:02 PM, Alexandra Tanner wrote:
>> Hi Doug,
>>
>> We don't want to do ROIs because we're trying to get a thickness map of
>> the entire subcortical region of the brain.
>>
>> Prior to trying this, we ran a within subjects paired ana
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
e very 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
>>
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 w
Hi Alex
> The dicoms should be enough
> Bruce
>
>
>
> On Aug 16, 2012, at 4:10 PM, "Alexandra Tanner"
> wrote:
>
>> Dear Doug,
>>
>> We're getting T1 DICOM files from the Clinical PACS System (via mi2b2)
>> and
>> would like to pul
dir -src -targ
-run 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 B
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
recon-
arts of the image, you might be able
> 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 ol
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
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 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 map
the fsaverage space, 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
e COPE 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,
nction 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:
>> Th
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 individ
, Joshua L.,M.D."
Date:Wed, December 10, 2014 11:52 am
To: "Alexandra Tanner"
--
Maybe...if we take this approach I guess we would want the cube root of
age, not age cubed? The relationship we are testin
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