Dear FS experts,
I got an error while running selxavg3-sess for a single subject. The log
(attached) says the following:
*
** Input 018/tmp.mc-afni2.7515/invol.nii.gz and base
018/tmp.mc-afni2.7515/tempvol.nii.gz don't have same dimens
onday, March 09, 2015 2:38 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] selxavg3-sess error
It looks like different runs have different number of slices. Is that right?
On 3/9/15 1:13 PM, Eryilmaz, H. Hamdi wrote:
Dear FS experts,
I got an error while running selxavg3-sess
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, March 09, 2015 2:49 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] selxavg3-sess error
What is your mris_preproc command? And your mkanalysis-sess command?
On 3/9/15 2:
Hello Doug and Freesurfers,
I am trying to compute a structural measure called 'BrainSegVolNotVent' as an
approximate value of total brain volume. 'BrainSegVolNotVent' is now present in
aseg.stats files but the dataset I'm working on was preprocessed using FS 5.0,
which did not produce this var
patibility with v5
On 07/07/2016 03:50 PM, Eryilmaz, H. Hamdi wrote:
> Hello Doug and Freesurfers,
>
> I am trying to compute a structural measure called
> 'BrainSegVolNotVent' as an approximate value of total brain volume.
> 'BrainSegVolNotVent' is now present in
Dear Doug/FreeSurfers,
We are looking at effects of age-squared on cortical thickness in two different
groups. We are interested in age-squared by group interactions on cortical
thickness across the surface. Nuisance covariates include age, sex, scanner,
and total brain volume.
The sig map f
Dear FreeSurfers,
I was wondering if there is a standardized way to construct a label that is the
complement of a regional label on freesurfer. For example, I have a customized
DLPFC label and would like to create another label that encompasses the entire
cortex except that DLPFC region.
Thank
Dear FS experts,
I have a question about extracting average cortical thickness from a manually
created ROI. I am comparing 2 groups, namely PostFort and PreFort and my fsgd
file appears as the following:
GroupDescriptorFile 1
Title PostPreFortification
Class PostFort
Class PreFort
InputSub
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] cortical thickness - comparing two groups within a ROI
On 10/30/2015 01:36 PM, Eryilmaz, H. Hamdi wrote:
> Sorry, the figures I inserted in the text did not appear in the email.
> I attach them now.
>
> B
else everything will be bogus). The y.mgh file
contains all the subjects in fsaverage space, so you don't need to run
it for each subject or resample back into native space
On 11/03/2015 02:29 PM, Eryilmaz, H. Hamdi wrote:
> Hi Doug,
>
> Thanks for the reply. Sure I will try this comman
Dear experts,
I am using aparcstats2table to extract values on a number of measures like
thickness, curvature, folding index, and surface area for specific ROIs. Is it
possible to create a table (using aparcstats2table) with all these measures
included or do I have to run it separately and cre
, Eryilmaz, H. Hamdi wrote:
> Dear experts,
>
> I am using aparcstats2table to extract values on a number of measures
> like thickness, curvature, folding index, and surface area for
> specific ROIs. Is it possible to create a table (using
> aparcstats2table) with all these measure
t: Re: [Freesurfer] aparcstats2table -- extracting multiple measures
Use foldind
On 11/12/15 12:06 PM, Eryilmaz, H. Hamdi wrote:
> Thanks Doug for the quick reply! Is there an option in aparcstats2table that
> allows to make a table with the folding i
2:28 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] aparcstats2table -- extracting multiple measures
what version of FS are you using? When I run
aparcstats2table --hemi lh -s subject --meas foldind --tablefile table.dat
it runs fine
On 11/16/2015 10:24 AM, Eryilmaz, H. Hamdi wrote:
Hi Anastasia and FS experts,
I am trying to create a white matter ROI mask underneath a cortical ROI label
(e.g., 2 mm into the white matter) created in fsaverage space. I will then use
this mask to extract values from individual dtifit_FA and dtifit_MD maps
generated by trac-all. What would be
Dear all,
We are modeling changes in cortical thickness over time using a cross-sectional
design. We have two groups of participants, age 8 to 18. In the cortical
regions that interest us, there is generally a linear decline in thickness with
age. Each group can be fitted to a best-fit line.
Hello all,
How can I simply smooth a surface map (constructed using MRIwrite) using a
specific FWHM? mri_surf2surf requires source subject as an input but all I want
to do is to smooth a single group map.
Thanks in advance for your help!
Best,
Hamdi
__
Dear freeview experts,
Is it possible to display multiple seeds (i.e., as a small circle) on freeview
surface view by specifying their coordinates? If there is no such feature,
could you suggest an alternative way to visualize seeds?
Thanks in advance!
Best,
Hamdi
___
Subject: Re: [Freesurfer] visualizing seeds on surface
What coordinate system are the seed coordinates in? Do you know the
vertex number on the surface?
On 05/02/2018 03:13 PM, Eryilmaz, H. Hamdi wrote:
>
> Dear freeview experts,
>
> Is it possible to display multiple seeds (i.e., as a
Dear all,
I would like to use the fsfast functional connectivity pipeline to compute
connectivity between two binarized ROIs. One of the ROIs is a surface ROI, the
other is a hippocampal subfield. Based on the tutorial on
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWal
Hi Doug and Freesurfers,
I am using fcseedcor to compute the correlation between two time courses for
each subject in my group. The command that I run is as follows:
fcseedcor -s $subject -fsd resting -seed seed1.dat -seed seed2.dat -xreg
global.waveform.dat 1 -xreg vcsf.dat 5 -xreg wm.dat 5 -x
...@nmr.mgh.harvard.edu
on behalf of Douglas Greve
Sent: Friday, July 20, 2018 9:23:58 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fcseedcor -- pca output for vcsf.dat and wm.dat
Hi Hamdi, sorry for the delay. Answers below.
On 6/26/18 2:50 PM, Eryilmaz, H. Hamdi wrote:
Hi Doug and
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