Dear Freesurfers,
I am trying to use the longitudinal 2-stage model to run a mri_glmfit
analysis. How do I specify my FSGD file so that I compared spc or pc1 maps
instead of the regular thickness maps? Also, it is my understanding that I do
not have to run mris_preproc and mri_surf2su
FSGD file specifies the order of subjects and other co-variates
(e.g. age, IQ, gender). You do not specify the Y (dependent variable) in there.
That is only passed on the command line.
Best, Martin
On 07/22/2015 04:00 PM, Govindarajan, Koushik Athreya wrote:
Dear Freesurfers,
I am try
e
equally spaced in time) you could manually compute t2-t1 and t3-t2 and then the
difference of that yielding: 2*t2-t1-t3, then test for difference from zero
(OSGM).
Cheers, Martin
On 07/22/2015 04:55 PM, Govindarajan, Koushik Athreya wrote:
Thanks for the detailed reply Martin. When you say “he
list
Subject: Re: [Freesurfer] FSGD file for mri_glmfit in longitudinal 2-stage
model {Disarmed}
Hi Koushik,
If that is what you want to do, the first option works:
(tp2-tp1) - (tp3-tp1) = tp2 - tp3
Best, Martin
On 07/22/2015 06:25 PM, Govindarajan, Koushik Athreya wrote:
> Thanks again Mar
...@nmr.mgh.harvard.edu] On Behalf Of Govindarajan,
Koushik Athreya
Sent: Wednesday, July 22, 2015 8:12 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] FSGD file for mri_glmfit in longitudinal 2-stage
model {Disarmed}
Thanks Martin. I will try that.
Regards
Koushik
2-tp1 ..." but if you have
those stacks, just subtract them:
(tp2-tp1) - (tp3-tp1) the results is equivalent to: tp2-tp3 and do a osgm there.
Cheers, Martin
On 07/23/2015 09:38 AM, Govindarajan, Koushik Athreya wrote:
> Hi Martin,
>
> Just had a quick follow-up on the conversatio
Hello Freesurfers,
I am trying to use mri_surf2vol to convert my thickness files into
analyze/nifty format to use with a custom code. Is there a way I can write all
output files from mri_surf2vol in axial format? Also, is there a way in
FreeSurfer to combine these thickness files fro
: [Freesurfer] mri_surf2vol questions
To get them both in one file, run mri_surf2vol to get the left
hemisphere. When you run it a 2nd time for the right hemisphere add
"--merge vol.lh.nii". I think FSL has software to swap dimensions
doug
On 11/04/2013 09:53 AM, Govindarajan, Koushik Ath
Hi all,
I am trying to compute differences between 2 runs of my same set of
subjects (repeatability) using the steps from the paired analysis wiki page.
After I finish the mris_preproc and the mri_surf2surf steps, when I do the
glmfit, should I be using the osgm option ? Since it is the sa
Dear Freesurfers,
I am trying to export the cortical thickness maps in nifti format
using the mri_surf2vol command. Is it possible to get these output files in the
fsaverage space (1x1x1 mm3) instead of the native space.
Thanks
Koushik
___
Behalf Of Douglas N Greve
Sent: Tuesday, December 03, 2013 9:13 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_surf2vol in fsaverage space
Convert the thickness maps to fsaverage using mri_surf2surf, then use
mri_surf2vol
doug
On 12/03/2013 10:00 AM, Govindarajan, Koushik Athreya
Dear Freesurfers,
I have a question regarding how Freesurfer's paired glmfit and
monte-carlo analysis compares with SPM8 GLM design analysis on cortical
thickness. If I were to export thickness maps as nifti files and do a paired
comparison on SPM8, would that be a fair comparison wit
change the results. Cluster-based correction for multiple
comparisons will be different/wrong without taking into account the
surface geometry.
doug
On 12/11/2013 10:58 AM, Govindarajan, Koushik Athreya wrote:
>
> Dear Freesurfers,
>
> I have a question regarding how Freesurfer's
Dear FS experts,
I have a serial study in which I have run cross-sectional and
longitudinal analysis on 5 time points. Now, I want to add a 6th time point to
my dataset. Do I have to rerun my base template creation step from scratch or
is there a way to just add further time points t
Dear FS experts,
I am trying to add a 6th and 7th timepoint to my longitudinal
analysis that already has a base template from 5 timepoints. I saw an earlier
response on the mailing list about doing this using a 'patch' script but there
was no further information on this. Is this scrip
Thanks Martin, I will try it out.
K
From: Martin Reuter [mailto:mreu...@nmr.mgh.harvard.edu]
Sent: Friday, March 14, 2014 9:31 AM
To: Govindarajan, Koushik Athreya; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] adding time points to longitudinal base template
Hi Koushik,
there is a
ailto:mreu...@nmr.mgh.harvard.edu]
Sent: Friday, March 14, 2014 9:31 AM
To: Govindarajan, Koushik Athreya; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] adding time points to longitudinal base template
Hi Koushik,
there is a way to add time points without recreating the base:
recon
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Martin Reuter
Sent: Wednesday, March 19, 2014 11:21 AM
To: Govindarajan, Koushik Athreya; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] adding time points to longitudinal base template
{Disarmed}
Hi Koushik,
What version
Thanks Martin, I tried that on version 5.1 and it worked.
Regards
Koushik
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Martin Reuter
Sent: Tuesday, March 25, 2014 9:55 AM
To: Govindarajan, Koushik Athreya; freesurfer
Dear all,
I am trying to run a group analysis between 2 groups of subjects. I
did the mris_preproc and mri_surf2surf steps. When I set up my mri_glmfit, the
end of the output is:
Reshaping mriglm->mask...
search space = 74485.691578
DOF = 1344
Starting fit and test
Fit completed in 0
to do with the search space? I'm not sure what the
problem is here.
dough
On 04/01/2014 05:05 PM, Govindarajan, Koushik Athreya wrote:
>
> Dear all,
>
> I am trying to run a group analysis between 2 groups of subjects. I
> did the mris_preproc and mri_surf2surf ste
Hi there,
I have run my subjects from multiple time points through a cross-sectional
stream and a longitudinal stream. When I look at the 'stats' directory for the
same subject from the cross-sectional pipeline and the longitudinal pipeline, I
see that the numbers are different. For example
year, Martin
On 12/29/2015 01:09 PM, Govindarajan, Koushik Athreya wrote:
> Hi there,
>
> I have run my subjects from multiple time points through a
> cross-sectional stream and a longitudinal stream. When I look at the 'stats'
> directory for the same subject
Dear FS experts,
I ran into an error with one of my mri_glmfit-sim execution and was not
sure what was going on. The same simulation is currently running for the left
hemisphere without any hiccups but I get this following error for the right
hemisphere:
estimate of the FWHM for that run. Can you
re-run mri_glmfit and send me the command line and terminal output?
On 05/06/2016 10:27 AM, Govindarajan, Koushik Athreya wrote:
> Dear FS experts,
>
> I ran into an error with one of my mri_glmfit-sim execution
> and was not sure what was g
nan). Can you
send the actual terminal output and not just the log file?
On 05/06/2016 11:55 AM, Govindarajan, Koushik Athreya wrote:
> Thanks for the reply Doug. This is content of my mri_glmf
: 0.00
Found 65950 voxels in mask
How did you create rh.paired-diff.thickness.sm05.mgh?
On 05/09/2016 10:24 AM, Govindarajan, Koushik Athreya wrote:
> This is the command line output for mri_glm
Dear Freesurfers,
I had a question about interpreting the results of the Monte-Carlo
simulation. It is my understanding that the clusters are labeled based on the
value of the maximum significant vertex in a cluster. So, assuming that a
cluster kind of borders or extends over 2 adjacent
ould satisfy you. No matter what the labeling
scheme, you'll always end up with overlap.
doug
On 06/04/2012 10:35 AM, Govindarajan, Koushik Athreya wrote:
> Dear Freesurfers,
>
> I had a question about interpreting the results of the Monte-Carlo
> simulation. It is m
you might want to look into this:
http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation
cheers
K
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Rashmi Singh
[rsi...@laureateinstitute.org]
Sent:
Hello group,
This may be just a naive question, I tried finding answers in the
archives but did not get a straight forward way to do it. So, I need the aseg
and aparc files in fsaverage in the MNI152 space (181x217x181) so that it can
be compared with data processed elsewhere. Is there
URFER_HOME/average in future versions
of FS.
doug
On 10/22/2012 11:34 AM, Govindarajan, Koushik Athreya wrote:
> Hello group,
>
> This may be just a naive question, I tried finding answers in the
> archives but did not get a straight forward way to do it. So, I need the aseg
Dear Freesurfers,
When I do the Monte-Carlo simulation after mri_glmfit between my
groups, I get an output summary file for each of my contrast. In that summary
file, there are multiple columns for coordinates, threshold values, number of
vertices and size (mm2). My question is, how
Dear FS experts,
I am trying to do a paired analysis between 2 time points obtained
from the longitudinal pipeline and had some trouble interpreting the results. I
have 2 different treatment groups I and II. I ran the paired analysis at p =
0.05, p = 0.01 and p = 0.001 vertex-wise th
ehalf Of Douglas N Greve
Sent: Wednesday, July 16, 2014 10:40 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_glmfit-sim question
I'm not sure I understand what you mean. Do you expect the two groups to yield
the same result?
On 07/16/2014 10:03 AM, Govindarajan, Koush
:59 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_glmfit-sim question
What do you mean that G1 does worse?
On 07/16/2014 11:59 AM, Govindarajan, Koushik Athreya wrote:
> Dear Doug, Thanks for writing back. I don't mean the 2 groups should yield
> same result. I j
10 PM, Govindarajan, Koushik Athreya wrote:
> Dear Doug, Group I shows larger cortical thinning from timepoint 1 to
> timepoint 2 compared to Group II at p = 0.05. At p = 0.01 and p = 0.001,
> Group II shows larger cortical thinning from timepoint 1 to timepoint 2
> compared to Group
Thanks for your response Martin.
From: Martin Reuter [mailto:mreu...@nmr.mgh.harvard.edu]
Sent: Monday, October 20, 2014 12:56 PM
To: Govindarajan, Koushik Athreya
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] adding time points to longitudinal base template
Hi Koushik,
no, I cc
Hello group,
I am a new user of Freesurfer and just learning to process data
through the pipeline. Sorry if this is an amateur question. I was just trying
to look at cortical thickness differences between a patient group and a control
group. So, my fsgd file would just list the input f
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Friday, December 23, 2011 11:20 AM
To: Govindarajan, Koushik Athreya
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] GLM question
Hi Koushik, it's very hard to diagnose these problems wit
Hello group,
I am running the multiple comparisons simulation after my mri_glmfit
finished. I see that it went through all the iterations and then quit with the
following error message it could not find the talairach.xfm file in my average
brain. I did not use the fsaverage and instead
it have to be
a separate mri_glmfit-sim again?
Thanks
Regards
Koushik
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, February 15, 2012 10:09 AM
To: Govindarajan, Koushik Athreya
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, February 15, 2012 10:41 AM
To: Govindarajan, Koushik Athreya
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] monte carlo simulation question
In principal, it should be the same
Hi Charlotte,
Can you try adding the path before your lh.test.thickness.10.mgh file?
Sometimes, if not all files are in SUBJECTS_DIR, I have had that problem.
Cheers
Koushik
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.h
Dear FS group,
This may be a trivial question. Could not find answer in the archives.
When Freesurfer outputs cluster summary files, it displays number of vertices
(NVtxs). What is the size of each of these vertices. In other words, is there a
standard correspondence between number of v
Hi,
I have a question regarding how the clusters are labeled after the results of
a Monte-Carlo Simulation. Similar regions from 2 different patient populations
seem to be labeled differently. On one of my results, the cluster has been
labeled as in the precentral region and a similar region
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