Hi all,
I was adviced to use PALM for permutation of non-orthogonal surface data.
However, I have some questions regarding the design matrix en contrast files
to be used in PALM, but somehow I cannot subscribe to the FSL mailing list, and
I was hoping one of the freesurfer users could help me
Hi all,
Is using forced permutation for non-orthogonal design matrices wrong or is it
allowed to do this instead of using tools like palm (what happens eg with the
covariates when using forced permutation)? I used forced permutation and it
seemed to work, results were (partly) comparable to w
Dear Douglas,
Sorry to bother you with this, but after reading the thread about the Eklund
papers I'm getting confused about what I actually did when correcting for
multiple comparisons and I'd also like to know whether I'm on the safe side.
I used pre-cashed Monte Carlo simulation with a c
On 2/8/15 1:48 PM, maaike rive wrote:
But how can i run the appropriate preprocessing
and smoothing? The --X flag s not recognised using
mris_preproc.
mri_preproc only uses the fsgd file to get the list of subjects to
Dear Freesurfer experts,
I have a question regarding tk surfer. If I load the
cache.h13.abs.sig.cluster.mgh file, I'll only see the clusters surviving the
statistical threshold I set, don't I? (e.g. I set the cluster finding
threshold at 0.05 (Monte carlo simulation), keeping all clusters with
:
freesurfer@nmr.mgh.harvard.edu; marie.sch...@unige.ch> From:
gr...@nmr.mgh.harvard.edu> Date: Thu, 5 May 2016 12:32:11 -0400> Subject: Re:
[Freesurfer] does lGI needs correction for any global measure?> > > > On
05/02/2016 07:39 AM, maaike rive wrote:> > Dear freesurfer e
Dear freesurfer experts,I have a question regarding correction of cortical
measures or global measures (ICV, total surface area). As I understand from
literature and the freesurfer wiki, a model for thickness should not be
corrected for ICV (since thickness does not scale with total brain vol
ructure.
> > However, you can create your own design matrix and include anything you
> > want in it and pass it to mri_glmfit with --X instead of --fsgd.
> >
> > doug
> >
> >> On 02/05/2015 06:13 AM, maaike rive wrote:
> >>
> >> Hi Doug,
&g
and pass it to mri_glmfit with --X instead of --fsgd.
>
> doug
>
>> On 02/05/2015 06:13 AM, maaike rive wrote:
>>
>> Hi Doug,
>>
>> I hope I'm not driving you crazy, but I have some additional questions
>> regardig the DOSS/DODS models. Also
rect. Is this what you fed to SPSS?
On 1/30/15 2:07 PM, maaike rive wrote:
Ok, I'm so sorry, I'm afraid I mixed things up. I indeed used DODS, and assumed
these were may regressors:
diagn1*state1*gender1
diagn1*state1*gender2
diagn1*state2*gender1
diagn1*state2*gender2
diagn2*st
eesur...@nmr.mgh.harvard.eduSubject: Re: [Freesurfer] defining
ROIs/clustersJust run mris_preproc on your healthy group, then run mri_segstats
using the cluster annotation from your first analysis and the HC stack as the
input. Does that make sense?doug
On 2/3/15 9:18 AM, maaike rive wrote:
Hi all, Does a
Hi all,
Does anyone know how to extract average (thickness/area/GI) values of a cluster
A for subjects in a group which was NOT included in the model where this
cluster A emerged? For example: in a t-test for diagnosis1>dagnosis2 there is
an effect in an insulacluster (found with mri_glmfit
ks correct. Is this what you fed to SPSS?
On 1/30/15 2:07 PM, maaike rive wrote:
Ok, I'm so sorry, I'm afraid I mixed things up. I indeed used DODS, and assumed
these were may regressors:
diagn1*state1*gender1
diagn1*state1*gender2
diagn1*state2*gender1
diagn1*state2*gender2
as soon as I'm sure.
Date: Fri, 30 Jan 2015 14:12:32 -0500
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] average values per cluster
Actually, that looks correct. Is this what you fed to SPSS?
On 1/30/15 2:07
er cluster
Actually, that looks correct. Is this what you fed to SPSS?
On 1/30/15 2:07 PM, maaike rive wrote:
Ok, I'm so sorry, I'm afraid I mixed things up. I
indeed used DODS, and assumed these
state is a categorical variable with 2 levels, you'd
have 4 regressors (gender by state) + 4 more regressors (gender by
state by age). If the SPSS model did not have 8 regressors, then it
is not the same.
doug
On 1/30/15 1:26 PM, maaike rive wrote:
How should I have described the model
ovariates
This is not a sufficient description. Several design matrices could
be derived from this description.
On 1/30/15 11:58 AM, maaike rive wrote:
The p value from SPSS is 0.156. I checked with a
statistician, just to be sure, but he
en it would be worrisome, but it is only a check and cannot be
used for anything. What p-value did you get from SPSS? I'd be
curious to know what the source of the descrpancy is since this has
happened several times now.
doug
On 1/30/15 3:25 AM, maaike
t; SPSS to output the design matrix. Did you try the matlab code below?
>
> On 01/29/2015 01:40 PM, maaike rive wrote:
> > Hi Douglas,
> >
> > I checked but as far as I see it I used the same models. I attached
> > the SPSS model and output as wel as the FSGD file and
t; is just an unsigned t. I don't know anything about SPSS so I can't tell
> from what you have sent whether it is the same model or not. Try to get
> SPSS to output the design matrix. Did you try the matlab code below?
>
> On 01/29/2015 01:40 PM, maaike rive wrote:
> &g
er-forming threshold (ie, abs), then it is
> possible that some of the voxels are pos and some are neg so that they
> average out
>
> doug
>
>
>
>
> On 01/26/2015 09:03 AM, maaike rive wrote:
> > Dear Freesurfer experts,
> >
> > Sorry to bother you a
Dear Freesurfer experts,
Sorry to bother you again, but I have two more questions about extracting
(thickness/surface/GI) values from a certain cluster.
As I understood, the abs.y.ocn.dat file gives the average values for a given
significant cluster (e.g. a cluster where there is a significant Ax
t only the value for the vertex, add --id 1
> doug
>
>
> On 01/05/2015 03:52 AM, maaike rive wrote:
> > Dear Freesurfer experts,
> >
> > I have a question about extracting vertex values of VtxMax for each
> > subject (for surface eara, in this case).
> >
Dear Freesurfer experts,
I have a question about extracting vertex values of VtxMax for each subject
(for surface eara, in this case).
Based on earlier postings, I used the command mri_segstats (--seg
${x}/surf/lh/area.pial --i ${x}/surf/lh/area.pial --vox vertexno 0 0).
First, I'm not
Subject: Re: [Freesurfer] DODS design and demeaning
On 12/24/14 5:21 AM, maaike rive wrote:
Dear Freesurfer experts,
I would be very greatful if you could help me with
three (probably basic) questions regarding
Dear Freesurfer experts,
I would be very greatful if you could help me with three (probably basic)
questions regarding an mri_glmfit design.
For the design and contrasts I used FSGDF. I have a 2x2 factorial design with
one covariate (age). I specified all four groups (A1B1, A1B2, A2B1, A2B2)
26 matches
Mail list logo
