Freesurfers-
When running analysis in qdec is it possible to use each individual
subjects brain volume (white matter + gray matter) as a covariate? If so,
what would be the easiest way to go about getting this information.
Best-
Michael
--
Michael D. Kruepke
PhD - University of Illinois at Urba
Freesurfers-
Question, when looking for interactions to justify using DOSS say i am
looking at cortical thickness and i have two discrete variables (G1 and G2)
and 4 continious variables (V1, V2, V3, V4). My thinking is that i should
look to see if there are interactions with the groups and each i
.harvard.edu/fswiki/UserContributions/Scripts/Two
>
> substitute "-all" with "-qcache"..you can also pick specific measure
> and fwhm if you dont want all others to be ran.
>
> hope this helps
>
>
> kk
>
> - Original Message -
> From: md
Perfect that should make things a bit easier on me, also according to this
post
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12406.html
it is not possible to run multiple subjects with this set up (recon-all -s
(subjectid) -qcache -fwhm 10, however this was from 2009, so not sure
Freesurfers-
For pre-smoothing subject surfaces for qdec using:
recon-all -s -qcache
Is it necessary to have all the variations of smoothing done (ie - fwhm
0,5,10,15,20,25) or is it possible to run with only a subsection of these?
Best-
Michael
--
Michael D. Kruepke
PhD - University of Illi
Freesurfers-
When choosing the simulation type does the ending have to match the sim
sign? for instance i see examples with
--sim mc-z 1 3 mc-z.pos.3 --sim sign pos
or
--sim mc-z 1 3 mc-z.neg.3 --sim sign neg
I guess what i am asking is what does the first sign (in the mc-z.(SIGN).3
me
Freesurfers
A real real general question here: if i am running a glm_fit for cortical
thickness with a fsgd with 2 groups (G1, G2) and 3 continues variables and
have a matrix of 1 -1 0 0 0, red/yellow areas mean that G1 is thicker in
this area than G2, correct?
Best-
Michael
--
Michael D. Kr
then use abs. Choosing a sign will yield stronger results
>(ie, smaller p-values), but you will lose the other sign.
>
> The FWHM is obtained from the data (glmdir/fwhm.dat)
>
> doug
>
>
>
> On 06/13/2012 02:04 PM, mdkrue...@uwalumni.com wrote:
> > Free
Freesurfers-
When correcting for multiple comparisons using:
mri_glmfit-sim \
--glmdir lh.gender_age.glmdir \
--sim mc-z 5 4 mc-z.negative \
--sim-sign neg --cwpvalthresh 0.4\
--overwrite
What does the sign mean (ie - the neg, pos, abs). Also for the mc-z
simulation type do we no longer
mfit to do grp analysis
>
>
> lemme knw if this helps
>
> kk
>
> - Original Message -
> From: mdkrue...@uwalumni.com
> To: "freesurfer"
> Sent: Wednesday, June 13, 2012 11:33:27 AM
> Subject: [Freesurfer] cortical thickness with a continuous va
Freesurfers-
I am looking to investigate the whether cortical thickness varies in
regards to a continues variable, while controlling for other continues
variables. I am having a little trouble wrapping my head around this as i
am unsure how to compare thickness in regards to a continues variable,
Hey all-
This may be a simple question to answer, but in an analysis looking at say
cortical thickness between Group 1 and Group 2 with say 3 continues
variables (age, anxiety, IQ) there would be a contrast matrix of 1 -1 0 0 0
. How does free surfer correctly remove the effects of the continues
v
?
michael
On 6/4/12, Douglas N Greve wrote:
> you should be able to run make_average_subject with --no-aseg
>
> On 06/04/2012 06:25 PM, mdkrue...@uwalumni.com wrote:
>> so what i should be able to do is run make_average_surface and
>> make_average_volume separately wit
t
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in erro
12:25 PM, Douglas N Greve
wrote:
> not unless you are trying to visualize the label
>
>
> On 06/01/2012 01:16 PM, mdkrue...@uwalumni.com wrote:
>
>> Thanks, i am also still able to display the rh in tksurfer without issue,
>> shouldnt that also fail with the curren
put is newer or older than rh.cortex.label. If older, it is
> probably ok.
>
> On 06/01/2012 12:53 PM, mdkrue...@uwalumni.com wrote:
> > Actually one last question-
> >
> > I used label2label to transfer some labels and grab ROI thickness
> > averages from the labels
to redo them?
Best-
Michael
> On Fri, Jun 1, 2012 at 11:05 AM, mdkrue...@uwalumni.com <
> mdkrue...@uwalumni.com> wrote:
>
>> Doug -
>>
>> That does indeed seem to be the problem! Ill just rerun some things here
>> to rectify that. Thanks for all th
if it is much different than the other rh files
>
> On 06/01/2012 11:55 AM, mdkrue...@uwalumni.com wrote:
> > Bruce-
> >
> > It is, and i agree, for instance here is the lh.cortex.label file
> >
> > #label , from subject ??
> > 149955
> > 22 -10.3
ike it
>>
>> On Fri, 1 Jun 2012, mdkrue...@uwalumni.com
>> wrote:
>>
>>> Bruce-
>>>
>>> Here you go. Subjects recoded.
>>>
>>> Graph: name
>>>
>>> Data: path
>>> Variable: Subject
>>> Measu
0.00
249 -10.766 45.545 6.476 0.00
507 -11.087 42.990 18.865 0.00
On 6/1/12, Bruce Fischl wrote:
> that is the rh.cortex.label file? It doesn't look like it
>
> On Fri, 1 Jun 2012, mdkrue...@uwalumni.com
> wrote:
>
>> Bruce-
>>
-93.203 -16.969 0.00
> 5 11.020 -93.855 -17.042 0.00
> 6 10.248 -93.745 -16.712 0.00
> 7 11.591 -93.603 -17.551 0.00
>
>
>
> and please cc the list so others can answer!
> On Fri, 1 Jun 2012,
> mdkrue...@uwalumni.com wrote:
>
>
To anyone who can help -
I am trying to tun a GLM on a set of data and am currently receiving an
error during the mri_surf2surf portion. When running this portion i receive
an error ( could not scan # of lines from (path to rh.cortex.label)). This
does not happen when running this portion for the
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