If you are asking whether you can mix versions of FS, the answer is no.
You should analyze all your data using a single version.
On 12/30/17 3:27 AM, Giovanni de Marco wrote:
Hello,
I’ve got a question concerning qdec running with freesurfer. I just
downloaded the latest version of freesurfe
Try using the data in the csdbase.y.ocn.dat file rather than
transferring the clusters back into the individual space. What are you
using to do the ROI-based analysis? You have to make sure that the
design matrix and contrasts are exactly the same. You can do this in
matlab with FS commmands, e
Hello Dr Greve,
Many thanks for replying to me. We are not including eTIV as a covariate.
Since we did not find any correlation with the thickness.
Kind regards,
Sampada
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I don't know what is going on with that, but one thing you should do is
to normalize the eTIV (ie, remove it's mean and divide by the std dev).
Also, why are you including eTIV in the first place? Thickness does not
change with head size, only volume and surface area.
doug
On 7/24/15 2:34 AM,
Dear freesurfer experts,
I was able to figure out the problem! I was not supposed to write the eTIV
values in my .dat.table which I did and for that reasons my continuous
factors were being read as 4 instead of 3.
Thanks and regards,
Sampada
AIIMS, Delhi
>
__
Dear Freesurfer experts,
Thanks for your valuable input. Since, comparison with global thickness
does not provide any valuable information we have decided to forego the
average thickness and lh-thickness comparison and now added eTIV as another
covariate with age
and
lh/rh thickess (
please s
The statements are automatically generated based on the names of the
variables you provide. In this case, you've included (global?) lh
thickness as a covariate. This will have a slope when plotted against
thickness at a given vertex, and this slope my differ between genders.
The "average" th
Does /home/anup/Desktop/QDEC/fsaverage/surf/lh.white exist? If not,
cd /home/anup/Desktop/QDEC/
ln -s $FREESURFER_HOME/subjects fsaverage
It looks like you will have a second problem in that the subject class
GenderFemale-DiagnosisSCA1 does not have any members
doug
On 07/17/2015 08:17 AM, Dr S
If you know the vertex you want to extract, then you can run something like
mri_segstats --i y.mgh --crs vertexno 0 0 --avgwf out.dat
where y.mgh is the stack created by qdec and out.dat is the data file
you want
doug
On 8/28/14 8:37 AM, Abrishamchi, Aurash David wrote:
Hello,
I still c
If you don't see an effect of gender, then it is ok to leave it out of
the model. I could be affecting the power as you suspect.
doug
On 5/6/14 3:55 AM, Anna Jonsson wrote:
thank you. I have another question; I am getting several significant
clusters for group, when correcting for multiple c
thank you. I have another question; I am getting several significant
clusters for group, when correcting for multiple comparisons and total
brain size and age, but when I enter sex in, msot of these disappear, but i
do not understand whether this is a power issue (as qdec automatically
incorporates
DOSS is not working in QDEC. It should be disabled in 5.3
doug
On 05/05/2014 09:39 AM, Anna Jonsson wrote:
> Dear group,
>
> when using the qdec gui interface, I was wondering where the "button"
> or the likes is to change the estimation from its standard doss to
> dods (different osnet, differ
You can do it in QDEC by going running QDEC, then loading the surface,
curvature, and overlay files (they are in the output folder (default
"Untitled")). Load the "sig.mgh" file for the overlay. This can also be
done in tksurfer.
doug
On 01/24/2014 11:11 AM, Estephan Moana wrote:
> Dear Frees
Hi Maria, can you tar up the qdec output folder and send it to our file
drop? I'm traveling now, so it might be the 1st week of august before I
can take a look. You can also go into the qdec output folder and run
tksurfer to show you the results.
doug
On 7/26/13 1:37 PM, Maria Kharitonova wro
I think the right way to do it is to use the symmetric template
(fsaverage_sym) as the target (instead of fsaverage). You will need to
run the symmetric registration. See
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi (if you have 5.2, you do
not need to download anything). You can map either
Hi Maria, you can do it with the commandline tools (mri_glmfit) by
specifying --mask or --label. This is a common thing to do, but you will
need to run simulations for multiple comparisons correction.
doug
On 01/04/2013 06:35 AM, Nick Schmansky wrote:
> Maria,
>
> In qdec there is not a built
Maria,
In qdec there is not a built-in mechanism to restrict analysis to a
particular region. By design it runs a whole-cortex analysis, masking
just the medial (non-cortical) region, and then i suppose if your lucky
(if your ROI is significant compared to everything else) your region will
appear
Nevermind, I figured out both my questions! I just have to read the
instructions carefully :)
Manish
On 2/2/12 3:02 PM, "Manish Dalwani" wrote:
Ok I figured that it is ctrl and mouse click on the co-ordinate of interest.
How can I get the cluster size out?
Thanks,
Manish
On 2/2/12 2:47 PM
Ok I figured that it is ctrl and mouse click on the co-ordinate of interest.
How can I get the cluster size out?
Thanks,
Manish
On 2/2/12 2:47 PM, "Manish Dalwani" wrote:
Hi Freesurfer users,
I ran a QDEC analysis and loaded annotation. Is there a way to click on the
activated cluster and p
t; >
> > -Original Message-
> > From: Allison Stevens [mailto:astev...@nmr.mgh.harvard.edu]
> > Sent: Friday, 10 July 2009 4:15 AM
> > To: Prapti Gautam
> > Cc: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] qdec question
> >
> &g
> Prapti
>
> -Original Message-
> From: Allison Stevens [mailto:astev...@nmr.mgh.harvard.edu]
> Sent: Friday, 10 July 2009 4:15 AM
> To: Prapti Gautam
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] qdec question
>
> The newest version of FreeS
your help,
Prapti
-Original Message-
From: Allison Stevens [mailto:astev...@nmr.mgh.harvard.edu]
Sent: Friday, 10 July 2009 4:15 AM
To: Prapti Gautam
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] qdec question
The newest version of FreeSurfer does not contain any changes
The newest version of FreeSurfer does not contain any changes to qdec I
believe.
Allison
--
On Thu, 9 Jul 2009, Prapti Gautam wrote:
Dear Freesurfers,
I just have some quick questions regarding qdec:
1. How many covariates does the latest version of qdec allow you to
select? I am
hi Dev,
You might have wrong SUBJECTS_DIR,
check it using echo $SUBJECTS_DIR
> Hi,
> I have been running into an error while using Qdec.
> *Error in Analyze: Couldn't open file
> <$SUBJECT_DIR>//surf/lh.thickness.fwhm10.fsaverage.mgh*
>
> I checked and the file is there in that folder. I know t
Xiangchuan Chen,
You might want to look at the slides downloadable from the top of this page:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial
which contain pictures showing the meaning of 'curv' and 'sulc'.
Nick
> sulc = "average convexity" from our 1999 reconII paper. Essentially
> measu
sulc = "average convexity" from our 1999 reconII paper. Essentially
measures the depth/height of each point above the average surface.
curv = smoothed mean curvature.
jacobian_white = the jacobian of the spherical transform. Measures the
amount of distortion needed to warp a subject into regis
Narly,
You can use qdec on data processed with the v3.0 processing stream, as
long as you create the 'qcached' files that qdec needs, which is done
using v4.0 recon-all, as you have done.
You can ignore those warning message. They are informative (I will
change it to say INFO). The ?h.volume fi
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