Hi there,
I am running an analysis to examine differences in cortical thickness
between two groups (clinical vs control) and have entered ICV as a nuisance
variable and age as a covariate. The analysis results in qdec do not appear
to give a result that answers the question: does the average
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
Hello,
I’ve got a question concerning qdec running with freesurfer. I just
downloaded the latest version of freesurfer.
Before to run qdec, I read than I have to run "recon-all -s ID -all" (about
7 hours) and then recon-all -s ID -qcache (about 5'). So I tried it with
one subject and everything
Dear Freesurfer experts,
I would like to use "Qdec" tool to study the between groups changes of
volume/cortical thickness
of one region (Perirhinal) belonging to the Brodmann areas. As I understand
Qdec load only the aparc and aseg stat lists and not the BA stat list. I am
wondering
if we
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,
Dear Experts,
I'm looking at differences in area between two groups of subjects in FreeSurfer
using qdec.
I've delineated an ROI based on a cluster that showed significant differences
in surface area between the two groups (taking gender into account, and with
age and ICV as nuisance
Hi all - When you get a significant cluster after doing monte-carlo simulation,
we get peak vertex/Talairach coordinates and also saved in *summary files. Is
there a way to find all the parcellated regions (Desikan, or, Destriuex) in the
significant clusters?
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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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
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
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
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
Dear freesurfer experts,
I am trying to do cortical thickness-age correlation in Spinocerebellar
ataxia patients (SCA1 and SCA2).
## I successfully ran qcache command on these 10 subjects of SCA1 and SCA2.
##Since my discrete factors are *Gender *(Male and Female) and* Diagnosis*
(SCA1 and SCA2),
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
Hello,
I still cannot solve this issue. All help will be appreciated.
I am running Qdec analysis on about 100 subjects and correcting with FDR. Once
I do this I click the find clusters and go to max button and Qdec gives me a
plot of all the data as well as taking me to the max vertex in the
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
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
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, different slope). I believe I can do this somewhere on
the qdec gui without changing to mri_glmfit?
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, different
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
Hello,
I have another newbie question. I'm running qdec, trying to compare cortical
thickness in children with and without ADHD. However, I'm seeing a discrepancy
between the clusters that are significant according to the terminal (after
applying the Monte-Carlo simulation with default
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
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
Hello!
I am running qdec group analysis on my patient data and have one very
important question. I am studying the differences between two Epilepsy
subtypes. Each one of my patients has a hemisphere of onset, either Left or
Right, that I would like to use in looking for differences between
Hello!
I am running qdec group analysis on my patient data and have one very
important question. I am studying the differences between two Epilepsy
subtypes. Each one of my patients has a hemisphere of onset, either Left or
Right, that I would like to use in looking for differences between
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
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
Dear Freesurfer users,
I have a question regarding qdec and I would like your help. When
conducting qdec analyses, is it possible to restrict the analyses to
specific brain regions? I would like to limit my qdec analyses to brain
regions typically associated with social cognition and have
Hi Freesurfer users,
I ran a QDEC analysis and loaded annotation. Is there a way to click on the
activated cluster and print the region with co-ordinates?
Thanks,
Manish Dalwani
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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 manish.dalw...@ucdenver.edu wrote:
Hi Freesurfer users,
I ran a QDEC analysis and loaded annotation. Is there a way to click on
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 manish.dalw...@ucdenver.edu 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,
Dear FreeSurfer experts,
Hello, I started to use FreeSurfer recently.
I want to do group analysis with QDEC in order to compare 2 groups
(control group and patient group), regressing out age and gender.
When I include 2 discrete factors (diagnosis and gender) and 1
continuous factor (age), and
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] qdec question
The newest version of FreeSurfer does not contain any changes to qdec I
believe.
Allison
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu
...@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 to qdec I
believe.
Allison
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr
for 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
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 using FS version 4.3.0 and I cannot select more than 2
continuous variables. I am just wondering if a newer version allows you
to
Hi,
I am using qdec for analysis and noticed that in addition to thickness
measures I can select others such as area and volume. I have been trying to
figure out what exactly the area measure refers to (surface area, etc.). I
did not find it on the website. Can someone clarify that for me? If
Hi,
I have been running into an error while using Qdec.
*Error in Analyze: Couldn't open file
$SUBJECT_DIR/SUBJECT_FOLDER/surf/lh.thickness.fwhm10.fsaverage.mgh*
I checked and the file is there in that folder. I know this file is created
when recon-all is run with -qcache option. I have run
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/SUBJECT_FOLDER/surf/lh.thickness.fwhm10.fsaverage.mgh*
I checked and the file is there in that folder. I
Hi all,
I am using Qdec to examine the anatomical differences between two groups of
subjects. The surface-based measures I can select are thickness, area,
area.pial, sulc, curv, and jacobian_white. Could anybody tell me what
anatomical features the later three (sulc, curv, and jacobian_white)
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
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
measures
Dear all,
I have 2 questions regarding doing analyses using QDEC:
1) can I use QDEC to analyse results on data for which I ran recon-all
using the last (ie: older, not most recent) version of Freesurfer, or
should I rerun recon-all on all the data using the new version of
Freesurfer? (I hope
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
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