the 'generate stats data tables' button in the Subjects tab will do
this. see the section 'Stats Data Import' in the tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis
which is copied here:
It is possible to import the aseg and aparc data from the
Hi
I have recently tried to create a new table and I received the following
message after loading it in QDEC:
Loading data table
/home/virtualuser/apps/freesurfer/subjects/qdec.table.dat...
Number of columns: 5
fsid column:1
Number of factors: 4
Number of subjects: 10
ERROR3:
can you email me the qdec.table.dat file? probably something is not
being parsed properly and i'll have to eyeball what it might be.
n.
On Wed, 2011-07-06 at 14:50 -0400, Ignacio Letelier wrote:
Hi
I have recently tried to create a new table and I received the
following message after
Ignacio,
I think it is the dashes in the factor name, try changing this:
Left-Cerebral-Cortical-Thickness
to this:
Left_Cerebral_Cortical_Thickness
n.
On Wed, 2011-07-06 at 14:50 -0400, Ignacio Letelier wrote:
Hi
I have recently tried to create a new table and I received the
Dear all,
I run a controls vs patients thickness analysis using qdec and got
several results. Now, it is not entirely clear to me how to refine my
surface-based analysis (still using qdec) into a ROI, the middle
orbitofrontal region.
Cheers,
Fabrizio
---
Fabrizio
on the tutorial page:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis
at the end there is a section on how to manually draw an ROI (must do so
on the inflated surface), which you would then map to each subject after
which stats info can be extracted and from there an
Hi Nick,
Thank you for your response. I carefully read the whole tutorial but
still did not find what I was looking for.
I don't want to manually draw an ROI but rather use one of the
existing labels (i.e. the middle orbitofrontal). Moreover, I don't
wanto to extract mean ROI thickness and
what version of freesurfer does this happen with?
n.
On Wed, 2011-05-25 at 14:17 +1000, Olivier Piguet wrote:
Good afternoon,
When running qdec, I receive the following error message:
Writing to
/Volumes/workingdata/FTD/T1/subjects/qdec/Untitled/contrasts.sig.mgh
reading group avg
Hi Nick
I run Qdec 1.2 and all cases have been processed with
freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0
Olivier
On 25/05/2011, at 21:18, Nick Schmansky wrote:
what version of freesurfer does this happen with?
n.
On Wed, 2011-05-25 at 14:17 +1000, Olivier Piguet wrote:
Good
Good afternoon,
When running qdec, I receive the following error message:
Writing to /Volumes/workingdata/FTD/T1/subjects/qdec/Untitled/contrasts.sig.mgh
reading group avg surface area 822 cm^2 from file
ERROR: could not find volume
Hello all,
In voxel based morphometry is not recommended use images from different
scanners. This recommendation also apply in the qdec analysis?
Thanks in advance
John Ochoa
Universidad de Antioquia
Instituto Neurológico de Antioquia
___
Freesurfer
Yes it does. However you can maybe use the scanner as a covariate.
On Wed, Apr 27, 2011 at 09:24, John Fredy jfochoas...@gmail.com wrote:
Hello all,
In voxel based morphometry is not recommended use images from different
scanners. This recommendation also apply in the qdec analysis?
Thank you Doug !
regards,
alex.
--- En date de : Lun 14.3.11, Douglas N Greve gr...@nmr.mgh.harvard.edu a
écrit :
Hi Alex, you can compute the difference in those slopes using an appropriate
contrast matrix passed to mri_glmfit. QDEC should do so autotmatically (this
would be an
Dear Freesurfer Experts,
We have
two groups at similar ages and the thickness-age correlation shows
many cluster of significant values. Pointing to this maximum the
plots present similar regressions coefficients for both groups. Actually
it would be intresting to have the regions were the
Hi Alex, you can compute the difference in those slopes using an
appropriate contrast matrix passed to mri_glmfit. QDEC should do so
autotmatically (this would be an interaction between group and age).
doug
Alex Hanganu wrote:
Dear Freesurfer Experts,
We have two groups at similar ages and
?? wrote:
Hi,all:
I have several problems about the qdec in freesurfer 5.0.
Firstly,can somebody explain the function of the buttons in the qdec's
third step (display),such as Set using FDR in the False Discovery Rate
,Monte Carlo Null-Z simulation.If I just let these buttons as the
Wang,
have a look at:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis
and also:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecMultipleComparisons
which itself has some links explaining the necessity for correcting for
multiple comparisons. the newer qdec has the
Hi,all:
I have several problems about the qdec in freesurfer 5.0.
Firstly,can somebody explain the function of the buttons in the qdec's third
step (display),such as Set using FDR in the False Discovery Rate ,Monte Carlo
Null-Z simulation.If I just let these buttons as the default ,is it
Dear FreeSurfer,
Can QDEC take 1 discrete and 2 continuous in addition to group variable (2
groups)? I received error messages when I add group+gender and 2 continous
variables.
thanks
Aifeng
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
...@nmr.mgh.harvard.edu
Objet: Re: [Freesurfer] Qdec - ROI - different thickness results
À: Alex Hanganu hanganu.alexan...@yahoo.de
Cc: FS Mailing List Freesurfer@nmr.mgh.harvard.edu
Date: Dimanche 27 février 2011, 0h28
the easiest way to determine X from Y and blue from red (ie, which group
Hi all,
I want to analyse the thickness difference between patients and normals,but I
can not understand the results that I got from qdec-analysis .I hope someone
can help me.
Firstly,as the papers says, the Cortical (surface-based) Analysis measures the
Distance between white and pial
Hi Wang,
you can do different types of analysis. You can do a vertex-wise
comparison, in which case you'll have about 150,000 tests/hemisphere.
This makes the multiple comparison problem pretty bad, so people frequently
collapse into regions of interest (ROIs). We provide anatomical ROIs
i think part of the confusion results from the option in qdec to import
the ROI thickness values into qdec for selection as factors in an
analysis. if what you want to do is simply look for cortex-wide (ie
vertex-wide) differences in thickness between two groups (patients vs.
controls), then you
the easiest way to determine X from Y and blue from red (ie, which group
is getting thicker or thinner) is to Ctrl-right click on a vertex within
the region of interest on the cortex result display. a plot will appear
showing the raw thickness values for your groups, and which-is-which
should
Dear Freesurfer Experts,
In qdec for question:
Does the average thickness differ between X and Y
we received blue colored regions, meaning that thickness for group Y is lower
then X ?
We created ROIs for each region, and extracted cortical thickness for each ROI
for each subject using
blue means that XY. So that sounds like it is compatible with your ROI
results, yes?
doug
Alex Hanganu wrote:
Dear Freesurfer Experts,
In qdec for question:
Does the average thickness differ between X and Y
we received blue colored regions, meaning that thickness for group Y
is lower then
...@nmr.mgh.harvard.edu a
écrit :
De: Douglas N Greve gr...@nmr.mgh.harvard.edu
Objet: Re: [Freesurfer] Qdec - ROI - different thickness results
À: Alex Hanganu hanganu.alexan...@yahoo.de
Cc: FS Mailing List Freesurfer@nmr.mgh.harvard.edu
Date: Vendredi 25 février 2011, 16h52
blue means that XY. So that sounds
Doug !
Have a great day,
Alex.
--- En date de : *Ven 25.2.11, Douglas N Greve
/gr...@nmr.mgh.harvard.edu/* a écrit :
De: Douglas N Greve gr...@nmr.mgh.harvard.edu
Objet: Re: [Freesurfer] Qdec - ROI - different thickness results
À: Alex Hanganu hanganu.alexan...@yahoo.de
: [Freesurfer] Qdec - ROI - different thickness results
À: Alex Hanganu hanganu.alexan...@yahoo.de
Cc: FS Mailing List Freesurfer@nmr.mgh.harvard.edu
Date: Vendredi 25 février 2011, 17h12
sorry, I should have said mri_label2label, not mri_surf2surf
doug
Alex Hanganu wrote:
right, qdec shows
healthy (X
Does this mean that if you label them something else, the problem goes away?
doug
Dominic Dwyer wrote:
Hi all,
It seems that the post below is the case for both QDEC1.2 and 1.4, but only
when you have two discrete variables with cases labeled as 1 and 2 in
both.
Cheers,
Dominic
On
Hi all,
It seems that the post below is the case for both QDEC1.2 and 1.4, but only
when you have two discrete variables with cases labeled as 1 and 2 in
both.
Cheers,
Dominic
On 28/1/11 1:58 PM, Dominic Dwyer dwy...@unimelb.edu.au wrote:
Dear developers,
I recently found that if you
Hi everybody,
I tried to run the qdec-tool, but experienced some problems . I got different
thickness in one area.
In detail:
1. When I open the qdec.table.dat ,the thickness is different from the
thickness got from the display in Find Clusters and Goto Max,I really do not
know why?
2. Can
You can't analyze 3 levels in QDEC, you'll have to create an FSGD file
and use mri_glmfit. See
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
doug
Lena Palaniyappan wrote:
I have a single factor with three levels (diagnosis) and trying to
setup qdec, but I get the following message –
I have a single factor with three levels (diagnosis) and trying to setup qdec,
but I get the following message - I have a .levels file with all 3 groups
specified - the contrasts are not getting generated automatically.
Data table loading completed successfully.
SUBJECTS_DIR is
Yes, that looks fine. The only other thing to decide is whether to use
DODS (different offset different slope) or DOSS (different offset same
slope). The default is DODS, but if you don't think that there is an
age-by-group interaction, then you can get more power using DOSS. If you
use DODS,
Hi,
We are doing a group analysis using qdec with two groups, and we would like
to include gender and age as covariates.
Which is the best option in order to perform a simple t-test (group1group2
and group2group1) and including the two covariates? (we would like them to
have 'zero' weighting in
Hi Everyone,
I am trying to extract volume and thickness data from a list of subjects for
several ROIs that Freesurfer does not automatically define (ie. Broca's
area). My plan was to load a .dat table into Qdec with a column of subject
IDs and a column with a dummy continuous variable. Then I
Hi,
My data is not in the usual SUBJECTS_DIR/fsid structure.
1. Is it possible to run qdec so that it loads each subject from a
full path instead of expecting them all to be under the same
SUBJECTS_DIR? ie. with something like this:
qdec.table.dat
path_to_fsid gender age
/full/path/fsid1 Male
option 2. should work fine (a subjects dir with symlinks).
On Tue, 2010-11-09 at 15:26 -0500, Mishkin Derakhshan wrote:
Hi,
My data is not in the usual SUBJECTS_DIR/fsid structure.
1. Is it possible to run qdec so that it loads each subject from a
full path instead of expecting them all
Hi all,
I do group analysis using QDEC to detect the difference between the normal
group and the patient group, the result shows some significant difference brain
area (normal patient, red, uncorrected p=0.001). I extract the average
cortical thickness in this area(ROI), then export
its hard to say without more details, but if i'm reading your email
correctly, one notable difference is that you state that you extracted
the cortical thickness data for an ROI and conducted the analysis in
SPSS using that data. that would not be the same analysis as what qdec
is doing. qdec is
you also must verify that you are using the same exact model for the
analysis.
doug
Nick Schmansky wrote:
its hard to say without more details, but if i'm reading your email
correctly, one notable difference is that you state that you extracted
the cortical thickness data for an ROI and
its not possible to do what you want in qdec. but if you're good with
matlab data slinging, here is how it can be done:
goto the directory named 'Untitled' underneath your qdec dir in your
subjects dir. it could be named something other than Untitled if you
changed the name in the qdec design
(How) Can I modify the plots produced using the Ctrl click on a vertex
of interest in the brain map on the qdec GUI?
I have two groups, 12 subjects each, currently using the Ctrl Click I
get the measure of interest on the y-axis, and my subjects along the
x-axis. I would like just two abcissae -
Hi,
I am wondering what is going on under the hood when one makes a choice under
the Design tab in the Measure (Dependant Variable) box for Measure. For example
if one chooses Volume instead of Thickness, what exactly is being used as
volume? Where does the information on volume come from? I
If you're referring to VERTEX-WISE analyses of area and volume, there
are issues with the interpretability of those measures.
Don Hagler has posted on this several times.
For example, most recently see:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15205.html
cheers,
-MH
On
the selection of 'volume' as a dependent variable in qdec is not yet
implemented. only thickness is currently available as the dependent
measure. the command-line mri_glmfit can be used for a volume analysis
though (outside of qdec).
for an independent variable, a volume measure, whether it be
You can say 4.x. The statistical part did not change that much in version 5.
doug
Manabu Kubota wrote:
Hi,
I'm interested in this issue.
If I use a former FreeSurfer version (ver. 4.x) for all the
preprocessing of each data and apply the new QDEC in FreeSurfer ver.
5.0.0 JUST to make
Hi,
I'm interested in this issue.
If I use a former FreeSurfer version (ver. 4.x) for all the
preprocessing of each data and apply the new QDEC in FreeSurfer ver.
5.0.0 JUST to make analyses easier (say, use of mri_glmfit-sim),
do I have to specify both FreeSurfer ver. 4.x and FreeSurfer 5.0.0
Hi,
I was wondering if it were possible/advisable to use data processed and
cached using earlier versions of FreeSurfe with the new 5.0 QDEC, since it has
enhanced capabilities.
Sincerely,
Mira
Mira Michelle Raman
Scientific Programmer
Center for Interdisciplinary Brain Sciences Research
yes, you may use v5 qdec with prior processed data.
n.
On Thu, 2010-09-30 at 21:04 +0200, Christian Scheel wrote:
Dear Mira,
I posted a similar question some days ago. It seems to be possible to
use the new qdec version for the group analysis for data that has been
processed and cached
there a line break script, which is somehow installed in my system (Sentos),
which cleans this up. you basically type lb FILENAME
i can't try and find out what it contains, if you can't get it to work
On 22 September 2010 11:28, James Porter port...@umn.edu wrote:
Hello-
I'm having a
Dear all,
a while ago I have processed a set of brains making use of recon-all in
freesurfer version 4.02. After a longer break I have now come back to my
data and wonder whether it is possible to employ qdec 1.4 (as shipped
with freesurfer version 5) for the group analysis. In particular I
you can use the new qdec with your existing data. qdec, and mri_glmfit,
are not dependent on any particular version of data. you could either
4.02 or 5 to run -qcache, but for consistency, i'd just use 4.02. the
method that is used to sample subject data to fsaverage is unchanged
between the
Hello-
I'm having a resurgence of an old problem
(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12152.html)
but the old solution is not cutting it. When I try to load a table
in QDEC 1.4, I get the following error:
Loading
can you send me the file?
n.
On Wed, 2010-09-22 at 10:28 -0500, James Porter wrote:
Hello-
I'm having a resurgence of an old problem
(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12152.html)
but the old solution is not cutting it. When I try to load a table in QDEC
Of course, once I ask
for help I stumble immediately upon the solution. There appears to
be a limit to the number of columns that QDEC is willing to put up
with when reading in tables. If I create a table that only has the
few columns that I'm interested in (as
there shouldn't be a limit on the number of columns it will read. the
thing to be careful about is the name of a column. sometimes when
importing a spreadsheet, a column name will consist of two words (thus
messing-up the detected number of columns), or it will have a minus -
char in the name,
Hi there,
I am having a problem with qdec when trying to rerun analyses (meaning this
worked before), I get the following error message:
Data table loading completed successfully.
SUBJECTS_DIR is '/Users/bruehh01/Borderline_2'
ERROR: QdecGlmDesign::Create: could not create directory
qdec by defaults puts its results in the directory
$SUBJECTS_DIR/qdec/Untitled, which can create problems when qdec is run
multiple times. try either deleting that Untitled dir (it might have
permissions set to another user), or try changing the name of the design
in the Design tab (look for the
what does the error message in the terminal say?
n.
On Mon, 2010-07-26 at 17:01 -0400, aekai...@umich.edu wrote:
Hello FS experts,
I have attached a gimped image of an error I have encountered.
it seems to only occur when I choose diagnosis as a discrete variable.
however I made the
, it works perfectly fine.
Thanks for your help,
Gaëlle.
-Message d'origine-
De : Krish Subramaniam [mailto:kr...@nmr.mgh.harvard.edu]
Envoyé : mardi 6 juillet 2010 17:47
À : Gaëlle Leroux
Cc : freesurfer@nmr.mgh.harvard.edu
Objet : Re: [Freesurfer] Qdec - problem with the Generate Stats
Hi Gaelle
This seems to be an error due to Python's warning module being
deprecated in Python 2.6. I'll update the sources so as to accommodate
this change.
Meanwhile, the quickest fix is to open up
nano $FREESURFER_HOME/bin/asegstats2table
and comment out the following lines ( put a # at
Hello all,
I'm running a cortical thickness group analysis in qdec with two groups and one
covariate (age). By default, does qdec use the DODS option, or DOSS?
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
It uses DODS by default.
doug
Dankner, Nathan (NIH/NIMH) [F] wrote:
Hello all,
I'm running a cortical thickness group analysis in qdec with two groups and
one covariate (age). By default, does qdec use the DODS option, or DOSS?
___
Freesurfer
Hello Support,
how can i calculate the value of the slope of a a plot when displaying the
data for a particular vertex in qdec?
thank you
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
Dear Experts,
I'm trying to use QDEC for a Multigroupal analysis. I've read in the wiki
that QDEC uses a GLM method to perform the analysis, but when I load a table
with 43 subjects aprox. of three different groups and I run the analysis, at
70% QDEC shows me the following error:
Error in
qdec currently only supports two levels to a group. i thought qdec
issued a better error message in this case, so that will need to be
improved.
to do a three-level group analysis, you will need to do it manually.
see:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
and
Hello All,
I have a very simple qdec question.
I have three groups (relatively age and sex matched), each grp has 8 subjects.
I have created a qdec.table.dat file with contents as follows
SUBJECT_DIR /jet/rito/freesurfer_data/
fsid gender age diagnosis
01 Female 40 Group1
02 Female 32 Group1
Hi all,
We're using QDEC DODS to compare the average thickness maps of patients
V. controls using sex and age as covariates. The results are identical
for Does the average thickness differ between patientsVscontrols with
sex and age as covariates and Does the average thickness differ
between
Hi All,
I am trying to use Qdec to analyze a dataset, and am getting the following
error:
ERROR: All stat files should have the same segmentations
If one or more stats file have different segs from others,
use --common-segs or --all-segs flag depending on the need.
The problem is that I haven't
Hi Tyler
qdec makes use of bunch of scripts. In this case, when you analyze it
makes use of asegstats2table. To know more about it type
asegstats2table --help
in your environment. The error is: one of the aseg.stats is has
different number of segmentations than all other ( or there is a
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
Hello,
When I get to the last step of qdec 1.2, when I choose the Description
under Scalers on the Display tab, I get a couple of errors relating to
fonts:
ERROR: In
/usr/pubsw/packages/vtk/5.2.0/src/Rendering/vtkFreeTypeUtilities.cxx, line
1659
vtkTextProperty (0x217178e0): Unable to create
Dear Freesurfers,
in my qdec analysis I want to compare
my patients group with a control group. The analysis should be
corrected for age effects, so I used group as discrete factor and age
as covariate. If I choose „Does the average thickness differ
between the two groups“, how can I
You have done the right thing, but you need to know a little more. When
QDEC says mean thickness it really means the thickness at age=0, so it
is extrapolating the results back to age=0. Since you have a covariate
and you are using DODS, you have to specify an age at which to do the
test (you
Can you send your fsgd file and your command-line?
doug
lordowen wrote:
Dear Professor Greve:
Thanks for your advisement. After re-value the covariates, the same
error report still popup. The value of age goes between 6.5-10.5
(origin SD =2.9), and mean_thickness goes around 31-35 (origin
Dear freesurfer experts:
We are using freesurfer to preform a cortical thickness analysis
between patients and controls. We plan to use the mean_thickness and
subject age as covariates. It's fine to analysis as group x age or
group x mean_thickness, respectively. But when we set design as group
x
you can divide the continuous variables by the standard deviation.
doug
lordowen wrote:
Dear freesurfer experts:
We are using freesurfer to preform a cortical thickness analysis
between patients and controls. We plan to use the mean_thickness and
subject age as covariates. It's fine to
Dear Professor Greve:
Thanks for your advisement. After re-value the covariates, the same
error report still popup. The value of age goes between 6.5-10.5
(origin SD =2.9), and mean_thickness goes around 31-35 (origin SD =
0.07). Can you give us some suggestions?
Any other comments also welcome
Hi,
I have a problem using qdec, which I don't know how to solve- I get
the following error message:
Error in Analyze: command failed: mri_glmfit --y /Users/Hannah/
Borderline/subjects/qdec/Untitled/y.mgh --fsgd /Users/Hannah/
Borderline/subjects/qdec/Untitled/qdec.fsgd dods --glmdir
what is the error message that is output to the terminal after this
command is run? qdec outputs everything it is doing to the terminal
window.
n.
On Mon, 2010-02-08 at 13:48 +0100, Hannah wrote:
Hi,
I have a problem using qdec, which I don't know how to solve- I get
the following
if the first run of asegstats2table to table worked, but the second
failed, then that means that something is wrong with the stats data for
subject 'test1' (or possibly something unusual with the way it was
parsed). can you send me the aseg.stats files for both subjects.
for the qcache command:
Hi all,
What's wrong with my QDEC? Today, I use the FeeSurfer Tutorial: Surface
Group Analysis with Qdec to analysis my data , when I carried out to '' Stats
Data Import'', I press the 'Generate Stats Data Tables' button, but something
happend to with a error(red letters ):
mkdir -p
from the error output shown, the problem appears to occur in the
aparcstats2table script (line 322). its failing to parse a float.
which version of freesurfer is being used? (type 'bugr' for this info)
and which version of python? (type 'python -V')
also, try running:
asegstats2table
can you send me your qdec.table.dat and the two .levels files?
n.
On Mon, 2009-12-14 at 14:58 -0500, Weisinger, Brian (NIH/OD) [E] wrote:
I am trying to use qdec but it gave me this error. I don’t understand what is
wrong because it read the diagnosis factor level of COS NV but then says
I am trying to use qdec but it gave me this error. I don’t understand what is
wrong because it read the diagnosis factor level of COS NV but then says
subject 00308 has invalid level of COS in diagnosis column.
Any ideas?
CHP-MP2:freesurfer brianweisinger$ qdec
[1] 7902
CHP-MP2:freesurfer
Hi, there,
Does anyone can give me link or paper which explains all the QDEC output file,
such as F.mgh, gamma.mgh, beta.mgh ...
What are they, how are they related?
Thanks a lot!
Guang
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] qdec output
Try running mri_glmfit with the --help option. QDEC runs mri_glmfit.
doug
Guang Zeng wrote:
Hi, there,
Does anyone can give me link or paper which explains all the QDEC
output file, such as F.mgh, gamma.mgh, beta.mgh
!
Guang
Date: Mon, 14 Dec 2009 18:35:39 -0500
From: gr...@nmr.mgh.harvard.edu
To: freesurfer...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] qdec output
Try running mri_glmfit with the --help option. QDEC runs mri_glmfit.
doug
Guang Zeng wrote:
Hi
Hi all,
I am attempting to create a qdec.table.dat file, and have been unable to find a
way to paste my data into it in a way that will make it readable. When I paste
it in qdec always outputs an error when trying to open it, even if visually the
file appears to be correct. Is there an easy
If you're creating the file in windows, try running dos2unix on the file.
doug
Dankner, Nathan (NIH/NIMH) [F] wrote:
Hi all,
I am attempting to create a qdec.table.dat file, and have been unable to find
a way to paste my data into it in a way that will make it readable. When I
paste it
Unfortunately I'm not running windows. Are you familiar with any tricks I can
use on a mac?
On 11/17/09 5:15 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:
If you're creating the file in windows, try running dos2unix on the file.
doug
Dankner, Nathan (NIH/NIMH) [F] wrote:
Hi all,
I
Some programs notoriously add Ctrl-M at the end of every line ( or
every cell )
If you have the vi editor you can follow this method
http://www.tech-recipes.com/rx/150/remove-m-characters-at-end-of-lines-in-vi/
to remove all the instances of Ctrl-M and again try in qdec.
Unfortunately I
Nathan,
Here are the steps I use to create QDEC dat files on a Mac:
-Export/save your data in SPSS/Excel as a .csv file
-Open the .csv file in TextWrangler (a free text editor for Mac)
-Do a Find Replace of the , for spaces to make it a space
separated file
-Down at the bottom of the
Hi everyone:
When I launched qdec in our system, I got the following error:
X Error of failed request: GLXBadRenderRequest
Major opcode of failed request: 151 (GLX)
Minor opcode of failed request: 1 (X_GLXRender)
Serial number of failed request: 1640
Current serial number in output
can you run that command from the terminal? that is:
cd [path]/qdec
mri_glmfit (as copied from terminal output).
it might give a more descriptive error. also, another obvious: make sure
you have enough disk space.
On Thu, 2009-10-08 at 11:14 -0400, Dankner, Nathan (NIH/NIMH) [F] wrote:
Hi all,
I am working with QDEC and I would like to know if it is possible to do
subcortical structures (e.g. hippocampus, amygdala, putamen) analyses in qdec??
I only have cortical structures mapped in my analyses.
Thanks for the help,
Miguel.
Miguel,
No, not yet. Sorry.
You can use the command-line tool mri_glmfit to do the analysis though.
Also, its pretty easy to export a table of the data and use a plain
stats tools. See:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI
Nick
On Tue, 2009-10-06 at 08:45 -0700,
Hi all,
I am using qdec and I would like to know if it is possible to do any comparison
with whit matter in qdec.
Thank you for the help,
Miguel.
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