Dear All,
When I tried to running qdec, I'm getting the following error.
qdec.bin: error while loading shared libraries: libjpeg.so.62: cannot open
shared object file: No such file or directory
What is the solution for this.?
Any help will be greatly appreciated.
_
Hi,
I am in the testing process of Freesurfer on a 64-bit Ubuntu installed
personal computer.
However when I run the qdec command as suggested in the testing stages I
receive the following error.
qdec.bin: error while loading shared libraries: libXss.so.1: cannot open
shared object file: No such
I got an error beginning with this.
Thanks for any help
Error in analyze: command failed: mri_glmfit --y
//qdec/LH_insula_thick/y.mgh --fsgd
**
Electronic Mail is not secure, may not be read every day, and should not be
used for urgent or
Hello,
First, ... Happy New Year!
When trying to run a basic qdec analysis between two groups (using qdec
from FS v4.0.2), I get an error in a pop-up window, which I've screen-
captured and attached as a gif. This is a Linux-centos4 installation,
and it doesn't have a /usr/pubsw directory, so I
When trying to analyze some data in qdec, after I completed recon-all -all and
-qcache for the subjects in my qdec table, I get to the Display tab and pick an
option under Scalar. It doesn't matter which option, as they all give me the
same two errors repeatedly (forcing me to quit qdec). These
Hi,
I pasted an error that I am receiving in qdec below. SUBJECTS_DIR is
/space/lightning/2/users/NEAA-freesurfer. If you need any more information
from me I will be happy to provide it. Any help is much appreciated.
Thanks,
troy:cameo[87] ERROR: QdecGlmDesign::GenerateContrasts: factor 1 mus
Hello Freesurfers,
I am having troubles analyzing some data in the qdec tool. I have two
groups of the same subjects that were run with different versions of FS
and I have put them in the same SUBJECTS_DIR and smoothed and created an
average subject. I have made a qdec.table.dat file and the appr
Hi, I am getting a qdec error on FreeSurfer 4.0.2 on Tiger. The error has
been mentioned on the forum before. In particular qdec.bin seems to be
calling for tcl/tk libs in /usr/pubsw which doesn't exist. Below are the
first two lines from the ldd profile for qdec.bin.
> ldd /Applications/frees
Hello,
I am seeing the following error in the terminal window when I run an
analysis in QDEC:
INFO: ignoring tag Creator
INFO: ignoring tag SUBJECTS_DIR
INFO: ignoring tag SynthSeed
INFO: demeaning continous variables
Continuous Variable Means (all subjects)
Class Means of each Continuous
Hi,
I’ve run across the following error while trying to run qdec in my linux 64 bit
computer,
qdec.bin: error while loading shared libraries: libtiff.so.3: cannot open
shared object file: No such file or directory
Is there any specific file that I need to download or change configuration of?
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
Dear FS experts:
I am trying to qdec to analysis FS results. when I loading qdec.table.dat,
it shows cannot open the data (could not fine column name of fsid or ID)
Following is my qdec files:
/home/Lawrence/Lawrence_data
fsid Gender age diagnosis L_frontal_V L_cingulate_V L_occipital_V
L_tempor
Dear Fressurfer Experts,
My table.dat file loaded fine. However, I came across the following error when
I was running the Qdec generate stats data table. If you can let me know what I
can do to fix the following error I would greatly appreciate it.
Uncaught exception: command failed: asegstats2
Dear Experts,
I tried to see if the average area/thickness differ between the 2 groups (HC
and A) with IQ, Age and Gender as covariates using Qdec, but encountered the
error (pls see attached). I tried the same thing for comparison between A and
PC and it works fine... please kindly help?
Man
Sorry, I am re-posting below again for help...
Dear Experts,
I tried to see if the average area/thickness differ between the 2 groups (HC
and A) with IQ, Age and Gender as covariates using Qdec, but encountered the
error (pls see attached). I tried the same thing for comparison between A and
P
Dear Freesurfer,
I have a question during qdec.
I tried to compare the surface area between two groups using qdec program.
Strange to say, if I control some combination of confounding factors, then
the error develops and qdec is closed.
When I control age, sex, HAMD (hamilton depression) score,
Hello All:
I am hoping someone can help me with qdec. I am running -qcache and running
into the following error:
ERROR: number of vertices in /Recon/subj1/surf/lh.volume does not match
surface (129774,129379)
I tried running "recon-all -s subj1 -make all" but still getting the same
error. I did
Hi FS community,
After I open QDEC, when I try to load my qdec data table, QDEC crashes for
some reason. The error message that comes out at the terminal is:
Returned Error on line 1:
missing close-brace
Stack trace:
missing close-brace
while executing
".vtkKWLoadSaveDialog5.vtkKWFileBrowserW
Dear group, I now have error loading my qdec table into qdec, for this error
fsid column:1
Number of factors: 8
Number of subjects: 168
ERROR: QdecSubject::GetContinuousFactor failure: could not find factor
name: age_demeaned for subject XXX
However those 5 of those "factors" are contini
HI freesurfer experts,
I am running a qdec analysis, my first factor has 3 levels, my other 2 factors
have 2 levels, I select my first and second factors and hit "Analyze"
I get the error ? :
Error in Analyze: command failed
ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 level
I'm getting the following erorr when running Qdec "Analyze"
Model Factors:
Discrete (fixed factors)
ADHD_Persist
MJ_group
Nuisance factor:
Age
ERROR: matrix is ill-conditioned or badly scaled, condno = 10355.4
Possible problem with experimental design:
External Email - Use Caution
Dear FreeSurfer experts
I ran QDEC and got the following error.
Design matrix --
1.0 1.04000 -1.38574 2.0 29.0 19.0;
1.0 1.04000 -0.55066 2.0 35.0 19.0;
1.0 1.03000 2.31721
External Email - Use Caution
Dear FS experts,
I have freesurfer-linux-centos7_x86_64-7.1.1 on my computer and when I run
qdec, I get the following error:
Tk_Init error: invalid command name "tcl_findLibrary"
Error initializing Tcl.
Could anyone please tell me what this means?
_
Hello Anupa,
Did you try to open the files in their directory?
Ye
On Mon, Jul 1, 2013 at 12:23 AM, Anupa AV wrote:
> Dear All,
>
> When I tried to running qdec, I'm getting the following error.
>
> qdec.bin: error while loading shared libraries: libjpeg.so.62: cannot open
> shared object file
Hello,
Is this running in Ubuntu? If so, it should be solved by running the
following command:
$ sudo apt-get install libjpeg62
-Zeke
> Dear All,
>
> When I tried to running qdec, I'm getting the following error.
>
> qdec.bin: error while loading shared libraries: libjpeg.so.62: cannot open
> s
Dear expert,
I got an error while clicking the Monte Carlo simulation in qdec.
I am using Mac 10.6 and qdec version 1.4, freesufer 5.1
Have no clue why it always gives this error in the terminal:
mri_surfcluster --in
/Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thi
Mike,
This qdec error results from a slightly out-of-date tcl script (an
oversight on my part when I updated qdec for v4.0.2). Attached to this
email is the file fsgdfPlot.tcl, which contains the function
FsdgfPlot_IsWindowShowing, and should be copied to
$FREESURFER_HOME/lib/tcl (overwriting the
Ryan,
Can you send me the output of:
ldd $FREESURFER_HOME/bin/qdec.bin
This error, and one seen by George He, who also is using Fedora release
8, tells me that the problem is related to Tcl/Tk on that platform.
Freesurfer includes a Tcl/Tk/Tix/BLT bundle in its distribution, so I
dont know why
Woo-Suk,
A file was missing from the distribution. That file, fsgdfPlot.tcl, is
attached to this email. Copy it to:
$FREESURFER_HOME/lib/tcl
Nick
On Mon, 2008-02-11 at 11:03 +0900, Woo-Suk, Tae wrote:
> I've processed my data with FreeSurfer 3.04,
> and ran the group data with qdec of Fre
Hi All,
I am trying to use Qdec to analyze a dataset, and am getting the following
error:
ERROR: All stat files should have the same segmentations
If one or more stats file have different segs from others,
use --common-segs or --all-segs flag depending on the need.
The problem is that I haven't
what does the error message in the terminal say?
n.
On Mon, 2010-07-26 at 17:01 -0400, aekai...@umich.edu wrote:
> Hello FS experts,
>
> I have attached a gimped image of an error I have encountered.
>
> it seems to only occur when I choose diagnosis as a discrete variable.
> however I made the
Good afternoon,
When running qdec, I receive the following error message:
Writing to /Volumes/workingdata/FTD/T1/subjects/qdec/Untitled/contrasts.sig.mgh
reading group avg surface area 822 cm^2 from file
ERROR: could not find volume
/Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/../mri/ori
Hi all,
I'm trying to run qdec on a SL 4.5:
[EMAIL PROTECTED] ~]$ uname -a
Linux neuro01.pic.es 2.6.9-55.0.12.ELsmp #1 SMP Thu Nov 1 08:41:34 CST 2007
i686 i686 i386 GNU/Linux
[EMAIL PROTECTED] ~]$ /lib/libc.so.6
GNU C Library stable release version 2.3.4, by Roland McGrath et al.
Copyright (C)
Hi Sky,
what are the first few lines of:
/cind/00/FSv4Test/Freesurfer/subjects/average/label/lh.cortex.label
is your partition full?
Bruce
On Wed,
16 Apr 2008, Sky Raptentsetsang
wrote:
Hello Freesurfers,
I am having troubles analyzing some data in the qdec tool. I have two
groups of th
Sky,
Can you load the lh.cortex.label file in tksurfer? If not, then its
corrupted somehow, and would need to be recreated outside of qdec.
Nick
On Wed, 2008-04-16 at 17:49 -0700, Sky Raptentsetsang wrote:
> Hello Freesurfers,
>
> I am having troubles analyzing some data in the qdec tool. I ha
Hi Bruce,
Here are the first few lines of the lh.cortex.label:
#label , from subject ??
149955
==>
/cind/00/FSv4Test/Freesurfer/subjects/average/make_cortex_label.tmp.20230/lh.G_and_S_occipital_inferior.label
<==
161841 -37.845 -74.578 -13.988 0.00
161842 -37.786 -74.111 -14.300 0.0
Hi Nick,
When I try to load the lh.cortex.label in tksurfer I get the following
error print out in the SSh tool window:
[EMAIL PROTECTED] subjects]$ tksurfer average lh pial
Using Freesurfer version 4.
Subjects Directory is /cind/00/FSv4Test/Freesurfer/subjects
Sessions Directory is /home/sky
that looks okay. What about the last two lines?
On Thu, 17 Apr 2008, Sky
Raptentsetsang wrote:
Hi Bruce,
Here are the first few lines of the lh.cortex.label:
#label , from subject ??
149955
==>/cind/00/FSv4Test/Freesurfer/subjects/average/make_cortex_label.tmp.20230/lh.G_a
nd_S_occipital_inf
what are the last couple of lines of that file?
On Thu, 17 Apr 2008, Sky
Raptentsetsang wrote:
Hi Nick,
When I try to load the lh.cortex.label in tksurfer I get the following
error print out in the SSh tool window:
[EMAIL PROTECTED] subjects]$ tksurfer average lh pial
Using Freesurfer versio
Here's the last two:
==>
/cind/00/FSv4Test/Freesurfer/subjects/average/make_cortex_label.tmp.20230/lh.S_temporal_superior.label
<==
161249 -45.309 4.980 -29.869 0.00
161250 -45.807 4.629 -30.666 0.00
161325 -45.049 6.874 -30.794 0.00
161326 -45.879 6.790 -32.199 0.00
1
Ming,
I'm planning on releasing a new freesurfer v4.0.5 this week, which will
include a distribution for Tiger on Intel.
Nick
On Tue, 2008-06-10 at 02:39 -0500, Ming Hsu wrote:
> Hi, I am getting a qdec error on FreeSurfer 4.0.2 on Tiger. The error has
> been mentioned on the forum before. In
Hi Prapti,
I think you have to modify the $LD_LIBRARY_PATH shell variable.
first find where libtiff.so.3 is. Usually "locate libtiff.so.3" will tell
you
where the file is at. On my machine, it is in /usr/lib/ and /usr/lib64/
then
LD_LIBRARY_PATH = $LD_LIBRARY_PATH:/usr/lib64/
export LD_LIBRARY_PATH
It's possible that you are running a Debian-based distro and just
don't have libtiff.so.3; but you probably have libtiff.so.4, so you
can create a symlink so that libtiff.so.3 points to libtiff.so.4.
I have to do this In Debian "etch" and later
mjp
On Nov 26, 2008, at 4:26 PM, "Siddharth
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
(reposting the answer to the list)
be sure to create the .levels and qdec.table.dat files in an editor that
doesnt add control characters. on both the mac and much of linux, a
handy editor to do this is 'pico'. so:
pico gender.levels
and delete stuff that's not an alpha-numeric char (usually t
How did you create the file? If on a mac or windows, there might be
hidden characters that prevent it from being parsed correctly
On 07/08/2016 02:34 PM, shi yao wang wrote:
> Dear FS experts:
> I am trying to qdec to analysis FS results. when I loading
> qdec.table.dat, it shows cannot open the
Hello,
When I'm loading qdec, I get the following error messages. Can you please help.
Thanks.
Kaja
ERROR: In
/usr/pubsw/packages/vtk/5.6.0/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx,
line 405
vtkXOpenGLRenderWindow (0x7084e40): Could not find a decent visual
ERROR: In
/usr/pubsw/package
16 00:30
Kopi: freesurfer@nmr.mgh.harvard.edu
Emne: Re: [Freesurfer] qdec error
Hi. My first answer in this list. So
Hello,
When I'm loading qdec, I get the following error messages. Can you please help.
Thanks.
Kaja
ERROR: In
/usr/pubsw/packages/vtk/5.6.0/src/VTK/Rendering/vtkXOpenGLRender
He Lena, can you repost with the error message as part of the email
instead of as a word doc file.
doug
On 09/28/2015 12:45 PM, Lim, Lena wrote:
>
> Sorry, I am re-posting below again for help…
>
> Dear Experts,
>
> I tried to see if the average area/thickness differ between the 2
> groups (HC
urfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: 28 September 2015 18:26
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] qdec error
He Lena, can you repost with the error message as part of the email instead of
as
pjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender/qdec.fsgd
> dods --glmdir
> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender --surf
> fsaverage lh --label
> /home/spjwker_PAC/Lena/CT_SA/FSL/fsaverage/label/lh.aparc.label --C
> /home/spjwker_PA
ss-PCHC-covIQAgeGender
> /y.mgh --fsgd
> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender
> /qdec.fsgd dods --glmdir
> /home/spjwker_PAC/Lena/CT_SA/FSL/qdec/lh-thickness-PCHC-covIQAgeGender
> --surf fsaverage lh --label
> /home/spjwker_PAC/Lena/CT_SA/FSL/fsa
Lena
Sent: 29 September 2015 12:42
To: 'Freesurfer support list'
Subject: Re: [Freesurfer] qdec error
Thanks, Doug. I used the qdec table attached.
L
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of
: 'Freesurfer support list'
Subject: Re: [Freesurfer] qdec error
Hi Lena,
Have you changed your Group.levels file to include the two groups you are
currently looking at? If this doesn't match your qdec table it will not work.
Best wishes,
Amanda
__
age-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Worker, Amanda
> Sent: 29 September 2015 14:11
> To: 'Freesurfer support list'
> Subject: Re: [Freesurfer] qdec error
>
> Hi Lena,
>
> Have you changed
hi, i never recieved answer for this problem...any ideas?
On Tue, Jul 8, 2014 at 11:13 AM, Anna Jonsson wrote:
> Dear group, I now have error loading my qdec table into qdec, for this
> error
>
> fsid column:1
> Number of factors: 8
> Number of subjects: 168
> ERROR: QdecSubject::GetC
you can't in QDEC. You'll have to use the command line stream
doug
On 07/29/2014 10:43 AM, Jon Alan Wieser wrote:
>
> HI freesurfer experts,
>
> I am running a qdec analysis, my first factor has 3 levels, my other 2
> factors have 2 levels, I select my first and second factors and hit
> "Analy
Try removing the mean from the age. By this I mean to compute the mean
age over all subjects regardless of group, then subtract the mean from
all ages.
doug
On 07/29/2014 02:39 PM, Jon Alan Wieser wrote:
>
> I'm getting the following erorr when running Qdec "Analyze"
>
> Model Factors:
>
>
> Di
that fixed the problem
Thanks
Jon
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N Greve
Sent: Tuesday, July 29, 2014 4:27 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] qdec error
Try removing the mean from the
Try normalizing your covariates (ie, remove the mean and divide by the stddev)
On 1/21/2020 7:39 AM, vittal korann wrote:
External Email - Use Caution
Dear FreeSurfer experts
I ran QDEC and got the following error.
Design matrix --
1.0 1.04000 -1.38574 2.0
External Email - Use Caution
Dear Douglas
I did normalize ICV values. This is something else I guess.
With regards
Vittal
On Tue, Jan 21, 2020 at 6:09 PM vittal korann
wrote:
> Dear FreeSurfer experts
>
> I ran QDEC and got the following error.
>
> Design matrix
I would normalize all the variables. Eg, column 2 is nearly identical to column
1
On 1/22/2020 1:03 AM, vittal korann wrote:
External Email - Use Caution
Dear Douglas
I did normalize ICV values. This is something else I guess.
With regards
Vittal
On Tue, Jan 21, 2020 at 6:09 PM vit
We are not supporting qdec anymore. Try using the "command line stream",
ie, mris_preproc, FSGD, etc
On 12/1/2021 6:47 PM, Arian Klows wrote:
External Email - Use Caution
Dear FS experts,
I have freesurfer-linux-centos7_x86_64-7.1.1 on my computer and when I
run qdec, I get the fol
Hello Experts,
This QDEC error is one that appears in the archives, but I did not see a
solution that solves my problem. The error (after some information about
initialization of the program) is as follows:
SUBJECTS_DIR : /home/freesurfer_ocd
Parsing the .stats files
ERROR: The stats file /hom
Dear list,
Sorry to repost it again, but i had rechecked it and found that all the
directories have no permission problems, but qdec could not load this CSD
file. Not sure why it is like this.
Thank you for the help again!
natalia
On Tue, Jul 10, 2012 at 3:20 PM, Natalia h wrote:
> Dear expert
Does
/Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm9/abs/th20/mc-z.csd
exist and do you have read permission?
doug
On 07/10/2012 09:20 AM, Natalia h wrote:
> Dear expert,
>
> I got an error while clicking the Monte Carlo simulation in qdec.
> I am using Mac 10.6 and qde
You have either too many effects that you are trying to fit or you don't
have enough subjects. Decrease one or increase the other!
doug
On 01/28/2013 01:00 PM, Pablo Emanuel wrote:
> Hi,
> My name is Pablo. I am using the freesurfer in my analyses, but when I
> try use the QDEC to statistical an
I downloaded some packages for tcl and tk, but they didn't have any effect. I
also get this error, which I forgot to include:
ERROR: In /usr/pubsw/packages/KWWidgets/CVS/src/KWWidgets/vtkKWTkUtilities.cxx,
line 221
vtkKWQdecApp (0x881c1f0): Script:
FsgdfPlot_IsWindowShowing 0
Returned Error on
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 go
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 av
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 aft
Gonzalo,
Attached is a file called fsgdfPlot.tcl, which was missing from
freesurfer v4.0.2. Copy it to your $FREESURFER_HOME/lib/tcl directory.
Nick
On Wed, 2008-03-05 at 12:42 +0100, Gonzalo Sanchez Benavides wrote:
> Hi all,
>
> I'm trying to run qdec on a SL 4.5:
>
> [EMAIL PROTECTED] ~]$
Dear FS-Experts,
I am trying to run Freesurfer on a Ubuntu 7.10 (Gutsy Gibbon) system and
unfortunately I encounter the same problem that Gonzalo Sanchez
Benavides and also William McGarry described in earlier emails. Copying
the new fsgdfPlot.tcl into the $FREESURFER_HOME/lib/tcl directory
s
Thanks Nick, (sorry I did't response this mail before in the proper way)
I copied your file and the IsWindowShowing error was fixed, but the second
error persists:
ERROR: In /usr/pubsw/packages/KWWidgets/CVS/src/KWWidgets/vtkKWApplication.cxx,
line 1182
vtkKWQdecApp (0x87903e0): TclTk error: inva
Hello to all the kind people at FreeSurfer! We are having difficulty running
qdec. After solving my issues loading tables, qdec is having difficulty
loading certain files.
Our current error is that qdec says it cannot find the lh.curv file for the
fsaverage subject.
-I have verified that this file
Hi,
Running Freesurfer v405 on RHEL5. Tried to launch qdec from the command prompt.
While the splash screen did appear with the inflated brain surface, the qdec
interface did not appear (even after 10min). When I tried to CTRL-C the
terminal window, the following error message appeared:
[EMAIL
Julia,
If you haven't already tried this, can you make sure that your display
is set to use 'millions' of colors (thats the Mac OS's way of setting
24bit color).
If that doesnt matter, you can try using the newest freesurfer, v4.1.0,
which is built against vtk v5.2, which is newer than what is in
Dear all,
I've come across a similar problem to the one described before in qdec,
but cannot find a solution for it,
I've previously visualised my data using qdec, but when I tried to run
it again I get the following error. I've checked to make sure my subject
is named correctly and I am in the
Hi,
I'm a new user of qdec and I'm trying to run a cortical thickness analysis
in qdec between Schizophrenic patients and healthy controls.
I have run "recon-all -i" and "recon-all -s -qcache" on my data
and it says that this has run successfully without any errors.
But when I hit analyze on the
Hi,
I'm a new user of qdec and I'm trying to run a cortical thickness analysis
in qdec between Schizophrenic patients and healthy controls.
I have run "recon-all -i" and "recon-all -s -qcache" on my data
and it says that this has run successfully without any errors.
But when I hit analyze on the
Hi all,
I am running surface area analysis in qdec and I get this error:
$Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $
cwd /Users/vinagoghari/Documents/Wanda/Wanda_SFS
cmdline mri_glmfit --y
/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/lh_area_covariates/y.mgh
--fsgd
/Users/v
Dear all,
I am trying to run statistical analysis on cortical thickness data using
Qdec. I have one group of control subjects that are split into three
genotype groups. I want to investigate if cortical thickness significantly
between the three genotype groups. Is it possible to look at difference
Ken, can you send the offending file and the file from the 6th subject?
doug
On 08/08/2013 03:09 PM, Rando, Kenneth wrote:
> Hello Experts,
>
> This QDEC error is one that appears in the archives, but I did not see
> a solution that solves my problem. The error (after some information
> about in
Hi everyone,
I got the error I just mentioned. Terminal window says "no contrasts specified".
I am trying to use "timepoint" (1-4) as a discrete factor to look at thickness
across time. I guess I will have to resort to longitudinal processing?
Thanks for the help
-Anson
***
Ryan,
It appears that tcsh is not being used. Enter tcsh by typing:
tcsh
then initialize freesurfer by typing:
source $FREESURFER_HOME/SetUpFreeSurfer.csh
then try the qdec utility again (and if still gives the same problems,
then run the ldd command and send me the results).
You can als
[EMAIL PROTECTED] qdec]$ source FREESURFER_HOME/bin/tcl_setup
bash: /usr/local/freesurfer/bin/tcl_setup: line 48: syntax error near
unexpected token `setenv'
bash: /usr/local/freesurfer/bin/tcl_setup: line 48: `if ( -e
$TCLLIBPATH/tcl8.3 ) setenv TCL_LIBRARY $TCLLIBPATH/tcl8.3'
[EMAIL PROTECT
[EMAIL PROTECTED] ~]$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
freesurfer-Linux-rh9-stable-pub-v4.0.2
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer
FSFAST_HOME /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii
SUBJECTS_DIR
Ryan,
I forgot to mention, prior to running the ldd command, type this:
source $FREESURFER_HOME/bin/tcl_setup
source $FREESURFER_HOME/bin/vtk_setup
source $FREESURFER_HOME/bin/kww_setup
Also, it should not be necessary to download a tcl/tk package, as the
tcl/tk package included with freesurfer
Christian,
Unfortunately, I can't find a solution to this problem. We don't have a
Ubuntu system to experiment with, so I can't recreate the problem to
debug it. We use Linux Centos4. Have you tried the centos4 freesurfer
distribution? The rh9 freesurfer distribution is for old Linux systems
(
Dear experts,
For reporting purposes,
we have the same problem with VTKKWWidgets running qdec in freesurfer rh9
release both, on Scientific Linux, as reported in "qdec error (2)" thread,
and also now on Fedora 8.
Cheers
2008/3/13, Nick Schmansky <[EMAIL PROTECTED]>:
>
> Christian,
>
> Unfortunate
Mischka,
You mention that you created your own average subject (this is fine,
although the default 'fsaverage' subject is sufficient in most cases, as
the average is used just for display). If you do choose to create and
use your own average subject, two things to keep in mind are:
- include the
-
Hi
FOrgot to attach the file of lh.cortex.label with my last email. Here it is.
My error message is the same as Sky's: see
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07271.html
Looked like there was no solution for it at the time (April 17th, 2008),
what about now please
Jenifer,
Is this new to v405, or have prior versions also had this problem?
Are you running directly from the terminal? Or over an ssh or vnc
connection? If over vnc, from what kind of machine?
Nick
On Wed, 2008-07-23 at 11:14 -0500, Juranek, Jenifer wrote:
> Hi,
> Running Freesurfer v405 on
-
From: Nick Schmansky [mailto:[EMAIL PROTECTED]
Sent: Wed 7/23/2008 3:47 PM
To: Juranek, Jenifer
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] qdec ERROR: Rendering vtkXOpenGLRenderWindow
Jenifer,
Is this new to v405, or have prior versions also had this problem?
Are you running directly
ox (not across VPN or SSH
> or VNC).
>
> Thanks for any help you can provide,
> Jenifer
>
> -Original Message-
> From: Nick Schmansky [mailto:[EMAIL PROTECTED]
> Sent: Wed 7/23/2008 3:47 PM
> To: Juranek, Jenifer
> Cc: Freesurfer Mailing List
> Su
dSection
Any other sections of the xorg.conf file I should check?
Is there a particular screen resolution I should check under Section "Screen"
Options or Modes?
Thanks,
Jenifer
-Original Message-
From: Nick Schmansky [mailto:[EMAIL PROTECTED]
Sent: Wed 7/23/2008 4:04 PM
Prapti,
Try deleting the directory 'qdec/Untitled' and run it again. Prior to
v4.2.0, qdec did not delete that directory, which is the default working
directory, so its possible some incompatible files from a prior run were
lingering.
Nick
On Thu, 2009-03-05 at 09:42 +1100, Prapti Gautam wrote
Deleting 'qdec/Untitled' worked! Thanks,
Prapti
-Original Message-
From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu]
Sent: Thursday, 5 March 2009 11:10 AM
To: Prapti Gautam
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] qdec error in analyze
Prapti,
Try de
;
> Prapti
>
> -Original Message-
> From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu]
> Sent: Thursday, 5 March 2009 11:10 AM
> To: Prapti Gautam
> Cc: Freesurfer Mailing List
> Subject: Re: [Freesurfer] qdec error in analyze
>
> Prapti,
>
> Try deleti
Hello,
I am getting an error when I try to use the "Analyze" feature in the Design
tab of Qdec.
The error is:
Error in Analyze: Couldn't open file
//FREESUFER_SUBJECTS/106966-100/surf/lh.thickness.fwhm10.fsaverage.mgz
or .mgh file
However, when I go into the 106966-100 subject directory, the fi
1 - 100 of 150 matches
Mail list logo
