Re: [Freesurfer] Qdec error

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

[Freesurfer] Qdec error

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?

Re: [Freesurfer] QDEC error Two Groups three covariates

Sorry, one of the reasons we stopped supporting QDEC was because it became impossible to debug these kinds of things. Please use the command line stream (ie, create an FSGD file and contrast matrices, run mris_preproc, mris_fwhm, and mri_glmfit). I can help you once you recreate the error On

[Freesurfer] QDEC error Two Groups three covariates

External Email - Use Caution Dear FreeSurfer Developers, I’m attempting to run a cortical thickness correlation analysis regressing out the effect of brain size, age and gender. However, when attempting to run this analysis in qdec (or trying to use mri_glmfit separately) I get

Re: [Freesurfer] Qdec error

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

Re: [Freesurfer] Qdec error

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

Re: [Freesurfer] Qdec error

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

[Freesurfer] Qdec error

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

[Freesurfer] qdec error

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,

Re: [Freesurfer] Qdec error in analysis

Can you send the command line, your key strokes and button presses, and the terminal output leading up to the error message? On 07/06/2017 12:27 AM, AYUSHI SHUKLA wrote: > Hi, > > Thank you for your response. > > Yes, I checked, and I do have the permission to read the file. > > Warm Regards >

Re: [Freesurfer] Qdec error in analysis

Hi, Thank you for your response. Yes, I checked, and I do have the permission to read the file. Warm Regards Ayushi On Thu, 6 Jul 2017 at 09:42, Douglas Greve wrote: > Do you have read permission to that file? > > On 6/29/17 7:04 AM, AYUSHI SHUKLA wrote: > > Hi, >

Re: [Freesurfer] Qdec error in analysis

Do you have read permission to that file? On 6/29/17 7:04 AM, AYUSHI SHUKLA wrote: 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

[Freesurfer] Qdec error in analysis

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

[Freesurfer] QDEC Error in Analysis

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

[Freesurfer] QDEC error writing fsgd and generating contrasts

Dear FreeSurfer Developers, I have the following problem and would be very happy if you could help me. I have searched the list and did not find the solution to my problem. I am using FS 5.1 because I have to reanalyze data which I preprocessed in 2014. Back then recon-all and all the

[Freesurfer] QDEC error writing fsgd and generating contrasts

Dear FreeSurfer Developers, I have the following problem and would be very happy if you could help me. I have searched the list and did not find the solution to my problem. I am using FS 5.1 because I have to reanalyze data which I preprocessed in 2014. Back then recon-all and all the

Re: [Freesurfer] Qdec Error: Couldn't open qcache file

I have already solved the problem. Thank you for your support. Best regards Jana Dinges -- Diese Nachricht wurde von meinem Android Mobiltelefon mit GMX Mail gesendet.Am 07.09.16, 23:57, Douglas N Greve schrieb: *Can you send the terminal output for recon-all

Re: [Freesurfer] Qdec Error: Couldn't open qcache file

*Can you send the terminal output for recon-all -s subjid -qcache* On 09/01/2016 02:53 PM, Jana Dinges wrote: > Dear freesurfer community, > we are conducting cortical-thickness analysis using freesurfer-5.3.0 and have > been experiencing some problems with the final analysis steps. > We are

Re: [Freesurfer] qdec error

: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/vtkXOpenGLRenderWindow.cxx

Re: [Freesurfer] qdec error

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

[Freesurfer] Qdec Error

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:

Re: [Freesurfer] qdec error

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

[Freesurfer] qdec error

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

Re: [Freesurfer] QDEC. Error in Analyze: command failed: mri_glmfit

Hi Douglas, Thank you for the response. I didn't know I couldn't do it without the command line. I will try it and think like this should work. Best, Max On 21/01/2016, at 18:57, Douglas N Greve wrote: > As the error message says, you can only have two levels. With 3 levels, > you must

Re: [Freesurfer] QDEC. Error in Analyze: command failed: mri_glmfit

As the error message says, you can only have two levels. With 3 levels, you must use the "command line" stream, ie, mris_preproc, mri_surf2surf, mri_glmfit, and mri_glmfit-sim. There are tutorials on the wiki. On 01/20/2016 08:53 AM, BAUTISTA-PERPINYA Maximilià wrote: > Thank you for the reply

Re: [Freesurfer] QDEC. Error in Analyze: command failed: mri_glmfit

Thank you for the reply Douglas, Factor 1 (diagnosis) has 3 levels (BPD, CCP, NPC). I created using the vi editor, one line for each level. Same as factor 2. Max On dijous 14 gener 2016 22:20 CET, Douglas N Greve wrote: > how many levels does factor 1 have?

Re: [Freesurfer] QDEC. Error in Analyze: command failed: mri_glmfit

Thank you for the reply Douglas, Factor 1 (diagnosis) has 3 levels (BPD, CCP, NPC). I created using the vi editor, one line for each level. Same as factor 2. Max On dijous 14 gener 2016 22:20 CET, Douglas N Greve wrote: > how many levels does factor 1 have?

Re: [Freesurfer] QDEC. Error in Analyze: command failed: mri_glmfit

I have the same problem. I observed that this error appears when you select a factor with 3 or more levels. Factors of 2 levels works fine. 2016-01-18 9:32 GMT+01:00 BAUTISTA-PERPINYA Maximilià < maximila.bautista-perpi...@etu.unistra.fr>: > Thank you for the reply Douglas, > > Factor 1

[Freesurfer] QDEC. Error in Analyze: command failed: mri_glmfit

Hi there experts, I'm runing qdec to analyze my subject data. I am able to import the qdec.table.dat, but the problem comes in the Design step. I select 'Volume-based' measure, 'Diagnosis' as my discrete independent variable and 'LeftAmygdala' as the continuous variable. I don't select any

Re: [Freesurfer] QDEC. Error in Analyze: command failed: mri_glmfit

how many levels does factor 1 have? How did you make the factor file? On 01/14/2016 05:30 AM, BAUTISTA-PERPINYA Maximilià wrote: > Hi there experts, > > I'm runing qdec to analyze my subject data. I am able to import the > qdec.table.dat, but the problem comes in the Design step. I select >

Re: [Freesurfer] qdec error

To: '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 From

Re: [Freesurfer] qdec error

oun...@nmr.mgh.harvard.edu> on behalf of Lim, Lena <lena@kcl.ac.uk> 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

Re: [Freesurfer] qdec error

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 your Group

Re: [Freesurfer] qdec error

vIQAgeGender > /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/fsaverage/lab

[Freesurfer] qdec error

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

Re: [Freesurfer] qdec error

...@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 a word doc

Re: [Freesurfer] qdec error

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

Re: [Freesurfer] qdec error

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_PAC/Lena/CT_

[Freesurfer] qdec error

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?

[Freesurfer] QDEC error- Couldn't open file

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 /personal_path_to_file/FREESUFER_SUBJECTS/106966-100/surf/lh.thickness.fwhm10.fsaverage.mgz or .mgh file However, when I go into the 106966-100

Re: [Freesurfer] qdec error

Subject: Re: [Freesurfer] qdec error 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

[Freesurfer] QDEC error and analysis termination during 'concatenating volumes' and different results from Monte Carlo Simulation from QDEC Command line

: [Freesurfer] QDEC error and analysis termination during 'concatenating volumes' To: freesurfer@nmr.mgh.harvard.edu Message-ID: 53d678b8.7060...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=UTF-8; format=flowed I can't make anything out of the error msg gif. Somewhere

[Freesurfer] qdec error

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 levels

[Freesurfer] qdec error

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:

Re: [Freesurfer] QDEC error and analysis termination during 'concatenating volumes' and different results from Monte Carlo Simulation from QDEC Command line

shot? doug Thank you so much for your time and help. Best wishes, Hanna -- Date: Mon, 28 Jul 2014 12:22:16 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] QDEC error and analysis termination during 'concatenating volumes

Re: [Freesurfer] qdec error

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 Analyze I

Re: [Freesurfer] qdec error

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: Discrete

Re: [Freesurfer] Freesurfer] QDEC error and analysis termination during 'concatenating volumes'

: Fri, 25 Jul 2014 09:50:51 -0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] QDEC error and analysis termination during 'concatenating volumes' To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.03.1407250949560.20

Re: [Freesurfer] QDEC error and analysis termination during 'concatenating volumes'

I can't make anything out of the error msg gif. Somewhere in there, there should be a mris_preproc command line. Can you try cutting and pasting that into a shell? Trying to do this in the context of qdec will be difficult doug On 07/25/2014 05:09 AM, Isotalus, Hanna wrote: Dear FreeSurfer

[Freesurfer] Freesurfer] QDEC error and analysis termination during 'concatenating volumes'

-- Date: Fri, 25 Jul 2014 09:50:51 -0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] QDEC error and analysis termination during 'concatenating volumes' To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID

[Freesurfer] QDEC error and analysis termination during 'concatenating volumes'

Dear FreeSurfer gurus, I am using QDEC to run my analyses on a large data set. The analysis works fine with up to 1224 subjects but as soon as I add subject 1225 I get an error and the analysis stops. The error displays during 'concatenating volumes' and it just displays file names. When I try

Re: [Freesurfer] QDEC error and analysis termination during 'concatenating volumes'

Hi Hanna seems like you are running out of memory. How much RAM do you have on your machine? Are there other things running on it that you can kill, or is there a larger RAM machine you can use? Doug will be back next week and perhaps will comment also. If you don't hear from him you should

Re: [Freesurfer] qdec error

hi, i never recieved answer for this problem...any ideas? On Tue, Jul 8, 2014 at 11:13 AM, Anna Jonsson ajonsso...@gmail.com 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:

[Freesurfer] qdec error

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

[Freesurfer] QDEC Error loading the data table

Hello FreeSurfer Experts, I am trying to run QDEC for a group comparison study. I am following the tutorial found on http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis_freeview However, when I try to load my data table it returns the error.

Re: [Freesurfer] QDEC Error loading the data table

That does look pretty silly. How did you create your qdec.table.dat and level files? If you created them under windows, then that could be the problem. If not, post your qdec.table.dat file and the gender.level file and I'll take a look On 06/23/2014 01:33 PM, Mohammed Goryawala wrote: Hello

Re: [Freesurfer] QDEC Error loading the data table

Hi Doug, I did create them in windows. I will recreate them on the linux machine and carry out the processing. Thanks for the help. Mohammed On Mon, Jun 23, 2014 at 1:38 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: That does look pretty silly. How did you create your qdec.table.dat

[Freesurfer] QDEC Error

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

[Freesurfer] QDEC error loading y

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

Re: [Freesurfer] QDEC error loading y

Is the disk full? On 01/27/2014 04:55 PM, Wanda Truong wrote: 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

[Freesurfer] qdec error

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

[Freesurfer] QDEC error in asegstats2table

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

Re: [Freesurfer] QDEC error in asegstats2table

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

Re: [Freesurfer] Qdec error

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 shared

[Freesurfer] Qdec error

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.

Re: [Freesurfer] Qdec error

Hello Anupa, Did you try to open the files in their directory? Ye On Mon, Jul 1, 2013 at 12:23 AM, Anupa AV av.an...@yahoo.com 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

[Freesurfer] Qdec error and design problem

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

Re: [Freesurfer] Qdec error and design problem

Hi Sinead, you cannot use QDEC for this design since it has one factor with 3 levels (only 2 levels possible now). You can create an FSGD file, follow the example here: http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V doug On 05/09/2013 06:42 AM, Sinead Kelly wrote: Dear all, I am

Re: [Freesurfer] QDEC ERROR ANALYSE

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

Re: [Freesurfer] qdec - ERROR: CSDread():

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 qdec

Re: [Freesurfer] qdec - ERROR: CSDread():

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

[Freesurfer] qdec - ERROR: CSDread():

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

[Freesurfer] Qdec error

I got an error beginning with this. Thanks for any help Error in analyze: command failed: mri_glmfit --y /mypath/qdec/LH_insula_thick/y.mgh --fsgd ** Electronic Mail is not secure, may not be read every day, and should not be used for

[Freesurfer] Qdec Error (more/better info)

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

[Freesurfer] qdec Error

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

[Freesurfer] Qdec Error in analyze: command failed

Hi, I'm getting an error in analyze: command failed: mri_concat notification when trying to run qdec on a within subjects analysis (N=29, looking at thickness and social functioning whilst controlling for ICV). I'm not sure what this means. See the output below. Thanks! Laura. Data table

Re: [Freesurfer] Qdec Error: MatrixMultiply: ml is null!

Hi Doug, I saw on a previous mailing earlier this week that someone has been having a similar error and that your advice was to demean the ICV. I apologise if this is a stupid question, but what does it mean to demean? And, how do i do that? Thanks in advance! Laura. On Wed, Feb 29, 2012 at

Re: [Freesurfer] Qdec Error: MatrixMultiply: ml is null!

it means to subtract the mean of the icv values from each. that way the values are close to zero, and closer in value to the other values in the glm (which seems to make the glm happier). n. On Thu, 2012-03-01 at 11:04 -0500, Laura Tully wrote: Hi Doug, I saw on a previous mailing

Re: [Freesurfer] Qdec Error: MatrixMultiply: ml is null!

In the terminal output, it says that it will exclude a subject because there is a NaN data point. NaN = not a number. Check your data table to make sure that everything is ok. doug Nick Schmansky wrote: it means to subtract the mean of the icv values from each. that way the values are close

Re: [Freesurfer] Qdec Error: MatrixMultiply: ml is null!

Hi Nick and Doug, Thanks for the help, I'll give the demeaning a try. Re: the missing values - all my missing data points are denoted with NaN so that I can include those subjects on the measures that they do have, but exclude them on measures they don't have (I think this is the only way to

Re: [Freesurfer] Qdec Error: MatrixMultiply: ml is null!

If it's working with demeaning, then that was the problem. The subjects with NaNs are going to be excluded entirely as we have no way to estimate missing fields. doug Laura Tully wrote: Hi Nick and Doug, Thanks for the help, I'll give the demeaning a try. Re: the missing values - all my

Re: [Freesurfer] Qdec Error: MatrixMultiply: ml is null!

The demeaning/mean centering worked a treat! Thank you freesurfer experts! Laura. On Thu, Mar 1, 2012 at 11:36 AM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: If it's working with demeaning, then that was the problem. The subjects with NaNs are going to be excluded entirely as we have no

Re: [Freesurfer] Qdec Error: MatrixMultiply: ml is null!

btw, to tie-in and follow-up on a related posted question about missing values, if NaN is used for the missing value (as you did), then qdec will automatically exclude that subject in an analysis if that variable is used. the rejected subject(s) will be printed to the terminal. N. On Thu,

Re: [Freesurfer] Qdec Error: MatrixMultiply: ml is null!

Hi Doug, Below is the output in the terminal window from running the analysis to the crash. Attached are the qdec.fsgd and y.fsgd files from the qdec output. I'm not actually sure what these file represent - could you enlighten me? Thanks! Laura. Number of subjects: 55 Number of factors:

[Freesurfer] Qdec Error: MatrixMultiply: ml is null!

Hi, I am trying to run a between group analysis in QDEC whilst controlling for intrancranial volume. The design has one dichotomous variable (group2, group2), one continuous (performance on behavioral task), and one nuisance variable (intracranial volume). each time I run it qec crashes with the

Re: [Freesurfer] Qdec Error: MatrixMultiply: ml is null!

Can you send the fsgd file that is created? Also, please send more text output. It's hard to tell from a single line. doug Laura Tully wrote: Hi, I am trying to run a between group analysis in QDEC whilst controlling for intrancranial volume. The design has one dichotomous variable

[Freesurfer] QDEC : Error loading the data table.

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:

Re: [Freesurfer] QDEC : Error loading the data table.

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

Re: [Freesurfer] QDEC : Error loading the data table.

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

Re: [Freesurfer] qdec error message

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

Re: [Freesurfer] qdec error message

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

[Freesurfer] qdec error message

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

Re: [Freesurfer] qdec error

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

[Freesurfer] Qdec Error Question

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

Re: [Freesurfer] Qdec Error Question

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

Re: [Freesurfer] QDEC error

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

[Freesurfer] QDEC error

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

[Freesurfer] qdec error in analyze

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

Re: [Freesurfer] qdec error in analyze

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

RE: [Freesurfer] qdec error in analyze

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 deleting

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