Re: [Freesurfer] QDEC Alternative

External Email - Use Caution no plans for a new gui. you might look up qdecr. this is a 3rd party altenative that uses R; I've never used it myself, so I don't know how well it works on voxel-wise analysis or if there is a gui On 5/1/2023 2:00 PM, Lauren Stephens wrote:   

[Freesurfer] QDEC Alternative

External Email - Use Caution Dear Freesurfers, We are looking to do a voxel-wise analysis on cross sectional and longitudinal data. We wanted to use QDEC but see that it is no longer maintained and has been removed in version 7.3.2 which we are using. Is there going to be a

Re: [Freesurfer] Qdec: Can't find a usable init.tcl

External Email - Use Caution Hello Rosa, The qdec program is deprecated in 7.X releases and is no longer maintained. In the 7.X releases, you can try using freeview for images and from the command line there are the mri* commands (mris_surf2surf, mri_glmfit, mri_glmfit-sim,

[Freesurfer] Qdec: Can't find a usable init.tcl

External Email - Use Caution Dear FreeSurfer Developers, I'm attempting to open Qdec on my linux server. I used to open it with freesurfer 6.0.0 activated to analyze our local gyrification index data. That version is not available anymore in our service; hence, the Freesurfer

Re: [Freesurfer] qdec analysis error

Sorry, we are not supporting qdec anymore. You will need to use the command-line stream On 3/23/2022 8:02 AM, David wrote: External Email - Use Caution Hello FreeSurfer Developers, I have a problem. Can you help me freesurfer version : 6.0.0 Load qdec when I run qdec.table.dat,

[Freesurfer] qdec analysis error

External Email - Use Caution Hello FreeSurfer Developers, I have a problem. Can you help me freesurfer version : 6.0.0 Load qdec when I run qdec.table.dat, the data is loaded correctly, but when I design, I choose discrete and continuous factors for analysis The error log is

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 command not found

We are no longer supporting qdec On 9/21/2021 2:15 PM, Fabiola Macruz wrote: External Email - Use Caution External Email - Use Caution Dear freesurfer experts, I have installed the freesurfer version 7.1.1 in my computer (Mac). After running the longitudinal pipeline in all

[Freesurfer] QDEC command not found

External Email - Use Caution Dear freesurfer experts, I have installed the freesurfer version 7.1.1 in my computer (Mac). After running the longitudinal pipeline in all the patients, I tried to open qdec for the analysis by typing qdec and the answer is "command not found".

Re: [Freesurfer] Qdec vertex-wise clustering question

I think i'm misunderstanding your question. Typically, you are running the stats on the thickness, so of course anything that changes thickness would impact the stats. Am I missing something? On 7/15/2021 2:34 PM, Alejandro Meruelo wrote: > External Email - Use Caution > > I see, thank

Re: [Freesurfer] Qdec vertex-wise clustering question

External Email - Use Caution I see, thank you. Would statistics on cortical thickness calculations be impacted? Many thanks again, Alejandro On Thu, Jul 15, 2021 at 8:38 AM Douglas N. Greve wrote: > > if you are doing statistics on the surface measures, then they will > impact

Re: [Freesurfer] Qdec vertex-wise clustering question

if you are doing statistics on the surface measures, then they will impact the calculations On 7/14/2021 7:07 PM, Alejandro Meruelo wrote: > External Email - Use Caution > > This is very helpful, thank you! Do the recon-all generated FreeSurfer > data (e.g., surfaces) impact any of the

Re: [Freesurfer] Qdec vertex-wise clustering question

External Email - Use Caution This is very helpful, thank you! Do the recon-all generated FreeSurfer data (e.g., surfaces) impact any of the statistical calculations or are they primarily used for figure generation for Qdec? Many thanks again, Alejandro On Mon, Jul 12, 2021 at

Re: [Freesurfer] Qdec vertex-wise clustering question

Not sure I know what you mean. For creating the design matrix, it uses the info from the qdec table. BTW, qdec is deprecated. On 7/12/2021 5:27 PM, Alejandro Meruelo wrote: > External Email - Use Caution > > Hello, > > I had a brief question regarding Qdec vertex-wise clustering. Does >

[Freesurfer] Qdec vertex-wise clustering question

External Email - Use Caution Hello, I had a brief question regarding Qdec vertex-wise clustering. Does Qdec use the data in the raw imaging files or the qdec.tables.dat file to generate the vertex-wise clustering results for cortical thickness group comparisons? Many thanks for

Re: [Freesurfer] QDEC/mri_glmfit questions

You can't do it in tandem. The 2nd command should work, just don't include -surf or -label Also, when you do use -surf, you need a subject and a hemi, eg, -surf fsaverage lh On 2/24/2021 12:03 PM, Erin Moe wrote: > External Email - Use Caution > > Hi Doug, > Thank you for the advice! I

Re: [Freesurfer] QDEC/mri_glmfit questions

External Email - Use Caution Hi Doug, Thank you for the advice! I tried plugging the output of aparc2stats into mri_glmfit both in tandem with —y (mri_preproc_output).mgh as well as on its own and got an error message from mri_reshape saying the elements cannot be changed

Re: [Freesurfer] QDEC/mri_glmfit questions

It might be easiest to start with running the ROI values in mri_glmfit. How did you extract the ROI values for use in SPSS? You can use aparcstats2table to create a table, and then feed that table into mri_glmfit --table table.dat --o glmdir —fsgd inflammatory_markers.fsgd —C

[Freesurfer] QDEC/mri_glmfit questions

External Email - Use Caution Hi Freesurfer experts, I’ve been running mri_glmfit and QDEC to investigate the effect of inflammatory markers on cortical thickness and don’t really get much. However, when I extract the cortical thickness values (with aparc/asegstats2table) and run

Re: [Freesurfer] Qdec crash while analysis almost finished

downloaded different versions(v5.3,v6.0,v7.1). So I think using which one is OK maybe. Chan -原始邮件- 发件人:"Greve, Douglas N.,Ph.D." 发送时间:2021-01-15 00:05:53 (星期五) 收件人: "freesurfer@nmr.mgh.harvard.edu" 抄送: 主题: Re: [Freesurfer] Qdec crash while analysis almost fini

Re: [Freesurfer] Qdec crash while analysis almost finished

I'm not sure I understand. Are you using v6 qdec with a 5.3 license file? On 1/13/2021 2:54 AM, chenb...@mail.sysu.edu.cn wrote: External Email - Use Caution Hi, dear Freesurfer experts, I recently came across an invalid Freesurfer license key error

[Freesurfer] Qdec crash while analysis almost finished

External Email - Use Caution Hi, dear Freesurfer experts, I recently came across an invalid Freesurfer license key error while using v5.3, and I tried apply for another license key, it just sent me the same license key as I have apply before. Then I put the licence file to

Re: [Freesurfer] qdec replacement

We don't have a GUI, if that is what you mean. The default now is to use the command line stream where you create your own FSGD file and contrast matricies, then run mri_glmfit and mri_glmfit-sim On 11/17/2020 10:44 AM, Pagliaccio, David (NYSPI) wrote:

[Freesurfer] qdec replacement

External Email - Use Caution Hello I was just wondering if there were any updates on a FSv7 replacement for QDEC for vertex-wise cortical thickness analyses? Or if there were any recommendations for analyses in other programs? Thanks! David -- David Pagliaccio, Ph.D.

Re: [Freesurfer] Qdec - talairach to vertex for display purposes

We don't use qdec anymore, so I can't remember what the interface is like. You can transfer your coordinates to fsaverage space, see https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems and then go to that point in freeview On 10/13/2020 9:45 AM, Paul Dhami wrote: External

[Freesurfer] Qdec - talairach to vertex for display purposes

External Email - Use Caution Dear Freesurfer community, I have an experiment in which participants received brain stimulation using anatomical coordinates which I have in talairach space. I have run a whole-brain analysis using qdec, and I have a surviving cluster. For display

[Freesurfer] qdec problems not receiving keyboard input

External Email - Use Caution Dear Freesurfer Experts, Although I haven't had any problems with the qdec until now, this week the qdec is having some errors when receiving inputs from the keyboard. For example, I can't write in the design name box, nor can I change the minimum or

Re: [Freesurfer] qdec problems not receiving keyboard input

Sorry, qdec has been mothballed and we are not supporting it anymore On 10/7/2020 7:12 AM, Agurne Sampedro Calvete wrote: External Email - Use Caution Dear Freesurfer Experts, Although I haven't had any problems with the qdec until now, this week the qdec is having some errors when

Re: [Freesurfer] QDEC command not found

We are no longer distributing or supporting qdec On 10/2/2020 6:17 AM, Enrico Collantoni wrote: External Email - Use Caution Dear freesurfer experts, I installed the 7.1.1 version of freesurfer in iOS enviroment (10.15.4). I could run the recon-all without any problems. However,

[Freesurfer] QDEC command not found

External Email - Use Caution Dear freesurfer experts, I installed the 7.1.1 version of freesurfer in iOS enviroment (10.15.4). I could run the recon-all without any problems. However, trying to open qdec I obtain "command not found". I've never had this problem with previous

Re: [Freesurfer] QDEC analyses

er"; *Subject:* Re: [Freesurfer] QDEC analyses How you did you do your analysis? As an exploratory/map-based analysis? Or as an ROI analysis? How did you correct for multiple comparisons? Generally, in a map-based analysis, the correction for multiple comparisons incorporates the fact that there are

Re: [Freesurfer] QDEC analyses

External Email - Use Caution Thanks for your timely response. To assess the two group differences in cortical thickness, whole-brain vertex-wise analyses were performed using the graphical user interface of FreeSurfer known as QDEC. We used a general linear model to compare the

Re: [Freesurfer] QDEC analyses

External Email - Use Caution Thanks for your timely response. To assess the two group differences in cortical thickness, whole-brain vertex-wise analyses were performed using the graphical user interface of FreeSurfer known as QDEC. We used a general linear model to compare the

Re: [Freesurfer] QDEC analyses

How you did you do your analysis? As an exploratory/map-based analysis? Or as an ROI analysis? How did you correct for multiple comparisons? Generally, in a map-based analysis, the correction for multiple comparisons incorporates the fact that there are two hemispheres being tested. On

[Freesurfer] QDEC analyses

External Email - Use Caution Hello Freesurfer developers, Recently, I have used QDEC of freesurfer 6.0.0 to examine the cortical thickness differences between two groups, and the manuscript has been submitted to a journal. One reviewer raised a question -"The manuscript

[Freesurfer] QDEC analyses

External Email - Use Caution Hello Freesurfer developers, Recently, I have used QDEC of freesurfer 6.0.0 to examine the cortical thickness differences between two groups, and the manuscript has been submitted to a journal. One reviewer raised a question -"The manuscript

Re: [Freesurfer] QDEC correlation analysis

In the qdec  output, there should be a file called Xg.dat and one called contrast/C.dat (where contrast is the name of the contrast of interest) X = load('Xg.dat'); C = load('contrast/C.dat'); y = MRIread('input-to-qdec.mgz'); % Not sure what this is called ymat = fast_vol2mat(y); yvertex =

[Freesurfer] QDEC correlation analysis

External Email - Use Caution Hello FreeSurfer Developers, I have a few questions about the p value in QDEC. I want to use matlab to calculate the p value in a vertex in the QDEC result. 1. In my design, there is a continuous variable A and two Nuisance factors B and C. How to

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

Re: [Freesurfer] qdec and mris_anatomical_stats help

On 5/15/2020 8:17 PM, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience wrote: External Email - Use Caution Dear Freesurfer experts, Hope everyone is doing well! Could someone please clarify some things about mris_anatomical_stats, done

Re: [Freesurfer] qdec and mris_anatomical_stats help

External Email - Use Caution Hello Freesurfer experts, Just wanted to follow-up from my last email. If any clarification is needed regarding what I'm trying to understand from mris_anatomical_stats, please let me know! Kind regards, Alex On Fri, May 15, 2020 at 8:17 PM Lab of

[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

[Freesurfer] qdec and mris_anatomical_stats help

External Email - Use Caution Dear Freesurfer experts, Hope everyone is doing well! Could someone please clarify some things about mris_anatomical_stats, done after running qdec + mapping label to all subjects? From what I can understand, the following code should be used:

Re: [Freesurfer] Qdec not running ("image not found" error message)

External Email - Use Caution Hello Alex, It looks like you need to install Xquartz on your Mac with the X Windows libraries including libGLU.1.dylib. Download from here, open and run the installer package. https://www.xquartz.org/ - R. On Feb 25, 2020, at 23:27, Lab of Autism

[Freesurfer] Qdec not running ("image not found" error message)

External Email - Use Caution Dear Freesurfer experts, Please help me with this simple error for running Qdec: - First I try to open qdec: qdec & - Then this occurs: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer/bin/qdec.bin

Re: [Freesurfer] qdec / tksurfer GUI

Have you tried freeview? On 2/7/2020 2:50 PM, Rockers, Elijah D. wrote: External Email - Use Caution I've noticed an issue when trying to manually input values into fields with Qdec. This problem has been reported before. I thought perhaps it was because Qdec is deprecated, so I

[Freesurfer] qdec / tksurfer GUI

External Email - Use Caution I've noticed an issue when trying to manually input values into fields with Qdec. This problem has been reported before. I thought perhaps it was because Qdec is deprecated, so I loaded the results into tksurfer, and I can't change fields in this

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 and TkSurfer input boxes

I don't know. Can you reconfigure to English to do a test? On 1/21/2020 12:14 PM, Marcos Martins da Silva wrote: External Email - Use Caution FreeSurfer 6 over CentOS 7. I have the same problem with 5.3 too. One more information: CentOS 7 is configured as PT-br instead of English.

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 and TkSurfer input boxes

External Email - Use Caution FreeSurfer 6 over CentOS 7. I have the same problem with 5.3 too. One more information: CentOS 7 is configured as PT-br instead of English. Could it be the reason? Em ter, 21 de jan de 2020 12:29, Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu>

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

Re: [Freesurfer] Qdec and TkSurfer input boxes

Which version of FS are you using? I don't have this problem in v6 or dev. What OS are you using? On 1/17/2020 9:09 AM, Marcos Martins da Silva wrote: External Email - Use Caution Thank you, Doug! Yes, there is an option to load a fsgd file in Freeview, but when you try to use this

[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

Re: [Freesurfer] Qdec and TkSurfer input boxes

External Email - Use Caution Thank you, Doug! Yes, there is an option to load a fsgd file in Freeview, but when you try to use this option Freeview closes wirh error. I tried to use the y.fsgd generated by Qdec process. This file works great when you use it in TkSurfer, but not in

Re: [Freesurfer] Qdec and TkSurfer input boxes

Sorry, qdec and tksurfer are becoming (have become?) obsolete. I think you can load an fsgd file in freeview On 1/15/2020 11:02 AM, Marcos Martins da Silva wrote: External Email - Use Caution Hi! I use FreeSurfer 6.0 over CentOS 7. I have just notice a problem with input/entry/edit

[Freesurfer] Qdec and TkSurfer input boxes

External Email - Use Caution Hi! I use FreeSurfer 6.0 over CentOS 7. I have just notice a problem with input/entry/edit boxes in Qdec and TkSurfer. I can see box content, click inside the box and even select the content but it seems read only: I can't change it. So it is

Re: [Freesurfer] Qdec support {Disarmed}

External Email - Use Caution Hello Leona, What is the error that you are seeing? Qdec is a 32 bit program (*not* 64 bit), so even Mac OS 10.14 (Mojave) may put up a warning that it is not optimized and needs to be re-compiled, but it should still run. It will not however run if

[Freesurfer] Qdec support

External Email - Use Caution Dear experts, i was trying to run Qdec on macOS Mojave, in the past it always worked well. But now I am not able to generate stats data any more, an error message pops up every time I try running it. Is there a general problem running Qdec or is it

Re: [Freesurfer] QDEC cluster output

Hi Lara, sorry, we don't really support qdec anymore for the very reason that we can't get into the code easily and answer these questions. Can you use the command-line stream? doug On 10/17/19 6:17 PM, Lara Foland-Ross wrote: External Email - Use Caution Hi Freesurfer experts, I’m

[Freesurfer] QDEC cluster output

External Email - Use Caution Hi Freesurfer experts, I’m running a simple qdec analysis to examine group differences in surface measures between a patient and control group, controlling for age and TBV. I noticed that when I run Monte Carlo Simulations (threshold=1.3, sign=abs),

Re: [Freesurfer] qdec contrast and data extraction

file should I load? I see cluster.mgh, > cluster.summary, sign.ocn.annot, sig.ocn.mgh, sig.vertex.mgh, and > pdf.dat./ > >// > >/How can I extract the values from fsaverage space?/ > >// > >/Basically, what is the correct way to extract values from th

Re: [Freesurfer] qdec contrast and data extraction

ace? > > Basically, what is the correct way to extract values from these significant > clusters? > > Many thanks, > Omar > > Date: Tue, 3 Sep 2019 15:15:02 + > From: "Greve, Douglas N.,Ph.D." > Subject: Re: [Freesurfer] qdec contrast and data extrac

[Freesurfer] qdec contrast and data extraction

these significant clusters? Many thanks, Omar Date: Tue, 3 Sep 2019 15:15:02 + From: "Greve, Douglas N.,Ph.D." Subject: Re: [Freesurfer] qdec contrast and data extraction To: "freesurfer@nmr.mgh.harvard.edu" Message-ID: <2286f9bf-37a4-1be9-2252-0bccc

Re: [Freesurfer] qdec contrast and data extraction

You might have done something wrong along the way. When you run the montecarlo correction, it will create a file with the thickness values in it for each cluster. the first thing to do is to load that and see if you see the expected differences. The other thing is to not go back into native

[Freesurfer] QDEC interpretation question - Please respond

External Email - Use Caution Hi, I have a question regarding interpreting results from QDEC. I am investigating lGI in individuals with ASD and controls (which I will refer to as 'TD' here). I understand from the archives that when "TD" is listed first and "ASD" is listed second

Re: [Freesurfer] Qdec Message to Mailing List

<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Qdec Message to Mailing List can you send the command line, full terminal output, your fsgd file, and the Xg.dat created in the output? On 7/3/2019 11:05 AM, Marie Hill wrote: External Email - Use Caution Thanks. When I ru

Re: [Freesurfer] Qdec Message to Mailing List

rfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <mailto:dgr...@mgh.harvard.edu> Sent: 03 July 2019 16:22 To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Qdec Message to Mailing List can you send the command line, full te

Re: [Freesurfer] Qdec Message to Mailing List

) ... could not determine the cause of the problem Kind Regards, Marie From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. Sent: 03 July 2019 16:22 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Qdec Message to Mailing

Re: [Freesurfer] Qdec Message to Mailing List

mgh.harvard.edu> Sent: 03 July 2019 15:24 To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Qdec Message to Mailing List yes, qdec can only have 2 factors with 2 levels. both qdec and mri_glmfit are linear methods (in fact, qdec just calls m

Re: [Freesurfer] Qdec Message to Mailing List

of Greve, Douglas N.,Ph.D. Sent: 03 July 2019 15:24 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Qdec Message to Mailing List yes, qdec can only have 2 factors with 2 levels. both qdec and mri_glmfit are linear methods (in fact, qdec just calls mri_glmfit). On 7/3/2019 9:39 AM

Re: [Freesurfer] Qdec Message to Mailing List

yes, qdec can only have 2 factors with 2 levels. both qdec and mri_glmfit are linear methods (in fact, qdec just calls mri_glmfit). On 7/3/2019 9:39 AM, Marie Hill wrote: External Email - Use Caution Dear Sir/Madam, Could I post the following message to the mailing list: I am running

[Freesurfer] Qdec Message to Mailing List

External Email - Use Caution Dear Sir/Madam, Could I post the following message to the mailing list: I am running a regression testing for significant difference in cortical volume, thickness etc with 3 factors: diagnosis, genotype and gender, with age as a nuisance factor. I

[Freesurfer] QDEC ROI Analysis

External Email - Use Caution Hello FreeSurfers, I had the same question as below, but did not see a response. Does anyone know if this feasible in QDEC? Best, Jessica - fabrizio

Re: [Freesurfer] QDEC Longitudinal Analysis: Missing spc option from dropdown menu

Hi Arsenije, the file name should be (with a starting “.” and no file extension): $SUBJECTS_DIR/qdec/.Qdecrc Best, Martin > On 22. Feb 2019, at 00:22, Arsenije Subotic > wrote: > > Dear Freesurfer experts, > > I am having issues choosing the spc option for my QDEC two stage

Re: [Freesurfer] QDEC Longitudinal Analysis: Missing spc option from dropdown menu

qdec is not really being supported anymore. It is better if you use the command line stream On 2/21/19 6:22 PM, Arsenije Subotic wrote: External Email - Use Caution Dear Freesurfer experts, I am having issues choosing the spc option for my QDEC two stage longitudinal analysis as it

[Freesurfer] QDEC Longitudinal Analysis: Missing spc option from dropdown menu

External Email - Use Caution Dear Freesurfer experts, I am having issues choosing the spc option for my QDEC two stage longitudinal analysis as it is not there. The spc files are all present in my participants files and the Qdecrc file is in the qdec subdirectory containing

[Freesurfer] Qdec tutorial video

External Email - Use Caution Hello Freesurfers, I was wondering if anyone has access to a Qdec tutorial, other than the one on the Freesurfer website. The one on the website only covers the basics and it does not have a video component. In case you have a better tutorial

[Freesurfer] QDEC - command not found

External Email - Use Caution Dear freesurfer experts, we installed the last version of freesurfer dev in a centos7 system (8th january 2019) and the matlab runtime to run segmentHA_T1.sh. We could obtain all the files without problems. However, today we tried to open qdec typing

[Freesurfer] Qdec table

External Email - Use Caution Hi Freesurfer devs, How can I create a qdec.table.dat file? I tried using a txt file but it doesn´t works. I attached the qdec.table.dat file that I have created. Sorry for this absurd question and thanks in advance. Cheers, -- *Miguel Ángel Rivas

Re: [Freesurfer] QDEC analysis with more that 2 fixed factors

They are the same thing underneath. On 10/18/18 11:12 AM, Azeez, Azeezat wrote: External Email - Use Caution Thank you for the response. Which smoothing option would you recommend, there is one in mris_preproc, but there is also mris_smooth. Thanks You On Wed, Oct 17, 2018 at 1:56 PM

Re: [Freesurfer] QDEC analysis with more that 2 fixed factors

External Email - Use Caution Thank you for the response. Which smoothing option would you recommend, there is one in mris_preproc, but there is also mris_smooth. Thanks You On Wed, Oct 17, 2018 at 1:56 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > You cannot use

Re: [Freesurfer] QDEC analysis with more that 2 fixed factors

You cannot use QDEC for this. You must use the "command line" stream, ie, create your FSGD file, run mris_preproc, smooth, run mri_glmfit, then mri_glmfit-sim. See the tutorial on the wiki. On 10/17/2018 01:30 PM, Azeez, Azeezat wrote: > > External Email - Use Caution > > Hello, > > I

[Freesurfer] QDEC analysis with more that 2 fixed factors

External Email - Use Caution Hello, I would like to know how I can run statistical analysis in QDEC on a data set where there are 3 fixed factors each with 2 contrast levels. (DEVELOPMENT : old vs young, SEX: male vs female, DIAGNOSE: Control Vs disease ) Any help would be much

Re: [Freesurfer] qdec analysis with more than 2 covariates

That looks like the terminal output for qdec. You cannot use qdec with your design. If you have questions about the FSGD, I'll be happy to answer them. On 10/16/2018 11:00 AM, vittal korann wrote: > > External Email - Use Caution > > Hi Doug, > > Thank you for your response. > I tried

Re: [Freesurfer] qdec analysis with more than 2 covariates

External Email - Use Caution Hi Doug, Thank you for your response. I tried the link which you sent yesterday. But got stuck while creating qdec.fsgd file. Below i have pasted the terminal output after loading the data. 1 Left-Lateral-Ventricle continuous 0 2 Left-Inf-Lat-Vent

Re: [Freesurfer] qdec analysis with more than 2 covariates

You cannot use QDEC. For this case you'll need to use the "command line" stream. You'll need to start by creating an FSGD file https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples On 10/15/18 10:15 AM, vittal korann wrote: External Email - Use Caution Hi Doug, Recently I started

[Freesurfer] qdec analysis with more than 2 covariates

External Email - Use Caution Hi Doug, Recently I started working on freesurfer for volume based analysis. For QDEC, I need to include more than 2 variables. For example if I include patients who hail from different places like statutory town, census town and rural. In present

Re: [Freesurfer] QDEC, order of groups for interpretation of results

I'm pretty sure that is uses the order in the .levels file. It will create a y.fsgd file in the output folder. Look at the order in that as that will be definitive. On 5/29/18 2:15 PM, Avi Gharehgazlou wrote: Hello experts, I am using QDEC to compared LGI values between groups (typically

Re: [Freesurfer] QDEC, order interpretationof Gracias @batmarandua for aqaa

External Email - Use Caution On Tue, May 29, 2018, 20:16 Avi Gharehgazlou wrote: > External Email - Use Caution > > Hello experts, > > I am using QDEC to compared LGI values between groups (typically develping > and ASD). I made a "diagnosis.levels" file, putting my 2

[Freesurfer] QDEC, order of groups for interpretation of results

External Email - Use Caution Hello experts, I am using QDEC to compared LGI values between groups (typically develping and ASD). I made a "diagnosis.levels" file, putting my 2 groups in the following order: Typically developing ASD However, when I upload my qdec.table.dat file

Re: [Freesurfer] QDEC vs. Command Line Stream

They both give the same results for the same analysis. It is harder to do proper correction for multiple comparisons in QDEC On 4/20/18 12:50 PM, Arsenije Subotic wrote: Dear experts, I'm about to start my cortical thickness analysis for my groups, and I was just wondering what seems to

[Freesurfer] QDEC vs. Command Line Stream

External Email - Use Caution Dear experts, I'm about to start my cortical thickness analysis for my groups, and I was just wondering what seems to be the consensus when it comes to using QDEC as opposed to using the command line stream? I've seen QDEC used plentifully in the

Re: [Freesurfer] QDEC Interaction of Two Covariates

QDEC is mostly depreicated. Use the command-line stream. See the group analysis on this page https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial On 04/19/2018 04:48 PM, David S Lee wrote: > > > Hi FreeSurfer Experts, > > I want to test the relationship between cortical thickness and two >

[Freesurfer] QDEC Interaction of Two Covariates

External Email - Use Caution Hi FreeSurfer Experts, I want to test the relationship between cortical thickness and two continuous covariates (interaction) while controlling for one categorical variable. In QDEC, I can only choose one covariate, so I created a new variable that is

[Freesurfer] Qdec+Table format issue ?????

Dear Recipient, I am a Master student new comer in FS. I am trying toi use the QDEC ti analyse some longitudinal data. Most probably my issue is related with the file format. I tried to use several text editors (mac text editor, gedit and text wrangler) however I end up in 2 different errors

[Freesurfer] Qdec question when examining group differences with continuous covariate and nuisance factor

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

Re: [Freesurfer] QDEC Set Up

Yes, that is the same On 02/12/2018 07:15 PM, Martin Juneja wrote: > Since I have 4 groups here: X1-M, X2-M, X1-F and X2-F, so can someone > please confirm if this is identical to this example: > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V > If so, then I can follow instructions on

Re: [Freesurfer] QDEC Set Up

Since I have 4 groups here: X1-M, X2-M, X1-F and X2-F, so can someone please confirm if this is identical to this example: https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V If so, then I can follow instructions on this page and set up my contrast files accordingly. Thanks. On Mon, Feb 12, 2018

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