Re: [Freesurfer] QDEC - Controlling for gender

Just include it as a categorical factor. When you look at your contrast of interest, it will be with respect to regressing out gender On 01/15/2017 08:55 PM, Jennifer Szeto wrote: > > Hi Freesurfer experts, > > > I am trying to compare cortical thickness between groups while > controlling for

[Freesurfer] QDEC - Controlling for gender

Hi Freesurfer experts, I am trying to compare cortical thickness between groups while controlling for age and gender using QDEC. However, gender is not showing up as a covariate variable or a nuisance factor (only showing up as a fixed factor), I am wondering how I could control for gender in

Re: [Freesurfer] QDEC table import issue

It was the spaces! Thanks for the help On Jan 13, 2017, at 11:40 AM, Douglas N Greve > wrote: I'm not sure that QDEC can read in a CSV file. Can you remove the commas and try again? You'll also have to remove the spaces between column

Re: [Freesurfer] QDEC table import issue

I'm not sure that QDEC can read in a CSV file. Can you remove the commas and try again? You'll also have to remove the spaces between column headings On 01/13/2017 10:55 AM, Paul Rowley wrote: > Good morning, > I’m experiencing issues importing data into QDEC. When I upload the table, > this

[Freesurfer] QDEC table import issue

Good morning, I’m experiencing issues importing data into QDEC. When I upload the table, this is the error I receive: Loading data table /Applications/freesurfer/subjects/qdec/qdec.table.dat... Number of columns: 10 fsid column:1 Number of factors: 9 Number of subjects: 19 ERROR:

Re: [Freesurfer] qdec question

Try using the data in the csdbase.y.ocn.dat file rather than transferring the clusters back into the individual space. What are you using to do the ROI-based analysis? You have to make sure that the design matrix and contrasts are exactly the same. You can do this in matlab with FS commmands,

Re: [Freesurfer] QDEC versus R

Hi Marine, these are two different analyses. In the first analysis, you have used a voxel-wise analysis, and in the second you've done an ROI analysis. They are not guaranteed to give the same results. Also, it is possible that the actual GLM design matrices are different. QDEC will create a

[Freesurfer] qdec question

Dear Experts, I'm looking at differences in area between two groups of subjects in FreeSurfer using qdec. I've delineated an ROI based on a cluster that showed significant differences in surface area between the two groups (taking gender into account, and with age and ICV as nuisance

[Freesurfer] QDEC versus R

Hello, As a PhD student, I send you this mail because i am meeting a misunderstanding with QDEC. In a few words : I made an analysis thanks to the QDEC tool : * I tested a correlation between an inhibition score and cortical thickness, corrected for age (continuous = inhibition score ;

Re: [Freesurfer] Qdec plot design

FDR does not have blobs either, but I think I get what you mean:). You should run mri_surfcluster specifying the FDR-determined voxel-wise threshold as the --thmin, the sig.mgh as the --in, --subject fsaverage --hemi the-hemi-you-use, and --ocn ocn.mgh Then mri_segstats --i y.mgh --seg

Re: [Freesurfer] Qdec plot design

I'm sorry, I might not have used the right word. Let's say 'blob' instead of cluster. It's something like the plot attached. Each circle/square is a subject. I would like to export that so I can make the plot myself. Best, Mihaela On Mon, Nov 7, 2016 at 4:38 PM, Douglas N Greve

Re: [Freesurfer] Qdec plot design

What do you mean a "plot"? I had assumed you wanted to average over clusters, but FDR does not produce clusters On 11/07/2016 04:26 PM, Mihaela Stefan wrote: > That seems to be for Monte Carlo simulation. What if I use FDR or if I > want to look at a plot from an uncorrected map? > > Thanks! >

Re: [Freesurfer] Qdec plot design

That seems to be for Monte Carlo simulation. What if I use FDR or if I want to look at a plot from an uncorrected map? Thanks! Mihaela On Mon, Nov 7, 2016 at 3:16 PM, Douglas N Greve wrote: > Run mri_glmfit-sim using the Qdec output folder as the --glmdir and >

Re: [Freesurfer] Qdec plot design

Run mri_glmfit-sim using the Qdec output folder as the --glmdir and setting the thresholds and signs as you had them in qdec. The output will then be in a file called something like cache.th20.pos.y.ocn.dat. the cluster summary table will be in cache.th20.pos.sig.cluster.summary On 11/07/2016

[Freesurfer] Qdec plot design

Hello Freesurfers, I am doing a group analysis using Qdec. I have a few significant clusters and I would like to plot one of them. Qdec does that if I click on 'Find Clusters and Goto Max' but I don't see options for the design of the plot. How can I export the thickness values from my cluster to

Re: [Freesurfer] qdec long parsing table to look in non-existant directory

Hi Katherine, You need to run the data through all three steps of the longitudinal pipeline. The *.long.* directories are created in the last step (recon_all -long ... ). See also the wiki ( Google longitudinal processing freesurfer ) Best Martin On Oct 8, 2016 21:19, Katherine Damme

[Freesurfer] qdec long parsing table to look in non-existant directory

Hello everyone, I am running qdec for longitudinal data for the first time and although I have a file that matches the guide on the wiki, the script is looking in a non-exsistant file location (see below). While there is a 1001 file and a 1001_MR1, I am not sure where it is getting 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

[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

[Freesurfer] qdec problem

Hi,Douglas maybe, you are right. i have tried most of new versions, as follows, but the problem still has. I don't know whether Fedora (3.14-288,fc20.x86_64) 20 (Heisenbug) match with these versions. thank you very much. freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

Re: [Freesurfer] qdec: Generate Stats Data tables {Disarmed}

: [Freesurfer] qdec: Generate Stats Data tables {Disarmed} Is that all the terminal output it gave? If not, can you provide the rest? Did it print out an asegstats2table command in the terminal? On 09/07/2016 05:40 PM, c.anastasopou...@lumc.nl wrote: > F5_removeLastScript(document,'F5_cookieIni

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 problem

Sounds like the GUI is doing strange things. What platform are you running on? What version of FS? Can you try it on a different type of computer? On 09/07/2016 08:20 AM, wanghaibao wrote: > Hi, /Douglas/ > thank you for your reply. > > yes, the number in the text box cannot be changed,

Re: [Freesurfer] qdec: Generate Stats Data tables {Disarmed}

Is that all the terminal output it gave? If not, can you provide the rest? Did it print out an asegstats2table command in the terminal? On 09/07/2016 05:40 PM, c.anastasopou...@lumc.nl wrote: > F5_removeLastScript(document,'F5_cookieInitId');F5_initializeCookiesFromMeta(); > > > Hello, > > I

[Freesurfer] qdec: Generate Stats Data tables {Disarmed}

Hello, I am facing a problem similar to what others in the community have reported: when trying to "Generate Stats Data tables" in qdec, I get following error: SUBJECTS_DIR is '/home/ubuntubeast/Documents/freesurfer_subj_dir' mkdir -p

[Freesurfer] qdec problem

Hi, Douglas thank you for your reply. yes, the number in the text box cannot be changed, including threshold and False Discovery Rate in display. and also when i Save the picture of Display in File menu, the name cannot be input into the text box. Can you not just change the number in the text

Re: [Freesurfer] qdec problem

Can you not just change the number in the text box? On 09/06/2016 12:49 PM, wanghaibao wrote: > Hello,*Douglas* > I used the freesurfer 5.3 in fedora 20,there is a question in my > reseach,may be not a question! > When i view the results of analysis in the qdec window,why did i > cannot change

[Freesurfer] qdec problem

Hello,Douglas I used the freesurfer 5.3 in fedora 20,there is a question in my reseach,may be not a question! When i view the results of analysis in the qdec window,why did i cannot change the value of the Threshold,such as min(which had been seted with the value of 2) ,in the same way,the

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

Re: [Freesurfer] Qdec Generate Stats Data Table Error

did you look at the file it points to as the source of the error? /local/limachiagv/freesurfer/subjects/CON_201/stats/aseg.stats On 07/27/2016 05:00 PM, Limachia, Gaurang (NIH/NINDS) [F] wrote: > Hello All, > > My table.dat file loaded fine. However, I came across the following > error when I

[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:

[Freesurfer] Qdec Generate Stats Data Table Error

Hello All, 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: asegstats2table

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-correction for multiple comparison

834 Fax: +1 (603) 646-1419     Sent: Wednesday, July 06, 2016 at 1:44 PM From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Qdec-correction for multiple comparison There is no recommendation between FDR and monte c

Re: [Freesurfer] Qdec-correction for multiple comparison

There is no recommendation between FDR and monte carlo. The question of which one is "better" is an emperical question that depends on your data. On 06/29/2016 06:38 AM, John Anderson wrote: > Dear FS experts, > I will re post this thread again looking for your help and support: > I ran cortical

[Freesurfer] Qdec-correction for multiple comparison

Hi Doug, I ran cortical thickness analysis between two groups using Qdec and I want to correct the results for multiple comparison. In Qdec there are two choices to correct the data for multiple comparison (FDR and montecarlo) . Which method do you recommend to correct the results of cortical

Re: [Freesurfer] qdec load error missing BLT

Dear Joshua, we had the same problem with freeSurfer 5.3.0 on Debian GNU/Linux 8.3 (jessie). In our case this was warning, the qdec launched, however the fsgd plot functionality (interactive vertex-wise GLM plot display) did not work. It seems that the error is caused by interference of tk/blt

[Freesurfer] Qdec-correction for multiple comparison

Dear FS experts, I will re post this thread again looking for your help and support:   I ran cortical thickness analysis between two groups using Qdec and I want to correct the results for multiple comparison. In Qdec there are two choices to correct the data for multiple comparison (FDR and

[Freesurfer] Qdec-correction for multiple comparison

Dear FS experts, I will re post this thread again looking for your help and support:   I ran cortical thickness analysis between two groups using Qdec and I want to correct the results for multiple comparison. In Qdec there are two choices to correct the data for multiple comparison (FDR and

[Freesurfer] Qdec-correction for multiple comparison

Dear FS experts, I ran cortical thickness analysis between two groups using Qdec and I want to correct the results for multiple comparison. In Qdec there are two choices to correct the data for multiple comparison (FDR and montecarlo) . Which method do you recommend montecarlo or FDR. Are there

Re: [Freesurfer] qdec load error missing BLT

contents of $FREESURFER_HOME/lib/tcl/ allisons_surfaces.tcl offsetmovie.tcl TclChartWindow.tcl curv-flat.tcl phasemovie.tcl test_layers.tcl curv-views.tcl polar-flat.tcl test_ScubaFrame.tcl dara_data.tcl polar-views.tcl test_ScubaLayers.tcl

[Freesurfer] qdec load error missing BLT

When loading qdec I get can't find package BLT FsgdfPlot::InitFsgdf: Couldn't find fsgdfPlot.tcl on Ubuntu with FreeSurfer5.3 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

[Freesurfer] Qdec

Dear Freesurfer experts, I wanted to run cortical thickness analysis between two groups to check the diffetence in thickness between the groups. I used Qdec My question is regarding correcting for multiple comparisons. There are two options FDR and montecarlo. Which option do you recommend? Are

Re: [Freesurfer] QDEC - cannot allocate memory

That fixed the error. Thank you so much for your help! Marissa Pifer On Wed, May 11, 2016 at 11:32 AM, Douglas N Greve wrote: > Try re-running recon-all -qcache for that subject and see if the error > goes away > > On 05/11/2016 10:56 AM, Marissa Pifer wrote: > >

Re: [Freesurfer] QDEC - cannot allocate memory

The error was generated on that first subject 03-1, but it was successful on all of the other subjects. Is there something wrong with that file that we have to exclude that subject from the analysis? Marissa On Wed, May 11, 2016 at 10:38 AM, Douglas Greve wrote: >

Re: [Freesurfer] QDEC - cannot allocate memory

Here is everything in the terminal after I hit analyze: Data table loading completed successfully. SUBJECTS_DIR is '/Users/marchaut/Documents/myprojects/SOARmaster' lh-Avg-Intercept-thickness --- Does the average thickness differ from zero? 1.000 1.000;

Re: [Freesurfer] QDEC - cannot allocate memory

Is that all it says? At one point (about 3-4 years ago) we would see that error because some of our files got corrupted. Can you send more of the terminal output? On 05/10/2016 12:56 PM, Marissa Pifer wrote: > Hi freesurfers, > > I am on a macbook pro OSX 10.9.5, trying to run an analysis on

[Freesurfer] QDEC - cannot allocate memory

Hi freesurfers, I am on a macbook pro OSX 10.9.5, trying to run an analysis on qdec - freesurfer version 5.3. I am looking to analyze T2weighted scans for 27 subjects through the qdec system. I keep getting this error that it cannot allocate memory for the task. I'v been talking with our IT

Re: [Freesurfer] Qdec stats question

In general, qdec should be used to "play" with your data in an interactive way. For many designs, you may need to run the command-line stream. This is probably one of them. If you have continuous nuisance variables, then you should run the analysis using DODS and test for an interaction of the

Re: [Freesurfer] Qdec stats question

Hello Freesurfer Experts, I wanted to see if I am setting up qdec correctly. I am using cortical thickness as my measure. When using the Qdec gui in Freesurfer 6.0 i supplied the following files: qdec.table.dat which contains the following: Subject Group Gender Age Site Yrs_Education For

[Freesurfer] Qdec interface issue

Hello, I am working on measuring cortical thickness of a patient group. I am using Ubuntu 14.04 Somehow, if I use command line to perform the analysis, Freesurfer/qdec is working fine but if I use Qdec interface, it works fine initially but when I switch to display window, it doesn't allow me

Re: [Freesurfer] Qdec DOSS

Yes, if the contrast matrix is correct, then everything should be fine. Also check the design matrix (but I'm pretty sure that will be correct). On 04/05/2016 04:07 AM, tom parker wrote: > Hi Freesurfers, > > I posted this question a few days ago but didn't get any replies. > Would you mind

[Freesurfer] Qdec DOSS

Hi Freesurfers, I posted this question a few days ago but didn't get any replies. Would you mind answering this for me? I compared 2 groups, while controlling for 1 covariate in qdec using freesurfer 5.1. There were no significant interactions with the covariate so I need to use DOSS. I read

[Freesurfer] QDEC analysis

Dear FreeSurfer experts, I am trying to analyze some single time points of my longitudinal data in QDEC. I have 3 groups and created a file for the discrete factor "group" with three levels (1,2 and 3). I have done the same for gender (with 2 levels). The analysis with gender works just fine

[Freesurfer] QDEC GUI or in-line command for Monte Carlo simulation?

Dear Freesurfer Experts: I would appreciate your help in clarifying one issue I have when applying Monte Carlo simulation to control for multiple comparisons. First, I did the correction via QDEC GUI. In the section of Monte Carlo Null-Z simulation, I set Threshold: 2.0 (0.01) and Sign: neg.

Re: [Freesurfer] Qdec-statistical map

> *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] Qdec-statistical map > You will have to extract clusters (mri_surfcluster) to create an > annotation, then use mri_segstats with the --annot option

Re: [Freesurfer] Qdec-statistical map

surfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Qdec-statistical map You will have to extract clusters (mri_surfcluster) to create an annotation, then use mri_segstats with the --annot option and specifying the y.mgh file as input and the output using something like --avgwf output.txt (also add

Re: [Freesurfer] Qdec-statistical map

ect? > Bests, > John > *Sent:* Thursday, March 03, 2016 at 12:37 PM > *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] Qdec-statistical map > not sure what you mean. the statistical map will ha

Re: [Freesurfer] Qdec-statistical map

" <gr...@nmr.mgh.harvard.edu> To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Qdec-statistical map not sure what you mean. the statistical map will have a single value, not a value for each subject On 03/03/2016 12:31 PM, John Anderson wrote: > Dear FS experts, > I am using Qdec

Re: [Freesurfer] Qdec-statistical map

not sure what you mean. the statistical map will have a single value, not a value for each subject On 03/03/2016 12:31 PM, John Anderson wrote: > Dear FS experts, > I am using Qdec to study the differnce in cortical thicnkess between > two groups. > Qdec is running a GLM analysis. This will

[Freesurfer] Qdec-statistical map

Dear FS experts, I am using Qdec to study the differnce in cortical thicnkess between two groups. Qdec is running a GLM analysis. This will output a statistical map (sig.mgh) for the differnce between the groups in cortical thicnkess. How can I extract the numbers of cortical thickness for

Re: [Freesurfer] qdec

can you send one of them? On 02/22/2016 03:13 PM, levi solomyak wrote: > Hi Douglas, > > I get the same error for every subject individually. I'm guessing > there is a problem with my aseg.stats files but when I look through > them they look okay to me. What would be the best way to identify

Re: [Freesurfer] qdec

Hi Douglas, I get the same error for every subject individually. I'm guessing there is a problem with my aseg.stats files but when I look through them they look okay to me. What would be the best way to identify the problem? Thank you! LS On Mon, Feb 22, 2016 at 11:18 AM, Douglas N Greve

Re: [Freesurfer] qdec

Not sure. Can you run it separately for each subject? I suspect that there might be a subject with a bad stats file On 02/19/2016 02:58 PM, levi solomyak wrote: > Hi Douglas, > > Sure! Below is the terminal outputs when I try and run the command you > suggested on the first five subjects. Any

Re: [Freesurfer] qdec

Hi Douglas, Sure! Below is the terminal outputs when I try and run the command you suggested on the first five subjects. Any help you could provide would be much appreciated! Best, LS $asegstats2table --common-segs --meas volume --tablefile

Re: [Freesurfer] Qdec ROI Analysis

If all you want are the stats from Desikan/Destrieux, then use the provided stats files and load them into SPSS (or whatever). That note has to do with if you have your own ROI from which you want statistics. doug On 01/25/2016 09:47 PM, Larissa McKetton wrote: > Dear Freesurfer community, > >

[Freesurfer] Qdec ROI Analysis

Dear Freesurfer community, I am working on an ROI analysis using qdec. I have created all aseg and aparc stats files and would like to determine if there are any differences in volume, surface area, and thickness for certain structures between two groups. I was wondering with the analysis, would

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 >

[Freesurfer] Qdec Clusters Graph Extracted

Hello FreeSurfer Group I would like to make my own box plot out of a cluster that I identified as significant in Qdec. Is there any easy way to extract the information that appears in the graph window so that I can create a box plot? I've tried extracting it by drawing an roi and using

Re: [Freesurfer] Qdec visualization

n Qdec to get the stamdard > error (SE) ? > Bests, > John > *Sent:* Monday, December 21, 2015 at 11:43 AM > *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] Qdec visualization > The correc

Re: [Freesurfer] Qdec visualization

Bests, John Sent: Monday, December 21, 2015 at 2:20 PM From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Qdec visualization QDEC cannot but the information may be in the output folder. There should be a file called gam

Re: [Freesurfer] Qdec visualization

e size ( number of > subjects included in the analysis)? > Thanks a lot! > *Sent:* Monday, December 21, 2015 at 2:44 PM > *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] Qdec visualizati

Re: [Freesurfer] Qdec visualization

To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Qdec visualization it helps to see the error msg, but my guess is that you need to specify an mgh file, not a txt file. This will give you the voxel-wise stderr, not a standard error for the cluster (which does not make sense) On 12/21

Re: [Freesurfer] Qdec visualization

Thanks you very much Doug, Please one more question. Is there any way in Qdec to get the stamdard error (SE) ?   Bests, John      Sent: Monday, December 21, 2015 at 11:43 AM From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [

Re: [Freesurfer] Qdec visualization

ohn > *Sent:* Monday, December 21, 2015 at 2:20 PM > *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] Qdec visualization > QDEC cannot but the information may be in the output folder. There &g

Re: [Freesurfer] qdec

Can you run the command below outside of qdec and send us the error it prints to the terminal? asegstats2table --common-segs --meas volume --tablefile /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 100307 101006

[Freesurfer] Qdec

Dear Freesurfer experts, I just started using Freesurfer for performing MRI (T1)- group-based ROI analysis and managed to go through the first recon-all processing stream and making few manual edits. Then I followed first steps of the Qdec -procedure. However, there is a separate section on

Re: [Freesurfer] Qdec visualization

The correction for multiple comparisons is cluster-based. Each cluster gets a single number. In the display, all the vertices get that same number. On 12/18/2015 03:17 PM, John Anderson wrote: > Hi Freesurfer experts, > I am using Qdec in Freesurfer 5.3 to do some cortical thickness >

[Freesurfer] qdec

Dear experts, I've been attempting to generate a stats data table in qdec, but each time I get a "Index Error: list index is out of range" error. This is occurring when it is trying to parse the .stats file. I've made sure that the files all line up exactly with the qdec table and that

[Freesurfer] Qdec question

Hi all - When you get a significant cluster after doing monte-carlo simulation, we get peak vertex/Talairach coordinates and also saved in *summary files. Is there a way to find all the parcellated regions (Desikan, or, Destriuex) in the significant clusters?

[Freesurfer] Qdec - cluster labels

Hi all - When you get a significant cluster after doing monte-carlo simulation, we get peak vertex/Talairach coordinates and also saved in *summary files. Is there a way to find all the parcellated regions (Desikan, or, Destriuex) in the significant clusters? Thanks,Sabin

[Freesurfer] Qdec questions

Hi all - When you get a significant cluster after doing monte-carlo simulation, we get peak vertex/Talairach coordinates and also saved in *summary files. Is there a way to find all the parcellated regions (Desikan, or, Destriuex) in the significant clusters? Thanks

Re: [Freesurfer] QDEC statistic problems correlation between lgi and experimental variable

There are several places where there could be problems. 1. You did not transfer the cluster label files to the individual correctly. What was your command line? 2. The clusters are very small and do not transfer well back to the individual 3. You are not using the same model in SPSS as you

[Freesurfer] QDEC statistic problems correlation between lgi and experimental variable

Dear FreeSurfer experts, we calculated a GLM in qdec with our experimental variable (continuous), age and gender as covariates and LGI. We found significant clusters and corrected them for multiple comparisons with Monte Carlo Z Simulation. We found several significant clusters and looked at

[Freesurfer] qdec analysis with ICV

Hi Freesurfer Experts, I am hoping someone can help me solve this error I'm experiencing while conducting a simple qdec analysis. I have 4 subjects (3 vs 1) that I am trying to analyze for volume differences using a demeaned ICV as a nuisance factor (see attached fsgd file - note I changed the

Re: [Freesurfer] qdec analysis with ICV

Thanks for the suggestion David. I tried it but I still got the same error :/ Gabriella From: David Vazquez [mailto:dvazq...@ucr.edu] Sent: Friday, November 13, 2015 12:36 PM To: Hirsch, Gabriella Subject: Re: [Freesurfer] qdec analysis with ICV Hi Gabriella. I'm not an expert, but I've had

Re: [Freesurfer] qdec analysis with ICV

...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of O'Shea,Andrew Sent: Friday, November 13, 2015 1:55 PM To: freesurfer@nmr.mgh.harvard.edu; David Vazquez Subject: Re: [Freesurfer] qdec analysis with ICV Try mean centering your ICV values (I.e. Subtract the mean value from

Re: [Freesurfer] qdec analysis with ICV

vember 13, 2015 at 1:03 PM To: David Vazquez <dvazq...@ucr.edu<mailto:dvazq...@ucr.edu>> Cc: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurf

Re: [Freesurfer] qdec analysis with ICV

-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of O'Shea,Andrew Sent: Friday, November 13, 2015 4:07 PM To: Freesurfer support list Subject: Re: [Freesurfer] qdec analysis with ICV I believe your issue is you are trying to do a between group analysis but you

Re: [Freesurfer] qdec analysis with ICV

y, November 13, 2015 at 1:58 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] qdec analysis with ICV Hi Andrew, the values I’m using are already mean centered -- similarly, I’ve never been able to use the f

Re: [Freesurfer] QDEC output after Monte Carlo simulation

It may cover both, but the peak can only be in one, and it is the peak that is reported. On 10/25/15 9:55 AM, Annemarie Brandhofe wrote: Dear freesurfer experts, I have analyzed inter-group differences in cortical thickness using freesurfer 5.3.0 and QDEC. I have found one significiant

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