Re: [Freesurfer] QDEC Alternative

[Douglas N. Greve]

   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:


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  We wanted to use QDEC but see that it is no longer 
maintained and has been removed in version 7.3.2 which we are using.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 GUI replacement released in the near future? 
Are there alternatives for QDEC besides the command-line analysis, or 
potential third-party alternatives that are compatible with freesurfer?


Thank you,

Lauren





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[Freesurfer] QDEC Alternative

[Lauren Stephens]

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  We wanted to use QDEC but see that it is no longer maintained and has 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 GUI 
replacement released in the near future? Are there alternatives for QDEC 
besides the command-line analysis, or potential third-party alternatives that 
are compatible with freesurfer?

Thank you,

Lauren




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

[fsbuild]

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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The qdec program is deprecated in 7.X releases and is no longer maintained.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, 
etc.) for stream processing.
If you still need to run qdec in the Freesurfer 6 distribution, then you could 
ask your IT department to create a virtual machine or container to host an 
older copy of your linux OS that supports the correct version of tcl/tk for 
Freesurfer 6.X and install the Freesurfer 6 distribution in it.  Linux 
has quemu for built in virtualization which you may already have installed on 
your server(s). There is also docker for containers and VirtualBox for 
virtual machines which likewise can run an older version of an OS and run 
Freesurfer 6 in those. Your IT group may support docker and/or VirtualBox 
as well.
- R.
On Jul 24, 2022, at 14:41, Rosa de los Angeles Tanzi ta...@cbs.mpg.de 
wrote: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 version I can use 
is 7.1.0 and when I tried to open Qdec the following message appears: Can't 
find a usable init.tclWe tried to contact our IT sever to see if there 
was a way we could use our old Freesurfer version 6.0.0 (which we used to 
calculate the LGI). But they replied to us with the following:"A G6 compute 
server must be used for freesurfer 6.0.0.. The background is that the TCL 8.4.6 
used by Freesurfer is very old (from 2008) and is no longer supported by 
current operating systems. The same applies to the latest version 7.2.0.We have 
TCL 8.6.11 available."Is there anyway we can install Qdec for this new version 
of freesurfer 7.1..0? so we are able to continue with the analysis.I am 
open to any other possible solutions.Kind 
regards,Rosa___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer​
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[Freesurfer] Qdec: Can't find a usable init.tcl

[Rosa de los Angeles Tanzi]

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 version 
I can use is 7.1.0 and when I tried to open Qdec the following message appears: 
Can't find a usable init.tcl 

We tried to contact our IT sever to see if there was a way we could use our old 
Freesurfer version 6.0.0 (which we used to calculate the LGI). But they replied 
to us with the following:

"A G6 compute server must be used for freesurfer 6.0.0. The background is that 
the TCL 8.4.6 used by Freesurfer is very old (from 2008) and is no longer 
supported by current operating systems. The same applies to the latest version 
7.2.0.
We have TCL 8.6.11 available."

Is there anyway we can install Qdec for this new version of freesurfer 7.1.0? 
so we are able to continue with the analysis. 

I am open to any other possible solutions.

Kind regards,

Rosa


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Re: [Freesurfer] qdec analysis error

[Douglas N. Greve]

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, the data is loaded correctly, but 
when I design, I choose discrete and continuous factors for analysis

The error log is as follows
：

Input table: /media/root/Backup_Plus2/new/RECON/qdec/qdec5.table.dat
Subj#, SubjID, Data...
    1 bd1 d Male 15.00 8.00
    2 bd2 d Female 19.00 13.00
    3 bd3 d Male 25.00 9.00
    4 bd4 d Male 17.00 12.00
    5 bd5 d Male 16.00 10.00
    6 bd6 m Female 22.00 12.00
    7 bd7 d Male 17.00 11.00
    8 bd8 d Female 19.00 13.00
    9 bd9 m Female 26.00 7.00
   10 bd10 m Male 53.00 15.00
   11 bd11 m Female 56.00 4.00
   12 bd12 d Female 21.00 14.00
   13 bd13 m Female 19.00 12.00
   14 bd14 m Female 32.00 15.00
   15 bd15 d Male 21.00 9.00
   16 bd16 d Male 16.00 10.00
   17 bd17 d Male 15.00 11.00
   18 bd18 d Female 32.00 10.00
   19 bd19 d Female 20.00 15.00
   20 bd20 d Female 17.00 11.00
   21 bd22 m Male 22.00 11.00
   22 bd23 m Female 28.00 6.00
   23 bd24 d Male 26.00 11.00
   24 bd25 m Female 24.00 9.00
   25 bd26 m Female 30.00 6.00
   26 bd27 m Female 20.00 12.00
   27 bd28 d Female 28.00 16.00
   28 bd29 m Female 18.00 12.00
   29 bd30 d Male 21.00 15.00
   30 bd31 d Female 30.00 16.00
   31 bd32 d Male 18.00 11.00
   32 bd33 d Female 16.00 10.00
   33 bd34 d Male 21.00 11.00
   34 bd35 d Female 15.00 10.00
   35 bd36 d Female 16.00 10.00
   36 bd37 d Male 19.00 14.00
   37 bd39 d Male 16.00 10.00
   38 bd40 m Female 20.00 14.00
   39 bd41 m Female 21.00 15.00
   40 bd42 d Male 23.00 9.00
   41 bd43 m Male 27.00 9.00
   42 bd44 d Female 15.00 8.00
   43 bd45 m Male 19.00 9.00
   44 bd46 d Female 16.00 11.00
   45 bd47 m Female 23.00 15.00
   46 bd48 m Male 18.00 13.00
   47 bd49 d Female 22.00 15.00
   48 bd50 d Female 17.00 11.00
   49 bd51 d Male 17.00 10.00
   50 bd52 d Male 27.00 15.00
   51 bd53 m Male 16.00 9.00
   52 bd54 d Male 18.00 12.00
   53 bd55 d Female 18.00 11.00
   54 bd56 m Female 16.00 10.00
   55 bd57 d Male 16.00 9.00
   56 bd58 m Male 22.00 9.00
   57 bd59 m Male 16.00 8.00
   58 bd60 d Male 16.00 9.00
   59 bd61 m Female 18.00 10.00
   60 bd62 d Female 15.00 9.00
   61 hc1 h Male 52.00 7.00
   62 hc2 h Female 24.00 10.00
   63 hc3 h Male 45.00 7.00
   64 hc4 h Female 18.00 13.00
   65 hc5 h Female 19.00 10.00
   66 hc6 h Female 17.00 12.00
   67 hc7 h Female 19.00 7.00
   68 hc8 h Male 48.00 5.00
   69 hc9 h Female 53.00 6.00
   70 hc10 h Female 52.00 15.00
   71 hc11 h Female 19.00 12.00
   72 hc12 h Female 18.00 12.00
   73 hc13 h Female 20.00 12.00
   74 hc14 h Female 18.00 12.00
   75 hc15 h Female 19.00 13.00
   76 hc16 h Female 18.00 11.00
   77 hc17 h Female 19.00 12.00
   78 hc18 h Female 19.00 12.00
   79 hc19 h Female 19.00 12.00
   80 hc20 h Female 19.00 12.00
   81 hc21 h Female 18.00 12.00
   82 hc22 h Female 18.00 12.00
   83 hc23 h Female 18.00 11.00
   84 hc24 h Female 18.00 12.00
   85 hc25 h Female 18.00 12.00
   86 hc26 h Female 18.00 11.00
   87 hc27 h Female 18.00 12.00
   88 hc28 h Female 18.00 12.00
   89 hc29 h Female 18.00 11.00
   90 hc30 h Male 20.00 12.00
   91 hc31 h Female 29.00 17.00
   92 hc32 h Female 16.00 10.00
   93 hc33 h Female 17.00 10.00
   94 hc34 h Female 26.00 14.00
   95 hc35 h Female 24.00 17.00
   96 hc36 h Female 22.00 17.00
   97 hc37 h Male 25.00 17.00
   98 hc38 h Male 24.00 17.00
   99 hc39 h Male 25.00 17.00
1  groups  discrete 3
    1  d
    2  m
    3  h
2  gender  discrete 2
    1  Male
    2  Female
3  age  continuous 0
4  edu  continuous 0
    Continuous Factors: Mean: StdDev:
    --- - ---
    age    22.293 9.015
    edu    11.374 2.827

Number of subjects:   99
Number of factors:    4 (2 discrete, 2 continuous)
Number of classes:    6
Number of regressors: 18

Data table loading completed successfully.
SUBJECTS_DIR 

[Freesurfer] qdec analysis error

[David]

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 as follows
：

Input table: /media/root/Backup_Plus2/new/RECON/qdec/qdec5.table.dat
Subj#, SubjID, Data...
1 bd1 d Male 15.00 8.00
2 bd2 d Female 19.00 13.00
3 bd3 d Male 25.00 9.00
4 bd4 d Male 17.00 12.00
5 bd5 d Male 16.00 10.00
6 bd6 m Female 22.00 12.00
7 bd7 d Male 17.00 11.00
8 bd8 d Female 19.00 13.00
9 bd9 m Female 26.00 7.00
   10 bd10 m Male 53.00 15.00
   11 bd11 m Female 56.00 4.00
   12 bd12 d Female 21.00 14.00
   13 bd13 m Female 19.00 12.00
   14 bd14 m Female 32.00 15.00
   15 bd15 d Male 21.00 9.00
   16 bd16 d Male 16.00 10.00
   17 bd17 d Male 15.00 11.00
   18 bd18 d Female 32.00 10.00
   19 bd19 d Female 20.00 15.00
   20 bd20 d Female 17.00 11.00
   21 bd22 m Male 22.00 11.00
   22 bd23 m Female 28.00 6.00
   23 bd24 d Male 26.00 11.00
   24 bd25 m Female 24.00 9.00
   25 bd26 m Female 30.00 6.00
   26 bd27 m Female 20.00 12.00
   27 bd28 d Female 28.00 16.00
   28 bd29 m Female 18.00 12.00
   29 bd30 d Male 21.00 15.00
   30 bd31 d Female 30.00 16.00
   31 bd32 d Male 18.00 11.00
   32 bd33 d Female 16.00 10.00
   33 bd34 d Male 21.00 11.00
   34 bd35 d Female 15.00 10.00
   35 bd36 d Female 16.00 10.00
   36 bd37 d Male 19.00 14.00
   37 bd39 d Male 16.00 10.00
   38 bd40 m Female 20.00 14.00
   39 bd41 m Female 21.00 15.00
   40 bd42 d Male 23.00 9.00
   41 bd43 m Male 27.00 9.00
   42 bd44 d Female 15.00 8.00
   43 bd45 m Male 19.00 9.00
   44 bd46 d Female 16.00 11.00
   45 bd47 m Female 23.00 15.00
   46 bd48 m Male 18.00 13.00
   47 bd49 d Female 22.00 15.00
   48 bd50 d Female 17.00 11.00
   49 bd51 d Male 17.00 10.00
   50 bd52 d Male 27.00 15.00
   51 bd53 m Male 16.00 9.00
   52 bd54 d Male 18.00 12.00
   53 bd55 d Female 18.00 11.00
   54 bd56 m Female 16.00 10.00
   55 bd57 d Male 16.00 9.00
   56 bd58 m Male 22.00 9.00
   57 bd59 m Male 16.00 8.00
   58 bd60 d Male 16.00 9.00
   59 bd61 m Female 18.00 10.00
   60 bd62 d Female 15.00 9.00
   61 hc1 h Male 52.00 7.00
   62 hc2 h Female 24.00 10.00
   63 hc3 h Male 45.00 7.00
   64 hc4 h Female 18.00 13.00
   65 hc5 h Female 19.00 10.00
   66 hc6 h Female 17.00 12.00
   67 hc7 h Female 19.00 7.00
   68 hc8 h Male 48.00 5.00
   69 hc9 h Female 53.00 6.00
   70 hc10 h Female 52.00 15.00
   71 hc11 h Female 19.00 12.00
   72 hc12 h Female 18.00 12.00
   73 hc13 h Female 20.00 12.00
   74 hc14 h Female 18.00 12.00
   75 hc15 h Female 19.00 13.00
   76 hc16 h Female 18.00 11.00
   77 hc17 h Female 19.00 12.00
   78 hc18 h Female 19.00 12.00
   79 hc19 h Female 19.00 12.00
   80 hc20 h Female 19.00 12.00
   81 hc21 h Female 18.00 12.00
   82 hc22 h Female 18.00 12.00
   83 hc23 h Female 18.00 11.00
   84 hc24 h Female 18.00 12.00
   85 hc25 h Female 18.00 12.00
   86 hc26 h Female 18.00 11.00
   87 hc27 h Female 18.00 12.00
   88 hc28 h Female 18.00 12.00
   89 hc29 h Female 18.00 11.00
   90 hc30 h Male 20.00 12.00
   91 hc31 h Female 29.00 17.00
   92 hc32 h Female 16.00 10.00
   93 hc33 h Female 17.00 10.00
   94 hc34 h Female 26.00 14.00
   95 hc35 h Female 24.00 17.00
   96 hc36 h Female 22.00 17.00
   97 hc37 h Male 25.00 17.00
   98 hc38 h Male 24.00 17.00
   99 hc39 h Male 25.00 17.00
1  groups  discrete 3
1  d
2  m
3  h
2  gender  discrete 2
1  Male
2  Female
3  age  continuous 0
4  edu  continuous 0
Continuous Factors: Mean:   StdDev:
--- -   ---
age22.293 9.015
edu11.374 2.827

Number of subjects:   99
Number of factors:4 (2 discrete, 2 continuous)
Number of classes:6
Number of regressors: 18

Data table loading completed successfully.
SUBJECTS_DIR is '/media/root/Backup_Plus2/new/RECON'
ERROR: QdecGlmDesign::GenerateContrasts: factor 1 

Re: [Freesurfer] Qdec error

[Douglas N. Greve]

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 following error:


Tk_Init error: invalid command name "tcl_findLibrary"
Error initializing Tcl.

Could anyone please tell me what this means?

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[Freesurfer] Qdec error

[Arian Klows]

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?
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Re: [Freesurfer] QDEC command not found

[Douglas N. Greve]

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 the patients, I tried to open qdec for the 
analysis by typing*qdec *and the answer is "command not found".
Could you help me, please?
Many thanks,

*Dra. Fabíola Macruz *
MD from *Faculdade de Ciências Médicas da Santa Casa de São Paulo*
PhD from*Universidade de São Paulo*
Former Research Fellow from***Stanford University*
Former Clinical Innovation Fellow/ Project Leader from***Mass General 
Brigham*

Phone: + 1(650)686-0668 / + 55(11)99571-5906


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[Freesurfer] QDEC command not found

[Fabiola Macruz]

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".


Could you help me, please?


Many thanks,

Dra. Fabíola Macruz
MD from Faculdade de Ciências Médicas da Santa Casa de São Paulo
PhD from Universidade de São Paulo
Former Research Fellow from Stanford University
Former Clinical Innovation Fellow/ Project Leader from Mass General Brigham
Phone: + 1(650)686-0668 / + 55(11)99571-5906

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Re: [Freesurfer] Qdec vertex-wise clustering question

[Douglas N. Greve]

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 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 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 statistical calculations or
>>> are they primarily used for figure generation for Qdec?
>>>
>>> Many thanks again,
>>> Alejandro
>>>
>>> On Mon, Jul 12, 2021 at 6:29 PM Douglas N. Greve  
>>> wrote:
 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
> 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 your assistance,
> Alejandro
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] Qdec vertex-wise clustering question

[Alejandro Meruelo]

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 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 statistical calculations or
> > are they primarily used for figure generation for Qdec?
> >
> > Many thanks again,
> > Alejandro
> >
> > On Mon, Jul 12, 2021 at 6:29 PM Douglas N. Greve  
> > wrote:
> >> 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
> >>> 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 your assistance,
> >>> Alejandro
> >>>
> >>> ___
> >>> Freesurfer mailing list
> >>> Freesurfer@nmr.mgh.harvard.edu
> >>> https://secure-web.cisco.com/1X19qF3LTR7nmdOuf_f6RSfYImcif8WdsoOw4_5vapNU7CnFsQEzH1fm1UDi3V8fK2JRGXNuLLDIjbxr62xLUSqiyvmQf8D48SJGSDm3x7Y4WpUo-DuZFi9h-eENJY15FvkfkGrg0cHEA8LFoK1HyY6blwCNnzYwt_q_W6RRRLDozVGog9vgYUi9rAqBZ1ykzl_ow040xGVoQh1u-JF8zXZTpaLSTRllYVlJSwB_XCLOakCHcnbJytarlHiKqgPMIPsQrCqAlYcK-v-Csf71GHA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> >> ___
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> >> The information in this e-mail is intended only for the person to whom it 
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> >> e-mail contains patient information, please contact the Mass General 
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Re: [Freesurfer] Qdec vertex-wise clustering question

[Douglas N. Greve]

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 statistical calculations or
> are they primarily used for figure generation for Qdec?
>
> Many thanks again,
> Alejandro
>
> On Mon, Jul 12, 2021 at 6:29 PM Douglas N. Greve  
> wrote:
>> 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
>>> 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 your assistance,
>>> Alejandro
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://secure-web.cisco.com/1X19qF3LTR7nmdOuf_f6RSfYImcif8WdsoOw4_5vapNU7CnFsQEzH1fm1UDi3V8fK2JRGXNuLLDIjbxr62xLUSqiyvmQf8D48SJGSDm3x7Y4WpUo-DuZFi9h-eENJY15FvkfkGrg0cHEA8LFoK1HyY6blwCNnzYwt_q_W6RRRLDozVGog9vgYUi9rAqBZ1ykzl_ow040xGVoQh1u-JF8zXZTpaLSTRllYVlJSwB_XCLOakCHcnbJytarlHiKqgPMIPsQrCqAlYcK-v-Csf71GHA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>> ___
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>> addressed. If you believe this e-mail was sent to you in error and the 
>> e-mail contains patient information, please contact the Mass General Brigham 
>> Compliance HelpLine at 
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Re: [Freesurfer] Qdec vertex-wise clustering question

[Alejandro Meruelo]

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 6:29 PM Douglas N. Greve  wrote:
>
> 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
> > 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 your assistance,
> > Alejandro
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://secure-web.cisco.com/1X19qF3LTR7nmdOuf_f6RSfYImcif8WdsoOw4_5vapNU7CnFsQEzH1fm1UDi3V8fK2JRGXNuLLDIjbxr62xLUSqiyvmQf8D48SJGSDm3x7Y4WpUo-DuZFi9h-eENJY15FvkfkGrg0cHEA8LFoK1HyY6blwCNnzYwt_q_W6RRRLDozVGog9vgYUi9rAqBZ1ykzl_ow040xGVoQh1u-JF8zXZTpaLSTRllYVlJSwB_XCLOakCHcnbJytarlHiKqgPMIPsQrCqAlYcK-v-Csf71GHA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>
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> contains patient information, please contact the Mass General Brigham 
> Compliance HelpLine at 
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Re: [Freesurfer] Qdec vertex-wise clustering question

[Douglas N. Greve]

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
> 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 your assistance,
> Alejandro
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
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The information in this e-mail is intended only for the person to whom it is 
addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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continue to communicate over unencrypted e-mail. 

[Freesurfer] Qdec vertex-wise clustering question

[Alejandro Meruelo]

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 your assistance,
Alejandro

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Re: [Freesurfer] QDEC/mri_glmfit questions

[Douglas N. Greve]

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 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 nv1=163842, nv1=2. This was an iteration of the table with one data 
> column for the thickness of an ROI, however, I also got the same error with 
> the full table. This is also the same table we used in SPSS for a linear 
> regression there.
>
> Terminal inputs:
> mri_glmfit —y lh.thickness.inflammatory.10.mgh —fsgd 
> inflammatory_markers.fsgd —C Inflammatory_group.mtx —C group_inflammatory.mtx 
> —surf fsaverage —table entorhinal_table.dat —label entorhinal.label —glmdir 
> Inflammatory_entorhinal.lh.thickness.10.glmdir
>
> mri_glmfit —fsgd inflammatory_markers.fsgd —C Inflammatory_group.mtx —C 
> group_inflammatory.mtx —surf fsaverage —table aparc_table.dat —label 
> entorhinal.label —glmdir Inflammatory_entorhinal.lh.thickness.10.glmdir
>
> Thanks!
> Erin
>
>> On Feb 18, 2021, at 11:15 AM, Erin Moe  wrote:
>>
>> 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 a linear regression with those same 
>> inflammatory markers in SPSS, I get several significant results. I’m 
>> assuming it might be due to me setting up the QDEC/mri_glmfit analysis wrong.
>>
>> For QDEC I have a two column .dat file with the subject IDs in the FSID 
>> column and the inflammatory markers for each participant in the other column 
>> and running the QDEC thickness analysis on that and I don’t get much in 
>> terms of results.
>>
>> For mri_glmfit I used an FSGD file set up just like the .dat file for QDEC 
>> with the exception of formatting. However, we wanted to constrain the 
>> analysis to an ROI (entorhinal in this case), I ran mris_preproc with the 
>> following command:
>> mris_preproc —fsgd inflammatory_markers.fsgd —cache-in 
>> thickness.fwhm10.fsaverage —target fsaverage —hemi lh —out 
>> lh.thickness.inflammatory.10.mgh
>>
>> Then fed that output into mri_glmfit as:
>> mri_glmfit —y lh.thickness.inflammatory.10.mgh —fsgd 
>> inflammatory_markers.fsgd —C Inflammatory_group.mtx —C 
>> group_inflammatory.mtx —surf fsaverage —label entorhinal.label —glmdir 
>> Inflammatory_entorhinal.lh.thickness.10.glmdir
>> The results from this look the same as the QDEC analysis but just masked out 
>> for the entorhinal ROI. So, to constrain the analysis to the ROI, I ran a 
>> Monte Carlo correction with mri_surfcluster.
>>
>> So a few questions:
>> Would running mri_surfcluster on the sig.mgh output from the mri_glmfit 
>> analysis actually constrain the analysis to the ROI specified?
>>
>> How can I get my results to match that of what I’m seeing in SPSS?
>>
>> Is my analysis set up correctly for what I’m trying to do?
>>
>>
>>
>> Thank you in advance for your patience with this lengthy inquiry.
>>
>> Best,
>> Erin
>>
>>
>>
>>
>
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Re: [Freesurfer] QDEC/mri_glmfit questions

[Erin Moe]

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 nv1=163842, nv1=2. This was an iteration of the table with one data 
column for the thickness of an ROI, however, I also got the same error with the 
full table. This is also the same table we used in SPSS for a linear regression 
there. 

Terminal inputs:
mri_glmfit —y lh.thickness.inflammatory.10.mgh —fsgd inflammatory_markers.fsgd 
—C Inflammatory_group.mtx —C group_inflammatory.mtx —surf fsaverage —table 
entorhinal_table.dat —label entorhinal.label —glmdir 
Inflammatory_entorhinal.lh.thickness.10.glmdir 

mri_glmfit —fsgd inflammatory_markers.fsgd —C Inflammatory_group.mtx —C 
group_inflammatory.mtx —surf fsaverage —table aparc_table.dat —label 
entorhinal.label —glmdir Inflammatory_entorhinal.lh.thickness.10.glmdir 

Thanks!
Erin

> On Feb 18, 2021, at 11:15 AM, Erin Moe  wrote:
> 
> 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 a linear regression with those same 
> inflammatory markers in SPSS, I get several significant results. I’m assuming 
> it might be due to me setting up the QDEC/mri_glmfit analysis wrong. 
> 
> For QDEC I have a two column .dat file with the subject IDs in the FSID 
> column and the inflammatory markers for each participant in the other column 
> and running the QDEC thickness analysis on that and I don’t get much in terms 
> of results.
> 
> For mri_glmfit I used an FSGD file set up just like the .dat file for QDEC 
> with the exception of formatting. However, we wanted to constrain the 
> analysis to an ROI (entorhinal in this case), I ran mris_preproc with the 
> following command: 
> mris_preproc —fsgd inflammatory_markers.fsgd —cache-in 
> thickness.fwhm10.fsaverage —target fsaverage —hemi lh —out 
> lh.thickness.inflammatory.10.mgh 
> 
> Then fed that output into mri_glmfit as: 
> mri_glmfit —y lh.thickness.inflammatory.10.mgh —fsgd 
> inflammatory_markers.fsgd —C Inflammatory_group.mtx —C group_inflammatory.mtx 
> —surf fsaverage —label entorhinal.label —glmdir 
> Inflammatory_entorhinal.lh.thickness.10.glmdir 
> The results from this look the same as the QDEC analysis but just masked out 
> for the entorhinal ROI. So, to constrain the analysis to the ROI, I ran a 
> Monte Carlo correction with mri_surfcluster.
> 
> So a few questions:
> Would running mri_surfcluster on the sig.mgh output from the mri_glmfit 
> analysis actually constrain the analysis to the ROI specified? 
> 
> How can I get my results to match that of what I’m seeing in SPSS? 
> 
> Is my analysis set up correctly for what I’m trying to do?
> 
> 
> 
> Thank you in advance for your patience with this lengthy inquiry. 
> 
> Best,
> Erin
> 
> 
> 
> 


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Re: [Freesurfer] QDEC/mri_glmfit questions

[Douglas N. Greve]

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 Inflammatory_group.mtx —C 
group_inflammatory.mtx

The sig output will be in glmdir/sig.table.dat (or something like that).
Oftentimes, SPSS and mri_glmfit will be using different design matrices.

On 2/18/2021 1:15 PM, Erin Moe wrote:
>  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 a linear regression with those same 
> inflammatory markers in SPSS, I get several significant results. I’m assuming 
> it might be due to me setting up the QDEC/mri_glmfit analysis wrong.
>
> For QDEC I have a two column .dat file with the subject IDs in the FSID 
> column and the inflammatory markers for each participant in the other column 
> and running the QDEC thickness analysis on that and I don’t get much in terms 
> of results.
>
> For mri_glmfit I used an FSGD file set up just like the .dat file for QDEC 
> with the exception of formatting. However, we wanted to constrain the 
> analysis to an ROI (entorhinal in this case), I ran mris_preproc with the 
> following command:
> mris_preproc —fsgd inflammatory_markers.fsgd —cache-in 
> thickness.fwhm10.fsaverage —target fsaverage —hemi lh —out 
> lh.thickness.inflammatory.10.mgh
>
> Then fed that output into mri_glmfit as:
> mri_glmfit —y lh.thickness.inflammatory.10.mgh —fsgd 
> inflammatory_markers.fsgd —C Inflammatory_group.mtx —C group_inflammatory.mtx 
> —surf fsaverage —label entorhinal.label —glmdir 
> Inflammatory_entorhinal.lh.thickness.10.glmdir
> The results from this look the same as the QDEC analysis but just masked out 
> for the entorhinal ROI. So, to constrain the analysis to the ROI, I ran a 
> Monte Carlo correction with mri_surfcluster.
>
> So a few questions:
> Would running mri_surfcluster on the sig.mgh output from the mri_glmfit 
> analysis actually constrain the analysis to the ROI specified?
>
> How can I get my results to match that of what I’m seeing in SPSS?
>
> Is my analysis set up correctly for what I’m trying to do?
>
>
>
> Thank you in advance for your patience with this lengthy inquiry.
>
> Best,
> Erin
>
>
>
>
>
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[Freesurfer] QDEC/mri_glmfit questions

[Erin Moe]

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 a 
linear regression with those same inflammatory markers in SPSS, I get several 
significant results. I’m assuming it might be due to me setting up the 
QDEC/mri_glmfit analysis wrong. 

For QDEC I have a two column .dat file with the subject IDs in the FSID column 
and the inflammatory markers for each participant in the other column and 
running the QDEC thickness analysis on that and I don’t get much in terms of 
results.

For mri_glmfit I used an FSGD file set up just like the .dat file for QDEC with 
the exception of formatting. However, we wanted to constrain the analysis to an 
ROI (entorhinal in this case), I ran mris_preproc with the following command: 
mris_preproc —fsgd inflammatory_markers.fsgd —cache-in 
thickness.fwhm10.fsaverage —target fsaverage —hemi lh —out 
lh.thickness.inflammatory.10.mgh 

Then fed that output into mri_glmfit as: 
mri_glmfit —y lh.thickness.inflammatory.10.mgh —fsgd inflammatory_markers.fsgd 
—C Inflammatory_group.mtx —C group_inflammatory.mtx —surf fsaverage —label 
entorhinal.label —glmdir Inflammatory_entorhinal.lh.thickness.10.glmdir 
The results from this look the same as the QDEC analysis but just masked out 
for the entorhinal ROI. So, to constrain the analysis to the ROI, I ran a Monte 
Carlo correction with mri_surfcluster.

So a few questions:
Would running mri_surfcluster on the sig.mgh output from the mri_glmfit 
analysis actually constrain the analysis to the ROI specified? 

How can I get my results to match that of what I’m seeing in SPSS? 

Is my analysis set up correctly for what I’m trying to do?



Thank you in advance for your patience with this lengthy inquiry. 

Best,
Erin





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Re: [Freesurfer] Qdec crash while analysis almost finished

[chenbh35]

External Email - Use Caution

Hi Douglas,

I used to work with v5.3(centOS6) before and recently I changed a new computer, 
so I hope to keep using the same version(v5.3) in case of some version problem 
with old results. But I couldn't perform a qdec analysis because It kept giving 
me the invalid license key error when I press the analyze button. Owing to I am 
using different linux system(Ubuntu20), I install v6 to see if the error still 
exist. Qdec kept well during loading table file and generate stats file, but 
after I press the analyze  button and it almost finished, the interface 
suddenly crashed and disappear as the content of terminal I have sent before. 
Wheareas, I used the mri_glmfit command in the terminal and it can work. That 
really confused me. 

As to the license file, they have the same content as I have apply for license 
file three times after I 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 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 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 
/usr/local/freesurfer and has changed the name to .license as well. But it 
still doesn't work. Owing to the version I used last time was v6.0, so I 
reinstall a v6.0 and use the same license file. 

But here comes the new problem, when the analysis almost finished, qdec just 
crash and disappear, parts of the contents in the command window are:

""""""""""""""""""""""

Writing results
  lh-Avg-Intercept-thickness
maxvox sig=1e+10  F=3846.45  at  index 14 0 0seed=1611502349
  lh-Diff-PCE-CON-Intercept-thickness
maxvox sig=3.52355  F=15.3058  at  index 11472 0 0seed=1611502349
mri_glmfit done
ninputs = 2
Checking inputs
nframestot = 2
Allocing output
Done allocing
nframes = 2
Writing to /media/lava/DATA/ESSAY/FirstWave/qdec/Untitled/contrasts.sig.mgh

--
ERROR: Invalid FreeSurfer license key found in license file 
/usr/local/freesurfer/license.txt
  If you are outside the NMR-Martinos Center,
  go to 
http://secure-web.cisco.com/12IMz3Y7rTVztzuldpNKAzkOidv5aXs4jMwblK0uNWTRHT39sbFSESHbr6MlSyJSfw3U64yrVx7i9kelES7w6JlB43Y8Vk-KkYgRL0uUuZljVYMjYZ3SQg63KdDqU_t5ooLkrlkk_PNACjX6LLWlLAVMVxXKhp3b-pqIMQT0VciDmBgvmCpU8B85n8cPn1eWXnuaZhfzUL5ciYRZBw1Vffn5aNtHj8tcYSKaG0qPdEed-QcrxPauza2vgmTcvsv8L/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu
 to 
  get a valid license file (it's free).
  If you are inside the NMR-Martinos Center,
  make sure to source the standard environment.




"""""""""""""""""""""""

I wonder what was the question?  Appreciate for any suggestions.





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freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Qdec crash while analysis almost finished

[Greve, Douglas N.,Ph.D.]

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 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 
/usr/local/freesurfer and has changed the name to .license as well. But it 
still doesn't work. Owing to the version I used last time was v6.0, so I 
reinstall a v6.0 and use the same license file.

But here comes the new problem, when the analysis almost finished, qdec just 
crash and disappear, parts of the contents in the command window are:

""

Writing results
  lh-Avg-Intercept-thickness
maxvox sig=1e+10  F=3846.45  at  index 14 0 0seed=1611502349
  lh-Diff-PCE-CON-Intercept-thickness
maxvox sig=3.52355  F=15.3058  at  index 11472 0 0seed=1611502349
mri_glmfit done
ninputs = 2
Checking inputs
nframestot = 2
Allocing output
Done allocing
nframes = 2
Writing to /media/lava/DATA/ESSAY/FirstWave/qdec/Untitled/contrasts.sig.mgh

--
ERROR: Invalid FreeSurfer license key found in license file 
/usr/local/freesurfer/license.txt
  If you are outside the NMR-Martinos Center,
  go to http://surfer.nmr.mgh.harvard.edu to
  get a valid license file (it's free).
  If you are inside the NMR-Martinos Center,
  make sure to source the standard environment.

"""

I wonder what was the question?  Appreciate for any suggestions.



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[Freesurfer] Qdec crash while analysis almost finished

[chenbh35]

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 
/usr/local/freesurfer and has changed the name to .license as well. But it 
still doesn't work. Owing to the version I used last time was v6.0, so I 
reinstall a v6.0 and use the same license file. 

But here comes the new problem, when the analysis almost finished, qdec just 
crash and disappear, parts of the contents in the command window are:

""

Writing results
  lh-Avg-Intercept-thickness
maxvox sig=1e+10  F=3846.45  at  index 14 0 0seed=1611502349
  lh-Diff-PCE-CON-Intercept-thickness
maxvox sig=3.52355  F=15.3058  at  index 11472 0 0seed=1611502349
mri_glmfit done
ninputs = 2
Checking inputs
nframestot = 2
Allocing output
Done allocing
nframes = 2
Writing to /media/lava/DATA/ESSAY/FirstWave/qdec/Untitled/contrasts.sig.mgh

--
ERROR: Invalid FreeSurfer license key found in license file 
/usr/local/freesurfer/license.txt
  If you are outside the NMR-Martinos Center,
  go to 
http://secure-web.cisco.com/1l89yx4rr6CbgxQdMiHeY9D8oLAHswLvN7Y1eaaby-Qvn6BVAZuZXwQTAmP0xC7E_rBnRtenwucOyHla0XC9xw2XeIb4JxTVdGUe7DvwQWkZeHZrUqHnr9ytKduEorS6hP5vcMYSHddgx_sm5IuMyMwUIclL1iy7aEMQi4_WDwbqmWFSL9JHrJR0Pi8jESAhxmMm7PAdyF8HtflWq5QA7WU7ccAdPF1EbObmbe9JfgZ9HMqGuzIq5iaG5WpkQHMBFU-RRra2y1iv0boOXppQN-w/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu
 to 
  get a valid license file (it's free).
  If you are inside the NMR-Martinos Center,
  make sure to source the standard environment.


"""

I wonder what was the question?  Appreciate for any suggestions.___
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Re: [Freesurfer] qdec replacement

[Greve, Douglas N.,Ph.D.]

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:
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[Freesurfer] qdec replacement

[Pagliaccio, David (NYSPI)]

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.
Assistant Professor of Clinical Neurobiology (in Psychiatry)
Columbia University Irving Medical Center

Assistant Research Scientist
Division of Child and Adolescent Psychiatry
New York State Psychiatric Institute
1051 Riverside Drive
New York, NY 10032
phone: 646-774-5556
Email: 
david.pagliac...@nyspi.columbia.edu
Pronouns: he/him

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

[Douglas N. Greve]

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 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 purposes, I would like to show that the 
coordinates that were stimulated fall within this cluster.


Is there a way to plug in talairach coordinates within the qdec 
display so that the cross hair (or some sort of other marking) appears 
at that specific corresponding vertex?


Thank you,
Paul

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[Freesurfer] Qdec - talairach to vertex for display purposes

[Paul Dhami]

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 purposes, I would like to show that the coordinates
that were stimulated fall within this cluster.

Is there a way to plug in talairach coordinates within the qdec display so
that the cross hair (or some sort of other marking) appears at that
specific corresponding vertex?

Thank you,
Paul
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[Freesurfer] qdec problems not receiving keyboard input

[Agurne Sampedro Calvete]

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 maximum threshold in the display page. I've seen that other people have
had a similar problem too. How can I solve it?

Thanks in advance.

Kind regards,
Agurne Sampedro
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Re: [Freesurfer] qdec problems not receiving keyboard input

[Douglas N. Greve]

Sorry, qdec has been mothballed and we are not supporting it anymore

On 10/7/2020 7:12 AM, Agurne Sampedro Calvete wrote:


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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 maximum threshold in the display page. I've seen 
that other people have had a similar problem too. How can I solve it?


Thanks in advance.

Kind regards,
Agurne Sampedro



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Re: [Freesurfer] QDEC command not found

[Douglas N. Greve]

We are no longer distributing or supporting qdec

On 10/2/2020 6:17 AM, Enrico Collantoni wrote:


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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 versions.
Could you help me?
Many thanks
Enrico Collantoni

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[Freesurfer] QDEC command not found

[Enrico Collantoni]

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 versions.

Could you help me?

Many thanks


Enrico Collantoni
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Re: [Freesurfer] QDEC analyses

[Douglas N. Greve]

Sorry, I can't remember whether the qdec correction for mult comp 
included an option to specify that there were two hemispheres. If not, 
you can take the cluster p-value that you get from qdec and multiply it 
by 2 (bonferonni correction for 2 hemis), this is mentioned in Greve and 
Fischl, 2017, NI. False positive rates in surface-based anatomical analysis


On 6/22/2020 11:07 AM, xunzhang_hmrrc wrote:


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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 thickness between the patients and healthy controls with age and 
sex as covariates. The Monte Carlo Null-Z Simulation was conducted to 
control for multiple comparisons (cluster-wise corrected P< 0.05). 
But, as we all know, QDEC analyses have always be done for the two 
hemispheres separately, so the multiple comparisons are also conducted 
for two hemispheres separately, which, the reviewer assumed, is 
different from multiple comparisons for the whole brain? So, could you 
please provide some perspective and citation about the validation for 
such design of QDEC (i.e., the right and left hemisphere were tested 
separately)?





-- Original --
*From:* "Douglas N. Greve";
*Date:* Mon, Jun 22, 2020 10:17 AM
*To:* "freesurfer";
*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 two 
hemispheres being tested.



On 6/20/2020 10:04 PM, xunzhang_hmrrc wrote:


    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 stated that the right and left hemisphere were tested 
separately. Could the authors provide an explanation for this? I 
assume that testing over 68 (all ROIs) vs testing separately left and 
right (34 ROIs) would have an effect?" Unfornately, I don't know how 
to responde to this reviewer, so I would like to ask for your help. I 
just followed the tutorials of QDEC 
(http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysisV6.0), 
and I found QDEC analyses have always be done for the two hemispheres 
separately. So, could you please provide some perspective and 
citation about the validation for such design of QDEC?


Thank you in advance for your assistance,

Best regards,




Xun



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Re: [Freesurfer] QDEC analyses

[xunzhang_hmrrc]

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 
thickness between the patients and healthy controls with age and sex as 
covariates. The Monte Carlo Null-Z Simulation was conducted to control for 
multiple comparisons (cluster-wise corrected P< 0.05). But, as we all know, 
QDEC analyses have always be done for the two hemispheres 
separately, so the multiple comparisons are also conducted for two 
hemispheres separately, which, the reviewer assumed, is different from multiple 
comparisons for the whole brain? So, could you please provide some 
perspective and citation about the validation for such design of
 QDEC (i.e., the right and left hemisphere were tested  
   separately)?

 





-- Original --
From:"Douglas N. Greve"http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysisV6.0),
 and I found QDEC analyses have always be done for the two 
hemispheres separately. So, could you please provide some 
perspective and citation about the validation for such design of
 QDEC?
 
 
Thank you in advance for your assistance,
 
Best regards,
 
   



   
   
Xun
 
 
   
 
   
   
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Re: [Freesurfer] QDEC analyses

[xunzhang_hmrrc]

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 
thickness between the patients and healthy controls with age and sex as 
covariates. The Monte Carlo Null-Z Simulation was conducted to control for 
multiple comparisons (cluster-wise corrected P< 0.05). But, as we all 
know,QDEC analyses have always be done for the two 
hemispheres separately, so themultiple comparisons are also conducted 
fortwo hemispheres separately, which, the reviewer assumed, 
is different frommultiple comparisons for the whole brain?So, could 
you please provide some perspective and citation about the 
validation for such design of QDEC (i.e., the right and 
left hemisphere were tested separately)?

 





--Original--
From:"Douglas N. Greve"http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysisV6.0),
 and I found QDEC analyses have always be done for the two 
hemispheres separately. So, could you please provide some 
perspective and citation about the validation for such design of
 QDEC?
 
 
Thank you in advance for your assistance,
 
Best regards,
 
   



   
   
Xun
 
 
   
 
   
   
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Re: [Freesurfer] QDEC analyses

[Douglas N. Greve]

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 6/20/2020 10:04 PM, xunzhang_hmrrc wrote:


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 stated that the right and left hemisphere were tested 
separately. Could the authors provide an explanation for this? I 
assume that testing over 68 (all ROIs) vs testing separately left and 
right (34 ROIs) would have an effect?" Unfornately, I don't know how 
to responde to this reviewer, so I would like to ask for your help. I 
just followed the tutorials of QDEC 
(http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysisV6.0), 
and I found QDEC analyses have always be done for the two hemispheres 
separately. So, could you please provide some perspective and citation 
about the validation for such design of QDEC?


Thank you in advance for your assistance,

Best regards,




Xun



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[Freesurfer] QDEC analyses

[xunzhang_hmrrc]

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 stated that the 
right and left hemisphere were tested separately. Could the authors provide an 
explanation for this? I assume that testing over 68 (all ROIs) vs testing 
separately left and right (34 ROIs) would have an effect?" Unfornately, I don't 
know how to responde to this reviewer, so I would like to ask for your help. I 
just followed the tutorials of QDEC 
(http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysisV6.0), 
and I found QDEC analyses have always be done for the two hemispheres 
separately. So, could you please provide some perspective and citation about 
the validation for such design of QDEC?

 
Thank you in advance for your assistance,
 
Best regards,







Xun___
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[Freesurfer] QDEC analyses

[xunzhang_hmrrc]

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 stated that the 
right and left hemisphere were tested separately. Could the authors provide an 
explanation for this? I assume that testing over 68 (all ROIs) vs testing 
separately left and right (34 ROIs) would have an effect?" Unfornately, I don't 
know how to responde to this reviewer, so I would like to ask for your help. I 
just followed the tutorials of QDEC 
(http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysisV6.0), 
and I found QDEC analyses have always be done for the two hemispheres 
separately. So, could you please provide some perspective and citation about 
the validation for such design of QDEC?

 
Thank you in advance for your assistance,
 
Best regards,







Xun___
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Re: [Freesurfer] QDEC correlation analysis

[Douglas N. Greve]

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 = ymat(:,vertexno+1);
[beta rvar] = fast_glmfit(yvertex,X);
[F p] = fast_fratio(beta,X,rvar,C)



On 6/8/2020 3:55 AM, Jian Ou wrote:


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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 calculate the p value in the 
correlation analysis of A and thickness. 2. If there are two groups of 
subjects F, M. How to calculate the p value.

Thank for your help,
Jian Ou

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[Freesurfer] QDEC correlation analysis

[Jian Ou]

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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 calculate the p value in the correlation analysis of A and 
thickness. 2. If there are two groups of subjects F, M. How to calculate the p 
value.Thank for your help,Jian Ou___
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Re: [Freesurfer] QDEC error Two Groups three covariates

[Douglas N. Greve]

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 5/18/2020 9:07 AM, Mikael Novén wrote:


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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 the following error:

"MatrixMultiplyD(): m2 is null
 break matrix.c:415

No such file or directory”

Full output from the mri_glmfit call is last in this mail.

The first lines of my fsgd files look like this:
"GroupDescriptorFile 1
Title RTfMRI
Class M
Class F
Variables RT eICV Age
Input 101 M36.767 1046505.93 25
Input 102 F-58.589 955597.34 30
Input 103 M68.883 1107660.32 22”

My contrast matrix looks like this:
"+0.0 +0.0 +1.0 +1.0 +0.0 +0.0 +0.0 +0.0”

Any help is much appreciated.

Kind regards,
Mikael

mri_glmfit --y lh.thickness.fMRIRT_revision.10.mgh --fsgd 
fMRIRT_age_gender_eICV.fsgd --C RT_covNI_cp.mat --surf fsaverage lh 
--cortex --glmdir fMRIRT_revision_test2

gdfRead(): reading fMRIRT_age_gender_eICV.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 RT 82.6508 76.4669
1 eICV 980394 122148
2 Age 24.5294 3.23797
Class Means of each Continuous Variable
1 M  97.4687 1037828.2188  25.
2 F  74.5684 949066.0966  24.2727
INFO: gd2mtx_method is dods
Reading source surface 
/Applications/freesurfer/subjects/fsaverage/surf/lh.white

Number of vertices 163842
Number of faces    327680
Total area         65416.984375
AvgVtxArea       0.399269
AvgVtxDist       0.721953
StdVtxDist       0.195470

$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
cwd /Applications/freesurfer/subjects
cmdline mri_glmfit.bin --y lh.thickness.fMRIRT_revision.10.mgh --fsgd 
fMRIRT_age_gender_eICV.fsgd --C RT_covNI_cp.mat --surf fsaverage lh 
--cortex --glmdir fMRIRT_revision_test2

sysname  Darwin
hostname LUMAC1089
machine  x86_64
user     root
FixVertexAreaFlag = 1
UseMaskWithSmoothing     1
OneSampleGroupMean 0
y  /Applications/freesurfer/subjects/lh.thickness.fMRIRT_revision.10.mgh
logyflag 0
usedti  0
FSGD fMRIRT_age_gender_eICV.fsgd
labelmask 
 /Applications/freesurfer/subjects/fsaverage/label/lh.cortex.label

maskinv 0
glmdir fMRIRT_revision_test2
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory fMRIRT_revision_test2
Loading y from 
/Applications/freesurfer/subjects/lh.thickness.fMRIRT_revision.10.mgh

   ... done reading.
INFO: gd2mtx_method is dods
Saving design matrix to fMRIRT_revision_test2/Xg.dat
Computing normalized matrix
Normalized matrix condition is 3815.6
Matrix condition is 1e+08
Found 149955 points in label.
Pruning voxels by thr: 1.175494e-38
Found 149078 voxels in mask
Saving mask to fMRIRT_revision_test2/mask.mgh
Reshaping mriglm->mask...
search space = 74130.630564
DOF = 9
Starting fit and test
Fit completed in 0.0511667 minutes
Computing spatial AR1 on surface
Residual: ar1mn=0.995881, ar1std=0.003426, gstd=6.299149, fwhm=14.833361
Writing results
  RT_covNI_cp
    maxvox sig=-4.61019  F=62.3686  at  index 156731 0 0  seed=1590285961
MatrixMultiplyD(): m2 is null
 break matrix.c:415

No such file or directory



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Re: [Freesurfer] qdec and mris_anatomical_stats help

[Douglas N. Greve]

On 5/15/2020 8:17 PM, Lab of Autism and Developmental Neuroscience, Lab 
of Autism and Developmental Neuroscience wrote:


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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:

mris_anatomical_stats -l lh.supramarg.label \
  -t lh.thickness -b -f 004/stats/lh.supramarg.stats 004 lh

But if I created the ".label" file directly on qdec, by "mapping label 
to all subjects", and didn't use the mri_label2label code for "target 
subjects", how should I work around this to perform 
mris_anatomical_stat correctly?
Sorry, it's been about 10 years since I used qdec and don't remember 
what the "mapping label to all subjects" does. My guess is that it is 
using mri_label2label to create labels for each subject. You can copy 
those labels into the label folder for each subject, then use 
mris_anatomical_stats
Also, I'm confused on when + where this "lh.thickness" file is created 
and stored.

This is created by recon-all. You can find it in subject/surf/lh.thickness

Please let me know if you need any other information about my code or 
my qdec output.


Thank you,
Alex Job Said

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Re: [Freesurfer] qdec and mris_anatomical_stats help

[Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience]

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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 Autism and Developmental
Neuroscience, Lab of Autism and Developmental Neuroscience <
l...@email.gwu.edu> wrote:

> 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:
>
> mris_anatomical_stats -l lh.supramarg.label \
>   -t lh.thickness -b -f 004/stats/lh.supramarg.stats 004 lh
>
> But if I created the ".label" file directly on qdec, by "mapping label to
> all subjects", and didn't use the mri_label2label code for "target
> subjects", how should I work around this to perform mris_anatomical_stat
> correctly?
> Also, I'm confused on when + where this "lh.thickness" file is created and
> stored.
> Please let me know if you need any other information about my code or my
> qdec output.
>
> Thank you,
> Alex Job Said
>
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[Freesurfer] QDEC error Two Groups three covariates

[Mikael Novén]

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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 the following 
error:
"MatrixMultiplyD(): m2 is null
 break matrix.c:415

No such file or directory”

Full output from the mri_glmfit call is last in this mail.

The first lines of my fsgd files look like this:
"GroupDescriptorFile 1
Title RTfMRI
Class M
Class F
Variables RT eICV Age
Input 101 M 36.767 1046505.93 25
Input 102 F -58.589 955597.34 30
Input 103 M 68.883 1107660.32 22”

My contrast matrix looks like this:
"+0.0 +0.0 +1.0 +1.0 +0.0 +0.0 +0.0 +0.0”

Any help is much appreciated.

Kind regards,
Mikael

mri_glmfit --y lh.thickness.fMRIRT_revision.10.mgh --fsgd 
fMRIRT_age_gender_eICV.fsgd --C RT_covNI_cp.mat --surf fsaverage lh --cortex 
--glmdir fMRIRT_revision_test2
gdfRead(): reading fMRIRT_age_gender_eICV.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 RT 82.6508 76.4669
1 eICV 980394 122148
2 Age 24.5294 3.23797
Class Means of each Continuous Variable
1 M  97.4687 1037828.2188  25.
2 F  74.5684 949066.0966  24.2727
INFO: gd2mtx_method is dods
Reading source surface /Applications/freesurfer/subjects/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces327680
Total area 65416.984375
AvgVtxArea   0.399269
AvgVtxDist   0.721953
StdVtxDist   0.195470

$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
cwd /Applications/freesurfer/subjects
cmdline mri_glmfit.bin --y lh.thickness.fMRIRT_revision.10.mgh --fsgd 
fMRIRT_age_gender_eICV.fsgd --C RT_covNI_cp.mat --surf fsaverage lh --cortex 
--glmdir fMRIRT_revision_test2
sysname  Darwin
hostname LUMAC1089
machine  x86_64
user root
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y/Applications/freesurfer/subjects/lh.thickness.fMRIRT_revision.10.mgh
logyflag 0
usedti  0
FSGD fMRIRT_age_gender_eICV.fsgd
labelmask  /Applications/freesurfer/subjects/fsaverage/label/lh.cortex.label
maskinv 0
glmdir fMRIRT_revision_test2
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory fMRIRT_revision_test2
Loading y from 
/Applications/freesurfer/subjects/lh.thickness.fMRIRT_revision.10.mgh
   ... done reading.
INFO: gd2mtx_method is dods
Saving design matrix to fMRIRT_revision_test2/Xg.dat
Computing normalized matrix
Normalized matrix condition is 3815.6
Matrix condition is 1e+08
Found 149955 points in label.
Pruning voxels by thr: 1.175494e-38
Found 149078 voxels in mask
Saving mask to fMRIRT_revision_test2/mask.mgh
Reshaping mriglm->mask...
search space = 74130.630564
DOF = 9
Starting fit and test
Fit completed in 0.0511667 minutes
Computing spatial AR1 on surface
Residual: ar1mn=0.995881, ar1std=0.003426, gstd=6.299149, fwhm=14.833361
Writing results
  RT_covNI_cp
maxvox sig=-4.61019  F=62.3686  at  index 156731 0 0seed=1590285961
MatrixMultiplyD(): m2 is null
 break matrix.c:415

No such file or directory


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[Freesurfer] qdec and mris_anatomical_stats help

[Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience]

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:

mris_anatomical_stats -l lh.supramarg.label \
  -t lh.thickness -b -f 004/stats/lh.supramarg.stats 004 lh

But if I created the ".label" file directly on qdec, by "mapping label to
all subjects", and didn't use the mri_label2label code for "target
subjects", how should I work around this to perform mris_anatomical_stat
correctly?
Also, I'm confused on when + where this "lh.thickness" file is created and
stored.
Please let me know if you need any other information about my code or my
qdec output.

Thank you,
Alex Job Said
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Re: [Freesurfer] Qdec not running ("image not found" error message)

[fsbuild]

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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 and Developmental Neuroscience,
Lab of Autism and Developmental Neuroscience l...@email.gwu.edu 
wrote:External Email - Use 
CautionDear 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.dylibReferenced from: 
/Applications/freesurfer/bin/qdec.binReason: image not 
foundAbortAny ideas on how I could fixthis? Thanks!All the 
best,Alex___Freesurfer 
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[Freesurfer] Qdec not running ("image not found" error message)

[Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience]

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

  Reason: image not found

Abort


Any ideas on how I could fix this? Thanks!
All the best,
Alex
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Re: [Freesurfer] qdec / tksurfer GUI

[Douglas N. Greve]

Have you tried freeview?

On 2/7/2020 2:50 PM, Rockers, Elijah D. wrote:


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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 program either. It's as if the 
keyboard is not recognized. Mouse input has no problem.


For isntance, if I try to use the "Save Multiple Views as TIFFs ... " 
tool, I can't even type in a filename. Nor can I change threshold 
levels on the overlay configuration (besides dragging the threshold 
markers, which is less accurate than I need).


Any suggestions on how I might debug this?

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[Freesurfer] qdec / tksurfer GUI

[Rockers, Elijah D.]

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 program either. It's as if the keyboard is not recognized. Mouse 
input has no problem.

For isntance, if I try to use the "Save Multiple Views as TIFFs ... " tool, I 
can't even type in a filename. Nor can I change threshold levels on the overlay 
configuration (besides dragging the threshold markers, which is less accurate 
than I need).

Any suggestions on how I might debug this?

Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & 
World Report as the No. 1 hospital in Texas and among the top 20 hospitals 
nationwide. Houston Methodist is the only nationally ranked Honor Roll hospital 
in the state and is designated as a Magnet hospital for excellence in nursing.
houstonmethodist.org | twitter.com/MethodistHosp | 
facebook.com/HoustonMethodist ***CONFIDENTIALITY NOTICE*** This e-mail is the 
property of Houston Methodist and/or its relevant affiliates and may contain 
restricted and privileged material for the sole use of the intended 
recipient(s). Any review, use, distribution or disclosure by others is strictly 
prohibited. If you are not the intended recipient (or authorized to receive for 
the recipient), please contact the sender and delete all copies of the message. 
Thank you.
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Re: [Freesurfer] Qdec error

[Greve, Douglas N.,Ph.D.]

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 vittal korann 
mailto:vittalkor...@gmail.com>> wrote:
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   2.0   23.0   14.0;
 1.0   1.03000  -0.22919   2.0   23.0   16.0;
 1.0   1.03000  -2.69688  -2.0   28.0   19.0;
 1.0   1.01000   0.84981  -2.0   22.0   19.0;
 1.0   1.01000   0.43845   2.0   36.0   21.0;
 1.0   1.06000   1.32888   2.0   28.0   17.0;
 1.0   1.02000   0.52292   2.0   34.0   22.0;
 1.0   1.02000   0.18104   2.0   32.0   17.0;
 1.0   1.03000  -0.33783  -2.0   32.0   22.0;
 1.0   1.04000   0.65805   2.0   30.0   17.0;
 1.0   1.03000   1.21888   2.0   37.0   10.0;
 1.0   1.02000   2.11598   2.0   29.0   10.0;
 1.0   1.02000  -0.02853   2.0   27.0   16.0;
 1.0   1.04000   0.21777   2.0   36.0   16.0;
 1.0   1.01000   0.30821   2.0   29.0   15.0;
 1.0   1.03000  -0.69389   2.0   30.0   12.0;
 1.0   1.04000   0.44792   2.0   23.0   15.0;
 1.0   1.03000   0.15876   2.0   28.0   15.0;
 1.0   1.02000  -1.05796   2.0   36.0   10.0;
 1.0   1.05000  -1.51878   2.0   32.0   15.0;
 1.0   1.03000  -0.91870  -2.0   30.0   15.0;

ERROR: matrix is ill-conditioned or badly scaled, condno = 68200

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit.bin --y /usr/local/freesurfer/subjects/qdec/Untitled/y.mgh 
--fsgd /usr/local/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir 
/usr/local/freesurfer/subjects/qdec/Untitled --surf fsaverage lh --label 
/usr/local/freesurfer/subjects/fsaverage/label/lh.aparc.label --C 
/usr/local/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
 --C 
/usr/local/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-Vein_Avg_tort-Cor.mat
  2. The FSGD file (if using one)
  3. And the design matrix above
Attempting to diagnose further
SumSq: Min=4.795832 (col 1), Max=145.206757 (col 5)
 The scale is much different between columns 1 and 5, you may want to
 normalize by subtracting the mean and dividing by the standard deviation.

Any help would be appreciated!

With regards
Korann




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Re: [Freesurfer] Qdec and TkSurfer input boxes

[Greve, Douglas N.,Ph.D.]

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. Could it be 
the reason?

Em ter, 21 de jan de 2020 12:29, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> escreveu:
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 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 Freeview. I just need to get the thickness measure from my 
subjects at a particular vertex: vtmax. I can use mri-segstats to get average 
thickness from clusters, but not the thickness from each subject at vtmax. And 
I know if the input boxes were working I could get the scatter plot from vtmax, 
so I guess there is a function inside both Qdec and TkSurfer to return this 
information.

Em qui, 16 de jan de 2020 20:36, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> escreveu:
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 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 impossible to see the scatter plot from a specific vertex 
inputing its number. Any clue about what happened and how to fix it? Thank you 
for your attention.



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Re: [Freesurfer] Qdec error

[vittal korann]

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 --
>  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   2.0   23.0   14.0;
>  1.0   1.03000  -0.22919   2.0   23.0   16.0;
>  1.0   1.03000  -2.69688  -2.0   28.0   19.0;
>  1.0   1.01000   0.84981  -2.0   22.0   19.0;
>  1.0   1.01000   0.43845   2.0   36.0   21.0;
>  1.0   1.06000   1.32888   2.0   28.0   17.0;
>  1.0   1.02000   0.52292   2.0   34.0   22.0;
>  1.0   1.02000   0.18104   2.0   32.0   17.0;
>  1.0   1.03000  -0.33783  -2.0   32.0   22.0;
>  1.0   1.04000   0.65805   2.0   30.0   17.0;
>  1.0   1.03000   1.21888   2.0   37.0   10.0;
>  1.0   1.02000   2.11598   2.0   29.0   10.0;
>  1.0   1.02000  -0.02853   2.0   27.0   16.0;
>  1.0   1.04000   0.21777   2.0   36.0   16.0;
>  1.0   1.01000   0.30821   2.0   29.0   15.0;
>  1.0   1.03000  -0.69389   2.0   30.0   12.0;
>  1.0   1.04000   0.44792   2.0   23.0   15.0;
>  1.0   1.03000   0.15876   2.0   28.0   15.0;
>  1.0   1.02000  -1.05796   2.0   36.0   10.0;
>  1.0   1.05000  -1.51878   2.0   32.0   15.0;
>  1.0   1.03000  -0.91870  -2.0   30.0   15.0;
> 
> ERROR: matrix is ill-conditioned or badly scaled, condno = 68200
> 
> Possible problem with experimental design:
> Check for duplicate entries and/or lack of range of
> continuous variables within a class.
> If you seek help with this problem, make sure to send:
>   1. Your command line:
> mri_glmfit.bin --y /usr/local/freesurfer/subjects/qdec/Untitled/y.mgh
> --fsgd /usr/local/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir
> /usr/local/freesurfer/subjects/qdec/Untitled --surf fsaverage lh --label
> /usr/local/freesurfer/subjects/fsaverage/label/lh.aparc.label --C
> /usr/local/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
> --C
> /usr/local/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-Vein_Avg_tort-Cor.mat
>
>   2. The FSGD file (if using one)
>   3. And the design matrix above
> Attempting to diagnose further
> SumSq: Min=4.795832 (col 1), Max=145.206757 (col 5)
>  The scale is much different between columns 1 and 5, you may want to
>  normalize by subtracting the mean and dividing by the standard deviation.
>
> Any help would be appreciated!
>
> With regards
> Korann
>
>
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Re: [Freesurfer] Qdec and TkSurfer input boxes

[Marcos Martins da Silva]

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> escreveu:

> 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 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 Freeview. I just need to get the thickness
> measure from my subjects at a particular vertex: vtmax. I can use
> mri-segstats to get average thickness from clusters, but not the thickness
> from each subject at vtmax. And I know if the input boxes were working I
> could get the scatter plot from vtmax, so I guess there is a function
> inside both Qdec and TkSurfer to return this information.
>
> Em qui, 16 de jan de 2020 20:36, Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> escreveu:
>
>> 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 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 impossible to see the scatter plot from a specific
>> vertex inputing its number. Any clue about what happened and how to fix it?
>> Thank you for your attention.
>>
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>>
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>
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Re: [Freesurfer] Qdec error

[Greve, Douglas N.,Ph.D.]

Try normalizing your covariates (ie, remove the mean and divide by the stddev)

On 1/21/2020 7:39 AM, vittal korann wrote:

External Email - Use Caution

Dear FreeSurfer experts

I ran QDEC and got the following error.

Design matrix --
 1.0   1.04000  -1.38574   2.0   29.0   19.0;
 1.0   1.04000  -0.55066   2.0   35.0   19.0;
 1.0   1.03000   2.31721   2.0   23.0   14.0;
 1.0   1.03000  -0.22919   2.0   23.0   16.0;
 1.0   1.03000  -2.69688  -2.0   28.0   19.0;
 1.0   1.01000   0.84981  -2.0   22.0   19.0;
 1.0   1.01000   0.43845   2.0   36.0   21.0;
 1.0   1.06000   1.32888   2.0   28.0   17.0;
 1.0   1.02000   0.52292   2.0   34.0   22.0;
 1.0   1.02000   0.18104   2.0   32.0   17.0;
 1.0   1.03000  -0.33783  -2.0   32.0   22.0;
 1.0   1.04000   0.65805   2.0   30.0   17.0;
 1.0   1.03000   1.21888   2.0   37.0   10.0;
 1.0   1.02000   2.11598   2.0   29.0   10.0;
 1.0   1.02000  -0.02853   2.0   27.0   16.0;
 1.0   1.04000   0.21777   2.0   36.0   16.0;
 1.0   1.01000   0.30821   2.0   29.0   15.0;
 1.0   1.03000  -0.69389   2.0   30.0   12.0;
 1.0   1.04000   0.44792   2.0   23.0   15.0;
 1.0   1.03000   0.15876   2.0   28.0   15.0;
 1.0   1.02000  -1.05796   2.0   36.0   10.0;
 1.0   1.05000  -1.51878   2.0   32.0   15.0;
 1.0   1.03000  -0.91870  -2.0   30.0   15.0;

ERROR: matrix is ill-conditioned or badly scaled, condno = 68200

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit.bin --y /usr/local/freesurfer/subjects/qdec/Untitled/y.mgh 
--fsgd /usr/local/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir 
/usr/local/freesurfer/subjects/qdec/Untitled --surf fsaverage lh --label 
/usr/local/freesurfer/subjects/fsaverage/label/lh.aparc.label --C 
/usr/local/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
 --C 
/usr/local/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-Vein_Avg_tort-Cor.mat
  2. The FSGD file (if using one)
  3. And the design matrix above
Attempting to diagnose further
SumSq: Min=4.795832 (col 1), Max=145.206757 (col 5)
 The scale is much different between columns 1 and 5, you may want to
 normalize by subtracting the mean and dividing by the standard deviation.

Any help would be appreciated!

With regards
Korann




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Re: [Freesurfer] Qdec and TkSurfer input boxes

[Greve, Douglas N.,Ph.D.]

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 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 Freeview. I just need to get the thickness measure from my 
subjects at a particular vertex: vtmax. I can use mri-segstats to get average 
thickness from clusters, but not the thickness from each subject at vtmax. And 
I know if the input boxes were working I could get the scatter plot from vtmax, 
so I guess there is a function inside both Qdec and TkSurfer to return this 
information.

Em qui, 16 de jan de 2020 20:36, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> escreveu:
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 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 impossible to see the scatter plot from a specific vertex 
inputing its number. Any clue about what happened and how to fix it? Thank you 
for your attention.



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[Freesurfer] Qdec error

[vittal korann]

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   2.0   23.0   14.0;
 1.0   1.03000  -0.22919   2.0   23.0   16.0;
 1.0   1.03000  -2.69688  -2.0   28.0   19.0;
 1.0   1.01000   0.84981  -2.0   22.0   19.0;
 1.0   1.01000   0.43845   2.0   36.0   21.0;
 1.0   1.06000   1.32888   2.0   28.0   17.0;
 1.0   1.02000   0.52292   2.0   34.0   22.0;
 1.0   1.02000   0.18104   2.0   32.0   17.0;
 1.0   1.03000  -0.33783  -2.0   32.0   22.0;
 1.0   1.04000   0.65805   2.0   30.0   17.0;
 1.0   1.03000   1.21888   2.0   37.0   10.0;
 1.0   1.02000   2.11598   2.0   29.0   10.0;
 1.0   1.02000  -0.02853   2.0   27.0   16.0;
 1.0   1.04000   0.21777   2.0   36.0   16.0;
 1.0   1.01000   0.30821   2.0   29.0   15.0;
 1.0   1.03000  -0.69389   2.0   30.0   12.0;
 1.0   1.04000   0.44792   2.0   23.0   15.0;
 1.0   1.03000   0.15876   2.0   28.0   15.0;
 1.0   1.02000  -1.05796   2.0   36.0   10.0;
 1.0   1.05000  -1.51878   2.0   32.0   15.0;
 1.0   1.03000  -0.91870  -2.0   30.0   15.0;

ERROR: matrix is ill-conditioned or badly scaled, condno = 68200

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit.bin --y /usr/local/freesurfer/subjects/qdec/Untitled/y.mgh
--fsgd /usr/local/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir
/usr/local/freesurfer/subjects/qdec/Untitled --surf fsaverage lh --label
/usr/local/freesurfer/subjects/fsaverage/label/lh.aparc.label --C
/usr/local/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
--C
/usr/local/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-Vein_Avg_tort-Cor.mat

  2. The FSGD file (if using one)
  3. And the design matrix above
Attempting to diagnose further
SumSq: Min=4.795832 (col 1), Max=145.206757 (col 5)
 The scale is much different between columns 1 and 5, you may want to
 normalize by subtracting the mean and dividing by the standard deviation.

Any help would be appreciated!

With regards
Korann
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Re: [Freesurfer] Qdec and TkSurfer input boxes

[Marcos Martins da Silva]

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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 Freeview. I just need to get the thickness
measure from my subjects at a particular vertex: vtmax. I can use
mri-segstats to get average thickness from clusters, but not the thickness
from each subject at vtmax. And I know if the input boxes were working I
could get the scatter plot from vtmax, so I guess there is a function
inside both Qdec and TkSurfer to return this information.

Em qui, 16 de jan de 2020 20:36, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> escreveu:

> 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 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 impossible to see the scatter plot from a specific
> vertex inputing its number. Any clue about what happened and how to fix it?
> Thank you for your attention.
>
> ___
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>
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Re: [Freesurfer] Qdec and TkSurfer input boxes

[Greve, Douglas N.,Ph.D.]

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 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 impossible to see the scatter plot from a specific vertex 
inputing its number. Any clue about what happened and how to fix it? Thank you 
for your attention.



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[Freesurfer] Qdec and TkSurfer input boxes

[Marcos Martins da Silva]

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 impossible to see the scatter plot from a specific
vertex inputing its number. Any clue about what happened and how to fix it?
Thank you for your attention.
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Re: [Freesurfer] Qdec support {Disarmed}

[fsbuild]

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 you upgrade to Catalina (Mac 
OS 10.15). Mac OS 10.14 is the last version of the OS that will run any 
32 bit applications.

- R.
On Dec 23, 2019, at 08:34, leona.salew...@med.uni-duesseldorf.de 
wrote:External Email - Use 
CautionDear 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 
just a problem of mine?Kind regardsL. SalewskiUniklinikum 
DüsseldorfGermany___Freesurfer 
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[Freesurfer] Qdec support

[Leona.Salewski]

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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 just a problem of mine?

Kind regards

L. Salewski
Uniklinikum Düsseldorf
Germany
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Re: [Freesurfer] QDEC cluster output

[Greve, Douglas N.,Ph.D.]

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 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), I 
get the following output in my terminal window:



# ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZCWPCWPLow
CWPHi   NVtxs   Annot

   17.365  125481   2114.03-34.44.11.6  0.01660  0.01500  
0.01820  4933  insula

   23.851   73048   1830.45 -8.4   30.1   29.4  0.03440  0.03210  
0.03670  3210  superiorfrontal

   3   -3.248  128137   4923.73 -8.1  -64.05.8  0.00010  0.0  
0.00020  7680  lingual



Simulation complete.



However, when I click on “Find clusters and go to max”, the output in my 
terminal window changes to be as follows:



Generating cluster stats using min threshold of 1.3...

Found 3 clusters

Contrast: 'lh-Diff-Control-Klinefelter-Intercept-volume', 20fwhm, DOF: 35

ClusterNo  Max   VtxMax  Size(mm2)   TalX   TalY   TalZ NVtxs Annotation

-  ---   --  -          - --

1   -4.  334923.73   -12.0  -67.1   34.7 7680  precuneus

21.7799   92114.03   -26.3   23.8   -6.0 4933  
lateralorbitofrontal

31.4634  211830.45-6.6   33.8   49.8 3210  superiorfrontal


Lastly, I see that the x/y/z coordinates of the peak coordinates listed above 
are on the very edge of the corrected cluster. Yet, visual inspection of the 
peaks from uncorrected significance maps suggest that the peaks it is quite far 
from the “hottest” parts of the uncorrected significance maps.

My questions are:


  1.  Why are these values different, and what values should I report?
  2.  Are the peaks listed above the center of gravity? Or highest p value of 
the cluster? Curious as to why the heatmap values are so different from the 
values above.

Many thanks,
Lara



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[Freesurfer] QDEC cluster output

[Lara Foland-Ross]

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), I 
get the following output in my terminal window:



# ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZCWPCWPLow
CWPHi   NVtxs   Annot

   17.365  125481   2114.03-34.44.11.6  0.01660  0.01500  
0.01820  4933  insula

   23.851   73048   1830.45 -8.4   30.1   29.4  0.03440  0.03210  
0.03670  3210  superiorfrontal

   3   -3.248  128137   4923.73 -8.1  -64.05.8  0.00010  0.0  
0.00020  7680  lingual



Simulation complete.



However, when I click on “Find clusters and go to max”, the output in my 
terminal window changes to be as follows:



Generating cluster stats using min threshold of 1.3...

Found 3 clusters

Contrast: 'lh-Diff-Control-Klinefelter-Intercept-volume', 20fwhm, DOF: 35

ClusterNo  Max   VtxMax  Size(mm2)   TalX   TalY   TalZ NVtxs Annotation

-  ---   --  -          - --

1   -4.  334923.73   -12.0  -67.1   34.7 7680  precuneus

21.7799   92114.03   -26.3   23.8   -6.0 4933  
lateralorbitofrontal

31.4634  211830.45-6.6   33.8   49.8 3210  superiorfrontal


Lastly, I see that the x/y/z coordinates of the peak coordinates listed above 
are on the very edge of the corrected cluster. Yet, visual inspection of the 
peaks from uncorrected significance maps suggest that the peaks it is quite far 
from the “hottest” parts of the uncorrected significance maps.

My questions are:


  1.  Why are these values different, and what values should I report?
  2.  Are the peaks listed above the center of gravity? Or highest p value of 
the cluster? Curious as to why the heatmap values are so different from the 
values above.

Many thanks,
Lara
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Re: [Freesurfer] qdec contrast and data extraction

[Greve, Douglas N.,Ph.D.]

If you are getting negative values, it probably means that your model 
(instantiated by the X matrix) is not proper in some ranges. The formula 
below extrapolates the effects of the covariates in order to subtract 
them off of a subject's value. If the model is not quite right, then the 
extrapolation will not be quite right, and you can get uninterpretable 
numbers. I don't have a solution for it.

On 9/18/19 11:56 AM, Maximo, Jose Omar wrote:
>
> External Email - Use Caution
>
> Hi,
>
> I tried that and it seemed to work. My averages between the 2 groups 
> look different now instead of almost identical. Thanks!
>
> I have another similar question. I have a cluster that shows a 
> significant difference between the groups when looking at volume. When 
> I look at the y.ocn.dat file, the values are in the 0.74188 - 2.16321 
> range, which are pretty low for volume. I found a post where it says 
> that you can multiply those values with the cluster size(mm^2) from 
> the summary file to convert them to volume. Then, I tried using the 
> formula you provided below (beta, res, yhat), but then I get some 
> negative values. Negative volumetric values do not make sense, so I 
> was thinking if using the absolute value would correct for that.
>
> Any thoughts?
>
> Thanks for all the help so far.
>
> >If you say y = ocn.dat, then
>
> >beta = (X'*X)*X'*y;
>
> >res = y - X*beta;
>
> >yhat = X(:,1:2)*beta(1:2) + res;
>
> >yhat will be a score for each subject with the nuisance variables removed.
>
> >
>
> >On 9/11/19 2:40 PM, Maximo, Jose Omar wrote:
>
> >
>
> >    External Email - Use Caution
>
> >
>
> >Hi,
> >
> >I plotted the data from the *.y.ocn.dat file and the graph still shows 
> no apparent significant difference between the groups (see attached 
> pic). Then I >found a post with the following:
> >
> /the ocn.dat files have data that is uncorrected in that sense and 
> might need to nuisance factors removed before plotting./
> /There is a design matrix in there (Xg.dat). You can load that into 
> matlab along with the ocn.dat, compute beta = inv(X'*X)*(X'*ocn)/
> /to get the betas. You can then compute yhat = X2*beta2 where X2 has 
> nuisance columns removed and beta2 has the same nuisance coefficients 
> removed, then treat yhat as your data to be plotted./
> >
> >I tried that since I have 2 nuisance factors (age and TICV) and want 
> to plot my significant cluster w/o any nuisance effects. This is what 
> I get
> >
>    1.8973
>    1.8973
>    1.8973
>    …
>    3.4728
>    3.4728
>    3.4728
>    …
> >Are these the mean averages for each group (cortical thickness). If so, is 
> there a way to get a score for each subject?
> >
> >Best,
> >Omar
>   >
> >Look  in the *.y.ocn.dat file.
> > 
> > From mri_glmfit-sim --help
> > 
> >csdbase.y.ocn.dat - this is a summary of the input (y) over each
> >cluster. It has a column for each cluster. Each row is a subject. The
> >value is the average of the input (y) in each cluster. This is a
> >simple text file.
> > 
> > 
> > 
> >On 9/3/2019 5:16 PM, Maximo, Jose Omar wrote:
> >/  External Email - Use Caution/
> >//
> >/Hi,/
> >//
> >/Which specific 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 these 
> significant clusters?/
> >//
> >/Many thanks,/
> >/Omar/
> >//
> >/  Date: Tue, 3 Sep 2019 15:15:02 +/
> >/  From: "Greve, Douglas N.,Ph.D."  <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>/
> >/  Subject: Re: [Freesurfer] qdec contrast and data extraction/
> >/  To: "freesurfer at nmr.mgh.harvard.edu 
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>" 
>  <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>/
> >/  Message-ID: <2286f9bf-37a4-1be9-2252-0bccc833a218 at 
> mgh.harvard.edu 
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>/
> >/  Content-Type: text/plain; charset="utf-8"/
> >//
> >/      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 dif

Re: [Freesurfer] qdec contrast and data extraction

[Greve, Douglas N.,Ph.D.]

Look  in the *.y.ocn.dat file.

 From mri_glmfit-sim --help

csdbase.y.ocn.dat - this is a summary of the input (y) over each
cluster. It has a column for each cluster. Each row is a subject. The
value is the average of the input (y) in each cluster. This is a
simple text file.



On 9/3/2019 5:16 PM, Maximo, Jose Omar wrote:
>  External Email - Use Caution
>
> Hi,
>
> Which specific 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 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-37a4-1be9-2252-0bccc833a...@mgh.harvard.edu>
>  Content-Type: text/plain; charset="utf-8"
>  
>  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 space 
> to extract the numbers. There are several operations that happen as it moves 
> into fsaverage space and in preparation for group analysis (interpolation, 
> and smoothing); sometimes these make a big difference. if the ROI is small, 
> it may not map accurately back into the native space (and you should not need 
> to draw it in the first place)
>  
>  On 8/30/2019 11:36 AM, Maximo, Jose Omar wrote:
>  
>  External Email - Use Caution
>  Hi,
>  
>  I have a question:
>  
>  My design is 2 groups (HC and Patients in that respective order) and 2 
> nuisance factors (age and eTIV). When I look at the average volume difference 
> between the 2 groups, I get blue and red clusters. I presume the color coding 
> is where each group is greater than the other (Blue = Patients > HC and Red = 
> HC > Patients).
>  
>  Then, I processed to extract individual values from each cluster in 
> order to plot them. When I extract data from the blue clusters and plot them, 
> the two groups show no difference in thickness at all, whereas when I look at 
> volume, HC show more than patients in blue clusters (see attached figure). I 
> would assume that both figures would show patients > HC based on the negative 
> statistic.
>  
>  Am I interpreting the colors wrong? Or am I doing something wrong?
>  
>  These are my steps 1) After applying montecarlo correction, I drew my 
> ROIs to extract the data from; 2) map it onto every single subject; and then 
> 3) used mris_anatomical_stats to extract the data from each subject.
>  
>  Any suggestions are welcome.
>  
>  Best,
>  Omar
>  
>  Jose O. Maximo, Ph.D. | Postdoctoral Fellow
>  Department of Psychiatry & Behavioral Neurobiology
>  UAB School of Medicine
>  University of Alabama at Birmingham
>  Cell Phone: (619) 252-3492
>  Email: jomax...@uabmc.edu<mailto:jomax...@uabmc.edu>
>  
>  
>
>
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[Freesurfer] qdec contrast and data extraction

[Maximo, Jose Omar]

External Email - Use Caution

Hi,

Which specific 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 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-37a4-1be9-2252-0bccc833a...@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

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 space to 
extract the numbers. There are several operations that happen as it moves into 
fsaverage space and in preparation for group analysis (interpolation, and 
smoothing); sometimes these make a big difference. if the ROI is small, it may 
not map accurately back into the native space (and you should not need to draw 
it in the first place)

On 8/30/2019 11:36 AM, Maximo, Jose Omar wrote:

External Email - Use Caution
Hi,

I have a question:

My design is 2 groups (HC and Patients in that respective order) and 2 
nuisance factors (age and eTIV). When I look at the average volume difference 
between the 2 groups, I get blue and red clusters. I presume the color coding 
is where each group is greater than the other (Blue = Patients > HC and Red = 
HC > Patients).

Then, I processed to extract individual values from each cluster in order 
to plot them. When I extract data from the blue clusters and plot them, the two 
groups show no difference in thickness at all, whereas when I look at volume, 
HC show more than patients in blue clusters (see attached figure). I would 
assume that both figures would show patients > HC based on the negative 
statistic.

Am I interpreting the colors wrong? Or am I doing something wrong?

These are my steps 1) After applying montecarlo correction, I drew my ROIs 
to extract the data from; 2) map it onto every single subject; and then 3) used 
mris_anatomical_stats to extract the data from each subject.

Any suggestions are welcome.

Best,
Omar

Jose O. Maximo, Ph.D. | Postdoctoral Fellow
Department of Psychiatry & Behavioral Neurobiology
UAB School of Medicine
University of Alabama at Birmingham
Cell Phone: (619) 252-3492
Email: jomax...@uabmc.edu<mailto:jomax...@uabmc.edu>




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Re: [Freesurfer] qdec contrast and data extraction

[Greve, Douglas N.,Ph.D.]

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 space to extract the 
numbers. There are several operations that happen as it moves into fsaverage 
space and in preparation for group analysis (interpolation, and smoothing); 
sometimes these make a big difference. if the ROI is small, it may not map 
accurately back into the native space (and you should not need to draw it in 
the first place)

On 8/30/2019 11:36 AM, Maximo, Jose Omar wrote:

External Email - Use Caution
Hi,

I have a question:

My design is 2 groups (HC and Patients in that respective order) and 2 nuisance 
factors (age and eTIV). When I look at the average volume difference between 
the 2 groups, I get blue and red clusters. I presume the color coding is where 
each group is greater than the other (Blue = Patients > HC and Red = HC > 
Patients).

Then, I processed to extract individual values from each cluster in order to 
plot them. When I extract data from the blue clusters and plot them, the two 
groups show no difference in thickness at all, whereas when I look at volume, 
HC show more than patients in blue clusters (see attached figure). I would 
assume that both figures would show patients > HC based on the negative 
statistic.

Am I interpreting the colors wrong? Or am I doing something wrong?

These are my steps 1) After applying montecarlo correction, I drew my ROIs to 
extract the data from; 2) map it onto every single subject; and then 3) used 
mris_anatomical_stats to extract the data from each subject.

Any suggestions are welcome.

Best,
Omar

Jose O. Maximo, Ph.D. | Postdoctoral Fellow
Department of Psychiatry & Behavioral Neurobiology
UAB School of Medicine
University of Alabama at Birmingham
Cell Phone: (619) 252-3492
Email: jomax...@uabmc.edu



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[Freesurfer] QDEC interpretation question - Please respond

[Avi Gharehgazlou]

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 in my "diagnosis.levels" file, when I select the question
"Does average lGI, accounting for sex, differ between TD and ASD?" results
would be interpreted as: Yellow regions = greater lGI in TD; blue regions =
reduced lGI in TD.

Assuming the same order, I thought that since I listed "females" first and
"males" second on my "sex.levels" file, then results from selecting
question "Does average lGI, accounting for diagnosis, differ between
females and males?" would be interpreted as: Yellow regions= greater lGI in
females; blue regions = reduced lGI in females. Is this correct?

The reason I'm asking is that when I extract mean lGI values of significant
clusters (between females and males in the latter case above) and plot the
mean lGIs for males and females separately, I see that the yellow regions
show greater lGI in males instead of females!

Will you please clarify for me how I have to interpret these results

Thanks so much

Avi
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Re: [Freesurfer] Qdec Message to Mailing List

[Greve, Douglas N.,Ph.D.]

   0.0   1.0   0.0   0.0  
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0  -0.35444   0.0   0.0   0.0   0.0   0.0   0.0;
 0.0   0.0   0.0   0.0   1.0   0.0   0.0   0.0  
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
-0.92957   0.0   0.0   0.0   0.0   0.0   0.0   0.0;
 0.0   0.0   0.0   0.0   0.0   1.0   0.0   0.0  
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0  -0.06688   0.0   0.0   0.0   0.0   0.0   0.0;
 0.0   0.0   0.0   0.0   0.0   1.0   0.0   0.0  
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0  -1.31299   0.0   0.0   0.0   0.0   0.0   0.0;
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 1.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0   0.0   0.0   0.0   1.08339   0.0   0.0   0.0;
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0   1.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0   0.0   0.0   0.0   0.0   1.08339   0.0   0.0;
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0   1.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0   0.0   0.0   0.0   0.0   1.17924   0.0   0.0;
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0   1.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0   0.0   0.0   0.0   0.0  -0.92957   0.0   0.0;
 0.0   0.0   0.0   0.0   0.0   1.0   0.0   0.0  
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0  -1.12128   0.0   0.0   0.0   0.0   0.0   0.0;
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0   0.0   1.0   0.0   0.0   0.0   0.0   0.0  
 0.0   0.0   0.0   0.0   0.0   0.0   0.89168   0.0;
 0.0   0.0   0.0   0.0   0.0   0.0   1.0   0.0  
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0   0.0   1.65852   0.0   0.0   0.0   0.0   0.0;

ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit.bin --y lh.g4v1.10.mgh --fsgd g4v1.fsgd dods --C 
healthy-vs-bipolar-and-schizophrenia.mtx --C healthy-vs-bipolar.mtx --C 
healthy-vs-schizophrenia.mtx --C bipolar-vs-schizophrenia.mtx --C 
none-vs-risk-allele.mtx --surf fsaverage lh --cortex --glmdir lh.g4v1.glmdir
  2. The FSGD file (if using one)
  3. And the design matrix above
Attempting to diagnose further
SumSq: Min=0.354440 (col 16), Max=2.741043 (col 19)
 ... could not determine the cause of the problem




Kind Regards,


Marie


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-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 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 run mri-glmfit I get Error: matrix is ill-conditioned or badly 
scaled.


I have normalised the continuous variable Age.


Kind regards,


Marie


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Greve, Douglas N.,Ph.D. 
<mailto:dgr...@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 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 a regression testing for signi

Re: [Freesurfer] Qdec Message to Mailing List

[Greve, Douglas N.,Ph.D.]

   0.0   0.0   0.0   0.0   0.0   0.0;
 0.0   0.0   0.0   0.0   1.0   0.0   0.0   0.0  
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
-0.92957   0.0   0.0   0.0   0.0   0.0   0.0   0.0;
 0.0   0.0   0.0   0.0   0.0   1.0   0.0   0.0  
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0  -0.06688   0.0   0.0   0.0   0.0   0.0   0.0;
 0.0   0.0   0.0   0.0   0.0   1.0   0.0   0.0  
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0  -1.31299   0.0   0.0   0.0   0.0   0.0   0.0;
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 1.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0   0.0   0.0   0.0   1.08339   0.0   0.0   0.0;
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0   1.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0   0.0   0.0   0.0   0.0   1.08339   0.0   0.0;
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0   1.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0   0.0   0.0   0.0   0.0   1.17924   0.0   0.0;
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0   1.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0   0.0   0.0   0.0   0.0  -0.92957   0.0   0.0;
 0.0   0.0   0.0   0.0   0.0   1.0   0.0   0.0  
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0  -1.12128   0.0   0.0   0.0   0.0   0.0   0.0;
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0   0.0   1.0   0.0   0.0   0.0   0.0   0.0  
 0.0   0.0   0.0   0.0   0.0   0.0   0.89168   0.0;
 0.0   0.0   0.0   0.0   0.0   0.0   1.0   0.0  
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0   0.0   1.65852   0.0   0.0   0.0   0.0   0.0;

ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit.bin --y lh.g4v1.10.mgh --fsgd g4v1.fsgd dods --C 
healthy-vs-bipolar-and-schizophrenia.mtx --C healthy-vs-bipolar.mtx --C 
healthy-vs-schizophrenia.mtx --C bipolar-vs-schizophrenia.mtx --C 
none-vs-risk-allele.mtx --surf fsaverage lh --cortex --glmdir lh.g4v1.glmdir
  2. The FSGD file (if using one)
  3. And the design matrix above
Attempting to diagnose further
SumSq: Min=0.354440 (col 16), Max=2.741043 (col 19)
 ... could not determine the cause of the problem




Kind Regards,


Marie


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-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 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 run mri-glmfit I get Error: matrix is ill-conditioned or badly 
scaled.


I have normalised the continuous variable Age.


Kind regards,


Marie


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Greve, Douglas N.,Ph.D. 
<mailto:dgr...@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 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 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 

Re: [Freesurfer] Qdec Message to Mailing List

[Marie Hill]

;
 0.0   0.0   0.0   0.0   1.0   0.0   0.0   0.0  
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
-0.92957   0.0   0.0   0.0   0.0   0.0   0.0   0.0;
 0.0   0.0   0.0   0.0   0.0   1.0   0.0   0.0  
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0  -0.06688   0.0   0.0   0.0   0.0   0.0   0.0;
 0.0   0.0   0.0   0.0   0.0   1.0   0.0   0.0  
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0  -1.31299   0.0   0.0   0.0   0.0   0.0   0.0;
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 1.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0   0.0   0.0   0.0   1.08339   0.0   0.0   0.0;
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0   1.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0   0.0   0.0   0.0   0.0   1.08339   0.0   0.0;
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0   1.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0   0.0   0.0   0.0   0.0   1.17924   0.0   0.0;
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0   1.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0   0.0   0.0   0.0   0.0  -0.92957   0.0   0.0;
 0.0   0.0   0.0   0.0   0.0   1.0   0.0   0.0  
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0  -1.12128   0.0   0.0   0.0   0.0   0.0   0.0;
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0   0.0   1.0   0.0   0.0   0.0   0.0   0.0  
 0.0   0.0   0.0   0.0   0.0   0.0   0.89168   0.0;
 0.0   0.0   0.0   0.0   0.0   0.0   1.0   0.0  
 0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  
 0.0   0.0   1.65852   0.0   0.0   0.0   0.0   0.0;

ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit.bin --y lh.g4v1.10.mgh --fsgd g4v1.fsgd dods --C 
healthy-vs-bipolar-and-schizophrenia.mtx --C healthy-vs-bipolar.mtx --C 
healthy-vs-schizophrenia.mtx --C bipolar-vs-schizophrenia.mtx --C 
none-vs-risk-allele.mtx --surf fsaverage lh --cortex --glmdir lh.g4v1.glmdir
  2. The FSGD file (if using one)
  3. And the design matrix above
Attempting to diagnose further
SumSq: Min=0.354440 (col 16), Max=2.741043 (col 19)
 ... 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 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 run mri-glmfit I get Error: matrix is ill-conditioned or badly 
scaled.


I have normalised the continuous variable Age.


Kind regards,


Marie


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Greve, Douglas N.,Ph.D. 
<mailto:dgr...@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 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 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 am using qdec but receiving Error: factor 2 must have 2 levels.

Is it true that Qdec only supports factors with 2 levels? There is a page for 
qdec levels stating to create a file diagnosis.levels and state the three 
levels. I did this however t

Re: [Freesurfer] Qdec Message to Mailing List

[Greve, Douglas N.,Ph.D.]

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 run mri-glmfit I get Error: matrix is ill-conditioned or badly 
scaled.


I have normalised the continuous variable Age.


Kind regards,


Marie


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Greve, Douglas N.,Ph.D. 
<mailto:dgr...@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 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 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 am using qdec but receiving Error: factor 2 must have 2 levels.

Is it true that Qdec only supports factors with 2 levels? There is a page for 
qdec levels stating to create a file diagnosis.levels and state the three 
levels. I did this however the same error occurs.

I was going to use glm_fit instead but I think my study isn't a linear 
regression so isn't suitable (as I am not interested in the change with age, 
just between groups).

Kind regards,

Marie




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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




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Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
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Re: [Freesurfer] Qdec Message to Mailing List

[Marie Hill]

External Email - Use Caution

Thanks. When I run mri-glmfit I get Error: matrix is ill-conditioned or badly 
scaled.


I have normalised the continuous variable Age.


Kind regards,


Marie


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf 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, Marie Hill wrote:

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 am using qdec but receiving Error: factor 2 must have 2 levels.

Is it true that Qdec only supports factors with 2 levels? There is a page for 
qdec levels stating to create a file diagnosis.levels and state the three 
levels. I did this however the same error occurs.

I was going to use glm_fit instead but I think my study isn't a linear 
regression so isn't suitable (as I am not interested in the change with age, 
just between groups).

Kind regards,

Marie




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Re: [Freesurfer] Qdec Message to Mailing List

[Greve, Douglas N.,Ph.D.]

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 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 am using qdec but receiving Error: factor 2 must have 2 levels.

Is it true that Qdec only supports factors with 2 levels? There is a page for 
qdec levels stating to create a file diagnosis.levels and state the three 
levels. I did this however the same error occurs.

I was going to use glm_fit instead but I think my study isn't a linear 
regression so isn't suitable (as I am not interested in the change with age, 
just between groups).

Kind regards,

Marie




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[Freesurfer] Qdec Message to Mailing List

[Marie Hill]

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 am using qdec but receiving Error: factor 2 must have 2 levels.

Is it true that Qdec only supports factors with 2 levels? There is a page for 
qdec levels stating to create a file diagnosis.levels and state the three 
levels. I did this however the same error occurs.

I was going to use glm_fit instead but I think my study isn't a linear 
regression so isn't suitable (as I am not interested in the change with age, 
just between groups).

Kind regards,

Marie

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[Freesurfer] QDEC ROI Analysis

[Kraft, Jessica N]

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 
piras
 Mon, 20 Jun 2011 09:54:38 
-0700

Hi Nick,

Thank you for your response. I carefully read the whole tutorial but

still did not find what I was looking for.

I don't want to manually draw an ROI but rather use one of the

existing labels (i.e. the middle orbitofrontal). Moreover, I don't

wanto to extract mean ROI thickness and analyze it with SPSS or

whatever, I simply want to compute my vertex to vertex difference map

limiting the analysis to that region. Is it possible with qdec?

Best,

Fabrizio

---

Fabrizio Piras Ph.D.

---

Fondazione I.R.C.C.S. Santa Lucia

Laboratorio di Neuropsichiatria

via Ardeatina 306

tel +390651501547

fax +390651501213


Jessica Kraft, M.A.
Neuroscience Graduate Student
Woods Lab
Center for Cognitive Aging and Memory
McKnight Brain Institute
Department of Clinical and Health Psychology
College of Public Health and Health Professions
University of Florida
Phone: 352-294-5744
Email: jkr...@phhp.ufl.edu

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

[Martin Reuter]

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 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 the line 
> long.thickness-spc. Is there a way to bypass this problem somehow?
> 
> Thank you,
> Arsenije
> 
> ---
> Arsenije Subotic | MSc Student 
> Department of Clinical Neurosciences
> Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada
> Tel: (403) 918-6970 
> arsenije.subot...@ucalgary.ca  
> 
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Re: [Freesurfer] QDEC Longitudinal Analysis: Missing spc option from dropdown menu

[Greve, Douglas N.,Ph.D.]

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 is not there. The spc files are all present in my participants 
files and the Qdecrc file is in the qdec subdirectory containing the line 
long.thickness-spc. Is there a way to bypass this problem somehow?


Thank you,

Arsenije


---

Arsenije Subotic | MSc Student

Department of Clinical Neurosciences

Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada

Tel: (403) 918-6970

arsenije.subot...@ucalgary.ca




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

[Arsenije Subotic]

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 the line 
long.thickness-spc. Is there a way to bypass this problem somehow?


Thank you,

Arsenije


---

Arsenije Subotic | MSc Student

Department of Clinical Neurosciences

Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada

Tel: (403) 918-6970

arsenije.subot...@ucalgary.ca

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[Freesurfer] Qdec tutorial video

[Korom, Marta]

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
available or a video that goes into detail, please send it to me.

Thank you,
Marta
-- 
*Marta Korom  |  *PhD Candidate
University of Delaware, Clinical Science
e-mail: mko...@udel.edu
phone: 646 861 8461
http://www.abcintervention.org/
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[Freesurfer] QDEC - command not found

[Alba Castells Sánchez]

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 qdec like we used to do with
other versions without problem and the answer is "command not found". We
are really surprised, we haven't found any other comment on internet and
the mailing list with this same problem.

We have installed the same last version in a mac and we had the same
problem. qdec doesn't exist.

We have checked the files .sh  in Freesurfersetup  and similar files in the
freesurfer direcotry looking for qdec without success. HOwever, there is a
direcotry called Qdec in freesurfer/matlab/lme

We don't know where is our mistake.
We are also considering that maybe the issue is related with the version.
Is this possible?
Could you help us, please?

Thousand thanks
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[Freesurfer] Qdec table

[Miguel Ángel Rivas Fernández]

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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 Fernández*


qdec.table.dat
Description: Binary data
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Re: [Freesurfer] QDEC analysis with more that 2 fixed factors

[Greve, Douglas N.,Ph.D.]

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 Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
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 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 appreciated.
> Thank You,
>
>
> --
> Azeezat Azeez
> PhD Student
> Department of Biomedical Engineering || New Jersey Institute of
> Technology
> Graduate School of Biomedical Sciences || Rutgers University
> E: ak...@njit.edu 
> >
>
>
> ___
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--
Azeezat Azeez
PhD Student
Department of Biomedical Engineering || New Jersey Institute of Technology
Graduate School of Biomedical Sciences || Rutgers University
E: ak...@njit.edu



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

[Azeez, Azeezat]

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 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 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 appreciated.
> > Thank You,
> >
> >
> > --
> > Azeezat Azeez
> > PhD Student
> > Department of Biomedical Engineering || New Jersey Institute of
> > Technology
> > Graduate School of Biomedical Sciences || Rutgers University
> > E: ak...@njit.edu 
> >
> >
> > ___
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>
>
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-- 
Azeezat Azeez
PhD Student
Department of Biomedical Engineering || New Jersey Institute of Technology
Graduate School of Biomedical Sciences || Rutgers University
E: ak...@njit.edu
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Re: [Freesurfer] QDEC analysis with more that 2 fixed factors

[Greve, Douglas N.,Ph.D.]

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 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 appreciated.
> Thank You,
>
>
> -- 
> Azeezat Azeez
> PhD Student
> Department of Biomedical Engineering || New Jersey Institute of 
> Technology
> Graduate School of Biomedical Sciences || Rutgers University
> E: ak...@njit.edu 
>
>
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[Freesurfer] QDEC analysis with more that 2 fixed factors

[Azeez, Azeezat]

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 appreciated.
Thank You,


-- 
Azeezat Azeez
PhD Student
Department of Biomedical Engineering || New Jersey Institute of Technology
Graduate School of Biomedical Sciences || Rutgers University
E: ak...@njit.edu
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Re: [Freesurfer] qdec analysis with more than 2 covariates

[Greve, Douglas N.,Ph.D.]

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 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  continuous 0
> 3  Left-Cerebellum-White-Matter  continuous 0
> 4  Left-Cerebellum-Cortex  continuous 0
> 5  Left-Thalamus-Proper  continuous 0
> 6  Left-Caudate  continuous 0
> 7  Left-Putamen  continuous 0
> 8  Left-Pallidum  continuous 0
> 9  3rd-Ventricle  continuous 0
> 10  4th-Ventricle  continuous 0
> 11  Brain-Stem  continuous 0
> 12  Left-Hippocampus  continuous 0
> 13  Left-Amygdala  continuous 0
> 14  CSF  continuous 0
> 15  Left-Accumbens-area  continuous 0
> 16  Left-VentralDC  continuous 0
> 17  Left-vessel  continuous 0
> 18  Left-choroid-plexus  continuous 0
> 19  Right-Lateral-Ventricle  continuous 0
> 20  Right-Inf-Lat-Vent  continuous 0
> 21  Right-Cerebellum-White-Matter continuous 0
> 22  Right-Cerebellum-Cortex  continuous 0
> 23  Right-Thalamus-Proper  continuous 0
> 24  Right-Caudate  continuous 0
> 25  Right-Putamen  continuous 0
> 26  Right-Pallidum  continuous 0
> 27  Right-Hippocampus  continuous 0
> 28  Right-Amygdala  continuous 0
> 29  Right-Accumbens-area  continuous 0
> 30  Right-VentralDC  continuous 0
> 31  Right-vessel  continuous 0
> 32  Right-choroid-plexus  continuous 0
> 33  WM-hypointensities  continuous 0
> 34  Optic-Chiasm  continuous 0
> 35  CC_Posterior  continuous 0
> 36  CC_Mid_Posterior  continuous 0
> 37  CC_Central  continuous 0
> 38  CC_Mid_Anterior  continuous 0
> 39  CC_Anterior  continuous 0
> 40  diagnosis  discrete 2
>     1  Schizophrenia
>     2  Control
> 41  Age  continuous 0
> 42  Birthplace  discrete 3
>     1  Statutory
>     2  Census
>     3  Rural
> 43  Upbringingplace discrete 3
>     1  Statutory
>     2  Census
>     3  Rural
> 44  Livingplace  discrete 3
>     1  Statutory
>     2  Census
>     3  Rural
>                 Continuous Factors:  Mean:       StdDev:
>                 ---  -       ---
>              Left-Lateral-Ventricle 6784.459      3582.583
>                   Left-Inf-Lat-Vent  363.189       163.344
>        Left-Cerebellum-White-Matter  13393.085      2875.553
>              Left-Cerebellum-Cortex  50654.337      7634.479
>                Left-Thalamus-Proper 7044.259      1254.886
>                        Left-Caudate 3267.819       728.738
>                        Left-Putamen 5221.959       863.333
>                       Left-Pallidum 1961.781       357.087
>                       3rd-Ventricle 1068.711       447.579
>                       4th-Ventricle 1673.963       641.339
>                          Brain-Stem  18975.526      3907.934
>                    Left-Hippocampus 3852.407       684.810
>                       Left-Amygdala 1625.463       378.770
>                                 CSF  983.626       305.507
>                 Left-Accumbens-area  587.848       155.803
>                      Left-VentralDC 3977.841       673.114
>                         Left-vessel 28.378        21.035
>                 Left-choroid-plexus  558.441       330.333
>             Right-Lateral-Ventricle 6224.989      3745.143
>                  Right-Inf-Lat-Vent  440.070       168.625
>       Right-Cerebellum-White-Matter  13111.263      2744.138
>             Right-Cerebellum-Cortex  52495.385      7167.728
>               Right-Thalamus-Proper 6732.170      1748.668
>                       Right-Caudate 3305.363       949.074
>                       Right-Putamen 4908.819      1155.840
>                      Right-Pallidum 1774.204       489.167
>                   Right-Hippocampus 3766.470      1019.353
>                      Right-Amygdala 1686.874       437.019
>                Right-Accumbens-area  539.763       151.780
>                     Right-VentralDC 3818.130       666.970
>                        Right-vessel 23.344        16.649
>                Right-choroid-plexus  620.948       414.269
>                  WM-hypointensities 4434.148     10311.009
>                        Optic-Chiasm  198.937        65.369
>                        CC_Posterior  973.467       157.378
>                    CC_Mid_Posterior  637.400       597.617
>                          CC_Central  625.374       497.642
>                     CC_Mid_Anterior  681.052       419.940
>                         CC_Anterior  870.274       237.412
>                                 Age 31.963         7.019
>
> Number of subjects:   27
> Number of factors:    44 (4 discrete, 40 continuous)
> Number of classes:    54
> Number of regressors: 2214
> 
> Data table 

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

[vittal korann]

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  continuous 0
3  Left-Cerebellum-White-Matter  continuous 0
4  Left-Cerebellum-Cortex  continuous 0
5  Left-Thalamus-Proper  continuous 0
6  Left-Caudate  continuous 0
7  Left-Putamen  continuous 0
8  Left-Pallidum  continuous 0
9  3rd-Ventricle  continuous 0
10  4th-Ventricle  continuous 0
11  Brain-Stem  continuous 0
12  Left-Hippocampus  continuous 0
13  Left-Amygdala  continuous 0
14  CSF  continuous 0
15  Left-Accumbens-area  continuous 0
16  Left-VentralDC  continuous 0
17  Left-vessel  continuous 0
18  Left-choroid-plexus  continuous 0
19  Right-Lateral-Ventricle  continuous 0
20  Right-Inf-Lat-Vent  continuous 0
21  Right-Cerebellum-White-Matter  continuous 0
22  Right-Cerebellum-Cortex  continuous 0
23  Right-Thalamus-Proper  continuous 0
24  Right-Caudate  continuous 0
25  Right-Putamen  continuous 0
26  Right-Pallidum  continuous 0
27  Right-Hippocampus  continuous 0
28  Right-Amygdala  continuous 0
29  Right-Accumbens-area  continuous 0
30  Right-VentralDC  continuous 0
31  Right-vessel  continuous 0
32  Right-choroid-plexus  continuous 0
33  WM-hypointensities  continuous 0
34  Optic-Chiasm  continuous 0
35  CC_Posterior  continuous 0
36  CC_Mid_Posterior  continuous 0
37  CC_Central  continuous 0
38  CC_Mid_Anterior  continuous 0
39  CC_Anterior  continuous 0
40  diagnosis  discrete 2
1  Schizophrenia
2  Control
41  Age  continuous 0
42  Birthplace  discrete 3
1  Statutory
2  Census
3  Rural
43  Upbringingplace  discrete 3
1  Statutory
2  Census
3  Rural
44  Livingplace  discrete 3
1  Statutory
2  Census
3  Rural
Continuous Factors: Mean:   StdDev:
--- -   ---
 Left-Lateral-Ventricle  6784.459  3582.583
  Left-Inf-Lat-Vent   363.189   163.344
   Left-Cerebellum-White-Matter 13393.085  2875.553
 Left-Cerebellum-Cortex 50654.337  7634.479
   Left-Thalamus-Proper  7044.259  1254.886
   Left-Caudate  3267.819   728.738
   Left-Putamen  5221.959   863.333
  Left-Pallidum  1961.781   357.087
  3rd-Ventricle  1068.711   447.579
  4th-Ventricle  1673.963   641.339
 Brain-Stem 18975.526  3907.934
   Left-Hippocampus  3852.407   684.810
  Left-Amygdala  1625.463   378.770
CSF   983.626   305.507
Left-Accumbens-area   587.848   155.803
 Left-VentralDC  3977.841   673.114
Left-vessel28.37821.035
Left-choroid-plexus   558.441   330.333
Right-Lateral-Ventricle  6224.989  3745.143
 Right-Inf-Lat-Vent   440.070   168.625
  Right-Cerebellum-White-Matter 13111.263  2744.138
Right-Cerebellum-Cortex 52495.385  7167.728
  Right-Thalamus-Proper  6732.170  1748.668
  Right-Caudate  3305.363   949.074
  Right-Putamen  4908.819  1155.840
 Right-Pallidum  1774.204   489.167
  Right-Hippocampus  3766.470  1019.353
 Right-Amygdala  1686.874   437.019
   Right-Accumbens-area   539.763   151.780
Right-VentralDC  3818.130   666.970
   Right-vessel23.34416.649
   Right-choroid-plexus   620.948   414.269
 WM-hypointensities  4434.148 10311.009
   Optic-Chiasm   198.93765.369
   CC_Posterior   973.467   157.378
   CC_Mid_Posterior   637.400   597.617
 CC_Central   625.374   497.642
CC_Mid_Anterior   681.052   419.940
CC_Anterior   870.274   237.412
Age31.963 7.019

Number of subjects:   27
Number of factors:44 (4 discrete, 40 continuous)
Number of classes:54
Number of regressors: 2214

Data table loading completed successfully.
SUBJECTS_DIR is '/usr/local/freesurfer/subjects'
lh-Avg-Intercept-thickness ---
Does the average thickness differ from zero?
Nuisance factors: Age
 1.000   

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

[Greve, Douglas N.,Ph.D.]

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 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 scenario, can I include all three as covariates.
Here is the error that qdec showing while running GLM:

"ERROR: Subject 2 seems to have a mismatched number of discrete factors 
(expected 4, found 1)"
"Reading source surface /usr/local/freesurfer/subjects/fsaverage/surf/lh.white
ERROR: no contrasts specified."
"Error in Analyze: command fai;ed mri_glmfit --y
/usr/local/freesurfer/subjects/qdec/qdecAnalys/y.mgh --fsgd
/usr/local/freesurfer/subjects/qdec/qdecAnalys/qdec.fsgd dods -glmdir
/usr/local/freesurfer/subjects/qdec/qdecAnalys/ -surf fsaverage lh -label
/usr/local/freesurfer/subjects/fsaverage/label/lh.aparc.label"

Could you help us out in this regard.

Would appreciate any help!!

Korann






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[Freesurfer] qdec analysis with more than 2 covariates

[vittal korann]

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 scenario, can I include all three as covariates.
Here is the error that qdec showing while running GLM:

"ERROR: Subject 2 seems to have a mismatched number of discrete factors
(expected 4, found 1)"
"Reading source surface
/usr/local/freesurfer/subjects/fsaverage/surf/lh.white
ERROR: no contrasts specified."
"Error in Analyze: command fai;ed mri_glmfit --y
/usr/local/freesurfer/subjects/qdec/qdecAnalys/y.mgh --fsgd
/usr/local/freesurfer/subjects/qdec/qdecAnalys/qdec.fsgd dods -glmdir
/usr/local/freesurfer/subjects/qdec/qdecAnalys/ -surf fsaverage lh -label
/usr/local/freesurfer/subjects/fsaverage/label/lh.aparc.label"

Could you help us out in this regard.

Would appreciate any help!!

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

[Douglas Greve]

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 
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 on QDEC, it recognizes 
my diagnosis levels in the following order:


1  Diagnosis  discrete 2
    1  ASD
    2  TD
2  age  continuous 0
3  SA  continuous 0


Will you please tell me which order I have to interpret my results 
according to? i.e. significant regions in Blue colour would indicate 
less LGI in TD relative to ASD (if I consider TD first then ASD- like 
the order I designed my diagnosis.levels file) BUT blue regions would 
mean less LGI in ASD vs. TD if I consider order my groups appear on 
QDEC when I upload qdec.table.dat file.


Would appreciate your reply,

Avi


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

[Markus Gschwind]

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 groups in the
> following order:
>
> Typically developing
> ASD
>
> However, when I upload my qdec.table.dat file on QDEC, it recognizes my
> diagnosis levels in the following order:
>
> 1  Diagnosis  discrete 2
> 1  ASD
> 2  TD
> 2  age  continuous 0
> 3  SA  continuous 0
>
>
> Will you please tell me which order I have to interpret my results
> according to? i.e. significant regions in Blue colour would indicate less
> LGI in TD relative to ASD (if I consider TD first then ASD- like the order
> I designed my diagnosis.levels file) BUT blue regions would mean less LGI
> in ASD vs. TD if I consider order my groups appear on QDEC when I upload
> qdec.table.dat file.
>
> Would appreciate your reply,
>
> Avi
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[Freesurfer] QDEC, order of groups for interpretation of results

[Avi Gharehgazlou]

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 on QDEC, it recognizes my
diagnosis levels in the following order:

1  Diagnosis  discrete 2
1  ASD
2  TD
2  age  continuous 0
3  SA  continuous 0


Will you please tell me which order I have to interpret my results
according to? i.e. significant regions in Blue colour would indicate less
LGI in TD relative to ASD (if I consider TD first then ASD- like the order
I designed my diagnosis.levels file) BUT blue regions would mean less LGI
in ASD vs. TD if I consider order my groups appear on QDEC when I upload
qdec.table.dat file.

Would appreciate your reply,

Avi
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Re: [Freesurfer] QDEC vs. Command Line Stream

[Douglas Greve]

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 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 literature, but I am also aware that it has 
less glm capability.



Thank you for any input!

Arsenije



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[Freesurfer] QDEC vs. Command Line Stream

[Arsenije Subotic]

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 
literature, but I am also aware that it has less glm capability.


Thank you for any input!

Arsenije
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Re: [Freesurfer] QDEC Interaction of Two Covariates

[Douglas N. Greve]

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 
> 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 a dot product (covariate1*covariate2) 
> of the two to represent interaction. After analyzing, when I look at 
> the data points at a single voxel, there is no visual indication of 
> interaction. There also is no fitted line.
>
> Am I utilizing QDEC correctly?
>
> Thank you for your help!
>
> -- 
> David S. Lee
> Associate Research Specialist
> Center for Healthy Minds
> University of Wisconsin - Madison
> (608) 890-1115 
>
>
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[Freesurfer] QDEC Interaction of Two Covariates

[David S Lee]

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 a dot product (covariate1*covariate2) of the two to
represent interaction. After analyzing, when I look at the data points at a
single voxel, there is no visual indication of interaction. There also is
no fitted line.

Am I utilizing QDEC correctly?

Thank you for your help!

-- 
David S. Lee
Associate Research Specialist
Center for Healthy Minds
University of Wisconsin - Madison
(608) 890-1115
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[Freesurfer] Qdec+Table format issue ?????

[Dimitrios Trifonopoulos]

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 without be able to overcome the issue.

The 1st error was:


 ERROR: qdec table missing correct column headers?

   Make sure first column is labeled 'fsid' for the time point and

   second column is 'fsid-base' to specify the subject tempate (base), e.g.:


 fsidfsid-base   age

 me1 me  22.3

 me2 me  23.2

 you1you 21.6

 you2you 22.5


Simones-iMac:subjects SLMAC14$ long_mris_slopes --qdec 
/Applications/freesurfer/subjects/qdec/lala copy.dat.doc --meas thickness 
--hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time 
years --qcache fsaverage --sd /Applications/freesurfer/subjects/


and the 2nd one was:


Parsing the qdec table: /Applications/freesurfer/subjects/qdec/qdec.table.dat

ERROR: qdec table /Applications/freesurfer/subjects/qdec/qdec.table.dat not 
found or empty?


Even if I found a similar error im the forum, I didn't understand finally how 
this guy overcome it. I also attached you the 2 files that I used. Please 
answer me as soon as you are available. Thank you


All the Best,

Dimitris








qdec.table.dat
Description: qdec.table.dat
{\rtf1\ansi\ansicpg1252\cocoartf1561\cocoasubrtf200
{\fonttbl\f0\fnil\fcharset0 Menlo-Regular;\f1\fswiss\fcharset0 Helvetica;}
{\colortbl;\red255\green255\blue255;}
{\*\expandedcolortbl;;}
\paperw11900\paperh16840\margl1440\margr1440\vieww10800\viewh8400\viewkind0
\deftab720
\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\pardeftab720\ri380\partightenfactor0

\f0\fs22 \cf0 fsid fsid-base
\f1\fs24  age\
\pard\tx566\tx1133\tx1700\tx2267\tx2834\tx3401\tx3968\tx4535\tx5102\tx5669\tx6236\tx6803\pardeftab720\ri380\partightenfactor0
\cf0 20101DOJ_M0 20101DOJ_template 6420101DOJ_M12 20101DOJ_template 65\
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[Freesurfer] Qdec question when examining group differences with continuous covariate and nuisance factor

[James Allebone]

 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 cortical
thickness differ between clinical and control with both the nuisance factor
and the covariate accounted for. The only result comparing average
thickness between the groups lists ICV as a nuisance factor, and does not
include age as a covariate. Other results are examining correlation between
age and thickness accounting for group, or whether the thickness-age
correlation differs between groups accounting for ICV.

A second question: when i just include ICV as a nuisance factor and do not
enter age as a covariate (groups mean age is almost identical), there are
some areas of cortical thickening in the clinical group, which become much
larger after correction for multiple comparisons using Monte Carlo Null-Z
simulation (threshold 0.05).  This seems counterintuitave to me as I would
expect a reduction in significant clusters after correction. One of the
main clusters traverses the cingulate gyrus, however, when I extract cortical
thickness values for each individual subject and compare group means for
subregions of the cingulate in SPSS, there are no significant differences
on any of the subregions. In fact, they are almost identical. Could adding
ICV as a nuisance variable account for this? Mean ICV values are almost
identitical between groups. Or is there some additive affect at the cluster
level?

Many thanks for any clarity you can provide.

Kind regards,

James
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Re: [Freesurfer] QDEC Set Up

[Douglas N Greve]

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 this page and set up my 
> contrast files accordingly.
>
> Thanks.
>
> On Mon, Feb 12, 2018 at 3:18 PM, Martin Juneja  > wrote:
>
> Hi FS experts,
>
> I have two population groups X1 (controls) and X2 (patients). I am
> interested in calculating impact of sex (F or M) on causing
> difference between both groups e.g. I am interested in following 4
> contrasts:
>
> X1 (F) > X1 (M)
> X2 (F) > X2 (M)
> X1 (F) > X2 (F)
> X1 (M) > X2 (M)
> X1 (M+F) > X2 (M+F)
>
> Could you please provide any directions on how can I set this up
> in QDEC (if possible) and/or by command line?
>
> Thanks.
>
>
>
>
>
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Re: [Freesurfer] QDEC Set Up

[Martin Juneja]

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 at 3:18 PM, Martin Juneja  wrote:

> Hi FS experts,
>
> I have two population groups X1 (controls) and X2 (patients). I am
> interested in calculating impact of sex (F or M) on causing difference
> between both groups e.g. I am interested in following 4 contrasts:
>
> X1 (F) > X1 (M)
> X2 (F) > X2 (M)
> X1 (F) > X2 (F)
> X1 (M) > X2 (M)
> X1 (M+F) > X2 (M+F)
>
> Could you please provide any directions on how can I set this up in QDEC
> (if possible) and/or by command line?
>
> Thanks.
>
>
>
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