Re: [Freesurfer] gnumeric file

[Bruce Fischl]

Hi Caroline

the data are in native space. Summary statistics means e.g. the volume of 
the left hippocampus. You don't need any registration algorithm for this 
type of thing - you just tabulate it across subjects


cheers
Bruce


On Thu, 17 Mar 2016, Caroline Beelen wrote:


Hi Bruce,

Thank you very much! :)
I think somethings wrong with gnumeric indeed just discovered that gedit 
works fine.

As for 3, that would mean that the data are not in native space? I'm trying to understand 
this concept of "summary statistics" :-).

Thanks again in advance.

Caroline



-Oorspronkelijk bericht-
Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Bruce Fischl
Verzonden: donderdag 17 maart 2016 13:59
Aan: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Onderwerp: Re: [Freesurfer] gnumeric file

Hi Caroline

have you looked at the  lh.aparc.thickness.table? If it is correct then it is 
something strange with gnumeric and I'm not sure we are qualified to help you.

As for 3, the tables contain summary stats and so don't need to be mapped into 
any common space.

cheers
Bruce


On Thu, 17 Mar 2016, Caroline
Beelen wrote:



Dear FS,

 

1. I typed: aparcstats2table --hemi lh --meas thickness --subjects
A01_T1


A02_T1 etc... A10_T1 --tablefile lh.aparc.thickness.table (followed
by)

gnumeric lh.aparc.thickness.table. As soon as I typed in the latter,
it generated the table attached. Why are the mean cortical thickness
values sometimes depicted wrong and how can I change this (or do I
need to do this by hand)?

 

2. I noticed aparcstats2table doesn’t generate a mean volume (column
AJ is empty). Is that supposed to be the case?

 

3. A final question: the aparcstats2table and asegstats2table contain
data in native space. Before loading Qdec data needs to be smoothed
onto the average subject (using qcache). As s I understand correctly
from your answer below and the tutorial I could either just use these
values to create the qdectable.dat file or just load the tables in Qdec itself.

Does that mean that the values of these tables somehow (have)
change(d) during the smoothing process?

 

Sorry if my questions are rather basic…, but I try to fully
understand. J

Thanks again for responding in advance.

 

Kind regards,

 

Caroline


 


 

 

Van: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Douglas Greve
Verzonden: woensdag 16 maart 2016 15:38
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] gnumeric file

 

 

On 3/16/16 6:52 AM, Caroline Beelen wrote:

  Hi FS team,

   

  Sorry for these rather basic questions…

   

  I'm not sure whether the gnumeric file is an ascii file (see
  mails below). Attached you'll find the file. It seems the case
  when you open it in the terminal screen that the nr's look fine
  (with command cat). However as soon as you type the command
  gnumeric and so on, it creates a wrong table from the start (see
  file attached). Can I somehow change this?

How did you create this file? The aparcstats2table command produces a
simple ascii file.

   

  I have an additional question:

  I was looking at the Qdec info (tutorial) and I am not totally
  sure how to create the table.dat file… Where to get the volume
  measures from, if you’d like to include those? The statistical
  folder (where the tables are from)?

Run asegstats2table and/or aparcstats2table to create a table of the
volumes, then extract the values you need. BTW, you don't have to have
volume measures in the qdec table.

   

  Thank you for responding in advance.

   

  Kind regards, Caroline

   

  -Oorspronkelijk bericht-

  Van: freesurfer-boun...@nmr.mgh.harvard.edu
  [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Douglas N
  Greve

  Verzonden: dinsdag 8 maart 2016 0:24

  Aan: freesurfer@nmr.mgh.harvard.edu

  Onderwerp: Re: [Freesurfer] mean thickness

   

  the table file lh.aparc.thickness.table should be an ascii file.
  when you look at it with cat/more/less, what do you see? Can you
  send that table file?

   

   

   

  On 03/07/2016 04:33 AM, Caroline Beelen wrote:

 > Hi Bruce,

 >

 > I'm a beginner in FS, so I just followed tutorial instructions
  for generating the files carefully...

 > I generated it by typing in for instance (after recon-all
  process was

 > done): aparcstats2table --hemi lh --meas thickness --subjects
  A01_T1

 > A02_T1 etc... A10_T1 --tablefile lh.aparc.thickness.table
  followed by

 > the command: gnumeric lh.aparc.thickness.table

 >

 > It's a linux pc with Ubuntu 12.04 LTS (processor intel core
  i7-3770

 > CPU @ 3.4GHz x 8)

 >

 > Attached the

Re: [Freesurfer] gnumeric file

[Douglas Greve]

On 3/16/16 6:52 AM, Caroline Beelen wrote:


Hi FS team,

Sorry for these rather basic questions…

I'm not sure whether the gnumeric file is an ascii file (see mails 
below). Attached you'll find the file. It seems the case when you open 
it in the terminal screen that the nr's look fine (with command cat). 
However as soon as you type the command gnumeric and so on, it creates 
a wrong table from the start (see file attached). Can I somehow change 
this?


How did you create this file? The aparcstats2table command produces a 
simple ascii file.


I have an additional question:

I was looking at the Qdec info (tutorial) and I am not totally sure 
how to create the table.dat file… Where to get the volume measures 
from, if you’d like to include those? The statistical folder (where 
the tables are from)?


Run asegstats2table and/or aparcstats2table to create a table of the 
volumes, then extract the values you need. BTW, you don't have to have 
volume measures in the qdec table.


Thank you for responding in advance.

Kind regards, Caroline

-Oorspronkelijk bericht-

Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] 
Namens Douglas N Greve


Verzonden: dinsdag 8 maart 2016 0:24

Aan: freesurfer@nmr.mgh.harvard.edu 



Onderwerp: Re: [Freesurfer] mean thickness

the table file lh.aparc.thickness.table should be an ascii file. when 
you look at it with cat/more/less, what do you see? Can you send that 
table file?


On 03/07/2016 04:33 AM, Caroline Beelen wrote:

> Hi Bruce,

>

> I'm a beginner in FS, so I just followed tutorial instructions for generating the files 
carefully...


> I generated it by typing in for instance (after recon-all process was

> done): aparcstats2table --hemi lh --meas thickness --subjects A01_T1

> A02_T1 etc... A10_T1 --tablefile lh.aparc.thickness.table followed by

> the command: gnumeric lh.aparc.thickness.table

>

> It's a linux pc with Ubuntu 12.04 LTS (processor intel core i7-3770

> CPU @ 3.4GHz x 8)

>

> Attached the log file (A09).

>

> Thank you very much!

>

> Greetings, Caroline



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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] gnumeric file

[Caroline Beelen]

Hi Bruce,

Thank you very much! :) 
I think somethings wrong with gnumeric indeed just discovered that gedit 
works fine. 

As for 3, that would mean that the data are not in native space? I'm trying to 
understand this concept of "summary statistics" :-).

Thanks again in advance.

Caroline



-Oorspronkelijk bericht-
Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Bruce Fischl
Verzonden: donderdag 17 maart 2016 13:59
Aan: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Onderwerp: Re: [Freesurfer] gnumeric file

Hi Caroline

have you looked at the  lh.aparc.thickness.table? If it is correct then it is 
something strange with gnumeric and I'm not sure we are qualified to help you.

As for 3, the tables contain summary stats and so don't need to be mapped into 
any common space.

cheers
Bruce


On Thu, 17 Mar 2016, Caroline
Beelen wrote:

> 
> Dear FS,
> 
>  
> 
> 1. I typed: aparcstats2table --hemi lh --meas thickness --subjects 
> A01_T1
> 
> > A02_T1 etc... A10_T1 --tablefile lh.aparc.thickness.table (followed 
> > by)
> gnumeric lh.aparc.thickness.table. As soon as I typed in the latter, 
> it generated the table attached. Why are the mean cortical thickness 
> values sometimes depicted wrong and how can I change this (or do I 
> need to do this by hand)?
> 
>  
> 
> 2. I noticed aparcstats2table doesn’t generate a mean volume (column 
> AJ is empty). Is that supposed to be the case?
> 
>  
> 
> 3. A final question: the aparcstats2table and asegstats2table contain 
> data in native space. Before loading Qdec data needs to be smoothed 
> onto the average subject (using qcache). As s I understand correctly 
> from your answer below and the tutorial I could either just use these 
> values to create the qdectable.dat file or just load the tables in Qdec 
> itself.
> 
> Does that mean that the values of these tables somehow (have) 
> change(d) during the smoothing process?
> 
>  
> 
> Sorry if my questions are rather basic…, but I try to fully 
> understand. J
> 
> Thanks again for responding in advance.
> 
>  
> 
> Kind regards,
> 
>  
> 
> Caroline
> 
> > 
> 
>  
> 
>  
> 
> Van: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Douglas Greve
> Verzonden: woensdag 16 maart 2016 15:38
> Aan: freesurfer@nmr.mgh.harvard.edu
> Onderwerp: Re: [Freesurfer] gnumeric file
> 
>  
> 
>  
> 
> On 3/16/16 6:52 AM, Caroline Beelen wrote:
>
>   Hi FS team,
>
>    
>
>   Sorry for these rather basic questions…
>
>    
>
>   I'm not sure whether the gnumeric file is an ascii file (see
>   mails below). Attached you'll find the file. It seems the case
>   when you open it in the terminal screen that the nr's look fine
>   (with command cat). However as soon as you type the command
>   gnumeric and so on, it creates a wrong table from the start (see
>   file attached). Can I somehow change this?
> 
> How did you create this file? The aparcstats2table command produces a 
> simple ascii file.
>
>    
>
>   I have an additional question:
>
>   I was looking at the Qdec info (tutorial) and I am not totally
>   sure how to create the table.dat file… Where to get the volume
>   measures from, if you’d like to include those? The statistical
>   folder (where the tables are from)?
> 
> Run asegstats2table and/or aparcstats2table to create a table of the 
> volumes, then extract the values you need. BTW, you don't have to have 
> volume measures in the qdec table.
>
>    
>
>   Thank you for responding in advance.
>
>    
>
>   Kind regards, Caroline
>
>    
>
>   -Oorspronkelijk bericht-
>
>   Van: freesurfer-boun...@nmr.mgh.harvard.edu
>   [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Douglas N
>   Greve
>
>   Verzonden: dinsdag 8 maart 2016 0:24
>
>   Aan: freesurfer@nmr.mgh.harvard.edu
>
>   Onderwerp: Re: [Freesurfer] mean thickness
>
>    
>
>   the table file lh.aparc.thickness.table should be an ascii file.
>   when you look at it with cat/more/less, what do you see? Can you
>   send that table file?
>
>    
>
>    
>
>    
>
>   On 03/07/2016 04:33 AM, Caroline Beelen wrote:
>
>   > Hi Bruce,
>
>   >
>
>   > I'm a beginner in FS, so I just followed tutorial instructions
>   for generating the files carefully...
>
>   > I generated it by typing in for instanc

Re: [Freesurfer] gnumeric file

[Caroline Beelen]

Dear FS

I typed in: aparcstats2table --hemi lh --meas thickness --subjects A01_T1
> A02_T1 etc... A10_T1 --tablefile lh.aparc.thickness.table (followed by) 
> gnumeric lh.aparc.thickness.table. As soon as I typed in the latter, it 
> generated the table attached in the previous mail.

Thank you with regards to the second question.. However, for volumes 
aparcstats2table it doesn't generate a mean volume (column AJ is empty). Is 
that supposed to be?

Kind regards,
Caroline
>

Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Douglas Greve
Verzonden: woensdag 16 maart 2016 15:38
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] gnumeric file


On 3/16/16 6:52 AM, Caroline Beelen wrote:
Hi FS team,

Sorry for these rather basic questions...

I'm not sure whether the gnumeric file is an ascii file (see mails below). 
Attached you'll find the file. It seems the case when you open it in the 
terminal screen that the nr's look fine (with command cat). However as soon as 
you type the command gnumeric and so on, it creates a wrong table from the 
start (see file attached). Can I somehow change this?
How did you create this file? The aparcstats2table command produces a simple 
ascii file.


I have an additional question:
I was looking at the Qdec info (tutorial) and I am not totally sure how to 
create the table.dat file... Where to get the volume measures from, if you'd 
like to include those? The statistical folder (where the tables are from)?
Run asegstats2table and/or aparcstats2table to create a table of the volumes, 
then extract the values you need. BTW, you don't have to have volume measures 
in the qdec table.


Thank you for responding in advance.

Kind regards, Caroline

-Oorspronkelijk bericht-
Van: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Douglas N Greve
Verzonden: dinsdag 8 maart 2016 0:24
Aan: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Onderwerp: Re: [Freesurfer] mean thickness

the table file lh.aparc.thickness.table should be an ascii file. when you look 
at it with cat/more/less, what do you see? Can you send that table file?



On 03/07/2016 04:33 AM, Caroline Beelen wrote:
> Hi Bruce,
>
> I'm a beginner in FS, so I just followed tutorial instructions for generating 
> the files carefully...
> I generated it by typing in for instance (after recon-all process was
> done): aparcstats2table --hemi lh --meas thickness --subjects A01_T1
> A02_T1 etc... A10_T1 --tablefile lh.aparc.thickness.table followed by
> the command: gnumeric lh.aparc.thickness.table
>
> It's a linux pc with Ubuntu 12.04 LTS (processor intel core i7-3770
> CPU @ 3.4GHz x 8)
>
> Attached the log file (A09).
>
> Thank you very much!
>
> Greetings, Caroline





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Freesurfer@nmr.mgh.harvard.edu
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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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] gnumeric file

[Caroline Beelen]

Hi Bruce,

Ok, very clear. Thank you! :-)

Regards, Caroline

-Oorspronkelijk bericht-
Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Bruce Fischl
Verzonden: donderdag 17 maart 2016 15:47
Aan: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Onderwerp: Re: [Freesurfer] gnumeric file

Hi Caroline

the data are in native space. Summary statistics means e.g. the volume of the 
left hippocampus. You don't need any registration algorithm for this type of 
thing - you just tabulate it across subjects

cheers
Bruce


On Thu, 17 Mar 2016, Caroline Beelen wrote:

> Hi Bruce,
>
> Thank you very much! :)
> I think somethings wrong with gnumeric indeed just discovered that gedit 
> works fine.
>
> As for 3, that would mean that the data are not in native space? I'm trying 
> to understand this concept of "summary statistics" :-).
>
> Thanks again in advance.
>
> Caroline
>
>
>
> -Oorspronkelijk bericht-
> Van: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Bruce Fischl
> Verzonden: donderdag 17 maart 2016 13:59
> Aan: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Onderwerp: Re: [Freesurfer] gnumeric file
>
> Hi Caroline
>
> have you looked at the  lh.aparc.thickness.table? If it is correct then it is 
> something strange with gnumeric and I'm not sure we are qualified to help you.
>
> As for 3, the tables contain summary stats and so don't need to be mapped 
> into any common space.
>
> cheers
> Bruce
>
>
> On Thu, 17 Mar 2016, Caroline
> Beelen wrote:
>
>>
>> Dear FS,
>>
>>  
>>
>> 1. I typed: aparcstats2table --hemi lh --meas thickness --subjects
>> A01_T1
>>
>>> A02_T1 etc... A10_T1 --tablefile lh.aparc.thickness.table (followed
>>> by)
>> gnumeric lh.aparc.thickness.table. As soon as I typed in the latter, 
>> it generated the table attached. Why are the mean cortical thickness 
>> values sometimes depicted wrong and how can I change this (or do I 
>> need to do this by hand)?
>>
>>  
>>
>> 2. I noticed aparcstats2table doesn’t generate a mean volume (column 
>> AJ is empty). Is that supposed to be the case?
>>
>>  
>>
>> 3. A final question: the aparcstats2table and asegstats2table contain 
>> data in native space. Before loading Qdec data needs to be smoothed 
>> onto the average subject (using qcache). As s I understand correctly 
>> from your answer below and the tutorial I could either just use these 
>> values to create the qdectable.dat file or just load the tables in Qdec 
>> itself.
>>
>> Does that mean that the values of these tables somehow (have)
>> change(d) during the smoothing process?
>>
>>  
>>
>> Sorry if my questions are rather basic…, but I try to fully 
>> understand. J
>>
>> Thanks again for responding in advance.
>>
>>  
>>
>> Kind regards,
>>
>>  
>>
>> Caroline
>>
>>>  
>>
>>  
>>
>>  
>>
>> Van: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Douglas Greve
>> Verzonden: woensdag 16 maart 2016 15:38
>> Aan: freesurfer@nmr.mgh.harvard.edu
>> Onderwerp: Re: [Freesurfer] gnumeric file
>>
>>  
>>
>>  
>>
>> On 3/16/16 6:52 AM, Caroline Beelen wrote:
>>
>>   Hi FS team,
>>
>>    
>>
>>   Sorry for these rather basic questions…
>>
>>    
>>
>>   I'm not sure whether the gnumeric file is an ascii file (see
>>   mails below). Attached you'll find the file. It seems the case
>>   when you open it in the terminal screen that the nr's look fine
>>   (with command cat). However as soon as you type the command
>>   gnumeric and so on, it creates a wrong table from the start (see
>>   file attached). Can I somehow change this?
>>
>> How did you create this file? The aparcstats2table command produces a 
>> simple ascii file.
>>
>>    
>>
>>   I have an additional question:
>>
>>   I was looking at the Qdec info (tutorial) and I am not totally
>>   sure how to create the table.dat file… Where to get the volume
>>   measures from, if you’d like to include those? The statistical
>>   folder (where the tables are from)?
>>
>> Run asegstats2table and/or aparcstats2table to create a table of the 
>> volumes, then extract the values you need. BTW, you don't have to 

Re: [Freesurfer] gnumeric file

[Bruce Fischl]

Hi Caroline

have you looked at the  lh.aparc.thickness.table? If it is correct then it 
is something strange with gnumeric and I'm not sure we are qualified to 
help you.


As for 3, the tables contain summary stats and so don't need to be mapped 
into any common space.


cheers
Bruce


On Thu, 17 Mar 2016, Caroline 
Beelen wrote:




Dear FS,

 

1. I typed: aparcstats2table --hemi lh --meas thickness --subjects A01_T1

> A02_T1 etc... A10_T1 --tablefile lh.aparc.thickness.table (followed by)
gnumeric lh.aparc.thickness.table. As soon as I typed in the latter, it
generated the table attached. Why are the mean cortical thickness values
sometimes depicted wrong and how can I change this (or do I need to do this
by hand)?

 

2. I noticed aparcstats2table doesn’t generate a mean volume (column AJ is
empty). Is that supposed to be the case?

 

3. A final question: the aparcstats2table and asegstats2table contain data
in native space. Before loading Qdec data needs to be smoothed onto the
average subject (using qcache). As s I understand correctly from your answer
below and the tutorial I could either just use these values to create the
qdectable.dat file or just load the tables in Qdec itself.

Does that mean that the values of these tables somehow (have) change(d)
during the smoothing process?

 

Sorry if my questions are rather basic…, but I try to fully understand. J

Thanks again for responding in advance.

 

Kind regards,

 

Caroline

> 

 

 

Van: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Douglas Greve
Verzonden: woensdag 16 maart 2016 15:38
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] gnumeric file

 

 

On 3/16/16 6:52 AM, Caroline Beelen wrote:

  Hi FS team,

   

  Sorry for these rather basic questions…

   

  I'm not sure whether the gnumeric file is an ascii file (see
  mails below). Attached you'll find the file. It seems the case
  when you open it in the terminal screen that the nr's look fine
  (with command cat). However as soon as you type the command
  gnumeric and so on, it creates a wrong table from the start (see
  file attached). Can I somehow change this?

How did you create this file? The aparcstats2table command produces a simple
ascii file.

   

  I have an additional question:

  I was looking at the Qdec info (tutorial) and I am not totally
  sure how to create the table.dat file… Where to get the volume
  measures from, if you’d like to include those? The statistical
  folder (where the tables are from)?

Run asegstats2table and/or aparcstats2table to create a table of the
volumes, then extract the values you need. BTW, you don't have to have
volume measures in the qdec table.

   

  Thank you for responding in advance.

   

  Kind regards, Caroline

   

  -Oorspronkelijk bericht-

  Van: freesurfer-boun...@nmr.mgh.harvard.edu
  [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Douglas N
  Greve

  Verzonden: dinsdag 8 maart 2016 0:24

  Aan: freesurfer@nmr.mgh.harvard.edu

  Onderwerp: Re: [Freesurfer] mean thickness

   

  the table file lh.aparc.thickness.table should be an ascii file.
  when you look at it with cat/more/less, what do you see? Can you
  send that table file?

   

   

   

  On 03/07/2016 04:33 AM, Caroline Beelen wrote:

  > Hi Bruce,

  > 

  > I'm a beginner in FS, so I just followed tutorial instructions
  for generating the files carefully...

  > I generated it by typing in for instance (after recon-all
  process was

  > done): aparcstats2table --hemi lh --meas thickness --subjects
  A01_T1

  > A02_T1 etc... A10_T1 --tablefile lh.aparc.thickness.table
  followed by

  > the command: gnumeric lh.aparc.thickness.table

  > 

  > It's a linux pc with Ubuntu 12.04 LTS (processor intel core
  i7-3770

  > CPU @ 3.4GHz x 8)

  > 

  > Attached the log file (A09).

  > 

  > Thank you very much!

  > 

  > Greetings, Caroline

   




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