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. :) Thanks again for responding in advance.

Kind regards,

Caroline

Van: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens Douglas N Greve Verzonden: dinsdag 8 maart 2016 0:24 Aan: freesurfer@nmr.mgh.harvard.edumailto: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

_______________________________________________

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu

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

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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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-bounces@nmr.mgh.harvard.edu
  [mailto:freesurfer-bounces@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

   

---

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

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

Hi Bruce,

Ok, very clear. Thank you! :-)

Regards, Caroline

-----Oorspronkelijk bericht----- Van: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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-bounces@nmr.mgh.harvard.edu
  [mailto:freesurfer-bounces@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

   

---

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer