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 log file (A09).
>
> Thank you very much!
>
> Greetings, Caroline
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