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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