I'll bear that in mind next time!
Thank you!!
Andreia
Quoting Anastasia Yendiki :
> No problem, you can usually find the answers to most of these types
> of questions in the help text of the commands. For example if you
> run "mris_label2annot --help" you'll see:
>
> [...]
>
> --a annotname
No problem, you can usually find the answers to most of these types of
questions in the help text of the commands. For example if you run
"mris_label2annot --help" you'll see:
[...]
--a annotname
Name of the annotation to create. The actual file will be called
hemi.annotname.annot, and it wil
It was automatically created in the same folder of the old one -> label
However, inside this folder there are the old rh.BAxxx.label. The new
ones (BAxxx.thresh.label) were created inside the Freesurfer folder,
could it be related to that?
Quoting Anastasia Yendiki :
> What's the location
What's the location of the new rh.BA.annot that was created by
mris_label2annot? You need to pass that same file to mris_anatomical_stats
with the -a option.
On Tue, 26 Mar 2013, _andre...@sapo.pt wrote:
After running the mri_label2label and mris_label2annot a new rh.BA.annot file
was creat
After running the mri_label2label and mris_label2annot a new
rh.BA.annot file was created (I had to remove the old one since it
doesn't overwritte) but when running
[user@host87 Freesurfer]$ mris_anatomical_stats -mgz -f
../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab SUBJECT rh white
In the "BA label" section there are:
- Several mri_label2label commands that map each label from fsaverage
space to your indidvidual's space
- One mris_label2annot command that combines the mapped label into an
annotation file.
- One mris_anatomical_stats command that gets stats for that annot
Nevermind the last email... If I change the output (wich is the second
place where BAxx.label appears, right?) file name and give the subjs
id this won't be a problem... Anyway, what are these files for? Will I
need to use them somehow?
Thanks
Andreia
Quoting _andre...@sapo.pt:
> Addicion
Hi,
I run the command for each BA labels of the right hemisphere and then run:
[user@host87 Freesurfer]$ mris_anatomical_stats -mgz -f
../stats/rh.BA.thresh.stats -b -a ./rh.BA.annot -c ./BA.ctab SUBJECT
rh white
Which resulted in:
INFO: assuming MGZ format for volumes.
computing statistics
If you replace *every* occurence of BAxxx.label with BAxxx.thresh.label,
this will keep things simple and you won't have to worry about which one
is input and which one is output.
Run *all* the commands from the "BA labels" section, all the way to the
end of that section, this will get you t
Ok. So the first is the input and the second is the output, correct?
So I'll have a different file for each out put? Is it possible to have
a table with the different measures after the threshold?
Thank you very much and I apologize for the naive questions...
Andreia
Quoting Anastasia Yendi
What you call the output label is up to you. What you call the input label
is more important - it has to be a file that actually exists.
On Mon, 25 Mar 2013, _andre...@sapo.pt wrote:
Ah ok! Sorry... In both places?
Quoting Anastasia Yendiki :
It's .thresh.label, not .threshold.label.
On
Ah ok! Sorry... In both places?
Quoting Anastasia Yendiki :
> It's .thresh.label, not .threshold.label.
>
> On Mon, 25 Mar 2013, _andre...@sapo.pt wrote:
>
>>
>> Hi Anastasia!
>>
>> The command in the recon-all.log is this one:
>>
>> mri_label2label --srcsubject fsaverage --srclabel
>> /home/u
It's .thresh.label, not .threshold.label.
On Mon, 25 Mar 2013, _andre...@sapo.pt wrote:
Hi Anastasia!
The command in the recon-all.log is this one:
mri_label2label --srcsubject fsaverage --srclabel
/home/user/visao/Freesurfer/fsaverage/label/rh.BA1.label
--trgsubject SUSANAFERREIRA --trgla
Hi Anastasia!
The command in the recon-all.log is this one:
mri_label2label --srcsubject fsaverage --srclabel
/home/user/visao/Freesurfer/fsaverage/label/rh.BA1.label --trgsubject
SUSANAFERREIRA --trglabel ./rh.BA1.label --hemi rh --regmethod surface
And I tried substituing BAxxx.label by BA
Hi Andreia - What you're rerunning is using BAxxx.label instead of
BAxxx.thresh.label. So of course the results will be the same as before
you copied over the BAxxx.thresh.label files, b/c these new files aren't
being used in 5.0.
You'll need to find the "BA labels" section in recon-all.log an
Hello list!
Any suggestions on what I may be doing wrong?
Thanks!
Andreia
- Mensagem encaminhada de _andre...@sapo.pt -
Data: Sun, 24 Mar 2013 19:11:13 +
De: _andre...@sapo.pt
Assunto: Re: [Freesurfer] Brodmann area thickness, surface area and volume
Para: Anastasia Y
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