Hi Jenni,
thanks for the reply.
The log file says it finished without any eroors.
In the aseg.stats file, none of the structures have the NVoxels of
Volume_mm3 reported. I attached the file so you can see what I mean.
I am using freesurfer-Linux-rh9-stable-pub-v3.0.5 on debian sarge.
I ran another subject as well and my aseg.stats file appears to be the same.

The command lines I ran were:
recon-all -i hippo_test_subject1_t1g_nu.mnc -autorecon1 -subjid subject1
recon-all -subcortseg -subjid subject1

did I miss anything?
thanks,
mishkin



On 6/5/07, Jenni Pacheco <jpacheco@nmr.mgh.harvard.edu> wrote:

Hi Mishkin,

Are all the fields blank in the aseg.stats table, or just for some things?
It shouldn't be like this.  It may be that there are some structures
listed in that file that are not labeled in the aseg and then reported as
a zero, but it shouldn't be all of them.  Were there any error messages at
the end of this particular subject's scripts/recon-all.log?

Jenni

On Tue, 5 Jun 2007, Mishkin Derakhshan wrote:

> Hi,
> After running the -subcortseg option, i see the output volumes of
> certain structures on the screen. Are they stored anywhere in a text
> file?
> I checked stats/aseg.stats, and while the column headers indicate that
> there should be values for NVoxels and Volume_mm3, in the table those
> two fields are blank for all labels. Is this a bug, or is there
> another option I need to set to get those fields filled in?
> thanks,
> mishkin
>
>
> On 6/1/07, Doug Greve <greve@nmr.mgh.harvard.edu> wrote:
>> unfortunately, you have to go thru the segmentation as that is part of
>> the surface-based stream.
>>
>> doug
>>
>> David Perlman wrote:
>>
>> > On this topic, if I *don't* want subcortical segmentation, but rather
>> > only surface generation and thickness maps, what's the best option to
>> > use for that?  It seems like it might be -noaseg, but I couldn't find
>> > any references to this flag being used with human data, only with non-
>> > human primates, so I thought I'd ask before I assumed I'd figured it
>> > out.
>> >
>> > On Jun 1, 2007, at 1:49 PM, Bruce Fischl wrote:
>> >
>> >> yes, sorry. The subcortical segmentation is early in the processing
>> >> stream, and pretty much the slowest step.
>> >
>> >
>> > --
>> > -dave----------------------------------------------------------------
>> > Science arose from poetry... when times change the two can meet again
>> > on a higher level as friends. -Göthe
>> >
>> >
>> >
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>> >
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> greve@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
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Fax: 617-726-7422

In order to help us help you, please follow the steps in:
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