Thanks Mark,
The FreeSurfer segmentations look pretty good - perhaps a little
over-generous.
I actually am having trouble working out how to visualise the FIRST
segmentation output - can you please advise me?
Yes, I am running FSL 4.1.4
I got the volumes from FIRST using the commands:
fslstats subjectname_all_fast_firstseg.nii.gz -l 16 -u 18 -V
fslstats subjectname_all_fast_firstseg.nii.gz -l 52 -u 54 -V
The FreeSurfer volumes are in aseg.stats - as I'm sure you know.
Cheers.......J
----- Original Message -----
From: "Mark Jenkinson" <[log in to unmask]>
To: <[log in to unmask]>
Sent: Sunday, October 25, 2009 7:15 PM
Subject: Re: [FSL] First and hippocampus
> Hi,
>
> Firstly, did you look at the output images?
> This is the best way to tell if things are going wrong or not.
> It should give you an indication of whether there is some
> systematic over/under-estimation. You should look at
> both the FIRST output segmentations and the FreeSurfer
> output segmentations.
>
> Secondly, are you running the FSL4.1.4 version? There
> are significant differences which are worth making sure
> that you are running.
>
> Thirdly, what commands are you using to get the volume
> measurements from the segmentations?
>
> All the best,
> Mark
>
>
> On 25 Oct 2009, at 09:49, Jay Ives wrote:
>
>> Hmmm.....I've run FIRST and FreeSurfer on the same data for 2 subjects
>> and
>> got quite disparate results for hippocampus volumes. In fact, they are
>> not
>> even close.
>>
>> Subject 1: L 1317 (FIRST) 5068 (FreeSurfer)
>> R 1855 5054
>>
>> Subject 2: L 2916 4934
>> R 4300 5325
>>
>> My data is good quality T1 volumes from a 3T Verio system
>>
>> FIRST version is 1.2 (command run_first_all)
>> FS version is 4.4.0 (command recon-all -s subject -all)
>>
>> So no fancy stuff. Any comments?
>>
>> Thx............J
>>
>
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