Hi,
To look at the first segmentations you simply load the image
subjectname_all_fast_firstseg.nii.gz into FSLView and look at it.
You may need to set the colormap to the MGH-Subcortical
one (although this may be the default).
If it looks like the segmentations are doing badly, then please
upload the data to our upload site:
http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
and send us the reference number. We'll then have a look
and see if there's anything that can be done to improve them.
All the best,
Mark
On 25 Oct 2009, at 12:00, Jay Ives wrote:
> 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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