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Hi Mark, OK, that's fine...but can one overlay the segmentations on the original images to see how good the fit is? I tried this but the orientation of the segmentations is quite different from the original data. Why? Should I have fed axial data into FIRST? Thanks......J ----- Original Message ----- From: "Mark Jenkinson" <[log in to unmask]> To: <[log in to unmask]> Sent: Monday, October 26, 2009 5:27 PM Subject: Re: [FSL] First and hippocampus > 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 >>>> >> >