Hi Mark,

Thanks for the advice. Indeed this was the problem case. Processing with 
preliminary cropping makes a small difference (less than 2%).

I don't think the hippocampus segmentation is ideal, however it is 
interesting that FIRST demonstrates a 9% size difference between right and 
left which agrees with my clinical impression, whereas FreeSurfer measures 
both sides to be the same.

I read the paper "A comparison of automated segmentation and manual tracing 
for quantifying hippocampal and amygdala volumes
by Rajendra A. Morey et al. NeuroImage 45 (2009) 855-866"



Do you have any comments on this?



Cheers.................J


----- Original Message ----- 
From: "Mark Jenkinson" <[log in to unmask]>
To: <[log in to unmask]>
Sent: Tuesday, October 27, 2009 10:56 PM
Subject: Re: [FSL] First and hippocampus


> Hi,
>
> Your images have a reasonable amount of neck in them which makes
> registration difficult.  The best thing is to crop the images to  remove 
> the
> neck and then reorient to axial in order to make the registration work
> the best.  If you do the crop and reorient and then do run_first_all  then
> you should get a good segmentation.  At least it looks good to me, 
> although
> I'm not an anatomical expert.  Try the following and see what you think
> of the results:
>   fslroi jay_ives_data.nii head 0 512 145 335 0 175
>   fslswapdim head.nii.gz RL PA IS head_axial
>   run_first_all -i head_axial.nii.gz -o head_axial_seg
> and look at head_axial_seg_all_fast_firstseg overlayed on the
> head_axial image.  If you see things there which you think are
> not good then please let me know - ideally with some images
> or coordinates where you can point out the problems.
>
> If you are happy with the above then I suggest that you go
> through this process each time.  The first stage needs to be
> done by hand, determining the right place to crop the image
> using fslview - but it doesn't take very long to do - at most a
> minute per image, which isn't that onerous.
>
> By the way, I'm assuming that this was the difficult/problematic case
> from before - right?  If not, then I really need to see the problematic
> case.
>
> All the best,
> Mark
>
>
> On 27 Oct 2009, at 12:30, Jay Ives wrote:
>
>> Hi Mark,
>>
>> I have uploaded a file jay_ives_data.nii to your site. The reference 
>> number is 398602.
>>
>> Thanks
>>
>> J
>>
>> ----- Original Message ----- From: "Mark Jenkinson" <[log in to unmask]
>> >
>> To: <[log in to unmask]>
>> Sent: Tuesday, October 27, 2009 4:55 PM
>> Subject: Re: [FSL] First and hippocampus
>>
>>
>>> Hi,
>>>
>>> I suspect the problem is the initial registration if you find the 
>>> results change
>>> when you reslice to axial.  It will only affect the ability of the 
>>> model (which is
>>> in standard space) to be transferred to the native image.  Once  the 
>>> model
>>> is in the native image space it makes no difference what  orientation 
>>> it is in.
>>>
>>> As for trying to improve your fit - I'm afraid there really is  nothing 
>>> I can
>>> do based on a worded description.  I really need to see the data.   Can 
>>> you
>>> please upload some data so that we can see?
>>>
>>> All the best,
>>> Mark
>>>
>>>
>>> On 26 Oct 2009, at 23:38, Jay Ives wrote:
>>>
>>>> Hi Mark,
>>>>
>>>> Well, I ran it again after doing 'fslswapdim RL PA IS' to get an 
>>>> axial format, and the results were much improved and overlay   properly 
>>>> on the axial format data. I'm surprised I had to do  this,  but it's no 
>>>> big problem.
>>>>
>>>> I wrote to Brian Patenaude last July about the less-than-ideal  fit  of 
>>>> the model to the hippocampus. Unfortunately, this is still  an  issue 
>>>> despite the new version. I have run 'run_first' with  several 
>>>> different modes (30 to 60) and with intensity referencing  to the 
>>>> thalamus, but could not get a satisfactory fit. This is  most 
>>>> noticable at the pes hippocampus and at the lateral  hippocampus body.
>>>>
>>>> It is a pity beacause it would be nice to use the tool in  analysis, 
>>>> but it just isn't accurately defining the structure of  interest. If 
>>>> anything can be done, please let me know.
>>>>
>>>> Thx........J
>>>>
>>>> ----- Original Message ----- From: "Mark Jenkinson" 
>>>> <[log in to unmask]
>>>> >
>>>> To: <[log in to unmask]>
>>>> Sent: Monday, October 26, 2009 9:57 PM
>>>> Subject: Re: [FSL] First and hippocampus
>>>>
>>>>
>>>>> Hi,
>>>>>
>>>>> This is odd.
>>>>> The image that is fed into run_first_all as the input and
>>>>> the output segmentations of run_first_all should have
>>>>> exactly the same size.  They will be different from the
>>>>> FreeSurfer inputs and outputs normally, but there should
>>>>> be no inconsistency between the input and output to
>>>>> run_first_all.
>>>>>
>>>>> All the best,
>>>>> Mark
>>>>>
>>>>>
>>>>> On 26 Oct 2009, at 11:56, Jay Ives wrote:
>>>>>
>>>>>> 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
>>>>>>>>>>
>>>>>>>>
>>>>>>
>>>>
>>
>