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
>>>>>>>>>
>>>>>>>
>>>>>
>>>
>
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