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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