Hi Doug,
I didn't actually write the code that reads in analyze volumes so that's
why I'm not totally sure at this point. I'll look through the code though
and figure out what's what. My suspicion is that it is dim4 that's critical
(should be set to 1) or maybe bitpix or dim0.
Anyway, I'll double check and let you know if mri_convert needs modification.
Cheers,
Mark
Doug Greve wrote:
> I looked at the mri_convert code, and it appears that we are setting all
> those fields (ie, dim, pixdim, and bitpix). If there is only a single
> frame, I do assign 1 to pixdim[4] (and then set the dim to 4). Is this
> not a reasonable thing to do?
>
> Mark: if you can tell me which fields must be set for FSL compatibility,
> I can make sure that mri_convert sets them.
>
> doug
>
> Mark Jenkinson wrote:
>
>>Hi All,
>>
>>The problem with this data set would not have been that it was 8 bit.
>>Flirt runs perfectly well on 8 bit data.
>>There would have been some other problem associated with the
>>header which stopped flirt reading the data in correctly.
>>Possibly the dim0 and pixdim0 fields, or maybe bitpix.
>>In general, because avwmaths uses a different input routine (very simple)
>>it is able to cope with these problems and write out corrected files.
>>
>>It should have all worked fine if you'd kept the image at 8 bit too.
>>
>>All the best,
>> Mark
>>
>>On Friday, November 8, 2002, at 10:46 AM, Darren Weber wrote:
>>
>>
>>>I wonder also whether mri_convert should assign 1 to pixdim4; check the
>>>differences in header values between the mri_convert and avwmaths outputs.
>>> I
>>>suspect that this will be one of the differences. Why would flirt not
>>>work
>>>with 8bit data?
>>>
>>>Darren
>>>
>>>
>>>----- Original Message -----
>>>From: "Doug Greve" <[log in to unmask]>
>>>To: <[log in to unmask]>
>>>Sent: Friday, November 08, 2002 6:56 AM
>>>Subject: Re: Freesurfer & FSL - Segmentation fault with FLIRT
>>>
>>>
>>>
>>>>Yes, mri_convert will not change the precision, and since CORs are 8 bit
>>>>...
>>>>
>>>>doug
>>>>
>>>>Tim Souza wrote:
>>>>
>>>>>Steve,
>>>>>
>>>>>Thanks, That worked, I guess the T1 analyze needed to be 16 bit signed
>>>>
>>>integer!
>>>
>>>>>Doug,
>>>>>
>>>>>Here is the mri_convert command line I used, and the contents of the
>>>>
>>>COR-.info file:
>>>
>>>>>mri_convert ${SUBJECTS_DIR}/surfer/mri/T1
>>>>
>>>/home/jnsb/surfer_7.02/EMy/briks/
>>>
>>>>>struc_fs_T1.img
>>>>>
>>>>>Thanks,
>>>>>Tim Souza
>>>>>
>>>>>imnr0 1
>>>>>imnr1 256
>>>>>ptype 2
>>>>>x 256
>>>>>y 256
>>>>>fov 0.256
>>>>>thick 0.001
>>>>>psiz 0.001
>>>>>locatn 0
>>>>>strtx -0.128
>>>>>endx 0.128
>>>>>strty -0.128
>>>>>endy 0.128
>>>>>strtz -0.128
>>>>>endz 0.128
>>>>>tr 0.000000
>>>>>te 0.000000
>>>>>ti 0.000000
>>>>>ras_good_flag 0
>>>>>x_ras -1.000000 0.000000 0.000000
>>>>>y_ras 0.000000 0.000000 -1.000000
>>>>>z_ras 0.000000 1.000000 0.000000
>>>>>c_ras 0.000000 0.000000 0.000000
>>>>
>>>>--
>>>>Douglas N. Greve, Ph.D.
>>>>MGH-NMR Center
>>>>[log in to unmask]
>>>>Phone Number: 617-724-2358
>>>>Fax: 617-726-7422
>>>>
>>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> [log in to unmask]
> Phone Number: 617-724-2358
> Fax: 617-726-7422
|