Hi - could you send the header information from the offending structural
image? It may not be a "valid" header...run "avwhd" on it. Also, if you
put the data on a web/ftp site, we'll run flirt and have a look.
Thanks, Steve.
On Thu, 7 Nov 2002, Tim Souza wrote:
> Hello FSL community,
>
> I have been following the instructions posted on the FSL web pages for Freesurfer &
> FSL Interoperation (which have been very useful!). We primarily use AFNI, although
> we are currently using several of the FSL utilities such as BET and flirt. I am a
> relatively new user to Freesurfer.
> I have successfully created structural datasets in Freesurfer, including final surfaces,
> and I am attempting to overlay functional activation on these surfaces. Using
> mri_convert, I have created an analyze version of the Freesurfer Pre-processed
> structural (T1). I have also created an analyze version of a functional volume for the
> same subject (through AFNI).
> Here is where the problem arises: I am using flirt to register this functional volume to
> the Freesurfer preprocessed structural T1, as indicated, but I am getting a
> "segmentation fault" from Flirt. A dumb question, but, what are some of the reasons
> that Flirt might seg fault with this data?
>
> Here are some of the things I do know to be true about this data:
>
> 1)I use flirt quite often, so I know that it must be something about my data that is
> causing the problem. I am suspecting it is the (analyze) FS-pre-processed structural
> T1.
> 2) both datasets are in coronal slice order
> 3) both datasets can be viewed in an analyze image viewer (MRICro), and look fine
> 4) the functional volume CAN register to itself using Flirt
> 5) the analyze T1 from Freesurfer CANNOT register to itself using Flirt(seg fault)
>
> here is my flirt command line:
>
> flirt -in funcvol.hdr -ref struc_fs_T1.hdr -v -searchrx -180 180 -searchry -180 180 -
> searchrz -180 180 -out func_reg_to_FST1 -omat funcreg_to_fst1.mat
>
>
> Hopefully, someone may be able to shed some light on this problem, and offer a
> possible solution.
>
> Thanks in advance,
> Tim Souza
>
Stephen M. Smith
Head of Image Analysis, FMRIB
Oxford University Centre for Functional MRI of the Brain
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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