Dear Robin,

Convert_xfm shouldn't care whether it uses analyze or nifti
images.  The errors that you are seeing here are consistent
with what happens when an image is corrupted or does not
exist (which could happen if the link was broken).

Can you load the highres image here into FSLView and does
it look OK?

Try copying the image files into this directory too if they
happen to be links at the moment.  That might fix it,
especially if they are not standard unix links, but the
strange mac aliases instead.

Finally, can you try executing that single convert_xfm call
from the command line and see if it works or gives a
different error message.

If all that still fails to get the desired results then
I can't think of anything else I can do remotely.
In this case, please tar up the directory (but make sure all
images are copies, not links) then upload the tar file to us at:
   http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
and email me directly with the ID number for the upload session.

Hopefully we can get to the bottom of this soon.
All the best,
	Mark


On 18 Oct 2005, at 20:44, Robin Goldman wrote:

> is convert_xfm now not compatible with analyze images? Does it only  
> read nifti?
>
> [ni0bgoldman:R21_OddBall/RG_081805/ 
> volunteerrobin_18082005_epi_6823.feat] rig% updatefeatreg .
> ** ERROR: nifti_image_read(highres): can't open header file
> ** ERROR: nifti_image_open(highres): bad header info
> Error: failed to open file highres
> ERROR: Could not open image highres
> Image Exception : #22 :: Failed to read volume highres
> /usr/local/bin/fsl/bin/updatefeatreg: line 90:   843 Abort trap         
>       ${FSLDIR}/bin/convert_xfm -in example_func -ref standard  
> -middlevol highres -omat example_func2standard.mat -concat  
> highres2standard.mat example_func2highres.mat
> ** ERROR: nifti_image_read(highres): can't open header file
> ** ERROR: nifti_image_open(highres): bad header info
> Error: failed to open file highres
> ERROR: Could not open image highres
> Image Exception : #22 :: Failed to read volume highres
> /usr/local/bin/fsl/bin/updatefeatreg: line 95:   844 Abort trap         
>       ${FSLDIR}/bin/convert_xfm -in highres -ref standard -inverse  
> -omat standard2highres.mat highres2standard.mat
> ** ERROR: nifti_image_read(highres): can't open header file
> ** ERROR: nifti_image_open(highres): bad header info
> Error: failed to open file highres
> ERROR: Could not open image highres
> Image Exception : #22 :: Failed to read volume highres
> /usr/local/bin/fsl/bin/updatefeatreg: line 98:   845 Abort trap         
>       ${FSLDIR}/bin/convert_xfm -in example_func -ref highres -inverse  
> -omat highres2example_func.mat example_func2highres.mat
>
> [ni0bgoldman:R21_OddBall/RG_081805/ 
> volunteerrobin_18082005_epi_6823.feat] rig% ls reg/
> example_func.nii.gz@            example_func2standard.xfm        
> highres2standard.xfm
> example_func2highres.gif        highres.hdr@                     
> index.html
> example_func2highres.mat        highres.img@                     
> standard.hdr@
> example_func2highres.xfm        highres2example_func.mat         
> standard.img@
> example_func2standard.gif       highres2standard.gif             
> standard2example_func.mat
> example_func2standard.mat       highres2standard.mat             
> standard2highres.mat
> [ni0bgoldman:R21_OddBall/RG_081805/ 
> volunteerrobin_18082005_epi_6823.feat] rig%
>
> ________________________
> Robin Goldman, Ph.D.
> Hatch Center for MR Research
> Columbia University
> 710 W. 168th Street, NIB-1
> New York, NY  10032
> (212) 342-0867
>
> On Oct 18, 2005, at 12:04 PM, Robin Goldman wrote:
>
>> Hi Mark,
>>
>> Thanks. I ran updatefeatreg again, and still get a segmentation  
>> fault. I'm testing everything in feat directories that were run in  
>> full, so I know the reg directories contain everything they should  
>> (and I double checked as well). Running on OS X 10.3.9, here's what I  
>> get --
>>
>> [ni0bgoldman:R21_OddBall/RS_092105/ 
>> rs_r21odd_21092005_epi_tr_sync1_7837_brain.feat] rig% updatefeatreg .
>> /usr/local/bin/fsl/bin/updatefeatreg: line 98:   796 Segmentation  
>> fault      ${FSLDIR}/bin/convert_xfm -in example_func -ref highres  
>> -inverse -omat highres2example_func.mat example_func2highres.mat
>>
>> What happens when this script gets a segmentation fault at this  
>> point? It seems that it is the inverse matricies that cause the  
>> problem. Will the other essential files for higher level stats be  
>> created anyway? The inverse matrices aren't necessary for higher  
>> levels, are they?
>>
>> Best,
>> Robin
>> ________________________
>> Robin Goldman, Ph.D.
>> Hatch Center for MR Research
>> Columbia University
>> 710 W. 168th Street, NIB-1
>> New York, NY  10032
>> (212) 342-0867
>>
>> On Oct 16, 2005, at 9:35 AM, Mark Jenkinson wrote:
>>
>>> Hi Robin,
>>>
>>> The essential files required by feat in the reg directory are:
>>>
>>> example_func
>>> highres
>>> standard
>>>
>>> example_func2highres.mat
>>> highres2standard.mat
>>>
>>> example_func2standard.mat
>>> highres2example_func.mat
>>> standard2highres.mat
>>> standard2example_func.mat
>>>
>>>
>>> The first three are images, or links to images, and you should
>>> be able to view them with fslview.  If they view OK then that
>>> should be fine.
>>>
>>> The next two files are the affine transformation files that
>>> are created by running flirt to register the pairs of images
>>> together (first the example_func to the highres, then the
>>> highres to the standard).  These are the most essential two
>>> matrix files, as the others are derived from these two, and
>>> updatefeatreg *should* generate all other matrix files, but
>>> relies on these being present.
>>>
>>> Finally, the other affine matrix files are either concatenated
>>> versions of the above two affine matrices (in the case of
>>> example_func2standard.mat) or are inverses of the other
>>> matrices, including the concatenated one.
>>>
>>> So if you need to do everything by hand, then you can
>>> populate the reg directory with all of these files.  However,
>>> if you have the three images and the essential two matrix
>>> files then updatefeatreg should work OK.  Try running
>>> updatefeatreg from the feat directory itself.  That is:
>>>   cd blah/blah/DY004_novOdd_0_TestRegOnly.feat
>>>   updatefeatreg .
>>> Hopefully this will work better, as sometimes directory
>>> links or mountings can make relative paths (like you
>>> used in your example with ../../ a little tricky and
>>> error prone).
>>>
>>> So I would try and get updatefeatreg to work, as it is
>>> designed to do exactly what you want.  However, in
>>> your case you must make sure that you link (or copy) the
>>> standard image into the reg directory as well as creating
>>> a highres2standard.mat file by running flirt to register
>>> the highres to the standard image.  Once these are in
>>> place (along with the example_func2highres.mat) then
>>> updatefeatreg should be fine.  Let me know if it isn't.
>>>
>>> All the best,
>>> 	Mark
>>>
>>>
>>>
>>> On 14 Oct 2005, at 23:28, Robin Goldman wrote:
>>>
>>>> Hi there,
>>>>
>>>> I have run feat on a dataset without registering the images to  
>>>> standard space, and now I want to
>>>> add the srandard registration to the reg directory. I have looked  
>>>> at the FAQ, but since I did not run
>>>> the registration with the standard image originally and for some  
>>>> reason updatefeatreg is crashing
>>>> on me (see my prior post), I'm looking for a work around. If I add  
>>>> a link to the standard image and
>>>> a highres2standard.mat, what else is needed to run the higher level  
>>>> stats? I don't need to have it
>>>> all linked to the report page...
>>>>
>>>> Best,
>>>> Robin
>>>
>>