hmmm... converted those images to nifti_gz and got this:
[ni0bgoldman:R21_OddBall/RG_081805/test_updatefeatreg.feat] rig%
updatefeatreg .
/usr/local/bin/fsl/bin/updatefeatreg: line 98: 1411 Segmentation fault
${FSLDIR}/bin/convert_xfm -in example_func -ref highres -inverse
-omat highres2example_func.mat example_func2highres.mat
[ni0bgoldman:R21_OddBall/RG_081805/test_updatefeatreg.feat] rig% ls reg/
example_func.nii.gz@ example_func2standard.xfm
index.html
example_func2highres.gif highres.nii.gz@
standard.nii.gz@
example_func2highres.mat highres2example_func.mat
standard2example_func.mat
example_func2highres.xfm highres2standard.gif
standard2highres.mat
example_func2standard.gif highres2standard.mat
example_func2standard.mat highres2standard.xfm
________________________
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 3:44 PM, 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
>>>
>>
>
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