On 18 Oct 2005, at 23:34, Robin Goldman wrote: > Hi Mark, > > I had copied all the images into the directory to make sure links > were not the problem. All the images look fine in fslview. > > Do you want the whole feat directory, or just the reg directory? > > Thanks, > R > ________________________ > 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 5:53 PM, Mark Jenkinson wrote: > > >> 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 >>>>>> >>>>> >>>>> >>>> >>>> >> >