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Dear Steve, thank you for the response. The file system is not remotely mounted (everything on 1 computer, home dir is on another HD do). I get from your answer that it could be \ is likely that the problems are caused by lib incompatibilities? I will install a CENTOS 5 distribution this afternoon and see if I have more success. Cheers, Steven -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Steve Smith Sent: vrijdag 5 oktober 2007 10:18 To: [log in to unmask] Subject: Re: [FSL] FSL compilation choice Hi - it sounds like maybe you have a file system or system library problem. Are you running on a remotely mounted file system? If so, what type? Alternatively, is it a very large filesystem? Maybe you and Matthew could email each other directly to compare which glibc (etc) libraries you are using compared with what we built on, to see if it's a system library problem. Cheers. On 4 Oct 2007, at 20:42, H.Steven Scholte wrote: > Dear FSL experts, I am having a number of problems with the new FSL > 4.01 > upgrade and am wondering whether I installed the right compilation. > I use > OpenSuse 10.2 and tried both the Centos4 and Centos5 compilations. > Both > versions run without problems or error messages with the exception > of the > following: > > - for one or other reason fslview saves everything in Analyze > format. No > matter what the setting of FSLOUTPUTTYPE. > - tbss_deproject complains about not finding particular files and > crashes > with the message > terminate called after throwing an instance of 'std::bad_alloc' > what(): St9bad_alloc > > - When using fslvbm_2_template, all images seem to be properly > segmented > into GM, WM and CSF. The subsequent concatenation into the 4D Analyze > image "template_GM_4D" fails, however, because it tries to read the > wrong > filenames. > Please see the error message in the last logfile created by fslvbm: > > ** ERROR (nifti_image_read): failed to find header file for > 'np0002.nii.gz > _FAi_GM_to_T' > ** ERROR: nifti_image_open(np0002.nii.gz > _FAi_GM_to_T): bad header info > Error: failed to open file np0002.nii.gz > _FAi_GM_to_T > Cannot open volume np0002.nii.gz > _FAi_GM_to_T for reading! > ** ERROR (nifti_image_read): failed to find header file > for 'template_4D_GM' > ** ERROR: nifti_image_open(template_4D_GM): bad header info > Error: failed to open file template_4D_GM > Cannot open volume template_4D_GM for reading! > > Note that the file np0002_FAi_GM_to_T.nii.gz does exist and can be > read > with fslview. > It looks like the problem is the erroneous filenames because it > appends > the "_FA1_GM_to_T" after a [return] and after the [.nii.gz] extention. > I've tried leaving out the extension in the template file, but the > error > persists as the [return] seems to throw the script off. > Should i maybe make the template without returns as separators but > only > with blanks instead? > > - Feat (admittedly with 80 EV's [want to do SVM classification]) > /usr/local/fsl/bin/contrast_mgr stats design.con > ** ERROR: nifti_image_open(stats/corrections): bad header info > > On the plus side, the computers that I am using have 4-8 GB's of > memory > and 2 to 12 GB of swap and the 64-bits installation. Also, there is > not a > diskspace problem. > > Anyone any idea? > > Many thanks, > Steven Scholte ------------------------------------------------------------------------ --- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve ------------------------------------------------------------------------ ---