As a short-term fix, you could add an additional "../" to the start of those paths, and it would likely find it (because the main thing that appears wrong with the path is that "data" shows up twice). We have identified a few troublesome aspects of spec file relative path handling (especially involving ".." and symlinks) which will be improved in the next release. Additionally, if you use -add-to-spec-file with a spec file outside the current working directory, that can unfortunately generate wrong paths - this will also be fixed in the next release.
If these spec files are in unmodified data you downloaded from us, then we should take a closer look at our spec files. If you created or modified them yourself (as the paths seem to suggest), and you'd like to see if the current code in development allows you to modify/create them without issue, email me directly. Tim On Tue, Dec 22, 2015 at 2:52 PM, Mahmoud <zeydab...@gmail.com> wrote: > Dear experts, > > Trying to open the spec file in /MNINonlinear/fsaverage_LR32K it gives me > the following error in terminal: > > File: T2w_restore.nii.gz > Path: /data/data/home/mydata/HCPReady/111_Sigma7/MNINonLinear > File does not exist! > > File: T1w_restore.nii.gz > Path: /data/data/home/mydata/HCPReady/111_Sigma7/MNINonLinear > > Referring to the spec file itself it's obvious that the paths to those two > files are not correct: > > </DataFile> > <DataFile Structure="Invalid" > DataFileType="VOLUME" > Selected="true"> > > ../../../../../../../../../../data/home/mydata/HCPReady/111_Sigma7/MNINonLinear/T2w_restore.nii.gz > </DataFile> > <DataFile Structure="Invalid" > DataFileType="VOLUME" > Selected="true"> > > ../../../../../../../../../../data/home/mydata/HCPReady/111_Sigma7/MNINonLinear/T1w_restore.nii.gz > </DataFile> > </CaretSpecFile> > > Any idea how it happened and how to fix it ? > > Thank you, > Mahmoud > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
