Has anyone found the elusive $CASE.Flipped-R_For-LEFT.TEMPLATE.MedialWallSegments.SPHERE.border file?
Best Wishes Nik On May 9, 2012, at 7:46 PM, Donna Dierker wrote: > I'm putting this back on the list, because I don't know the answer to either > question. > > I searched for both MedialWallSegments and flipped (the latter with species > set to macaque), and I didn't find it either way. Maybe David or someone > else knows? > > The second issue is perplexing. Look at the script output carefully, and > pinpoint the line where it is complaining. Before that line, try adding this > line: > > caret_command -file-convert -format-convert BINARY *coord > > I had an issue a while back where certain Linux versions had a compiler issue > that was causing coord files to be read incorrectly. Switching versions > helped. Which version are you runing, and what is your OS? > > > On May 8, 2012, at 12:02 PM, Leon wrote: > >> Hi, Donna >> >> Thank you for your tip on searching files on the website. It is very >> helpful. >> >> I have a few related questions regarding the tutorial and would appreciate >> your help on it: >> >> 1) The file "Macaque.FS.R.TEMPLATE.MedialWallSegments.SPHERE.border" is >> found in the folder, but when processing left hemisphere according to the >> Stage-1.FS-to-F99 bash, it requires a file called " >> $CASE.Flipped-R_For-LEFT.TEMPLATE.MedialWallSegments.SPHERE.border", which I >> do not find on SumsDB. Do you have any idea where I should look for it or >> generate it? >> >> 2) I noticed that in the script, several coordinate files (WM, PIAL, >> MIDTICKNESS) are sharing the same topology files. During the running, I >> constantly get the error " MyMonkey.R.Midthickness.62227.coord: Topology >> File MyMonkey.R.CLOSED.62227.topo is not for use with coordinate file >> MyMonkey.R.Midthickness.62227.coord. Topo file has tiles with node numbers >> exceeding >> the number of coordinates in the coordinate file. >> >> I have checked the original rh.white, rh.pial and rh.inflated and they look >> fine in FreeSurfer. Do you know how I should solve this issue of mismatched >> topology and coordinate files? >> >> Thank you! >> Leon >> >> From: Donna Dierker <[email protected]> >> To: Leon <[email protected]>; "Caret, SureFit, and SuMS software users" >> <[email protected]> >> Sent: Tuesday, May 8, 2012 12:36 PM >> Subject: Re: [caret-users] A question about FS-to-F99 tutorial >> >> I went to http://sumsdb.wustl.edu and selected Browse/Search: Basic Archive >> Search. >> >> I entered TEMPLATE.MedialWallSegments in the filename box and got this >> search result: >> >> Macaque.FS.R.TEMPLATE.MedialWallSegments.SPHERE.border >> >> Selecting "Show Parent" led me here: >> >> FS-to-F99_Aug10.zip >> http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=8284563 >> >> I used a similar strategy to find Chip.LPI.nii: >> >> FS_MACAQUE.zip >> http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=8284039 >> >> Usually tutorials specify the archive_id of the datasets you need at the >> beginning. >> >> >> On May 7, 2012, at 8:48 PM, Leon wrote: >> >>> Hi, Caret experts >>> As I am going through the FS-to-F99 tutorial, I notice that the downloaded >>> package does not contain the following files that are needed for running >>> the State-1.FS-to-F99.sh bash: >>> >>> 1) $CASE.Flipped-R_For-LEFT.TEMPLATE.MedialWallSegments.SPHERE.border >>> >>> Also, if I want to run the tutorial files, I could not find the volume file >>> Chip.LPI.nii neither. >>> >>> Could someone help on locating these files? >>> >>> Thank you very much in advance! >>> >>> Leon >>> _______________________________________________ >>> caret-users mailing list >>> [email protected] >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> >> > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
