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
