I have found in my data that I have to do so much messing around with landmarks (adding some, removing some etc) that the left flip doesn't help that much (it might if I wrote better code, rather than hacking around).
Although the code isn't open in front of me I'd say surely that if one wanted to alter it for "left first" this would be pretty doable. I'd guess you'd use the code that flips the RH landmarks to LH after adjustment to make a LH flipped file them before processing starts, so that you have a landmark file(s) with initial left guess similar to the initial right guess. and everywhere in code else just change left to right. I think would surely be entirely ok. It is my own plan anyway, if I ever get to the other hemispheres! On 22 May 2012 16:00, <caret-users-requ...@brainvis.wustl.edu> wrote: > Send caret-users mailing list submissions to > caret-users@brainvis.wustl.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://brainvis.wustl.edu/mailman/listinfo/caret-users > or, via email, send a message with subject or body 'help' to > caret-users-requ...@brainvis.wustl.edu > > You can reach the person managing the list at > caret-users-ow...@brainvis.wustl.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of caret-users digest..." > > Today's Topics: > > 1. Re: A question about FS-to-F99 tutorial (Nikhil Sharma) > 2. Re: A question about FS-to-F99 tutorial (David Van Essen) > > > ---------- Forwarded message ---------- > From: Nikhil Sharma <ns...@cam.ac.uk> > To: "Caret, SureFit, and SuMS software users" < > caret-users@brainvis.wustl.edu> > Cc: > Date: Tue, 22 May 2012 07:08:59 +0100 > Subject: Re: [caret-users] A question about FS-to-F99 tutorial > 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 <do...@brainvis.wustl.edu> > >> To: Leon <leonad...@yahoo.com>; "Caret, SureFit, and SuMS software > users" <caret-users@brainvis.wustl.edu> > >> 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 > >>> caret-users@brainvis.wustl.edu > >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users > >> > >> > >> > > > > > > _______________________________________________ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > ---------- Forwarded message ---------- > From: David Van Essen <vanes...@wustl.edu> > To: "Caret, SureFit, and SuMS software users" < > caret-users@brainvis.wustl.edu> > Cc: > Date: Tue, 22 May 2012 09:03:03 -0500 > Subject: Re: [caret-users] A question about FS-to-F99 tutorial > Hello Nik, > > Here is the solution to the mystery: > The tutorial as it currently runs expects the user to *start with the > right hemisphere* (stated near bottom of p. 2). The file that you need > for stage 1 of the left hemisphere is created during Stage 3 for the right > hemisphere (see below). This is not meant to be perverse! Rather, the > intent is to capitalize on the effort put into revising the template > landmarks for the right hemisphere. By mirror-flipping a good set of right > hemisphere landmarks, you are likely to be much closer to the mark when you > start on the left hemisphere. > > The relevant operations in the stage 3 script are extracted below. If you > do not wish to do (or repeat) the full set of right hemisphere steps, you > can probably use this to kludge your way into generating the left > hemisphere template border. Basically you need to take the right > hemisphere medial wall borders and mirror-flip them to be approximately > aligned for the left hem. There are other ways to do this in Caret on an > ad hoc basis. > > I hope this helps. We should amend the tutorial to make this more clear. > If you learn something that could help in improving the tutorial, please > let us know. > > David > > Stage-3.FS-to-F99.sh > > if [ $HEM_FLAG = "R" ] ; then > ### Prepare flipped right hem landmarks (medial wall segments for stage 1 > and full landmarks for stage 2) as templates for left hem > # Mirror-flip right hem morphed sphere > MATRIX="-1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 1.0" > caret_command -surface-apply-transformation-matrix > $CASE.R.SPHERE_smooth.$NUMBER_NODES.coord $CASE.R.CLOSED.$NUMBER_NODES.topo > $CASE.R.SPHERE_smooth.X-Flip.$NUMBER_NODES.coord -matrix $MATRIX > > # unproject right hem medial wall borders from mirror-reflected initial > sphere in same subject. > caret_command -surface-border-unprojection > $CASE.R.SPHERE_smooth.X-Flip.$NUMBER_NODES.coord > $CASE.R.CLOSED.$NUMBER_NODES.topo $CASE.R.MedialWallSegments.borderproj > $CASE.Flipped-R_For-LEFT.TEMPLATE.MedialWallSegments.SPHERE.border > > # unproject right hem medial wall borders from mirror-reflected initial > sphere in same subject. > caret_command -surface-border-unprojection > $CASE.R.SPHERE_smooth.X-Flip.$NUMBER_NODES.coord > $CASE.R.CLOSED.$NUMBER_NODES.topo > $CASE.R.LANDMARKS.$NUMBER_NODES.borderproj > $CASE.Flipped-R_For-LEFT.TEMPLATE.LANDMARKS.SPHERE.border > fi > > > > On May 22, 2012, at 1:08 AM, Nikhil Sharma wrote: > > 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 <do...@brainvis.wustl.edu> > > To: Leon <leonad...@yahoo.com>; "Caret, SureFit, and SuMS software users" > <caret-users@brainvis.wustl.edu> > > 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 > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > > _______________________________________________ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > >
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