Hi Iman, See inline replies below.
Donna On 10/04/2010 01:59 PM, Iman J. wrote: > Dear Donna, > > I wrote to you a few weeks ago about creating borders and paint files > using the caret GUI, > I had some work to finish up and I had addressed the caret issue using > your advice. > > I was able to save my files with out receiving an error message > finally and everything seemed > to be going well. > > The original error message from before was that two of the Border > files for surface in the .spec file called > > IMANS_FINAL_CALLS_copy_of_Macaque.F99UA1.LEFT.FLAT.CartSTD.Std-MESH.clean.73730.coord > > > and > Macaque.F99.UA1.LEFT.FLAT.CartSTD.Std-Mesh.Clean.73730.coord > > (strangely searching for these files i cant even locate them on the > computer are they temporary files?) Hmmm. Not that I know of. The second one looks a lot like this one from the Sept 2006 tutorial: MACAQUE/Macaque.F99UA1.LEFT.FLAT.CartSTD.Std-MESH.clean.73730.coord > > could not be saved even though I went to Manage Loaded Files and > clicked Save all Files... > > Eventually what I ended up doing was going through the Spec file, file > by file and saving all files associated with it "As" and replacing > them with the current file, the one containing all the work I had > done... and it seemed to work at the time. The error went away and I > was able to access the files correctly. > > Since then I am now again trying to access the border and paint files > i had made and the entire .spec file is totally mixed up. > > I had made borders and paint associations for 2 maps from the figure > in the papers I showed you (Barbas2008 and Petrides1994) using > anatomical landmarks to visually project the regions on to the 3D F99 > brain. This method although tedious produced good results that I was > quite happy with. I would place green nodes on the brain in 3D > outlining the area I wanted to select then on the flat map I would > draw the border around the area indicated by the green nodes. The > program would then project my border and associated paint file and > color I had assigned... everything was working fine. > > But now again I am stuck. I went to access my work and things just > don't make sense. The Barbas paint files work. I can see the paint > colors just as I had made them previously. The Petrides paint files > don't work ... I can't see the areas that I had made at all but > strangely the file is in the drop down menu when i go to D/C overlay > underlay surface and i try to overlay the file it is there but it just > doesn't project anything. Then I wonder whether the area colors are just missing. The parcels are stored in the paint file, using node:index pairs, which are defined at the top of the file (paint index to paint name). The colors are defined in a separate area colors file, keyed to the same names used in the paint file. > And for both Barbas and Petrides, when I try to project the borders, > they don't exist. That is under D/C border names they don't exist but > they all exist under D/C border colors just as I had made them before > ... either way I cant project them onto the F99 Flat map. Did you save the files as border or borderproj? You can save as both, but only borderproj will display on all configurations (flat, inflated, etc.). If you still have the border representation, and the reference surface used to generate those borders, you can project them again and save as borderproj. > > I don't know what is going on ... I feel that my spec file has gotten > so mixed up with trying different things and redoing things, saving > and not saving things to try and keep my work everything is just chaos > right now. Before I closed caret I completed my figures incase > something would go wrong and everything seemed like it was working > still after I closed but now again it is lost... this makes no sense > to me as I saved it all and did not get any error messages and was > able to access it immediately afterwards... I have a feeling that it > is there somewhere in the background but I don't know how to access it. If your entire directory is less than one gigabyte (as reported by du -k .), then zip it up and upload it here: http://pulvinar.wustl.edu/cgi-bin/upload.cgi Otherwise, just upload your paint, area_color, border, borderproj, and bordercolor files. > > Please, is there any way you can help me retrieve my work I have no > idea what is going on and could really use some help. Or, if you have > a more optimal way of getting these maps onto the brain I am free and > open to suggestions. I am relatively new to caret and know that the > program is capable of so much more than my limited knowledge allows at > this time. If I can help clarify any thing else about what I did > please let me know and I will respond promptly. Just tell yourself: It could be worse. I could be patching segmentation generated from awful spgr scans. (Sorry to those who actually are doing that.) > > Thank you very much for your help so far I look forward to hearing > from you. > > Iman Janemi > > > > > > > On 4-Sep-10, at 1:00 PM, [email protected] wrote: > >> Send caret-users mailing list submissions to >> [email protected] >> >> 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 >> [email protected] >> >> You can reach the person managing the list at >> [email protected] >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of caret-users digest..." >> >> >> Today's Topics: >> >> 1. Re: Problems Saving on F99 Brain (Donna Dierker) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Fri, 03 Sep 2010 13:41:26 -0500 >> From: Donna Dierker <[email protected]> >> Subject: Re: [caret-users] Problems Saving on F99 Brain >> To: "Caret, SureFit, and SuMS software users" >> <[email protected]> >> Cc: Thilo Womelsdorf <[email protected]>, [email protected] >> Message-ID: <[email protected]> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> Hi Iman, >> >> I feel like I don't have enough detail to get a feel for what went >> wrong. >> >> You say, "i closed and all my work was lost." By this you mean when you >> open Caret later, you don't see the same thing as when you closed >> previously, right? Unless you save your current settings in a scene >> (Toolbar: D/C: Scene: Append New Scene), and then save the resulting >> scene file, you won't get exactly the same view when you open Caret >> later. You'll have to select the pertinent files when you load the spec >> file, make the surface-to-window assignments, toggle on the Borders >> button at the bottom of the D/C: Overlay/Underlay surface menu (or >> toggle on show borders on the D/C: Borders Main window). There are tons >> of settings, and that's why we have the Scenes feature -- to allow you >> to save them. >> >> I also feel like there's this big disconnect between the figures you >> show and the last capture, which is the only Caret one. How you are >> transforming from figure to Caret is a black box to me. >> >> Have you tried using the File: Save Data File: Border file feature to >> save your borders? I wouldn't think it should matter, but I would >> try it. >> >> Finally, I vaguely wonder whether you are projecting the borders, but >> failing to save a borderproj file. Even if you don't save a borderproj, >> it should be possible to recreate it if you still have the border file >> and its reference surface available. >> >> Donna >> >> On 09/03/2010 11:25 AM, Iman J. wrote: >>> Dear Caret users my colleague and I are having trouble saving our >>> work.... already I have had to redo my job 3 times each time taking >>> some 4 hours. We are in the process of reproducing the attached >>> figures from , >>> >>> Petrides M, Pandya DN (1994) Comparative architectonic analysis of the >>> human and the macaque frontal cortex. In: Handbook of neuropyschology, >>> Vol 9 (Boller F, Grafman J, eds), pp 17-57. Amsterdam: Elsevier, >>> >>> Barbas H. (2007) Specialized elements of orbitofrontal cortex in >>> primates. Annals of the New York Academy of Sciences Volume 1121, >>> Issue 1 >>> <http://onlinelibrary.wiley.com/doi/10.1111/nyas.2007.1121.issue-1/issuetoc> >>> >>> >>> >>> Saleem K. Kondo H. and Price J. (2008) Complementary Circuits >>> Connecting the Orbital and Medial Prefrontal Networks with the >>> Temporal, Insular, and Opercular Cortex in the Macaque Monkey. Journal >>> of Comparative Neurology. 506:659-693 >>> >>> >>> the first attempt I added the borders to the F99 brain then using >>> Manage files i changed the name of the border file to my own name and >>> then pressed save all checked files and it did then i finished the >>> work and went to close it said that there was a border and paint files >>> that was not saved, i rechecked manage loaded files all was saved .... >>> i closed and all my work was lost. >>> >>> the second time around i saved As new border files, paint files etc >>> ... basically any thing that had the word border or paint i saved As >>> my new version and again it failed and gave me the same error saying >>> that a certain border file had been saved but we couldn't save our >>> work .... >>> >>> i re did the work for a third time this time refusing to close caret >>> and have now finished all my figures but caret is still giving me this >>> error.... If you can help solve this issue i would greatly appreciate >>> it and also if you would like to add these border and paint files to >>> the F99 Standard brain in the Caret Data base we would be happy to >>> share our work with all caret users. >>> >>> Many thanks, >>> >>> Iman Janemi >>> >>> >>> >>> >>> >>> >>> >>> >>> ------------------------------------------------------------------------ >>> >>> >>> _______________________________________________ >>> 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 >> >> >> End of caret-users Digest, Vol 84, Issue 2 >> ****************************************** > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------ > > _______________________________________________ > 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
