Dear Donna thank you so much for your quick reply, I am uploading the file right now as you instructed it was much less than 1 gig. I did save both border and border projection files. one thing that puzzles me even more is that when i go to overlay/underlay surface --> paint then go to choose my paint mask there seems to be several copies of everything there for some reason... but still my Petrides paint does not work ... i will keep trying and let you know if i figure anything new out. Thank you again and I look forward to hearing from you.
Iman Janemi On 5-Oct-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. Xi-Nian Zuo invited you to Dropbox (Dropbox) > 2. Re: F99 borders and paint using GUI (Donna Dierker) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 05 Oct 2010 05:37:11 +0000 > From: Dropbox <[email protected]> > Subject: [caret-users] Xi-Nian Zuo invited you to Dropbox > To: [email protected] > Message-ID: <[email protected]> > Content-Type: text/plain; charset="utf8" > > Xi-Nian Zuo wants you to use Dropbox to sync and share files online > and across computers. > > Get started here: http://www.dropbox.com/link/20.AI89Dg_LF1/NjM3ODEwODU0Nw > > - The Dropbox Team > > ____________________________________________________ > To stop receiving invites from Dropbox, please go to > http://www.dropbox.com/bl/7c7f1e584bfa/caret-users%40brainvis.wustl.edu > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://brainvis.wustl.edu/pipermail/caret-users/attachments/20101005/4727f2d4/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Tue, 05 Oct 2010 10:52:46 -0500 > From: Donna Dierker <[email protected]> > Subject: Re: [caret-users] F99 borders and paint using GUI > 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, > > 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 > > > End of caret-users Digest, Vol 85, Issue 4 > ****************************************** _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
