You can subscribe to this list here.
2004 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
(1) |
Jul
(1) |
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
---|---|---|---|---|---|---|---|---|---|---|---|---|
2008 |
Jan
(2) |
Feb
(1) |
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
From: Keller, C. J. <CJKELLER@PARTNERS.ORG> - 2008-02-15 18:33:43
|
Hi fROI users, I am new to using the fROI tools and am trying to make a new ROI using make_roi. My code is below. multnomah:ckeller[114] make_roi -analysis simple_v_complex -contrast ROI_simple_v_complex -roi ROI_froi_test -sf sessid -df sesspar -signed Subroutine FSFAST::Misc::getcwd redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 65. at /usr/pubsw/common/froi/0.1.1/lib/perl5/site_perl/5.6.1/FSFAST/Misc.pm line 9 starting makeROI... ERROR 102: The contrast sig does not seem to exist in /space/multnomah/3/users/gow/PROZ06/fMRI/PROZ06004/bold/simple_v_complex/ROI_sim ple_v_complex/. Please ensure your parameters are correct. However, the file sig.nii is in that folder. Is there a specific file extension that the command is searching for? Thanks so much. Best, Corey -------------------- Corey Keller Epilepsy Unit Clinical Research Coordinator Massachusetts General Hospital VBK 830, 55 Fruit Street Boston, MA 02114 Phone 802.578.6292 Email cjk...@pa... ck...@nm... The information transmitted in this electronic communication is intended only for the person or entity to whom it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this information in error, please contact the Compliance HelpLine at 800-856-1983 and properly dispose of this information. |
From: nick k. <nknouf@MIT.EDU> - 2008-01-21 18:05:40
|
Hi Corey, I'm not really supporting froi much anymore as I'm not involved in =20 the neurosciences anymore. Anyway, I can help out in whatever way I =20 can, although I won't be writing any new code... There's a lot of good info in the manual about how to install and use =20= froi; I'd suggest checking it out: http://froi.sourceforge.net/documents/manual.pdf As to your question, you can change the location for installing perl =20 modules with the following: perl Makefie.pl PREFIX=3D/place/to/install/module PREFIX could be something like /home/username/perl/perl_version/, =20 replicating the perl file structure. You can then install by running the standard commands: make make test make install I've heard from others that the latest version of freesurfer changes =20 the file formats from bshort/bfloat to something else. froi won't =20 work with these new formats without some major changes to the code. =20 If you do make the changes, let me know and I'll commit them to the =20 repository (or, if you or anyone else wants to take over the project, =20= then let me know!) Best, nick On Jan 18, 2008, at 1:48 PM, Corey Keller wrote: > Hello froi users, > > I'm new to froi and am trying to install it. I am not a system =20 > administrator, so I used the second option and am getting errors. > > I run the perl Makefile.PL command to create the file and then run=85 > Make > Make test > Make install > > And it gives me the following error=85 > Warning: You do not have permission to install into /usr/lib/perl5/=20 > site_perl=85 > Permission denied. > > How do I change the location to which this module is installed to? =20= > Thanks for your help. > > Best, > Corey > > -------------------- > Corey Keller > Epilepsy Unit > Clinical Research Coordinator > Massachusetts General Hospital > Wang 735, 55 Fruit Street > Boston, MA 02114 > Phone 802.578.6292 > Email cjk...@pa... > ck...@nm... > > ----------------------------------------------------------------------=20= > --- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/=20 > _______________________________________________ > Froi-users mailing list > Fro...@li... > https://lists.sourceforge.net/lists/listinfo/froi-users |
From: Corey K. <ck...@nm...> - 2008-01-18 18:49:53
|
Hello froi users, I'm new to froi and am trying to install it. I am not a system administrator, so I used the second option and am getting errors. I run the perl Makefile.PL command to create the file and then run=85 Make Make test Make install And it gives me the following error=85 Warning: You do not have permission to install into /usr/lib/perl5/site_perl=85 Permission denied. How do I change the location to which this module is installed to? = Thanks for your help. Best, Corey -------------------- Corey Keller Epilepsy Unit Clinical Research Coordinator Massachusetts General Hospital Wang 735, 55 Fruit Street Boston, MA 02114=20 Phone 802.578.6292 Email cjk...@pa... ck...@nm... |
From: Nick K. <nknouf@MIT.EDU> - 2004-07-22 21:44:33
|
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi everyone, I thought I'd let people know the development status for froi. As I started working on bugfixes and new features, I realized that the first version of froi had become unwieldy. It was a pain to update, a pain to work worth, wrong language for the job, etc. I've learned all of this in the last year and a half (or so) of working off-and-on on the software. Thus, before froi got too out of hand, I wanted to begin fresh with the things I've learned in the last year about software engineering and development. Thus the version I'm working on right now, froi 0.2.0, will not only provide me an easier development environment, it will also give you, the end user, a number of improvements, most notably being a huge increase in speed as well as a much simplified installation procedure. For example, in the code that is used to read in a bshort or bfloat file, I've managed to decrease the loading time (for one of our standard bshort runs) from 9s to 0.5s. If you're interested, you can read some of the technical changes in the project at the end of the e-mail. I'm spending a lot of my time on this now and hope to have a release out by the end of the summer. Thanks for using froi, Nick Knouf For those interested in the technical details: The original version of froi was a mixture of perl scripts, modules, and matlab functions. What became apparent over time was the lack of a real object-oriented development environment in either perl or matlab. Sure, perl has "objects", and I used them in the modules, but it's not what perl was (or is) designed for. And in matlab the support is even worse; about the close you can get to an object is a structure. After some research I decided to reprogram froi in python. The reasons are numerous: 1. python is designed with object oriented development in mind, from the ground up. This makes the programer's life much, much easier and allows me to use current programming idioms like design patterns and test-driven-development. 2. There has been a lot of work by many groups to recreate a number of matlab functions in python. Many times these functions are faster than the native matlab code. 3. python has a very easy-to-use C extension architecture, which allows lengthy computations to be coded in C for speed. This is how I get the huge speed increase in reading bshort volumes. 4. With the object-oriented-environment comes the ability to write the code in a modular way, giving those who want to a base to extend froi. Those are the main technical reasons behind the change. I've also moved the building of the software from simply "copy and paste and run these perl scripts" to a GNU autoconf/automake system. For those of you who have installed software from source before, the "./configure && make && make check && make install" sequence ought to be familiar. This will greatly simplify configuration. If you were looking closely you saw "make check" in the last paragraph. I'm coding using test-driven-development which will mean that there are tests of all the functionality in froi that you can run before installation. This not only gives the you the piece of mind that the code works as advertised, it also give me the freedom to make changes without worrying about breaking something and not knowing about it. That's about it. If you're interested in the development at all you can download the "froip" (for froi in python) module from the sourceforge CVS. Simply run "./reconf" in the root directory of the distribution (with a quite recent version of autoconf, like 2.52) to generate the configure script. Thanks! -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.3 (Darwin) iD8DBQFBADU8x+5APqaSLB4RAqqGAJ9+2da8elxrwHBD/d/6E3wWh3Sr4ACgjTxb TKNPFn9Fi8ZYLV7kVbgQ/wk= =MixA -----END PGP SIGNATURE----- |
From: Tamara K. <kn...@nm...> - 2004-06-09 14:15:24
|
keep getting same error, followed installation instructions exactly, have no idea what's going on: whatever:knutsen[27] source ~knutsen/.environment whatever:knutsen[28] make_roi -analysis a1 -contrast cM_F -roi MT -sf sf -df df -threshold 6 Can't locate FSFAST/Parse.pm in @INC (@INC contains: /homes/6/knutsen/matlab/froi/lib/perl5/site_perl/5.6.1/i386-linux /usr/lib/perl5/5.6.1/i386-linux /usr/lib/perl5/5.6.1 /usr/lib/perl5/site_perl/5.6.1/i386-linux /usr/lib/perl5/site_perl/5.6.1 /usr/lib/perl5/site_perl/5.6.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.6.1/i386-linux /usr/lib/perl5/vendor_perl/5.6.1 /usr/lib/perl5/vendor_perl .) at /homes/6/knutsen/matlab/froi/bin/make_roi line 116. BEGIN failed--compilation aborted at /homes/6/knutsen/matlab/froi/bin/make_roi line 116. whatever:knutsen[29] source ~knutsen/.environment whatever:knutsen[30] make_roi -analysis a1 -contrast cM_F -roi MT -sf sf -df df -threshold 6 Can't locate FSFAST/Parse.pm in @INC (@INC contains: /homes/6/knutsen/matlab/froi/lib/perl5/site_perl/5.6.1/i386-linux/auto /usr/lib/perl5/5.6.1/i386-linux /usr/lib/perl5/5.6.1 /usr/lib/perl5/site_perl/5.6.1/i386-linux /usr/lib/perl5/site_perl/5.6.1 /usr/lib/perl5/site_perl/5.6.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.6.1/i386-linux /usr/lib/perl5/vendor_perl/5.6.1 /usr/lib/perl5/vendor_perl .) at /homes/6/knutsen/matlab/froi/bin/make_roi line 116. BEGIN failed--compilation aborted at /homes/6/knutsen/matlab/froi/bin/make_roi line 116. |