| Author |
 Topic  |
|
syam.gadde
BIAC Staff
USA
421 Posts |
 Posted - Nov 08 2006 : 3:52:08 PM
|
Dear golgi FSL users,
I have been working on a way to get FSL to use a directory other than /tmp for temporary storage, and think I have found a way for it to work. I have compiled FSL version 3.3.7 on golgi and have modified it to put some files in whatever your TMPDIR variable is set to. I intend to test this modification over the next day or two and when I am confident that it works, I intend to install 3.3.7 as the default version. The changes between FSL 3.3.5 (the current default version) and 3.3.7 as listed on the FSL web page are as follows:- 3.3.6 15/6/06 Fixed buglet in tbss_non_FA.
- 3.3.7 21/7/06 Fixed buglet in randomise which caused it to hang/crash under certain conditions.
As these look like minor changes, I don't think there will be any problems moving to the later version. The location of this installation and the date I intend to change over will be posted here when I have finished testing. FSL 3.3.5 will still be available when the change-over happens if there are any problems. Please reply to this post if you have any concerns about these plans. Thanks. |
|
|
syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Nov 16 2006 : 3:30:59 PM
|
OK, in light of the problems people are having with the temporary directories on golgi, I am planning to switch the installation to FSL-3.3.7 (with the new temporary directory functionality) tonight. The old version will still be available in /usr/local/packages/fsl-3.3.5, this change will only change the symbolic link in /usr/local/packages/fsl to point to fsl-3.3.7. Also, now, on login, your TMPDIR environment variable to be automatically set to /data/users/USERID/tmp and the directory created if it doesn't exist. To verify this is the case, log in to golgi and type the following:
echo $TMPDIR
ls -d /data/users/$USER/tmp
Both commands should print out /data/users/USERID/tmp where USERID is your user id. If there are any concerns about this switch, please respond to this post. |
 |
|
|
syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Nov 17 2006 : 07:08:16 AM
|
| FSL-3.3.7 is now the default on golgi. Please report any problems to the forums. |
|
|
|
petty
BIAC Staff
USA
453 Posts |
Posted - Nov 17 2006 : 07:49:30 AM
|
when fsl is open it still says 3.2, however i'm pointing to /usr/local/packages/fsl
the misc. tools are missing too.
|
Edited by - petty on Nov 17 2006 07:51:22 AM |
|
|
|
ckim
BIAC Alum
10 Posts |
Posted - Nov 17 2006 : 07:53:27 AM
|
| Mine says FSL 3.3, and it's pointing at /usr/local/bin/fsl. |
Edited by - ckim on Nov 17 2006 07:54:38 AM |
|
|
|
syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Nov 17 2006 : 07:54:29 AM
|
What happens if you type:
echo $FSLDIR
It should say /usr/local/packages/fsl if you are using the default installation. I get FSL 3.3 when I just type "fsl". |
|
|
|
jim.voyvodic
BIAC Faculty
138 Posts |
Posted - Nov 17 2006 : 08:14:16 AM
|
| I'm impressed by all these messages going back and forth before 8am. |
|
|
|
petty
BIAC Staff
USA
453 Posts |
Posted - Nov 17 2006 : 08:31:36 AM
|
quote:
Originally posted by jim.voyvodic
I'm impressed by all these messages going back and forth before 8am.
working hard as always.
hmmm... echo reveals: /usr/local/packages/fsl-3.2
in my .bash_profile i'm loading this:
export FSLDIR=/usr/local/packages/fsl
. ${FSLDIR}/etc/fslconf/fsl.sh
is there a possibility the .sh is still pointing to 3.2? |
Edited by - petty on Nov 17 2006 08:34:54 AM |
|
|
|
syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Nov 17 2006 : 08:39:36 AM
|
quote:
Originally posted by jim.voyvodic
I'm impressed by all these messages going back and forth before 8am.
Some of us need a little shot of BIAC to ease us into the day. |
|
|
|
syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Nov 17 2006 : 08:46:05 AM
|
quote:
Originally posted by petty
is there a possibility the .sh is still pointing to 3.2?
fsl.sh does not set FSLDIR. Something else must be
setting it. Though I can't seem to find anything in
your "dot" files to show where this is being set.
|
|
|
|
petty
BIAC Staff
USA
453 Posts |
Posted - Nov 17 2006 : 09:10:36 AM
|
| in SetUpFreeSurfer.sh there is a comment that sets the FSL_DIR to 3.2 |
|
|
|
petty
BIAC Staff
USA
453 Posts |
Posted - Nov 17 2006 : 09:12:21 AM
|
quote:
Originally posted by petty
in SetUpFreeSurfer.sh there is a comment that sets the FSL_DIR to 3.2
yep, that was the problem. so can you change the freesurfer file, its read-only. when i removed that path, i got the correct FSL |
|
|
|
syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Nov 17 2006 : 09:28:58 AM
|
quote:
Originally posted by petty
in SetUpFreeSurfer.sh there is a comment that sets the FSL_DIR to 3.2
Nice detective work! Thanks. I have updated the SetupFreesurfer files to point to the generic fsl link. |
|
|
|
jim.voyvodic
BIAC Faculty
138 Posts |
Posted - Nov 22 2006 : 5:03:32 PM
|
Since recent changes to FSL and FreeSurfer startup files I find that the CSH script I use to run FreeSurfer bombs ("grep gcc ..." error msg) when trying to run FSL's fsl.csh script (in $FSLDIR/etc/fslconf).
Has anyone else experienced similar problems?
Jim |
|
|
|
tankersley
BIAC Alum
USA
143 Posts |
Posted - Dec 01 2006 : 2:44:59 PM
|
I'm (still) a Unix novice.
I want to write a script that will sequentially execute another script. Specifically, I have a batchFSL script that will run first level FEAT on all the runs in an exam, which is executed as
./batchFSL exam#
I would like to write a script that will sequentially execute many times with different exam inputs.
I tried the obvious:
#!/bin/bash
\.batchFSL 43127
.\batchFSL 43129
but get this error:
./batchFSL_runall: batchFSL: command not found
./batchFSL_runall: batchFSL: command not found
Then I tried some other things which didn't work. Is there a way to do this in unix?
Thanks,
Dharol
|
|
|
|
petty
BIAC Staff
USA
453 Posts |
Posted - Dec 01 2006 : 2:50:04 PM
|
for a in 43127 43129; do
./batchFSL ${a} &
done
ps- that will start both of them ... if you want it to wait until the 1st is finished them remove the '&'
this will need to be in the same place your original batchFSL is, and once you've saved the script it has to be made executable (chmod +x scriptname). |
Edited by - petty on Dec 01 2006 2:54:34 PM |
|
|
|
Topic |
|
FSL-3.3.7
