| T O P I C R E V I E W |
| xu |
Posted - May 07 2007 : 3:56:05 PM
Hey all,
I got my FreeSurfer environment setting as below:
[xu@golgi: /] $ source /usr/local/packages/freesurfer-dev2-0-0/SetUpFreeSurfer.sh
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/packages/freesurfer-dev2-0-0
FSFAST_HOME /usr/local/packages/freesurfer-dev2-0-0/fsfast
SUBJECTS_DIR /data/users/xu/subjects
FUNCTIONALS_DIR /data/users/xu/sessions
MINC_BIN_DIR /usr/local/packages/freesurfer-mni/bin
MINC_LIB_DIR /usr/local/packages/freesurfer-mni/lib
PERL5LIB /usr/local/packages/freesurfer-mni/lib/5.8.0
Word too long.
Word too long.
Word too long.
Word too long.
FSL_DIR /usr/local/packages/fsl
But the correct results should be
SUBJECTS_DIR = /data/users/xu/freesurfer/subjects
FUNCTIONALS_DIR = /data/users/xu/freesurfer/sessions.
Someone can solve the problem for me will be much appreciated.
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| 15 L A T E S T R E P L I E S (Newest First) |
| xu |
Posted - Aug 13 2007 : 2:59:20 PM
Thanks Dr. Voyvodic and Syam,
I ran the runfreesurfer command as Dr. Voyvodic suggested above for FSE0013 this morning, it works very well. I will try Syam’s way later.
Thanks again,
Amy
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| jim.voyvodic |
Posted - Aug 10 2007 : 4:43:07 PM
Let us know if that works, Amy. I would not have expected it to.
If it doesn't, try:
runfreesurfer SUBJID series600/bia*_00360.dcm
I just modified runfreesurfer so that you can specify the first file explicitly if you want. If you use the directory name it will assume _00001.dcm
Jim |
| syam.gadde |
Posted - Aug 10 2007 : 4:17:12 PM
You can just copy the series directory, and in the copy, rename the first file to end in _00001.dcm. I think that should work (runfreesurfer only needs to send one file to Freesurfer, which finds the rest, and doesn't care what the files are named). |
| xu |
Posted - Aug 10 2007 : 4:07:26 PM
Thanks Syam!
I found the problem was: there is no *00001.dcm in series006 folder, the image slice starts with *00370.dcm. Now I can run Freesurfer with image slice start with *00001.dcm. Last time, FSE0012 had same problem!
Do you know any BIAC tool that I can change image slices number?
Thanks again,
Amy
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| syam.gadde |
Posted - Aug 10 2007 : 09:40:28 AM
Are you running from a directory where there is a series006 subdirectory, and does it have a file that matches *_00001.dcm? The script apparently can not find it.
Just so others are not confused, if you are running tcsh (or csh) as your shell (i.e. you either set this as your default shell, or you ran "tcsh" explicitly), then the commands Amy is using are the right ones:set SUBJECTS_DIR=/data/users/USER/freesurfer/subjects
set FUNCTIONALS_DIR=/data/users/USER/freesurfer/sessions
source /usr/local/packages/freesurfer-dev2-0-0/SetUpFreeSurfer.csh However, if you are running bash (true for most people), the commands are:export SUBJECTS_DIR=/data/users/USER/freesurfer/subjects
export FUNCTIONALS_DIR=/data/users/USER/freesurfer/sessions
. /usr/local/packages/freesurfer-dev2-0-0/SetUpFreeSurfer.sh (Don't forget to replace USER in the commands above with your golgi login name) |
| xu |
Posted - Aug 09 2007 : 4:38:20 PM
Thanks Syam, you are right!
But I still had problem to use runfreesurfer script, and got error message as following:
> runfreesurfer FSE0013 series006
SUBJECTS_DIR /data/users/xu/freesurfer/subjects
echo: No match.
AutoRecon1 did not finish properly
> cat recon.log
INFO: SUBJECTS_DIR is /data/users/xu/freesurfer/subjects
ERROR: cannot find /data/users/xu/freesurfer/subjects/FSE0013
>
I tried two ways that Josh and Petty suggested above.
Thanks again,
Amy
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| syam.gadde |
Posted - Aug 09 2007 : 3:47:54 PM
Did you mean to type:echo $SUBJECTS_DIR ? Otherwise, without the "echo" it is trying to run that path as a command, and that's why it is saying permission denied. |
| xu |
Posted - Aug 09 2007 : 3:29:59 PM
Hi all,
Why I got “Permission Denied.” problem after I set up SUBJECTS_DIR variable?
> set SUBJECTS_DIR = /data/users/xu/freesurfer/subjects
> set FUNCTIONALS_DIR = /data/users/xu/freesurfer/sessions
> source /usr/local/packages/freesurfer-dev2-0-0/SetUpFreeSurfer.csh
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/packages/freesurfer-dev2-0-0
FSFAST_HOME /usr/local/packages/freesurfer-dev2-0-0/fsfast
SUBJECTS_DIR /data/users/xu/freesurfer/subjects
FUNCTIONALS_DIR /data/users/xu/freesurfer/sessions
MINC_BIN_DIR /usr/local/packages/freesurfer-mni/bin
MINC_LIB_DIR /usr/local/packages/freesurfer-mni/lib
PERL5LIB /usr/local/packages/freesurfer-mni/lib/5.8.0
FSL_DIR /usr/local/packages/fsl
> $SUBJECTS_DIR
/data/users/xu/freesurfer/subjects: Permission denied.
>
Thanks a lot,
Amy
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| xu |
Posted - May 08 2007 : 1:14:42 PM
Thanks Dr. Voyvodic,
FreeSurfer is running well now. I am much appreciated all my helper.
Amy
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| jim.voyvodic |
Posted - May 08 2007 : 12:47:08 PM
Amy,
Since you are already in the FSE0012 directory you should not include that in your commands.
Try,
recon-all -i series005/*_00208.dcm -autorecon1 -subjid FSE0012
The 'runfreesurfer' command didn't work because it assumes that the first DICOM image is labelled *_00001.dcm, whereas yours actually starts at _00208. The recon-all command should do roughly the same thing as runfreesurfer.
Jim
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| xu |
Posted - May 08 2007 : 12:46:44 PM
Thanks Josh,
> cat recon.log
INFO: SUBJECTS_DIR is /data/users/xu/freesurfer/subjects
ERROR: cannot find /data/users/xu/freesurfer/subjects/FSE0012
Amy |
| petty |
Posted - May 08 2007 : 12:46:28 PM
there is no "FSE0012/series005" in "/data/users/xu/freesurfer/subjects"
your SUBJECTS_DIR path is incorrect for where your data actually is, set it to "/data/users/xu/freesurfer" and try the above commands again. |
| xu |
Posted - May 08 2007 : 12:38:07 PM
Thanks Dr. Voyvodic and Petty,
I tried two ways as following:
------------------------------------------
[xu@golgi: /data/users/xu/freesurfer/FSE0012] $ recon-all -i FSE0012/series005/*_00208.dcm -autorecon1 -subjid FSE0012
set: No match.
------------------------------
> runfreesurfer FSE0012 series005
SUBJECTS_DIR /data/users/xu/freesurfer/subjects
echo: No match.
AutoRecon1 did not finish properly
-----------------------------------
Why?
Thanks,
Amy |
| josh.bizzell |
Posted - May 08 2007 : 12:30:31 PM
Amy,
One problem I was having with the recon-all and runfreesurfer on a different machine (not Golgi) is that the recon-all script has a "-f" flag at the shell declaration line (i.e. "#!/bin/tcsh -f"), which as I understand it, causes any environment variables set in your .cshrc (or .tcshrc) file to be ignored.
I solved this by editing "runfreesurfer" to explicitly send the $SUBJECTS_DIR variable to the recon-all command using the -sd flag.
BTW: If you run "runfreesurfer", a file called recon.log should be created in the folder where you've saved your subject data and run the command. If the program crashes again, could you post the contents of this file?
Josh
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| xu |
Posted - May 08 2007 : 12:09:57 PM
Thanks Dr. Voyvodic and Petty,
Before I thought I got SUBJECTS_DIR problem, but it looks not now since I set SUBJECTS_DIR properly. My problem maybe that did not finish running runfreesurfer properly because some of my subjects running more than 10 days could not finish, so I just simply turn off my computer to stop it then I got this problem and still can not fix it. I can not run runfreesurfer now.
Thanks again,
Amy
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