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xu
Junior Member
25 Posts |
 Posted - May 08 2007 : 12:46:44 PM
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Thanks Josh,
> cat recon.log
INFO: SUBJECTS_DIR is /data/users/xu/freesurfer/subjects
ERROR: cannot find /data/users/xu/freesurfer/subjects/FSE0012
Amy |
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jim.voyvodic
BIAC Faculty
138 Posts |
Posted - May 08 2007 : 12:47:08 PM
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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
Junior Member
25 Posts |
Posted - May 08 2007 : 1:14:42 PM
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Thanks Dr. Voyvodic,
FreeSurfer is running well now. I am much appreciated all my helper.
Amy
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Edited by - xu on May 08 2007 1:15:49 PM |
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xu
Junior Member
25 Posts |
Posted - Aug 09 2007 : 3:29:59 PM
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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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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Aug 09 2007 : 3:47:54 PM
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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. |
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xu
Junior Member
25 Posts |
Posted - Aug 09 2007 : 4:38:20 PM
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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
BIAC Staff
USA
421 Posts |
Posted - Aug 10 2007 : 09:40:28 AM
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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) |
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xu
Junior Member
25 Posts |
Posted - Aug 10 2007 : 4:07:26 PM
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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
BIAC Staff
USA
421 Posts |
Posted - Aug 10 2007 : 4:17:12 PM
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| 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). |
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jim.voyvodic
BIAC Faculty
138 Posts |
Posted - Aug 10 2007 : 4:43:07 PM
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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 |
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xu
Junior Member
25 Posts |
Posted - Aug 13 2007 : 2:59:20 PM
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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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Topic |
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Problem in running FreeSurfer
