open-discussion > Brain Parcellation always fails
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Aug 23, 2012 10:08 AM | Markus Mertens
Brain Parcellation always fails
Whenever I try to run "Brain Parcellation" PANDA fails and
"BrainParcellation_pipeline.loginfo" does not contain more info
than this:
< M A T L A B (R) >
Copyright 1984-2012 The MathWorks, Inc.
R2012a (7.14.0.739) 64-bit (glnxa64)
February 9, 2012
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit http://www.mathworks.com.
What could be the reason and how do I have to use " Brain Parcellation"? There are not many options so what is wrong if I take sub_0001_FA.nii from a first successful run of PANDA and a T1-image from the same subject?
< M A T L A B (R) >
Copyright 1984-2012 The MathWorks, Inc.
R2012a (7.14.0.739) 64-bit (glnxa64)
February 9, 2012
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit http://www.mathworks.com.
What could be the reason and how do I have to use " Brain Parcellation"? There are not many options so what is wrong if I take sub_0001_FA.nii from a first successful run of PANDA and a T1-image from the same subject?
Aug 24, 2012 03:08 AM | Zaixu Cui
RE: Brain Parcellation always fails
You should
run bet command on t1 image to delete non-brain tissues.
Did you?
Best,
Zaixu
Did you?
Best,
Zaixu
Aug 24, 2012 11:08 AM | Markus Mertens
RE: Brain Parcellation always fails
Yes, I use "brain images" produced by bet. But BrainParcellation
does not finish. It stops sometime after writing something like
Setting subsampling
Setting reg mode
Setting lambda
several times in PartitionTemplate2FA_00001.log. But then suddenly this file disappears after the process has stopped.
After changing parameters in bet and catching some output of PartitionTemplate2FA_00001.log with "tail -f" I got the follwing messages:
# tail -f ./logs/PartitionTemplate2FA_00001.log
Setting lambda
Setting subsampling
Setting reg mode
Setting lambda
SpMat::SolveForx: Warning requested tolerence not obtained.
Requested tolerance was 0.001, and achieved tolerance was 0.0256171
This may or may not be a problem in your application, but you should look into it
Setting subsampling
Setting reg mode
Setting lambda
Setting subsampling
Setting reg mode
Setting lambda
invwarp -w /data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2MNI152_warp -r /data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2.nii.gz -o /data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2MNI152_warp_inv
WARNING!! Reference image has large non-zero ROI. Check that BET has run successfully on this.
applywarp -i /opt/spm/PANDA-1.1.0_64/data/atlases/AAL/AAL_116_2MM -o /data/fsl/projects/feye_dti/test/pat/00020/native_space/dti_00020_FA_Parcellated_AAL_116_2MM -r /data/fsl/projects/feye_dti/test/pat/00020/native_space/dti_00020_FA.nii.gz -w /data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2MNI152_warp_inv --postmat=/data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2FA.mat --interp=nn
** ERROR (nifti_image_read): failed to find header file for '/data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2MNI152_warp_inv'
** ERROR: nifti_image_open(/data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2MNI152_warp_inv): bad header info
ERROR: failed to open file /data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2MNI152_warp_inv
ERROR: Could not open image /data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2MNI152_warp_inv
Image Exception : #22 :: Failed to read volume /data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2MNI152_warp_inv
An error occured while reading file: /data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2MNI152_warp_inv
** ERROR (nifti_image_read): failed to find header file for '/data/fsl/projects/feye_dti/test/pat/00020/native_space/dti_00020_FA_Parcellated_AAL_116_2MM'
** ERROR: nifti_image_open(/data/fsl/projects/feye_dti/test/pat/00020/native_space/dti_00020_FA_Parcellated_AAL_116_2MM): bad header info
ERROR: failed to open file /data/fsl/projects/feye_dti/test/pat/00020/native_space/dti_00020_FA_Parcellated_AAL_116_2MM
Cannot open volume /data/fsl/projects/feye_dti/test/pat/00020/native_space/dti_00020_FA_Parcellated_AAL_116_2MM for reading!
/data/fsl/projects/feye_dti/test/pat/00020/native_space/dti_00020_FA_2T1
Finished. To view, point your web browser at
file:/data/fsl/projects/feye_dti/test/pat/00020/quality_control/FA_to_T1/slicesdir/index.html
/data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2MNI152
Finished. To view, point your web browser at
file:/data/fsl/projects/feye_dti/test/pat/00020/quality_control/T1_to_MNI152/slicesdir/index.html
****************
Checking outputs
****************
The output file or directory /data/fsl/projects/feye_dti/test/pat/00020/native_space/dti_00020_FA_Parcellated_AAL_116_2MM.nii.gz has not been generated!
************************************************
24-Aug-2012 14:13:06 : The job has FAILED
Total time used to process the job : 587.60 sec.
************************************************
Warning: File
'/data/fsl/projects/feye_dti/test/logs//PartitionTemplate2FA_00001.running'
not found.
> In psom_run_job at 178
ans =
1
Setting subsampling
Setting reg mode
Setting lambda
several times in PartitionTemplate2FA_00001.log. But then suddenly this file disappears after the process has stopped.
After changing parameters in bet and catching some output of PartitionTemplate2FA_00001.log with "tail -f" I got the follwing messages:
# tail -f ./logs/PartitionTemplate2FA_00001.log
Setting lambda
Setting subsampling
Setting reg mode
Setting lambda
SpMat::SolveForx: Warning requested tolerence not obtained.
Requested tolerance was 0.001, and achieved tolerance was 0.0256171
This may or may not be a problem in your application, but you should look into it
Setting subsampling
Setting reg mode
Setting lambda
Setting subsampling
Setting reg mode
Setting lambda
invwarp -w /data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2MNI152_warp -r /data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2.nii.gz -o /data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2MNI152_warp_inv
WARNING!! Reference image has large non-zero ROI. Check that BET has run successfully on this.
applywarp -i /opt/spm/PANDA-1.1.0_64/data/atlases/AAL/AAL_116_2MM -o /data/fsl/projects/feye_dti/test/pat/00020/native_space/dti_00020_FA_Parcellated_AAL_116_2MM -r /data/fsl/projects/feye_dti/test/pat/00020/native_space/dti_00020_FA.nii.gz -w /data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2MNI152_warp_inv --postmat=/data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2FA.mat --interp=nn
** ERROR (nifti_image_read): failed to find header file for '/data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2MNI152_warp_inv'
** ERROR: nifti_image_open(/data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2MNI152_warp_inv): bad header info
ERROR: failed to open file /data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2MNI152_warp_inv
ERROR: Could not open image /data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2MNI152_warp_inv
Image Exception : #22 :: Failed to read volume /data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2MNI152_warp_inv
An error occured while reading file: /data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2MNI152_warp_inv
** ERROR (nifti_image_read): failed to find header file for '/data/fsl/projects/feye_dti/test/pat/00020/native_space/dti_00020_FA_Parcellated_AAL_116_2MM'
** ERROR: nifti_image_open(/data/fsl/projects/feye_dti/test/pat/00020/native_space/dti_00020_FA_Parcellated_AAL_116_2MM): bad header info
ERROR: failed to open file /data/fsl/projects/feye_dti/test/pat/00020/native_space/dti_00020_FA_Parcellated_AAL_116_2MM
Cannot open volume /data/fsl/projects/feye_dti/test/pat/00020/native_space/dti_00020_FA_Parcellated_AAL_116_2MM for reading!
/data/fsl/projects/feye_dti/test/pat/00020/native_space/dti_00020_FA_2T1
Finished. To view, point your web browser at
file:/data/fsl/projects/feye_dti/test/pat/00020/quality_control/FA_to_T1/slicesdir/index.html
/data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2MNI152
Finished. To view, point your web browser at
file:/data/fsl/projects/feye_dti/test/pat/00020/quality_control/T1_to_MNI152/slicesdir/index.html
****************
Checking outputs
****************
The output file or directory /data/fsl/projects/feye_dti/test/pat/00020/native_space/dti_00020_FA_Parcellated_AAL_116_2MM.nii.gz has not been generated!
************************************************
24-Aug-2012 14:13:06 : The job has FAILED
Total time used to process the job : 587.60 sec.
************************************************
Warning: File
'/data/fsl/projects/feye_dti/test/logs//PartitionTemplate2FA_00001.running'
not found.
> In psom_run_job at 178
ans =
1
Aug 25, 2012 02:08 PM | Suyu Zhong
RE: Brain Parcellation always fails
Dear Markus,
Please replace the original g_PartitionTemplate2FA.m of PANDA with the attached one.
Best Regards
Suyu
Please replace the original g_PartitionTemplate2FA.m of PANDA with the attached one.
Best Regards
Suyu
Aug 28, 2012 08:08 AM | Markus Mertens
RE: Brain Parcellation always fails
Dear Suyu,
thanks a lot! It is working now.
Kind regards,
Markus
thanks a lot! It is working now.
Kind regards,
Markus