Hello, Allison,

Thanks a lot for your help and sorry for my delay! Yes, I agree. If I use -autorecon3 to rerun it, everything should be fine. But I also find something interesting. Please check the attached recon-all.log,

From line 10812 to line 10847, you will see

"ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, line 372 vtkMultiThreader (0x270e3480): Unable to create a thread. pthread_create() returned 12"

Normally, after this line, we will see something like,

"Segmentation fault (core dumped) recon-all exited with ERRORS at Thu Dec 10 00:58:33 CST 2009"

Once, I call -autorecon3, we can see the following lines in the recon-all.log, and the results will be fine.

" New invocation of recon-all

Thu Dec 10 15:50:19 CST 2009 /data1/radiology/m047599/subjects/002_S_0413_20060519 /usr/local/biotools/freesurfer/freesurfer-v4.5.0/bin/recon-all -s 002_S_0413_20060519 -autorecon3 -no-isrunning "

However, in the recon-all.log I sent to you, we only can see something like,

" ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, line 372 vtkMultiThreader (0x30bf9d90): Unable to create a thread. pthread_create() returned 12

loading input data... hemi masks overlap voxels = 4 writing volume /data1/radiology/m047599/subjects/002_S_0413_20060502/mri/ribbon.mgz writing ribbon files #----------------------------------------- #@# AParc-to-ASeg Wed Dec 9 20:07:25 CST 2009 /data1/radiology/m047599/subjects/002_S_0413_20060502

mri_aparc2aseg --s 002_S_0413_20060502 --volmask "

The trick thing is I do not do anything, it looks like to me, after few rounds of calling vtkMultiThreader and getting ERRORs, FS automatically go to the next step with a wrong ribbon.mgz by itself. And it will finish the whole process without "errors", however, when we load the results into tkmedit, we find lots of wm parcellation are wrong.

I have 38 subjects have this kind of problem, do you think it is because of FS or the SGE I use to run the subjects?

Thanks a lot! Guang

Date: Tue, 8 Dec 2009 17:43:09 -0500 From: astevens@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com Subject: Re: [Freesurfer] a question about the mris_volmask ERROR

Oh I just saw your earlier message which had a bit more detail.

If you are using -autorecon3 to rerun it so it finishes, you shouldn't see a difference in the stats. You may see a difference if you are running on different platforms.

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On Mon, 7 Dec 2009, Guang Zeng wrote:

...

Hi, there,

I have question about the mris_volmask ERROR.

I ran multiple subjects on our SUN Grid Engine system. sometimes some subjects are sent to the same cluster node, and limited memory is assigned to each subject. Because of this, I often met an ERROR at the mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance sub1 step in autorecon3., which gave me an error like:

ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, line 372 vtkMultiThreader (0x33d05a90): Unable to create a thread. pthread_create() returned 12

I knew this error is caused by some VTK function FS used to allocate memory. What I did is everytime when I met this kind of error, I use recon-all -s subj -autorecon3 -no-isrunning , and the process will finish.

However, I found if I did something like this, it will cause problems at the wm parcellation step. For example, I have the same subject which is sent to SGE, fails at mris_volmask, and then I call autorecon3 to finish the process, and I go to wmparc.stats, lotf of rois such as isthumus ctx-cingluate, ctx-posterior singulate are 0. While I ran the same subject at a local machine, and finished without any problems, I looked at isthumus cingluate and posterior singulate, they are not zeros.

So, does it mean that I need start from beginning when I met the errors cause by mris_volmask?

Thanks a lot! guang

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