Hi all,
I just ran recon-all -s (subject) -all for several subjects and it looked like they ran successfully, however when I went to check the data in tkmedit, I realized there were no aseg.mgz as wel as other vital files. The subject did not produce an error log.
Any one else ever have this happen?
Best,
Anson K.
University of Michigan
What does the recon-all.log file in the stats dir show for the steps it missed? Allison
the recon-all.log does not show anything missing, however it is apparent now that it definitly didn't finish. For most of my subjects it stopped running at:
Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (26249 voxels, overlap=0.958) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (26249 voxels, peak = 64), gca=64.5 gca peak = 0.12723 (61) mri peak = 0.03761 (63) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (27939 voxels, overlap=0.963) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (27939 voxels, peak = 63), gca=62.5 gca peak = 0.22684 (88) mri peak = 0.10929 (95) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (8347 voxels, overlap=0.476) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (8347 voxels, peak = 95), gca=94.6 gca peak = 0.21067 (87) mri peak = 0.11382 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (7525 voxels, overlap=0.506) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (7525 voxels, peak = 94), gca=93.5 ****STOPPED RUNNING HERE *******
if anyone can recognize this step so I don't have to run full recon again that would be great or any ideas as to why this happend
best,
Anson K.
University of Michigan
On Mon, 12 Jul 2010 11:39:10 -0400 (EDT), Allison Stevens astevens@nmr.mgh.harvard.edu wrote:
What does the recon-all.log file in the stats dir show for the steps it missed? Allison
If you run: recon-all -make all -s <subjid> It will pick up where it left off. Let us know if it doesn't run. Allison
how much RAM do you have on the machine that it's running on? What was the exit code of the process? On Mon, 12 Jul 2010 aekairys@umich.edu wrote:
the recon-all.log does not show anything missing, however it is apparent now that it definitly didn't finish. For most of my subjects it stopped running at:
Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (26249 voxels, overlap=0.958) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (26249 voxels, peak = 64), gca=64.5 gca peak = 0.12723 (61) mri peak = 0.03761 (63) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (27939 voxels, overlap=0.963) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (27939 voxels, peak = 63), gca=62.5 gca peak = 0.22684 (88) mri peak = 0.10929 (95) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (8347 voxels, overlap=0.476) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (8347 voxels, peak = 95), gca=94.6 gca peak = 0.21067 (87) mri peak = 0.11382 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (7525 voxels, overlap=0.506) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (7525 voxels, peak = 94), gca=93.5 ****STOPPED RUNNING HERE *******
if anyone can recognize this step so I don't have to run full recon again that would be great or any ideas as to why this happend
best,
Anson K.
University of Michigan
On Mon, 12 Jul 2010 11:39:10 -0400 (EDT), Allison Stevens astevens@nmr.mgh.harvard.edu wrote:
What does the recon-all.log file in the stats dir show for the steps it missed? Allison
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