You can run it with recon-all -s subject -make all

In the future, you can run recon-all with nohup, ie,

nohup recon-all -s subject ... &

ie, put "nohup" as the first item and "&" as the last item. This will cause it to run in the background and it should continue to run even if you log out

doug

On 11/3/14 12:50 PM, Tanev, Kaloyan,M.D. wrote:

Hi,

I just took the FreeSurfer course. I am using the command reconall --s <subj_ID> -i <t1w> -all. Frequently, because I log on remotely to the server and because of the time that it takes, the terminal disconnects and therefore the process is not complete entirely. Can you point me to a way to redo just the steps that have not been done yet.

I give an example of the latest files generated, with just a few files missing. How do I direct it to pick up from where it left?

Thank you.

Here is the list of files generated:

drwxrwsr-x 2 ktanev schiz 80 Oct 31 14:06 orig/

drwxrwsr-x 3 ktanev schiz 1.0K Oct 31 21:39 transforms/

-rw-rw-r-- 1 ktanev schiz 258K Oct 31 21:39 aseg.auto.mgz

-rw-rw-r-- 1 ktanev schiz 1.6K Oct 31 21:31 aseg.auto_noCCseg.label_intensities.txt

-rw-rw-r-- 1 ktanev schiz 257K Oct 31 21:38 aseg.auto_noCCseg.mgz

-rw-rw-r-- 1 ktanev schiz 258K Oct 31 21:39 aseg.mgz

-rw-rw-r-- 1 ktanev schiz 1.4M Oct 31 21:45 brain.finalsurfs.mgz

-rw-rw-r-- 1 ktanev schiz 1.4M Oct 31 14:53 brainmask.auto.mgz

-rw-rw-r-- 1 ktanev schiz 1.4M Oct 31 14:53 brainmask.mgz

-rw-rw-r-- 1 ktanev schiz 1.4M Oct 31 21:45 brain.mgz

-rw-rw-r-- 1 ktanev schiz 395K Oct 31 15:33 ctrl_pts.mgz

-rw-rw-r-- 1 ktanev schiz 145K Oct 31 21:49 filled.mgz

-rw-rw-r-- 1 ktanev schiz 12K Oct 31 14:12 mri_nu_correct.mni.log

-rw-rw-r-- 1 ktanev schiz 5.7K Oct 31 14:08 mri_nu_correct.mni.log.bak

-rw-rw-r-- 1 ktanev schiz 1.5M Oct 31 15:33 norm.mgz

-rw-rw-r-- 1 ktanev schiz 5.6M Oct 31 14:12 nu.mgz

-rw-rw-r-- 1 ktanev schiz 3.6M Oct 31 20:32 nu_noneck.mgz

-rw-rw-r-- 1 ktanev schiz 7.8M Oct 31 14:07 orig.mgz

-rw-rw-r-- 1 ktanev schiz 5.7K Oct 31 14:08 orig_nu.log

-rw-rw-r-- 1 ktanev schiz 7.8M Oct 31 14:08 orig_nu.mgz

-rw-rw-r-- 1 ktanev schiz 19M Oct 31 14:07 rawavg.mgz

-rw-rw-r-- 1 ktanev schiz 119 Oct 31 21:45 segment.dat

-rw-rw-r-- 1 ktanev schiz 5.5M Oct 31 14:16 T1.mgz

-rw-rw-r-- 1 ktanev schiz 1.6K Oct 31 16:35 talairach.label_intensities.txt

-rw-rw-r-- 1 ktanev schiz 214 Oct 31 15:30 talairach.log

-rw-rw-r-- 1 ktanev schiz 214 Oct 31 21:08 talairach_with_skull_2.log

-rw-rw-r-- 1 ktanev schiz 214 Oct 31 14:52 talairach_with_skull.log

-rw-rw-r-- 1 ktanev schiz 463K Oct 31 21:48 wm.asegedit.mgz

-rw-rw-r-- 1 ktanev schiz 464K Oct 31 21:48 wm.mgz

-rw-rw-r-- 1 ktanev schiz 507K Oct 31 21:47 wm.seg.mgz

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