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Dear Douglas,
I do not think -s and -sd is essential to the issue. I just wanted to draw attention to this not standard call in my set up. There are reasons for it and it worked for version 6.
Yes, all prior steps of recon-all were executed, sometimes one by one, some times in bunches. The real point, as far as I could see, is that -white was not executed before -smooth2 started. The exact same sequence of commands on the exact same data worked using version 6.
Since ReconAllTableStable for version 7 does not exist, I do not know if the order of steps is really the same as in version 6. I do not expect the order of steps to change and thus I expect the sequence that worked for version 6 should work. My expectation could be wrong, of course.
Does version 7 introduce different order of processing or some intermediate steps that did not exist in version 6?
The previous and successfully completed step was "-hemi lh -fix". Would you expect "-hemi lh -white -smooth2 -inflate2 -sphere -surfreg -cortparc -pial" to be the right next step?
Thank you,
Roman
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Monday, June 8, 2020 10:18 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ver 7.1: recon-all executes out of order?
I'm not sure what you are trying to communicate here abut -s and -sd. It is hard to debug without the log file. Had you run the earlier steps in the recon before running this command?
On 6/8/2020 1:25 AM, Roman Fleysher wrote:
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Dear FreeSurfer Develovers,
FreeSurfer 7.1 was recently installed on our cluster. I am testing it and stumbled on the error. It is difficult for me to debug it myself (perhaps if https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV7https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReconAllTableStableV6.0&data=02%7C01%7Croman.fleysher%40einsteinmed.org%7Cc0d8f01f3d12431b2d6f08d80bb6eccc%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637272227987921433&sdata=hHqlv%2B%2FyqadWq%2BPBuGhsvbpQlc%2FBTE7nsiBUowR1jJk%3D&reserved=0.1 existed it would help me). I hope you can help.
The symptom is that I run:
recon-all -s FOLDER_1 -hemi lh -white -smooth2 -inflate2 -sphere -surfreg -cortparc -pial -sd FOLDER_2
Notice strange combination: -s FOLDER_1 -sd FOLDER_2 . Data is actually in FOLDER_2 where specific subject is set up in the environmental variable. The error message in recon-all.log is:
mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm
smoothing for 3 iterations setting seed for random number generator to 1234 error: No such file or directory error: MRISread(../surf/lh.white.preaparc): could not open file error: No such file or directory error: mris_smooth: could not read surface file ../surf/lh.white.preaparc
Indeed, file ../surf/lh.white.preaparc does not exist. It seems to indicate that -white was not actually executed before -smooth2. This command worked on version 6.0. Is this a bug in recon-all script version 7.1? Is this expected?
Previous successful command on the same data was:
recon-all -s FOLDER_1 -hemi lh -fix -sd FOLDER_2
General info:
1) FreeSurfer version: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b 2) Platform: likely CentOS, not sure how to tell 3) uname -a: Linux loginnode4 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: not attached because folder structure contains sensitive information that is hard to remove.
Thank you,
Roman
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