External Email - Use Caution
I ran freesurfer 7.1 with the following options:-
-i ./study/T1_SAG/IM-0001-0001.dcm -FLAIR ./study/SAG_3D_FLAIR/IM-0001-0001.dcm -s TEST_050620 -3T -mprage -FLAIRpial -hires -parallel -all
The job failed, the logfile recon-all_hires.log is attached. I then reran the job with the same datasets but exchanged -hires with -conf2hires and used the subject ID TEST_050620c and the job completed successfully (the logfile for this job, recon-all_conf2hires.log, is also attached). Any idea what the problem is when using the -hires option?
Thanks
Richard
I don't know what is wrong. Can you upload the hires run? Instructions below
From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file.
On 5/21/2020 9:35 AM, Jones, Richard wrote:
External Email - Use Caution
I ran freesurfer 7.1 with the following options:-
-i ./study/T1_SAG/IM-0001-0001.dcm -FLAIR ./study/SAG_3D_FLAIR/IM-0001-0001.dcm -s TEST_050620 -3T –mprage –FLAIRpial –hires –parallel –all
The job failed, the logfile recon-all_hires.log is attached. I then reran the job with the same datasets but exchanged –hires with –conf2hires and used the subject ID TEST_050620c and the job completed successfully (the logfile for this job, recon-all_conf2hires.log, is also attached). Any idea what the problem is when using the –hires option?
Thanks
*Richard*
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Richard, the conclusion among us is that you have run out of memory. I'm not sure how much you will need, but with both hires and FLAIR, it will be a lot
On 5/21/2020 9:35 AM, Jones, Richard wrote:
External Email - Use Caution
I ran freesurfer 7.1 with the following options:-
-i ./study/T1_SAG/IM-0001-0001.dcm -FLAIR ./study/SAG_3D_FLAIR/IM-0001-0001.dcm -s TEST_050620 -3T –mprage –FLAIRpial –hires –parallel –all
The job failed, the logfile recon-all_hires.log is attached. I then reran the job with the same datasets but exchanged –hires with –conf2hires and used the subject ID TEST_050620c and the job completed successfully (the logfile for this job, recon-all_conf2hires.log, is also attached). Any idea what the problem is when using the –hires option?
Thanks
*Richard*
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Jones, Richard