Re: [Freesurfer] Errors with recon-all -autorecon2
Linda, You might want to check if the disk is full or not by using df command. Gen On Nov 19, 2011, at 12:13 AM, Linda Zhang wrote: Hi, I'd been having trouble with recon-all -all -subjid [mysubject], so I broke it down with -autorecon1 and -autorecon2. -autorecon1 worked fine, it seems that the problem is somewhere in -autorecon2. I've included the system information below, as well as the error message I got, and the recon-all log. I've tried this with another subject as well and the same error occurs. It'd be great if someone could tell me what the problem is and how I can fix it. - FREESURFER_HOME: /home/virtualuser/freesurfer Build stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 Debian version: squeeze/sid Kernel info: Linux 2.6.31-23-generic i686 - The command line: FreeSurfer:~/freesurfer/subjects recon-all -subjid avo0260 -autorecon2 The error message: GCAMwrite(transforms/talairach.m3z): gzip encountered error. writing output transformation to transforms/talairach.m3z... GCAMwrite GCAMwrite:: m3z loop GCAMwrite:: the command is: gzip -f -c transforms/talairach.m3z GCAMwrite:: the popen error code is: 12 mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed ERROR: mri_ca_register with non-zero status 252 but continuing despite the error #-- #@# CA Reg Inv Fri Nov 18 11:23:25 EST 2011 /home/virtualuser/freesurfer/subjects/avo0260/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux recon-all -s avo0260 exited with ERRORS at Fri Nov 18 11:23:26 EST 2011 The recon-all.log and recon-all.error files are attached. Thanks for your time and help! Regards, Linda Zhang University of Hong Kong recon-all.logrecon-all.error___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] when to invoke reg-feat2anat in fsl ppi
Dear Freesurfers, I am using seeds based on Freesurfer masks to run a PPI analysis and am wondering if I am using reg-feat2anat at the right fsl feat registration step. First, I ran an fsl analysis to generate a feat directory. Then I ran reg-feat2anat using that feat directory. Next I ran aseg2feat and fslmaths to generate binary masks Next I extracted the timeseries by using the filtered func of the feat and the binary masks from aseg2feat. So now I want to do another feat analysis, but this time using the extracted timeseries But this timeseries is based on the first feat and associated masks from the reg-feat2anat registration. 1) Is it still valid to use this timeseries in this new feat since FSL will be running another registration? 2) Do I have to run reg-feat2anat again? Thanks. Michelle ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] gcut memory requirements
Hello, Approximately how much memory does one need when using the -gcut option with FS 5.1? I had submitted 30+ recons to a cluster that alloted a default of 2.5 GB for processes submitted under this particular queue, and all of them aborted with a bad_alloc error at the gcut stage of skull stripping. Should 4 GB be sufficient? thanks, -MH -- Michael Harms, Ph.D. Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6604 Tel: 314-747-6173 660 South Euclid Ave.Fax: 314-747-2182 St. Louis, MO 63110 Email: mha...@wustl.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] gcut memory requirements
Hi Michael, I had the same issue a few months ago. In my experience 4GB was sufficient. If there are constraints on the memory, I think 3 GB should also work. I also had the same issue with -gcut and FS 5.0. Back then I had tried to figure out what was the minimum memory required since I had some memory constraints. I was running jobs on cluster where each node had 16 cores and 32 GB total memory (that could be divided between the 16 cores). At most I was able to run 12 recons on each node. So the minimum memory required was ~ 2.7 GB (32 GB/12). Mehul On Sat, Nov 19, 2011 at 12:46 PM, Michael Harms mha...@conte.wustl.eduwrote: Hello, Approximately how much memory does one need when using the -gcut option with FS 5.1? I had submitted 30+ recons to a cluster that alloted a default of 2.5 GB for processes submitted under this particular queue, and all of them aborted with a bad_alloc error at the gcut stage of skull stripping. Should 4 GB be sufficient? thanks, -MH -- Michael Harms, Ph.D. Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6604 Tel: 314-747-6173 660 South Euclid Ave.Fax: 314-747-2182 St. Louis, MO 63110 Email: mha...@wustl.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
