Hi Andrew, hi Bruce, thanks for the tip! Unfortunately, the dev version of mri_normalize did not work (resulted in the same error log) but simply manually checking the control points in the respective cross runs and deleting the ones outside the brain before rerunning worked!
Best, Anna 2018-04-11 23:22 GMT+02:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > p.s. you probably want to grab a new freeview also, as it lets you jump to > the voxel coords of each control point so you can see them > > On Wed, 11 Apr 2018, Hoopes, Andrew wrote: > > >> Hi Anna, >> >> >> >> You can download the new mri_normalize from this link - >> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_ >> binaries/centos6_x86_64/mri_normalize >> >> >> >> To get it into your FS installation, first set executable permissions and >> then move it into your >> $FREESURFER_HOME/bin directory (sudo might be required): >> >> >> >> chmod +x /path/to/downloaded/mri_normalize >> >> mv /path/to/downloaded/mri_normalize ${FREESURFER_HOME}/bin/ >> >> >> >> best >> >> Andrew >> >> >> >> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anna Daniels >> <anna.dani...@fu-berlin.de> >> Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu> >> Date: Monday, April 9, 2018 at 1:10 PM >> To: FS Help <freesurfer@nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] recon-all: exited with errors (white matter >> peak at 110, cannot allocate >> memory) >> >> >> >> Hi Bruce, >> >> thank you for the quick reply! >> >> Ubuntu 16.04 LTS 64-bit >> >> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c >> >> Please let me know how to incorporate the new version into the >> installation. >> >> Thank you very much and best, >> >> Anna >> >> >> >> Hi Anna >> >> no attachments :< >> >> Srishti's issue stemmed from control points outside of the head. The >> current (dev) version of mri_normalize detects and removes them. Can you >> grab a new version of mri_normalize and see if it fixes your problem? Let >> us know your hardware/software environment and we will get it to you >> >> cheers >> Bruce >> >> >> On Fri, 6 Apr 2018, Anna Daniels wrote: >> >> > Hi Bruce, hi Srishti, >> > >> > I have exactly the same problem with several subjects rerunning >> recon-all >> > and there was sufficient memory available. I also tried out the last >> command >> > directly which resulted in the same error log. >> > >> > ?mri_normalize -f/home/anna/FREESURFER/00_DAT >> A_MABT1T2/02a_MABT1T2_cross_edits_transfer/rrer >> > uncrosstest_cp17/22275_T1_fs_edit/tmp/control.dat -mprage -aseg >> > aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz >> > >> > Attached you can find the input file. >> > >> > Thank you and best, >> > Anna?[icon_10_generic_list.png] ?22275_T1_fs_edit.zip[IMAGE] >> >> >> >> > > 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. >
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