Should I re-run the recon-all after running the last command from recon-all.cmd?
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Thu, Apr 5, 2018 at 12:31 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Srishti > > if you look in the subject's scripts dir there should be a file named > "recon-all.cmd". Try rerunning the last command in it (probably from the > mri dir) > > > cheers > Bruce > On Thu, 5 Apr 2018, srishti goel wrote: > > I am sorry, I am not sure what do you mean by running the command line >> directly? >> I use the following command: >> >> sbatch --mem 2200 -t 6-00:00 --mail-type END --mail-user >> srish...@email.unc.edu --wrap "export >> SUBJECTS_DIR=/proj/hng/sheridanlab/freeSurfer/DukeYAS/Freesurfer_out/; >> recon-all -s 13166 -autorecon2-cp -autorecon3 -nowmsa" >> >> >> where sbatch..... until export is our local server submission command and >> I run this command from the command line itself, not >> using any script. >> >> >> Best, >> Srishti >> Social/Clinical Research Specialist >> Child Imaging Research and Life Experiences Lab >> University of North Carolina at Chapel Hill >> email (W): srish...@email.unc.edu >> skype: srishti.goel12 >> >> >> On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> wrote: >> if you run the command that failed again on the command line >> directly (that is, not in recon-all) does it fail >> again? >> >> On Thu, 5 Apr 2018, srishti goel wrote: >> >> Hi Bruce, >> >> The machine definitely hasn't run out of memory. Here is the >> memory usage >> from recon-all.log >> >> total used free >> >> shared buff/cache available >> Mem: 263726968 34330048 152102696 12944 >> 77294224 >> 191963372 >> Swap: 2097148 0 2097148 >> >> >> >> >> Best, >> Srishti >> Social/Clinical Research Specialist >> Child Imaging Research and Life Experiences Lab >> University of North Carolina at Chapel Hill >> email (W): srish...@email.unc.edu >> skype: srishti.goel12 >> >> >> On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Srishti >> >> are you sure that your machine didn't just run out of >> memory? >> The recon-all.log file includes the amount of free (and >> total) >> memory at the time the process was started. >> >> cheers >> Bruce >> >> On Thu, 5 Apr 2018, srishti goel wrote: >> >> Hi, >> I have been trying to edit structural brains and >> very few times I would get the following error >> while >> running recon-all -s >> subjID >> >> white matter peak found at 110 >> cannot allocate memory >> >> Upon looking at the archive, there was only one >> similar issue and it was recommend to check >> mri_info >> as the brain mask might >> have been corrupted. I did that and here is the >> output: >> >> Volume information for brainmask.mgz >> >> type: MGH >> >> dimensions: 256 x 256 x 256 >> >> voxel sizes: 1.000000, 1.000000, 1.000000 >> >> type: UCHAR (0) >> >> fov: 256.000 >> >> dof: 0 >> >> xstart: -128.0, xend: 128.0 >> >> ystart: -128.0, yend: 128.0 >> >> zstart: -128.0, zend: 128.0 >> >> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 >> msec, flip angle: 0.00 degrees >> >> nframes: 1 >> >> PhEncDir: UNKNOWN >> >> FieldStrength: 0.000000 >> >> ras xform present >> >> xform info: x_r = -1.0000, y_r = 0.0000, >> z_r >> = 0.0000, c_r = -1.0000 >> >> : x_a = 0.0000, y_a = 0.0000, >> z_a >> = 1.0000, c_a = 37.5000 >> >> : x_s = 0.0000, y_s = -1.0000, >> z_s >> = 0.0000, c_s = 4.7185 >> >> >> talairach xfm :/pine/scr/s/r/srishtig/Duke_T >> est/Freesurfer_out/11039/mri/transforms/talair >> ach.xfm >> >> Orientation : LIA >> >> Primary Slice Direction: coronal >> >> >> voxel to ras transform: >> >> -1.0000 0.0000 0.0000 >> 127.0000 >> >> 0.0000 0.0000 1.0000 >> -90.5000 >> >> 0.0000 -1.0000 0.0000 >> 132.7185 >> >> 0.0000 0.0000 0.0000 >> 1.0000 >> >> >> voxel-to-ras determinant -1 >> >> >> ras to voxel transform: >> >> -1.0000 -0.0000 -0.0000 >> 127.0000 >> >> -0.0000 -0.0000 -1.0000 >> 132.7185 >> >> -0.0000 1.0000 -0.0000 >> 90.5000 >> >> -0.0000 -0.0000 -0.0000 >> 1.0000 >> >> >> Is there any other way to resolve this issue than >> reconstruction the brain again and doing all the >> edits all over again hoping >> that the brain mask does not get corrupted this >> time? >> >> Appreciate any help with this. >> >> Best, >> Srishti >> >> >> _______________________________________________ >> 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. 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