It will, unless it doesn't find the anatomical segmentation of the subject ($SUBJECTS_DIR/$subj/mri/aparc+aseg.mgz).
On Fri, 22 Mar 2013, Jon Wieser wrote: > I ran the flirt command on command line and got the same error. > I noticed that the freesurfer/dlabel directory did not have an anatorig > directory in it. > I created this "anatorig" directory in the freesurfer/dlabel directory and > ran the flirt command again. > it ran ok. > > it created the /freesurfer/dlabel/anatorig/lowb_brain_mask.flt > > Is Trac-all supposed to create the freesurfer/dlabel/anatorig directory? > > > I will try running trac-all again > Jon > > > ----- Original Message ----- > From: "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu> > To: "Jon Wieser" <wie...@uwm.edu> > Cc: freesurfer@nmr.mgh.harvard.edu > Sent: Friday, March 22, 2013 2:23:10 PM > Subject: Re: [Freesurfer] trac-all -prep exited with errors > > > Can you run the flirt command that gives the error directly on the command > line? > > On Fri, 22 Mar 2013, Jon Wieser wrote: > >> Hi Anastasia, >> we have plenty of disk space, 386 GB >> the file does not exist >> >> freesurfer/dlabel/anatorig/lowb_brain_mask.flt.nii.gz >> >> the entire freesurfer directory has read,write, and executable permission >> >> Jon >> >> >> ----- Original Message ----- >> From: "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu> >> To: "Jon Wieser" <wie...@uwm.edu> >> Cc: freesurfer@nmr.mgh.harvard.edu >> Sent: Friday, March 22, 2013 1:06:22 PM >> Subject: Re: [Freesurfer] trac-all -prep exited with errors >> >> >> Hi Jon - The error says that it can't open a file *for writing*. Any >> chance it's a disk space issue or, if the file already exists, a >> permission issue? >> >> a.y >> >> On Fri, 22 Mar 2013, Jon Wieser wrote: >> >>> HI Ansatasia >>> I have attached the trac-all.log >>> Jon >>> >>> ----- Original Message ----- >>> From: "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu> >>> To: "Jon Wieser" <wie...@uwm.edu> >>> Cc: "freesurfer" <freesurfer@nmr.mgh.harvard.edu> >>> Sent: Friday, March 22, 2013 11:49:35 AM >>> Subject: Re: [Freesurfer] trac-all -prep exited with errors >>> >>> >>> Hi Jon - Can you please send all of trac-all.log? Sometimes there are >>> hints earlier than where the error actually occurs. >>> >>> Thanks, >>> a.y >>> >>> On Fri, 22 Mar 2013, Jon Wieser wrote: >>> >>>> Hi >>>> I ran trac-all -prep -c dmrirc_single_subject >>>> and got the following error: >>>> >>>> here's the end of the output from trac-all: >>>> >>>> >>>> RegMat --------------------------- >>>> 1.000 -0.016 -0.000 4.210; >>>> 0.000 -0.005 1.000 2.417; >>>> -0.016 -1.000 -0.005 0.018; >>>> 0.000 0.000 0.000 1.000; >>>> FSLOUTPUTTYPE NIFTI_GZ >>>> tkreg2FSL: mov det = -64, ref det = -1 >>>> Cleaning up >>>> >>>> Started at Fri Mar 22 11:35:44 CDT 2013 >>>> Ended at Fri Mar 22 11:38:10 CDT 2013 >>>> BBR-Run-Time-Sec 146 >>>> >>>> bbregister Done >>>> To check results, run: >>>> tkregister2 --mov >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/dwi.nii.gz >>>> --reg >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2diff.bbr.dat >>>> --surf >>>> >>>> convert_xfm -omat >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2diff.bbr.mat >>>> -inverse >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anatorig.bbr.mat >>>> convert_xfm -omat >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2diff.bbr.mat >>>> -concat >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2diff.bbr.mat >>>> >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2anatorig.mat >>>> convert_xfm -omat >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anat.bbr.mat >>>> -inverse >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2diff.bbr.mat >>>> #------------------------------------- >>>> #@# Inter-subject registration Fri Mar 22 11:38:10 CDT 2013 >>>> flirt -in >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/brain_anat.nii.gz >>>> -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/brain_anat_mni.nii.gz >>>> -omat >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat >>>> -cost mutualinfo >>>> >>>> convert_xfm -omat >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/mni2anat.mat >>>> -inverse >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat >>>> convert_xfm -omat >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.flt.mat >>>> -concat >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat >>>> >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anat.flt.mat >>>> convert_xfm -omat >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/mni2diff.flt.mat >>>> -inverse >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.flt.mat >>>> convert_xfm -omat >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.bbr.mat >>>> -concat >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat >>>> >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anat.bbr.mat >>>> convert_xfm -omat >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/mni2diff.bbr.mat >>>> -inverse >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.bbr.mat >>>> convert_xfm -omat >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2mni.mat >>>> -concat >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat >>>> >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2anat.mat >>>> convert_xfm -omat >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/mni2anatorig.mat >>>> -inverse >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2mni.mat >>>> #------------------------------------- >>>> #@# Masks Fri Mar 22 11:41:27 CDT 2013 >>>> flirt -in >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/diff/lowb_brain_mask.nii.gz >>>> -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/mni/lowb_brain_mask.flt.nii.gz >>>> -applyxfm -init >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.flt.mat >>>> -interp nearestneighbour >>>> flirt -in >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/diff/lowb_brain_mask.nii.gz >>>> -ref >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/brain_anat_orig.nii.gz >>>> -out >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/anatorig/lowb_brain_mask.flt.nii.gz >>>> -applyxfm -init >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anatorig.flt.mat >>>> -interp nearestneighbour >>>> Error: failed to open file >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/anatorig/lowb_brain_mask.flt.nii.gz >>>> ERROR: Could not open image >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/anatorig/lowb_brain_mask.flt >>>> Image Exception : #23 :: Failed to open volume >>>> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/anatorig/lowb_brain_mask.flt >>>> for writing >>>> terminate called after throwing an instance of 'RBD_COMMON::BaseException' >>>> Abort >>>> Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 >>>> 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 >>>> >>>> trac-preproc exited with ERRORS at Fri Mar 22 11:41:39 CDT 2013 >>>> >>>> >>>> >>>> >>> >>> >>> 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
