Hi Jon - You will have to email the list with specifics about your recon-all problem, including recon-all.log. I can't guess what the problem is with no other information. I recommend starting a different email thread about it.
a.y On Fri, 22 Mar 2013, Jon Wieser wrote: > > there is not a aparc+aseg.mgz file in the freesurfer/mri directory. > strange. I ran recon-all autorecon1, autorecon2, and autorecon3 successfully > and check the results. > they looked ok > 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 4:19:57 PM > Subject: Re: [Freesurfer] trac-all -prep exited with errors > > > 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
