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" ayendiki@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@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" ayendiki@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@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" ayendiki@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@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" ayendiki@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@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
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Anastasia Yendiki