Freesurfer March 2013

freesurfer@nmr.mgh.harvard.edu

155 participants
331 discussions

Re: [Freesurfer] Two questions regarding mri_fill and mris_fix_topology
by Bruce Fischl 23 Mar '13

23 Mar '13

Hi Falk have you tracked down the source of the defect in the wm.mgz? Sometimes very minor edits can correct even major defects. If you are having trouble with this feel free to upload the dataset and one of us will take a look Bruce On Sat, 23 Mar 2013, falk.luese(a)gmx.net wrote: > Hi Bruce, > > well, there is an option called -correct_defect within > mris_fix_topology, which is meant to correct just one defect at a time. > However, after the defect is corrected one is getting a message like: > > ?TERMINATING AFTER CORRECTED DEFECT > > no such file or directory? > > I haven?t been able to figure out how to save this or if this is even > possible. Maybe I am missing the correct flag to do so. May it otherwise be > possible to remove certain defects from ?h.defect_labels or something > similar? > > The errors of the filled.mgz result in a faulty surface > reconstruction of ?h.orig.nofix and every following surface like ?h.white > and ?.pial in that area. Therefore I wanted to remove these in before and, > if possible, automatically. > > Best, > Falk > > Von: Bruce Fischl > Gesendet: ?22?. ?März? ?2013 ?19?:?14 > An: ""Falk Lüsebrink"" <falk.luese(a)gmx.net> > Cc: FreeSurfer > Betreff: Re: [Freesurfer] Two questions regarding mri_fill and > mris_fix_topology > > Hi Falk > > I don't think it's possible to fix just one defect, unless Florent > included some option that I am not aware of. > > I also wouldn't worry too much about the filled.mgz. Make sure that the > aseg.mgz and the ?h.white and ?h.pial are accurate > cheers > Bruce > On Fri, 22 Mar 2013, > "Falk Lüsebrink" wrote: > > > Dear FreeSurfers, > > > > I am processing some T1-weighted images of the human brain with an > isotropic resolution of .5 mm using version 5.1. > > > > After mri_fill my hemispheres are separated nicely and the cerebellum is > completely removed. However, looking at the filled.mgz, posterior and > > superior of the corpus callosum some residual of white matter can be found > in the longitudinal fissure. It does not remain if I look at the > > conformed data, altough these leftovers are found in the wm.mgz of both > datasets. As this does not happen using conformed data I assume that the > > cutting plane is not "broad" enough in case of higher resolution data or > something related. Is there some way to tweak this? > > > > Secondly, I currently skip the -fix stage of recon-all completely while > processing this data, but I would like to correct at least some of its > > defects. I already I have seen in the help of mris_fix_topology that it is > possible to fix just one defect and I extracted the defects and their > > number of vertices using the defect-seg script. Is it possible to save the > resulting surface, so I am able to correct the defects I want > > to consecutively? > > > > Best, > > Falk > > > > > >

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Two questions regarding mri_fill and mris_fix_topology
by "Falk Lüsebrink" 23 Mar '13

23 Mar '13

3 2

Re: [Freesurfer] trac-all -prep exited with errors
by Anastasia Yendiki 22 Mar '13

22 Mar '13

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(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu> > Cc: freesurfer(a)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(a)nmr.mgh.harvard.edu> >> To: "Jon Wieser" <wieser(a)uwm.edu> >> Cc: freesurfer(a)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(a)nmr.mgh.harvard.edu> >>> To: "Jon Wieser" <wieser(a)uwm.edu> >>> Cc: freesurfer(a)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(a)nmr.mgh.harvard.edu> >>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>> Cc: "freesurfer" <freesurfer(a)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. >>>> >>>> >>>> >>> >>> >> >> > >

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Re: [Freesurfer] trac-all -prep exited with errors
by Anastasia Yendiki 22 Mar '13

22 Mar '13

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(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu> > Cc: freesurfer(a)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(a)nmr.mgh.harvard.edu> >> To: "Jon Wieser" <wieser(a)uwm.edu> >> Cc: freesurfer(a)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(a)nmr.mgh.harvard.edu> >>> To: "Jon Wieser" <wieser(a)uwm.edu> >>> Cc: "freesurfer" <freesurfer(a)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. >>> >>> >>> >> >> > >

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hippo subfield
by stdp82＠virgilio.it 22 Mar '13

22 Mar '13

I'm running: recon-all -s Diff02 -hippo-subfields with the following error. Thanks. Stefano Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova/Diff02Actual FREESURFER_HOME /Applications/freesurfer-rw-rw-r-- 1 Stefano wheel 499999 Mar 22 16:53 /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.logDarwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64#--------------------------------------------#@# Hippocampal Subfields processing Fri Mar 22 16:56:31 CET 2013\n mkdir -p /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults\n kvlSegmentHippocampalSubfields.sh Diff02 left /Applications/freesurfer/subjects/subject_prova/Diff02 /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults \nDoing left sidemeshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gzcompressionLookupTableFileName: /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txtboundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgzsubjectName: Diff02side: leftinputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02outputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResultsdirectory /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02 already existsdirectory /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left already existscd /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/leftcp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/nu.mgz .cp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/aseg.mgz .cp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/transforms/talairach.xfm .cp /Applications/freesurfer/data/GEMS/imageDump.mgz .kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939dyld: Library not loaded: libITKCommon.3.16.dylib Referenced from: /Applications/freesurfer/bin/kvlApplyTransform Reason: image not found/Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 77530 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939failed to do kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 recon-all -s Diff02 exited with ERRORS at Fri Mar 22 16:56:31 CET 2013 For more details, see the log file /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.logTo report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Re: [Freesurfer] trac-all -prep exited with errors
by Anastasia Yendiki 22 Mar '13

22 Mar '13

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(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu> > Cc: freesurfer(a)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(a)nmr.mgh.harvard.edu> >> To: "Jon Wieser" <wieser(a)uwm.edu> >> Cc: "freesurfer" <freesurfer(a)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. >> >> >> > >

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R: Re: R: Re: R: Re: hippo subfield
by stdp82＠virgilio.it 22 Mar '13

22 Mar '13

[iMac-di-Stefano:freesurfer/subjects] Stefano% otool -L kvlApplyTransformotool: Command not found. ----Messaggio originale---- Da: zkaufman(a)nmr.mgh.harvard.edu Data: 22-mar-2013 18.43 A: <stdp82(a)virgilio.it> Cc: <iglesias(a)nmr.mgh.harvard.edu>, <koen(a)nmr.mgh.harvard.edu>, <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: hippo subfield He's on a Mac, so the command would be: otool -L kvlApplyTransform and the output will be: kvlApplyTransform: libITKCommon.3.16.dylib (compatibility version 3.16.0, current version 3.16.0) libITKIO.3.16.dylib (compatibility version 3.16.0, current version 3.16.0) libITKznz.3.16.dylib (compatibility version 3.16.0, current version 3.16.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.5) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 159.1.0) /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 52.0.0) which is a little odd. Stefano, I will get back to you while I debug the issue. -Zeke On 03/22/2013 02:39 PM, stdp82(a)virgilio.it wrote: > From command line I obtain: > > Stefano% ldd kvlApplyTransform > ldd: Command not found. > > I do not know is useful, but I have done this analysis with the previous > version with any problem. > > > Stefano > > > ----Messaggio originale---- > Da: iglesias(a)nmr.mgh.harvard.edu > Data: 22-mar-2013 19.19 > A: <stdp82(a)virgilio.it> > Cc: <koen(a)nmr.mgh.harvard.edu>, <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] R: Re: hippo subfield > > Hi Stefano, > >From the command line, type: > ldd kvlApplyTransform > and send us the output that you get. > Cheers, > /Eugenio > > > On Fri, 2013-03-22 at 18:44 +0100, stdp82(a)virgilio.it wrote: > > I'm sorry but, what's meaning "ldd kvlApplyTransform"? What's I should > > do more simply? > > > > > > Stefano > > > > > > > > > > > > ----Messaggio originale---- > > Da: koen(a)nmr.mgh.harvard.edu > > Data: 22-mar-2013 18.22 > > A: <stdp82(a)virgilio.it> > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > Ogg: Re: [Freesurfer] hippo subfield > > > > Hi Stefano, > > > > Can you do "ldd kvlApplyTransform" and send us the result? > > > > Koen > > > > On 3/22/13, stdp82(a)virgilio.it <stdp82(a)virgilio.it Hippocampal > > Subfields > > > processing Fri Mar 22 16:56:31 CET 2013\n mkdir -p > > > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults\n > > > kvlSegmentHippocampalSubfields.sh Diff02 left > > > /Applications/freesurfer/subjects/subject_prova/Diff02 > > > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults > > > \nDoing left sidemeshFileName: > > > > /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gzcompressionLookupTableFileName: > > > > /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txtboundingBoxFileName: > > > /Applications/freesurfer/data/GEMS/imageDump.mgzsubjectName: > > Diff02side: > > > leftinputDirectory: > > > /Applications/freesurfer/subjects/subject_prova/Diff02outputDirectory: > > > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResultsdirectory > > > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02 > > > already existsdirectory > > > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left > > > already existscd > > > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/leftcp > > > > > -f > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/nu.mgz > > > .cp -f > > > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/aseg.mgz > > > .cp -f > > > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/transforms/talairach.xfm > > > .cp /Applications/freesurfer/data/GEMS/imageDump.mgz .kvlApplyTransform > > > imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 > > 2.6560 > > > 0.0255 0.0094 0.9996 -3.1939dyld: Library not loaded: > > > libITKCommon.3.16.dylib Referenced from: > > > /Applications/freesurfer/bin/kvlApplyTransform Reason: image not > > > found/Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: > > line > > > 18: 77530 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz > > -0.9991 > > > -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 > > 0.9996 > > > -3.1939failed to do kvlApplyTransform imageDump.mgz > > > -0.9991 -0.0328 0.0258 144.0010 > > > -0.0330 0.9994 -0.0086 2.6560 > > 0.0255 > > > 0.0094 0.9996 -3.1939Darwin iMac-di-Stefano.local 12.3.0 > > Darwin > > > Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; > > > root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 > > > recon-all -s Diff02 exited with ERRORS at Fri Mar 22 16:56:31 CET > > 2013 > > > For more details, see the log file > > > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.logTo > > > report a problem, see > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)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. 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(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > ------------------------------------------------------------------------------------- > Juan Eugenio Iglesias, PhD > http://www.jeiglesias.com > iglesias(a)nmr.mgh.harvard.edu > Athinoula A. Martinos Center for Biomedical Imaging > Department of Radiology, MGH, Harvard Medical School > 149 Thirteenth Street, Suite 2301 > Charlestown, Massachusetts 2129 > U.S.A. > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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R: Re: R: Re: R: Re: hippo subfield
by stdp82＠virgilio.it 22 Mar '13

22 Mar '13

otool: Command not found. ----Messaggio originale---- Da: zkaufman(a)nmr.mgh.harvard.edu Data: 22-mar-2013 18.43 A: <stdp82(a)virgilio.it> Cc: <iglesias(a)nmr.mgh.harvard.edu>, <koen(a)nmr.mgh.harvard.edu>, <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: hippo subfield He's on a Mac, so the command would be: otool -L kvlApplyTransform and the output will be: kvlApplyTransform: libITKCommon.3.16.dylib (compatibility version 3.16.0, current version 3.16.0) libITKIO.3.16.dylib (compatibility version 3.16.0, current version 3.16.0) libITKznz.3.16.dylib (compatibility version 3.16.0, current version 3.16.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.5) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 159.1.0) /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 52.0.0) which is a little odd. Stefano, I will get back to you while I debug the issue. -Zeke On 03/22/2013 02:39 PM, stdp82(a)virgilio.it wrote: > From command line I obtain: > > Stefano% ldd kvlApplyTransform > ldd: Command not found. > > I do not know is useful, but I have done this analysis with the previous > version with any problem. > > > Stefano > > > ----Messaggio originale---- > Da: iglesias(a)nmr.mgh.harvard.edu > Data: 22-mar-2013 19.19 > A: <stdp82(a)virgilio.it> > Cc: <koen(a)nmr.mgh.harvard.edu>, <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] R: Re: hippo subfield > > Hi Stefano, > >From the command line, type: > ldd kvlApplyTransform > and send us the output that you get. > Cheers, > /Eugenio > > > On Fri, 2013-03-22 at 18:44 +0100, stdp82(a)virgilio.it wrote: > > I'm sorry but, what's meaning "ldd kvlApplyTransform"? What's I should > > do more simply? > > > > > > Stefano > > > > > > > > > > > > ----Messaggio originale---- > > Da: koen(a)nmr.mgh.harvard.edu > > Data: 22-mar-2013 18.22 > > A: <stdp82(a)virgilio.it> > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > Ogg: Re: [Freesurfer] hippo subfield > > > > Hi Stefano, > > > > Can you do "ldd kvlApplyTransform" and send us the result? > > > > Koen > > > > On 3/22/13, stdp82(a)virgilio.it <stdp82(a)virgilio.it Hippocampal > > Subfields > > > processing Fri Mar 22 16:56:31 CET 2013\n mkdir -p > > > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults\n > > > kvlSegmentHippocampalSubfields.sh Diff02 left > > > /Applications/freesurfer/subjects/subject_prova/Diff02 > > > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults > > > \nDoing left sidemeshFileName: > > > > /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gzcompressionLookupTableFileName: > > > > /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txtboundingBoxFileName: > > > /Applications/freesurfer/data/GEMS/imageDump.mgzsubjectName: > > Diff02side: > > > leftinputDirectory: > > > /Applications/freesurfer/subjects/subject_prova/Diff02outputDirectory: > > > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResultsdirectory > > > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02 > > > already existsdirectory > > > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left > > > already existscd > > > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/leftcp > > > > > -f > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/nu.mgz > > > .cp -f > > > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/aseg.mgz > > > .cp -f > > > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/transforms/talairach.xfm > > > .cp /Applications/freesurfer/data/GEMS/imageDump.mgz .kvlApplyTransform > > > imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 > > 2.6560 > > > 0.0255 0.0094 0.9996 -3.1939dyld: Library not loaded: > > > libITKCommon.3.16.dylib Referenced from: > > > /Applications/freesurfer/bin/kvlApplyTransform Reason: image not > > > found/Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: > > line > > > 18: 77530 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz > > -0.9991 > > > -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 > > 0.9996 > > > -3.1939failed to do kvlApplyTransform imageDump.mgz > > > -0.9991 -0.0328 0.0258 144.0010 > > > -0.0330 0.9994 -0.0086 2.6560 > > 0.0255 > > > 0.0094 0.9996 -3.1939Darwin iMac-di-Stefano.local 12.3.0 > > Darwin > > > Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; > > > root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 > > > recon-all -s Diff02 exited with ERRORS at Fri Mar 22 16:56:31 CET > > 2013 > > > For more details, see the log file > > > > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.logTo > > > report a problem, see > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)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. 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(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > ------------------------------------------------------------------------------------- > Juan Eugenio Iglesias, PhD > http://www.jeiglesias.com > iglesias(a)nmr.mgh.harvard.edu > Athinoula A. Martinos Center for Biomedical Imaging > Department of Radiology, MGH, Harvard Medical School > 149 Thirteenth Street, Suite 2301 > Charlestown, Massachusetts 2129 > U.S.A. > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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R: Re: hippo subfield
by stdp82＠virgilio.it 22 Mar '13

22 Mar '13

I'm sorry but, what's meaning "ldd kvlApplyTransform"? What's I should do more simply? Stefano ----Messaggio originale---- Da: koen(a)nmr.mgh.harvard.edu Data: 22-mar-2013 18.22 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] hippo subfield Hi Stefano, Can you do "ldd kvlApplyTransform" and send us the result? Koen On 3/22/13, stdp82(a)virgilio.it <stdp82(a)virgilio.it Hippocampal Subfields > processing Fri Mar 22 16:56:31 CET 2013\n mkdir -p > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults\n > kvlSegmentHippocampalSubfields.sh Diff02 left > /Applications/freesurfer/subjects/subject_prova/Diff02 > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults > \nDoing left sidemeshFileName: > /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gzcompressionLookupTableFileName: > /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txtboundingBoxFileName: > /Applications/freesurfer/data/GEMS/imageDump.mgzsubjectName: Diff02side: > leftinputDirectory: > /Applications/freesurfer/subjects/subject_prova/Diff02outputDirectory: > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResultsdirectory > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02 > already existsdirectory > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left > already existscd > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/leftcp > -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/nu.mgz > .cp -f > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/aseg.mgz > .cp -f > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/transforms/talairach.xfm > .cp /Applications/freesurfer/data/GEMS/imageDump.mgz .kvlApplyTransform > imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 > 0.0255 0.0094 0.9996 -3.1939dyld: Library not loaded: > libITKCommon.3.16.dylib Referenced from: > /Applications/freesurfer/bin/kvlApplyTransform Reason: image not > found/Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line > 18: 77530 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 > -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 > -3.1939failed to do kvlApplyTransform imageDump.mgz > -0.9991 -0.0328 0.0258 144.0010 > -0.0330 0.9994 -0.0086 2.6560 0.0255 > 0.0094 0.9996 -3.1939Darwin iMac-di-Stefano.local 12.3.0 Darwin > Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; > root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 > recon-all -s Diff02 exited with ERRORS at Fri Mar 22 16:56:31 CET 2013 > For more details, see the log file > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.logTo > report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ Freesurfer mailing list Freesurfer(a)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. 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.

2 1

Re: [Freesurfer] trac-all -prep exited with errors
by Anastasia Yendiki 22 Mar '13

22 Mar '13

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(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu> > Cc: "freesurfer" <freesurfer(a)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. > > >

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Freesurfer March 2013