Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

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

1 0

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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R: Re: R: Re: R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts
by stdp82＠virgilio.it 22 Mar '13

22 Mar '13

Thank you Anastasia. I'm checking bvecs/bvals. I obtain it by DTI table creator (http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html) bvecs/bvals should be done. Gradients can be the unique responsable? Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 22-mar-2013 17.07 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts Your gradient table is wrong. See where I've marked the corpus callosum in your screenshot. The eigenvectors are not pointing along the corpus callosum, but perpendicular to it. So they're off by 90 degrees, which means the same is true about the vectors in your gradient table. On Fri, 22 Mar 2013, stdp82(a)virgilio.it wrote: > Hi Anastasia - I attacked the screenshots. > Thanks, > > > Stefano > > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 22-mar-2013 1.39 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts > > > Hi Stefano - There's nothing in these screenshots that tells you that the > eigenvectors are correct. These are vectors, so the way to check them is > to display them as lines. You display dtifit_V1 as lines, overlaid on > dtifit_FA. Then you see if the lines point in the right direction. > > a.y > > On Fri, 22 Mar 2013, stdp82(a)virgilio.it wrote: > > > Here they are attacked. > > Thanks, > > > > > > Stefano > > > > > > > > > > ----Messaggio originale---- > > Da: ayendiki(a)nmr.mgh.harvard.edu > > Data: 21-mar-2013 21.50 > > A: <stdp82(a)virgilio.it> > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > Ogg: Re: R: Re: [Freesurfer] R: R: Re: Problem with tracula: incomplete or > > lacking tracts > > > > > > Can you send a screenshot that shows dtifit_V1 and dtifit_FA? > > > > On Thu, 21 Mar 2013, stdp82(a)virgilio.it wrote: > > > > > I have checked the gradient directions. How can I resolve the brain mask > > > problem. > > > Can I send you my files of this subject? > > > Stefano > > > > > > > > > > > > ----Messaggio originale---- > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > Data: 20-mar-2013 22.46 > > > A: <stdp82(a)virgilio.it> > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > Ogg: Re: [Freesurfer] R: R: Re: Problem with tracula: incomplete or > > lacking > > > tracts > > > > > > > > > There are chunks of the brain missing from the brain mask. This may cause > > > some tracts to be incomplete or missing. > > > > > > But you should still check that the gradient directions are correct, so > > > you know if you have multiple problems or just one. The FA map can't tell > > > you if the gradient table was correct, you have to check the eigenvectors > > > in dtifit_V1 for that. > > > > > > > > > On Wed, 20 Mar 2013, stdp82(a)virgilio.it wrote: > > > > > > > File attacked > > > > > > > > ----Messaggio originale---- > > > > Da: stdp82(a)virgilio.it > > > > Data: 20-mar-2013 22.34 > > > > A: <ayendiki(a)nmr.mgh.harvard.edu> > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > Ogg: [Freesurfer] R: Re: Problem with tracula: incomplete or lacking > > > tracts > > > > > > > > Thank you Anastasia. I'm checking gradient table but I would like > > > underline that I'm noting some holes in > > > > dti_FA.nii.gz and not in dwi.nii.gz (I have attacked the relative > > > images). > > > > > > > > Stefano > > > > > > > > ----Messaggio originale---- > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > Data: 20-mar-2013 16.40 > > > > A: <stdp82(a)virgilio.it> > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > Ogg: Re: [Freesurfer] Problem with tracula: incomplete or lacking tracts > > > > > > > > > > > > Hi Stefano - Have you checked that your gradient table is correct by > > > > looking at the output of the tensor fit? > > > > > > > > a.y > > > > > > > > On Wed, 20 Mar 2013, stdp82(a)virgilio.it wrote: > > > > > > > > > Hi list and Anastasia, > > > > > if you remember the last week I had same problems with tracula output: > > > the final tract are lacking or > > > > > incomplete for same subjects. Some of these are less wrong (only > > forceps > > > major), other have more evident > > > > > error (you can see this in picture that I have attacked). > > > > > > > > > > To resolve this issue I have: > > > > > > > > > > 1-checked the correct overlap of dwi and dwi_mask > > > > > 2-rerun data with new version 5.2 > > > > > 3-rerun new registration using bbregister (fsl/spm option): for > > example, > > > in the subject of the picture > > > > > attacked, the .mincost file now contains as first value 0.87 (previous > > > it was 1.1) > > > > > > > > > > Please, give me an advise > > > > > > > > > > Thanks > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > > > > > > > > ----Messaggio originale---- > > > > > Da: stdp82(a)virgilio.it > > > > > Data: 12-mar-2013 17.47 > > > > > A: <ayendiki(a)nmr.mgh.harvard.edu> > > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > > Ogg: [Freesurfer] R: Re: R: Re: Question on tracula and dwi-T1 overlap > > > > > > > > > > I got it from mri directory but I'm understanding that this directory > > > isn't ok.I'm attacking the image > > > > > from dlabel/diff/aparc+aseg.bbr.nii > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > > > ----Messaggio originale---- > > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > > Data: 12-mar-2013 17.19 > > > > > A: <stdp82(a)virgilio.it> > > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > > Ogg: Re: [Freesurfer] R: Re: Question on tracula and dwi-T1 overlap > > > > > > > > > > > > > > > Can you please answer my question? I can't really tell if the issue is > > > due > > > > > poor dwi-aseg overlap unless you tell me where you got that aseg > > volume > > > > > from. > > > > > > > > > > On Tue, 12 Mar 2013, stdp82(a)virgilio.it wrote: > > > > > > > > > > > Thank you Anastasia. What do you think about the issue in the file > > > attacked > > > > > > (I'm noting that same subjects are lacking of same > > > > > > tracts or same tracts are incomplete) > > > > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > ----Messaggio originale---- > > > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > > > Data: 12-mar-2013 17.02 > > > > > > A: <stdp82(a)virgilio.it> > > > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > > > Ogg: Re: [Freesurfer] Question on tracula and dwi-T1 overlap > > > > > > > > > > > > > > > > > > Hi Stefano - Where did you get the aseg.nii.gz from? Anything that's > > > in > > > > > > the dlabel/diff/ directory has been mapped to the same space as the > > > DWI, > > > > > > so those are the volumes that can be compared directly to > > dwi.nii.gz. > > > > > > > > > > > > a.y > > > > > > > > > > > > On Tue, 12 Mar 2013, stdp82(a)virgilio.it wrote: > > > > > > > > > > > > > Hi list, > > > > > > > > > > > > > > I have two questions, please. > > > > > > > > > > > > > > I'm using version 5.1 to complete my analysis. > > > > > > > > > > > > > > 1- I have attacked two images from aseg.nii.gz and dwi.nii.gz of > > the > > > same > > > > > > > subject (figure 1 and 3). You can note the dwi do not overlap to > > the > > > aseg. > > > > > > > How can I resolve this issue? > > > > > > > > > > > > > > 2-After TRACULA analysis, I'm noting that same subjects are > > lacking > > > of > > > > > > same > > > > > > > tracts or same tracts are incomplete (figure 3). > > > > > > > > > > > > > > Could it depends from the issue in question 1? I'm thinking to > > rerun > > > all > > > > > > > using version 5.2 but before starting new analyses, I'd like to > > ask > > > you > > > > > > > which is the possible error. > > > > > > > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > >_______________________________________________ > > > > > > 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 > > > > > > > > > > > > > > > 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 > > > > > > > > > > > > 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 > > > > > > > > > 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 > > > 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 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: hippo subfield
by stdp82＠virgilio.it 22 Mar '13

22 Mar '13

>From command line I obtain: Stefano% ldd kvlApplyTransformldd: 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.

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