Freesurfer March 2013

freesurfer@nmr.mgh.harvard.edu

155 participants
331 discussions

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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trac-all -prep exited with errors
by Jon Wieser 22 Mar '13

22 Mar '13

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 -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219

2 1

Re: [Freesurfer] Gray matter
by Gabriel Gonzalez Escamilla 22 Mar '13

22 Mar '13

2 1

R: R: Re: correction on question: offset in qdec GUI
by stdp82＠virgilio.it 22 Mar '13

22 Mar '13

If I'd like to show a contrast map between two group, which is the correct form? If I set offset=1 the red area will be more larger, with more results than offset=0, the the blue (negative) will be stable. If I apply the Montecarlo Sim the results will seem to be in accord to offset=0. Which is the true map? Thanks, Stefano ----Messaggio originale---- Da: stdp82(a)virgilio.it Data: 22-mar-2013 14.59 A: <fischl(a)nmr.mgh.harvard.edu> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: [Freesurfer] R: Re: correction on question: offset in qdec GUI Hi Bruce, I'm referring to "offset" in qdec/Display threshold line, near Min/Mid/Max. For example, I'm noting that if set +1 as offset the red statistical area is more larger. Stefano ----Messaggio originale---- Da: fischl(a)nmr.mgh.harvard.edu Data: 22-mar-2013 13.48 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] correction on question: offset in qdec GUI Hi Stefano I believe it's the offset of the center of the color scale. So for example in the red/positive blue/negative one, the cross-over doesn't have to be at 0 cheers Bruce On Fri, 22 Mar 2013, stdp82(a)virgilio.it wrote: > Hi list, > I have a question, probably trivial, on OFFSET in qdec GUI. What's this? And > what I can do using it? > > > > Stefano > > 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.

1 0

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

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.

2 1

Re: [Freesurfer] help with contrasts
by Laura M. Tully 22 Mar '13

22 Mar '13

oops sorry! (I also miscalculated the # of regressors - there's actually 12 (not 10 as previously noted). Here is the list of column labels: Grp1male Grp1female Grp2male Grp2female Grp1maleVar1 Grp1femaleVar1 Grp1maleVar2 Grp1femaleVar2 Grp2maleVar1 Grp2femaleVar1 Grp2maleVar2 Grp2femaleVar2 And what I think is actually an F test looking for group x var 1 interaction OR group x variable 2 interaction whilst accounting for gender. .5 .5 -.5 -.5 0 0 0 0 0 0 0 0 0 0 0 0 .5 .5 -.5 -.5 But what I actually WANT to test is a multiple regression style model - i.e. if I put var 1 AND 2 into the model together do they explain more variance than either variable alone, AND does this vary by group (is this even a sensible contrast to make?). Which I *think* would look something like this... 0 0 0 0 .125 .125 .125 .125 .125 .125 .125 .125 Laura. On Thu, Mar 21, 2013 at 5:51 PM, MCLAREN, Donald <mclaren.donald(a)gmail.com>wrote: > Please include the list of the column labels. > > Best Regards, Donald McLaren > ================= > D.G. McLaren, Ph.D. > Research Fellow, Department of Neurology, Massachusetts General Hospital > and > Harvard Medical School > Postdoctoral Research Fellow, GRECC, Bedford VA > Website: http://www.martinos.org/~mclaren > Office: (773) 406-2464 > ===================== > This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED > HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is > intended only for the use of the individual or entity named above. If the > reader of the e-mail is not the intended recipient or the employee or agent > responsible for delivering it to the intended recipient, you are hereby > notified that you are in possession of confidential and privileged > information. Any unauthorized use, disclosure, copying or the taking of any > action in reliance on the contents of this information is strictly > prohibited and may be unlawful. If you have received this e-mail > unintentionally, please immediately notify the sender via telephone at > (773) > 406-2464 or email. > > > On Thu, Mar 21, 2013 at 6:43 PM, Laura M. Tully < > tully.laura(a)googlemail.com> wrote: > >> hi Experts, >> >> I'm struggling to conceptualize the appropriate contrasts for my cortical >> thickness analysis. I have four classes [two groups; two levels >> (patients,controls; male,female) and two behavioral variables. I want to >> see if together the two variables account significant proportion of the >> variance in y (thickness) and if this differs by group whilst regressing >> out gender. - i.e. if I enter both behavioral variables into the model does >> it account for more variance than either variable on their own (after >> controlling for gender)? What I have is this: >> >> .5 .5 -.5 -.5 0 0 0 0 >> 0 0 0 0 .5 .5 -.5 -.5 >> >> Does this look right? >> >> Thanks! >> >> Laura. >> >> >> >> >> -- >> -- >> Laura M. Tully, MA >> Social Neuroscience & Psychopathology, Harvard University >> Center for the Assessment and Prevention of Prodromal States, UCLA Semel >> Institute of Neuroscience >> ltully(a)mednet.ucla.edu >> ltully(a)fas.harvard.edu >> 310-267-0170 >> -- >> My musings as a young clinical scientist: >> http://theclinicalbrain.blogspot.com/ >> Follow me on Twitter: @tully_laura >> >> _______________________________________________ >> 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. >> >> > -- -- Laura M. Tully, MA Social Neuroscience & Psychopathology, Harvard University Center for the Assessment and Prevention of Prodromal States, UCLA Semel Institute of Neuroscience ltully(a)mednet.ucla.edu ltully(a)fas.harvard.edu 310-267-0170 -- My musings as a young clinical scientist: http://theclinicalbrain.blogspot.com/ Follow me on Twitter: @tully_laura

2 4

FreeSurfer 5.2 Segmentation & Talairach Registration Issues
by Daniel Carey 22 Mar '13

22 Mar '13

Dear All, We have been running the recon-all pipeline in 5.2 and have been encountering some difficulties with segmentations. We have isolated these issues to problems with Talairach registrations, and have been re-running recon-all with the Talairach registrations manually corrected in tkregister2; however, doing so appears to worsen our segmentation problems. In particular, the orig surface appears substantially shrunk away from the filled and white matter volumes. Has anyone encountered such difficulties with manually corrected Talairach registrations placed in the processing stream, or indeed, seen the surface shrink to such an extent? We initially provided recon-all with synthesised volumes obtained using MRI-synthesise from the developer version (our raw scans are high-resolution PDw and T1w volumes). Any insights would be greatly appreciated. Many thanks, Dan --- Daniel Carey, M.Sc., Marie Curie PhD Fellow, Centre for Brain and Cognitive Development, Birkbeck College, 32 Torrington Sq., London, WC1E 7JL UK

2 1

R: Re: correction on question: offset in qdec GUI
by stdp82＠virgilio.it 22 Mar '13

22 Mar '13

Hi Bruce, I'm referring to "offset" in qdec/Display threshold line, near Min/Mid/Max. For example, I'm noting that if set +1 as offset the red statistical area is more larger. Stefano ----Messaggio originale---- Da: fischl(a)nmr.mgh.harvard.edu Data: 22-mar-2013 13.48 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] correction on question: offset in qdec GUI Hi Stefano I believe it's the offset of the center of the color scale. So for example in the red/positive blue/negative one, the cross-over doesn't have to be at 0 cheers Bruce On Fri, 22 Mar 2013, stdp82(a)virgilio.it wrote: > Hi list, > I have a question, probably trivial, on OFFSET in qdec GUI. What's this? And > what I can do using it? > > > > Stefano > > 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

correction on question: offset in qdec GUI
by stdp82＠virgilio.it 22 Mar '13

22 Mar '13

Hi list, I have a question, probably trivial, on OFFSET in qdec GUI. What's this? And what I can do using it? Stefano

2 1

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Freesurfer March 2013