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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

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Whole Brain definition
by Akshay 22 Mar '13

22 Mar '13

Hello Freesurfer experts, I am currently doing some TBM analysis and to compute whole brain atrophy I consider all the structures except ventricles and CSF from aseg.mgz in my definition. Should I also include the cortex definition from aparc+aseg? If yes, should I then use aparc+aseg or aparc.a2009s+aseg segmentation file? Any help will be greatly appreciated. Akshay Univ. of Copenhagen

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offset in qdec GUI
by stdp82＠virgilio.it 22 Mar '13

22 Mar '13

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

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Gray matter
by Jordi Delgado 22 Mar '13

22 Mar '13

Dear FS experts, I have a double question about the gray matter calculations in FS: - Revising the aseg.stats, I noticed that there is a Total Gray Volume calculation. Is there a mgz volume with the gray matter? I cannot find it on the output mri folder... - How this total Gray Volume is calculated? Which structures are taken into account? Is there any file with this information Kind Regards, -- Jordi

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Re: [Freesurfer] subcortseg error - ?h.white surfaces not available
by A. Yamamoto 22 Mar '13

22 Mar '13

Still having issues with the subcortseg flag in v5.2.0 ... Trying to take a look at the source code, I did checkout from the cvs but it failed due to the following error: cvs [checkout aborted]: Could not map memory to RCS archive /usr/fscvsroot/dev/distribution/average/cvs_avg35.tar.gz,v: Cannot allocate memory Any problems with the cvs server? Your help will be very much appreciated. Akio ---------- Forwarded message --------- From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Date: 2013/3/20 Subject: Re: [Freesurfer] subcortseg error - ?h.white surfaces not available Cc: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> I think something must be inconsistent with that flag. Can you use the workaround for now? On Wed, 20 Mar 2013, Akio Yamamoto wrote: Hi Bruce, > > After completing autorecon1 stage, I run: > > recon-all -s test -autorecon2 -autorecon3 > > and confirmed that it finished without errors, so I suspect mri_segstats > did not work correctly with the "-subcortseg" > flag in the new version 5.2.0. > > Here is the full command line where the error occurred: > > mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz > --empty --brainmask mri/brainmask.mgz > --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --subcortgray --in > mri/norm.mgz --in-intensity-name norm > --in-intensity-units MR --etiv --ctab > /usr/local/freesurfer/5.2.0/dist/ASegStatsLUT.txt --subject test > > > Now my questions are: > 1. Is there any change in mri_segstats from the previous version 5.1.0? > Or, is the "-subcortseg" flag no longer supported > in v5.2.0? > > 2. Any workaround for the use of "-sobcortseg" just after completing > autorecon1 in v5.2.0? > > > Thanks for your help. > Akio > > > 2013/3/19 A. Yamamoto <a.mtbook(a)gmail.com> > Hi Bruce, > > Here are command lines I used: > > recon-all -s test -i ./sample-001.mgz -i ./sample-002.mgz -autorecon1 > recon-all -s test -subcortseg > > > The error occurred in the final process, i.e. calculation of stats on the > automatic segmentation. > > Thanks, > Akio > > > 2013/3/19 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Akio > > what was your full command line? > > cheers > Bruce > > On Mon, 18 Mar 2013, A. Yamamoto wrote: > > Hi, > > After upgrading to FreeSurfer 5.2.0, the command with > "-subcortseg" flag > exited with the following error. > > > MRISread(/usr/local/freesurfer/5.2.0/dist/subjects/test/surf/lh.white): > could not open file > > > I confirmed that the "-autorecon1" stage finished without > error. > In v5.1.0 it worked fine, so I'm wondering if there is any > change in > mri_segstats?? > > > FYI, I have attached the last part of recon-all.log file. > > Thanks for your help. > Akio > > > > > > 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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vox2ras and vox2ras-tkr
by Eric Larson 21 Mar '13

21 Mar '13

Does anyone have code available for reading the vox2ras-tkr transform from .mgz files? I am working on implementing the transform outlined on the Freesurfer wiki: MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]' TalXFM: subject/orig/transforms/talairach.xfm Norig: mri_info --vox2ras orig.mgz Torig: mri_info --vox2ras-tkr orig.mgz I can get vox2ras-tkr (a.k.a., Torig) using mri_info, but it would be better if they were available in the python package nibabel for use in mne-python (for easy conversion from surface to MNI coordinates). nibabel already supports reading the --vox2ras transform, but I need to code the other one in order to avoid a dependecy in our code. Does anyone have code to extract that information? MATLAB, Python, C code, or heck, even pseudocode would help. If not, if anyone has helpful information on the specs on the .mgz specification, maybe it won't be too difficult to code from scratch... Eric

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Re: [Freesurfer] R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts
by Anastasia Yendiki 21 Mar '13

21 Mar '13

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. > > > > > > > > > > >

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Re: [Freesurfer] Stat doubts
by Gabriel Gonzalez Escamilla 21 Mar '13

21 Mar '13

4 7

help with contrasts
by Laura M. Tully 21 Mar '13

21 Mar '13

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

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R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts
by stdp82＠virgilio.it 21 Mar '13

21 Mar '13

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.

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