Re: [Freesurfer] Otto: unsupported slice timing pattern 5
Hi, One option is to open the volume in 3D Slicer and save it in .mgz format. 3D Slicer is free to download. John On 2013-08-22, at 4:30 PM, Otto Muzik wrote: > > Hi, > > I am trying to convert a SIEMENS T1-weighted volume to the mgz > format (via mri_convert) but I am getting constantly the error message > > unsupported slice timing pattern 5 in file > > I saw in the archives that a lot of people had problems with this but > could not find any solutions posted - what am I missing? > > Many thanks > > Otto > ___ > Freesurfer mailing list > Freesurfer@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Labels for comparison
Hello, I have successfully developed an automated algorithm combining pixel intensity-based and shape based approaches to segment the lateral ventricles. I have applied my algorithm to a small data set of 1.5 T1 ADNI images consisting of 24 AD (subjects with Alzheimer Disease) 19 MCI (subjects with Mild Cognitive Impairment) and 24 NEC (elderly controls). In my cases, particularly AD cases, I noticed that the segmentation of the lateral ventricles is connected to the third ventricle with foramina (usually 1 on a side or on both sides). Also, sometimes I find a connection with the posterior horn and third ventricle. I have researched CSF flow and from the literature, and all of these are real connections. I am near completion of developing an automated cropping scheme with a colleague to crop the third ventricle at these junctions. Our implementation is a combination of C++ code that we have developed and modified ITK classes. We have been viewing our segmented label maps in Slicer3 and generated 3D renderings using Slicer3's Model Maker module which is based on Marching Cubes. I have viewed a Freesurfer segmentation in Slicer3 based on a tutorial on the Slicer web site. I presented a poster of our results at the AIC and AAIC conference which I am at now in Vancouver, and a few people have asked me to compare my volumes with other methods. They were particularly interested in comparing my volumes with Freesurfer ventricle volumes and cross-sectional and longitudinal data. I was told and found csv files on the ADNI web site of Freesurfer analysis. I plan to correlate my values with Freesurfer's values, but I would be interested if Freesurfer also finds these connections between the third ventricle and lateral ventricles and also if it includes isolated temporal horn pieces when the horns are discontinuous due to the MRI not being able to resolve a very thin portion of the temporal horn. So, would it be possible, if I gave you a list of my ADNI subjects, for you to provide me the freesurfer label maps that correspond to the volumes in the csv files that are on the ADNI web site please? I could run Freesurfer but I would prefer having the label maps that exactly correspond to the Freesurfer ventricle volumes that are on the ADNI website. These would be from the two versions of Freesurfer noted on the ADNI web site in the ADNI Study Data/MRI image analysis link. Thank you, John Sent from my iPhone 4S ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Labels for comparison
Hi Bruce, I apologize for my detailist nature. I found the csv files on the ADNI web site containing the numerical values of volume in mm^3 numbers. Do you mean that there should also be the corresponding label maps on the ADNI web site, particularly of the third and lateral ventricles? I know when I ran recon-all it gave all the label maps of each parcellation of the brain and I could overlay these labels on the grey scale images and render 3D surface models in Slicer. If this is the case, could you confirm this. Then I'll email ADNI to see if they have the label maps corresponding to the csv files that they have in the ADNI Study Data -> MRI Images -> Image Analysis link. I am particularly interested in where Freesurfer separates the lateral ventricles from the third ventricle at the foramina, or at the connection between the posterior horns and the third ventricle. If you have any insight in this, that would be helpful. I am glad that Freesurfer includes the isolated horn pieces, as you explained. I particularly found that accurate segmentation of the horns was very important for the significance statistics in comparing AD, MCI and NEC groups. The next step for me will be sub-regional ventricle volumes, not only left and right but separate volumes of horns. I am curious how you defined the division of left from right for the ventricles? Was it special landmarks on the atlas? Thank you, John Sent from my iPhone 4S On 2012-07-17, at 2:13 PM, Bruce Fischl wrote: > Hi John > > have you checked with the ADNI folks? I think they have FreeSurfer > segmentation on many if not most of their subjects. We place no connectivity > constraints on the ventricular segmentations because they get so thin that > indeed sometimes 1mm data cannot resolve the connections. So > sometimes the temporal or occipital horn are disconnected, and sometimes not. > > cheers > Bruce > > > On Tue, 17 Jul 2012, John Drozd wrote: > >> Hello, >> >> I have successfully developed an automated algorithm combining pixel >> intensity-based and shape based approaches to segment the lateral >> ventricles. I have applied my algorithm to a small data set of 1.5 T1 ADNI >> images consisting of 24 AD (subjects with Alzheimer Disease) 19 MCI >> (subjects with Mild Cognitive Impairment) and 24 NEC (elderly controls). In >> my cases, particularly AD cases, I noticed that the segmentation of the >> lateral ventricles is connected to the third ventricle with foramina >> (usually 1 on a side or on both sides). Also, sometimes I find a connection >> with the posterior horn and third ventricle. I have researched CSF flow and >> from the literature, and all of these are real connections. I am near >> completion of developing an automated cropping scheme with a colleague to >> crop the third ventricle at these junctions. >> >> Our implementation is a combination of C++ code that we have developed and >> modified ITK classes. We have been viewing our segmented label maps in >> Slicer3 and generated 3D renderings using Slicer3's Model Maker module which >> is based on Marching Cubes. >> >> I have viewed a Freesurfer segmentation in Slicer3 based on a tutorial on >> the Slicer web site. >> >> I presented a poster of our results at the AIC and AAIC conference which I >> am at now in Vancouver, and a few people have asked me to compare my volumes >> with other methods. They were particularly interested in comparing my >> volumes with Freesurfer ventricle volumes and cross-sectional and >> longitudinal data. I was told and found csv files on the ADNI web site of >> Freesurfer analysis. I plan to correlate my values with Freesurfer's values, >> but I would be interested if Freesurfer also finds these connections between >> the third ventricle and lateral ventricles and also if it includes isolated >> temporal horn pieces when the horns are discontinuous due to the MRI not >> being able to resolve a very thin portion of the temporal horn. >> >> So, would it be possible, if I gave you a list of my ADNI subjects, for you >> to provide me the freesurfer label maps that correspond to the volumes in >> the csv files that are on the ADNI web site please? I could run Freesurfer >> but I would prefer having the label maps that exactly correspond to the >> Freesurfer ventricle volumes that are on the ADNI website. These would be >> from the two versions of Freesurfer noted on the ADNI web site in the ADNI >> Study Data/MRI image analysis link. >> >> Thank you, >> John >> >> Sent from my iPhone 4S >> >> >> ___
Re: [Freesurfer] Labels for comparison
Hi Bruce, Thank you very much for your clarifications. I will ask ADNI for their permission and I will consult CMA for their definitions. Thank you, Have a great day, John Sent from my iPhone 4S On 2012-07-18, at 6:42 AM, Bruce Fischl wrote: > Hi John > > we follow the conventions of the Center for Morphometric Analysis (CMA) here > at MGH. I'm not actually sure what landmarks they use to separate what they > call "inferior lateral ventricle" from the main one, but you can check with > them. > > As for ADNI, we might have that data but I'm not sure we are allowed to > distribute it. If you check with them about it and let us know we'll give you > what we have. > > cheers > Bruce > > > On Tue, 17 Jul 2012, John Drozd wrote: > >> Hi Bruce, >> >> I apologize for my detailist nature. >> I found the csv files on the ADNI web site containing the numerical values >> of volume in mm^3 numbers. Do you mean that there should also be the >> corresponding label maps on the ADNI web site, particularly of the third and >> lateral ventricles? I know when I ran recon-all it gave all the label maps >> of each parcellation of the brain and I could overlay these labels on the >> grey scale images and render 3D surface models in Slicer. If this is the >> case, could you confirm this. Then I'll email ADNI to see if they have the >> label maps corresponding to the csv files that they have in the ADNI Study >> Data -> MRI Images -> Image Analysis link. >> >> I am particularly interested in where Freesurfer separates the lateral >> ventricles from the third ventricle at the foramina, or at the connection >> between the posterior horns and the third ventricle. If you have any >> insight in this, that would be helpful. I am glad that Freesurfer includes >> the isolated horn pieces, as you explained. I particularly found that >> accurate segmentation of the horns was very important for the significance >> statistics in comparing AD, MCI and NEC groups. The next step for me will >> be sub-regional ventricle volumes, not only left and right but separate >> volumes of horns. I am curious how you defined the division of left from >> right for the ventricles? Was it special landmarks on the atlas? >> >> Thank you, >> John >> >> Sent from my iPhone 4S >> >> >> On 2012-07-17, at 2:13 PM, Bruce Fischl wrote: >> >>> Hi John >>> >>> have you checked with the ADNI folks? I think they have FreeSurfer >>> segmentation on many if not most of their subjects. We place no >>> connectivity constraints on the ventricular segmentations because they get >>> so thin that indeed sometimes 1mm data cannot resolve the connections. So >>> sometimes the temporal or occipital horn are disconnected, and sometimes >>> not. >>> >>> cheers >>> Bruce >>> >>> >>> On Tue, 17 Jul 2012, John Drozd wrote: >>> >>>> Hello, >>>> >>>> I have successfully developed an automated algorithm combining pixel >>>> intensity-based and shape based approaches to segment the lateral >>>> ventricles. I have applied my algorithm to a small data set of 1.5 T1 ADNI >>>> images consisting of 24 AD (subjects with Alzheimer Disease) 19 MCI >>>> (subjects with Mild Cognitive Impairment) and 24 NEC (elderly controls). >>>> In my cases, particularly AD cases, I noticed that the segmentation of the >>>> lateral ventricles is connected to the third ventricle with foramina >>>> (usually 1 on a side or on both sides). Also, sometimes I find a >>>> connection with the posterior horn and third ventricle. I have researched >>>> CSF flow and from the literature, and all of these are real connections. I >>>> am near completion of developing an automated cropping scheme with a >>>> colleague to crop the third ventricle at these junctions. >>>> >>>> Our implementation is a combination of C++ code that we have developed and >>>> modified ITK classes. We have been viewing our segmented label maps in >>>> Slicer3 and generated 3D renderings using Slicer3's Model Maker module >>>> which is based on Marching Cubes. >>>> >>>> I have viewed a Freesurfer segmentation in Slicer3 based on a tutorial on >>>> the Slicer web site. >>>> >>>> I presented a poster of our results at the AIC and AAIC conference which I >>>> am at now
[Freesurfer] question on invoking partial volume calculations in freesurfer 4.3
Hello, My freesurfer version is freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0 I noticed that the aparc+aseg.mgz label map is resampled to 1mm x 1mm x 1mm voxels, eventhough the .mgz grayscale mri image file remains as per the original voxel size and is not 1x1x1. mri_convert .nii to .mgz translates the grayscale image down the y direction in the horizontal plane transverse/axial slices. I noticed that the aseg.stats files list the number of voxels and the volume, and these numbers match because the voxel size is 1 x 1 x 1. My question is whether freesurfer 4.3 can be invoked to perform partial volume error corrections, and if so how do you invoke this feature? My interests lie in segmentations of the lateral ventricles including their posterior and inferior horns. thank you, john ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] question on invoking partial volume calculations in freesurfer 4.3
Thanks Doug. Do you know if the Freesurfer volumes in mm^3 that are posted on the ADNI website (particularly the longitudinal studies) include partial volume corrections? i.e., if they were run to include partial volume calculations? Thank you, John On 2012-11-30, at 3:11 PM, Douglas N Greve wrote: > Hi John, it has been a long time since I looked at version 4.3, so I > don't know if it can or not. One thing you can try is to use the version > 5.x mri_segstats (the program which computes the aseg.stats table). You > could run this outside of recon-all and generate a file with a different > name. That way you won't have to worry about mixing version. > doug > > > On 11/30/2012 03:00 PM, John Drozd wrote: >> Hello, >> >> My freesurfer version is freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0 >> >> I noticed that the aparc+aseg.mgz label map is resampled to 1mm x 1mm >> x 1mm voxels, >> eventhough the .mgz grayscale mri image file remains as per the >> original voxel size and is not 1x1x1. mri_convert .nii to .mgz >> translates the grayscale image down the y direction in the horizontal >> plane transverse/axial slices. >> >> I noticed that the aseg.stats files list the number of voxels and the >> volume, and these numbers match because the voxel size is 1 x 1 x 1. >> >> My question is whether freesurfer 4.3 can be invoked to perform >> partial volume error corrections, and if so how do you invoke this >> feature? >> >> My interests lie in segmentations of the lateral ventricles including >> their posterior and inferior horns. >> >> thank you, >> john >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] downloading GradientUnwarping
Hello, I would like to download and install the software described at http://surfer.nmr.mgh.harvard.edu/fswiki/GradientUnwarping Your email address is listed on this website. I cannot find a download link. We would like to use this with Freesurfer. Do you know where I can download this software from? Thank you, John John J. Drozd, M.Sc., Ph.D. Post-Doctoral Fellow Robarts Research Institute Western University London, Ontario, Canada ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] downloading GradientUnwarping
Thanks Dan. It is already installed with Freesurfer as you say: [jdrozd@trumpet bin]$ pwd /trumpet/downloads/FreeSurfer/freesurfer/bin [jdrozd@trumpet bin]$ ./grad_unwarp USAGE: grad_unwarp -i infile : dcmdir or dcmfile or mghfile -s seriesno : dicom series - needed only if invoking -i dcmdir -unwarp: gradient unwarping : Optional type is the gradient unwarping displacements : map to use - supply either scanner gradient model (sonata, : allegra, brm, crm) or map filename. (BRM is GE like : UCSD's 1.5T; CRM is GE like MGH Bay 1, BWH-GE, Duke-GE.) : If unwarping an mgh volume, user _must_ supply a type. -nojac : don't do jacobian correction when unwarping -corfov : resample to cor FOV (bug: recenters volume on (0,0,0)) -cor : save as COR format instead of mgh (you should use -corfov as well) -interp : method (,linear,nearest,spline) -o outfile : MGH formatted by default (unless -cor is specified) -matlab matlab_binary : default is /space/lyon/6/pubsw/common/matlab/6.5/bin/matlab : grad_unwarp needs at least version 6.5 to handle the long. : filenames. And this installation has crucial dicom patches. -version : print version string -help: print help text On 12/20/12, dgw wrote: > Is it not included in your freesurfer installation? > > To check: > After sourcing Freesurfer type > > which grad_unwarp > > HTH > Dan > > On Thu, Dec 20, 2012 at 9:42 AM, John Drozd wrote: >> Hello, >> >> I would like to download and install the software described at >> >> http://surfer.nmr.mgh.harvard.edu/fswiki/GradientUnwarping >> >> Your email address is listed on this website. >> >> I cannot find a download link. >> >> We would like to use this with Freesurfer. >> >> Do you know where I can download this software from? >> >> Thank you, >> >> John >> >> John J. Drozd, M.Sc., Ph.D. >> Post-Doctoral Fellow >> Robarts Research Institute >> Western University >> London, Ontario, Canada >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] What is the correct way to cite Freesurfer in a journal paper?
Hello, I am writing a paper for publication in Neuroimage. I used Freesurfer 4.3 to segment brain anatomy. Lateral ventricles were my focus. Can someone please tell me what is the correct way to cite Freesurfer in a bibliography? Is there a paper I can cite? Thank you, John Drozd John Jan Drozd, M.Sc., Ph.D. Financial Secretary Knights of Columbus St. Pius X Council 10561 Holy Family Parish Post-Doctoral Scholar (Fellow) Imaging Department Robarts Research Institute Western University London, ON, Canada http://publish.uwo.ca/~jdrozd2 http://kong.apmaths.uwo.ca/~jdrozd/personal.html http://kong.apmaths.uwo.ca/~jdrozd/bio.html http://cfmm.robarts.ca/people/staff/bartha-group/#john cell phone: 519-282-3340 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] What is the correct way to cite Freesurfer in a journal paper?
Hi Bruce, Thank you very much. Enjoy your Sunday. John On 2013-01-13, at 9:01 AM, Bruce Fischl wrote: > Hi John > > if you are really only looking at the ventricles it would probably be: > > for the segmentation: > Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in > the Human Brain, Fischl, B., D.H. Salat, E. Busa, M. Albert, M. Dieterich, C. > Haselgrove, A. van der Kouwe, R. Killiany, D. Kennedy, S. Klaveness, A. > Montillo, N. Makris, B. Rosen, and A.M. Dale, (2002). Neuron, 33:341-355. > > Sequence-Independent Segmentation of Magnetic Resonance Images, Fischl, B., > Salat, D.H., van der Kouwe, A.J.W., Makris, N., Ségonne, F., and Dale, A.M. > (2004) NeuroImage 23:S69-S84. > > Atlas Renormalization for Improved Brain MR Image Segmentation Across Scanner > Platforms, Han, X. and B. Fischl, (2007). IEEE Transactions on Medical > Imaging, 26(4):479-486. > > for skull stripping: > A Hybrid Approach to the Skull-Stripping Problem in MRI, Ségonne, F., Dale, > A.M., Busa, E., Glessner, M., Salvolini, U., Hahn, H.K., Fischl, B. (2004). > NeuroImage, 22:1160-1075. > > cheers > Bruce > > On Sun, 13 Jan 2013, john.dr...@gmail.com wrote: > >> Hello, >> >> I am writing a paper for publication in Neuroimage. >> >> I used Freesurfer 4.3 to segment brain anatomy. Lateral ventricles were my >> focus. >> >> Can someone please tell me what is the correct way to cite Freesurfer in a >> bibliography? >> Is there a paper I can cite? >> >> Thank you, >> John Drozd >> >> John Jan Drozd, M.Sc., Ph.D. >> >> Financial Secretary >> Knights of Columbus >> St. Pius X Council 10561 >> Holy Family Parish >> >> Post-Doctoral Scholar (Fellow) >> Imaging Department >> Robarts Research Institute >> Western University >> >> London, ON, Canada >> >> http://publish.uwo.ca/~jdrozd2 >> http://kong.apmaths.uwo.ca/~jdrozd/personal.html >> http://kong.apmaths.uwo.ca/~jdrozd/bio.html >> http://cfmm.robarts.ca/people/staff/bartha-group/#john >> >> cell phone: 519-282-3340 >> >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: zero determinant error in using mri_convert rawavg.mgz orig.mgz --conform
S32496_I63397_76.dcm* > 70731171155016_S32496_I63397_151.dcm* 70731171155016_S32496_I63397_77.dcm* > 70731171155016_S32496_I63397_152.dcm* 70731171155016_S32496_I63397_78.dcm* > 70731171155016_S32496_I63397_153.dcm* 70731171155016_S32496_I63397_79.dcm* > 70731171155016_S32496_I63397_154.dcm* 70731171155016_S32496_I63397_7.dcm* > 70731171155016_S32496_I63397_155.dcm* 70731171155016_S32496_I63397_80.dcm* > 70731171155016_S32496_I63397_156.dcm* 70731171155016_S32496_I63397_81.dcm* > 70731171155016_S32496_I63397_157.dcm* 70731171155016_S32496_I63397_82.dcm* > 70731171155016_S32496_I63397_158.dcm* 70731171155016_S32496_I63397_83.dcm* > 70731171155016_S32496_I63397_159.dcm* 70731171155016_S32496_I63397_84.dcm* > 70731171155016_S32496_I63397_15.dcm* 70731171155016_S32496_I63397_85.dcm* > 70731171155016_S32496_I63397_160.dcm* 70731171155016_S32496_I63397_86.dcm* > 70731171155016_S32496_I63397_161.dcm* 70731171155016_S32496_I63397_87.dcm* > 70731171155016_S32496_I63397_162.dcm* 70731171155016_S32496_I63397_88.dcm* > 70731171155016_S32496_I63397_163.dcm* 70731171155016_S32496_I63397_89.dcm* > 70731171155016_S32496_I63397_164.dcm* 70731171155016_S32496_I63397_8.dcm* > 70731171155016_S32496_I63397_165.dcm* 70731171155016_S32496_I63397_90.dcm* > 70731171155016_S32496_I63397_16.dcm* 70731171155016_S32496_I63397_91.dcm* > 70731171155016_S32496_I63397_17.dcm* 70731171155016_S32496_I63397_92.dcm* > 70731171155016_S32496_I63397_18.dcm* 70731171155016_S32496_I63397_93.dcm* > 70731171155016_S32496_I63397_19.dcm* 70731171155016_S32496_I63397_94.dcm* > 70731171155016_S32496_I63397_1.dcm*70731171155016_S32496_I63397_95.dcm* > 70731171155016_S32496_I63397_20.dcm* 70731171155016_S32496_I63397_96.dcm* > 70731171155016_S32496_I63397_21.dcm* 70731171155016_S32496_I63397_97.dcm* > 70731171155016_S32496_I63397_22.dcm* 70731171155016_S32496_I63397_98.dcm* > 70731171155016_S32496_I63397_23.dcm* 70731171155016_S32496_I63397_99.dcm* > 70731171155016_S32496_I63397_24.dcm* 70731171155016_S32496_I63397_9.dcm* > > I first converted these files to an mgz file using: > > [jdr...@trumpet orig]$ mri_convert -it dicom > 70731171155016_S32496_I63397_0.dcm T1.mgz > mri_convert -it dicom 70731171155016_S32496_I63397_0.dcm T1.mgz > $Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $ > reading from 70731171155016_S32496_I63397_0.dcm... > Starting DICOMRead2() > dcmfile = > /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/mri/orig/70731171155016_S32496_I63397_0.dcm > dcmdir = > /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/mri/orig > WARNING: tag ImageNumber not found > Ref Series No = 63443 > Found 168 files, checking for dicoms > WARNING: tag ImageNumber not found > Found 166 dicom files in series. > WARNING: tag ImageNumber not found > First Sorting > WARNING: files are not found to be different and cannot be sorted > File1: > /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/mri/orig/70731171155016_S32496_I63397_0.dcm > File2: > /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/mri/orig/70731171155016_S32496_I63397_1.dcm > Computing Slice Direction > Vs: 1.2024 0 0 > Vs: 1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 166 > ndcmfiles = 166 > PE Dir = UNKNOWN (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2-- > jpegUID: --1.2.840.10008.1.2.4-- > Loading pixel data > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0, -0, -1) > j_ras = (-0, -1, 0) > k_ras = (-1, -0, 0) > writing to T1.mgz... > > Then I copied the outputted T1.mgz file using: > > [jdr...@trumpet orig]$ cp T1.mgz ../rawavg.mgz > [jdr...@trumpet orig]$ cd .. > [jdr...@trumpet mri]$ ls > 1.Bvq.Xml* 2.Bvq.Xml* error.log orig/ orig2/ rawavg.mgz transforms/ > [jdr...@trumpet mri]$ pwd > > /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/mri > > Then I tried to conform the data using: > > [jdr...@trumpet mri]$ mri_convert rawavg.mgz orig.mgz --conform > mri_convert rawavg.mgz orig.mgz --conform > $Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $ > reading from rawavg.mgz... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0, -0, -1) > j_ras = (-0, -1, 0) > k_ras = (-1, -0, 0) > Original Data has (0.93905, 0.93905, 0) mm size and (256, 256, 166) voxels. > Data is conformed to 1 mm size and 256 voxels for all directions > changing data type from 4 to 0 (noscale = 0)... > MRIchangeType: Building histogram > Reslicing using trilinear interpolation > MRIresa
Re: [Freesurfer] Re: zero determinant error in using mri_convert rawavg.mgz orig.mgz --conform
Hello Bruce and Nick, Thank you, Bruce, for the clarification that FreeSurfer when reading my dicom files, it thinks the slice thickness is 0, and thank you Nick for your help as well. Just for your information, 3D Slicer was able to read in the dicom files successfully. I find this perplexing. Anyways, I tried an alternate route with FreeSurfer which seemed to work reasonably well. The dicom files that I was using were derived from a nifti .nii file. So I used the original .nii file and everything worked with FreeSurfer, except when I tried to perform non-uniform intensity normalization (the program gave a segmentation crash) when I typed: mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 So I did the talairach transformation without performing the non-uniform intensity normalization, and then I was able to calculate the total intercranial volume when I typed: talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm mri_segstats --subject subjid --etiv-only Now that I am able to calculate the total intercranial volume with FreeSurfer, I am interested in the details of the procedure that FreeSurfer uses to calculate the intercranial volume. Afterall, the pudding is in the details. I am interested in what components of the head FreeSurfer includes/excludes in its calculation of total intercranial volume. I am also interested in the details of the mathematical and computer algorithm used to calculate the total intercranial volume (as well as for calculating ventricle volume). I am performing image analysis for research on Alzheimer's Disease and I need to understand these calculations in detail. Can you recommend any good references that would provide me information on how FreeSurfer calculates the total intracranial volume and ventricle volume? Also, please let me know if the source code is available for my viewing if at all possible, which would be really handy. Thank you, John Drozd PostDoctoral Fellow Robarts Research Institute, Imaging Department, The University of Western Ontario London, Ontario, Canada On Wed, May 13, 2009 at 5:28 PM, Bruce Fischl wrote: > looks like it thinks the slice thickness is 0, which is probably bad > > On Wed, 13 May 2009, Nick Schmansky wrote: > > John, >> >> What does the file look like when its opened in tkmedit? ie >> >> tkmedit -f T1.mgz >> >> does it look like our sample subject data bert? ie, a full brain t1 >> anatomical scan? >> >> Nick >> >> On Wed, 2009-05-13 at 16:41 -0400, John Drozd wrote: >> >>> >>>Hello, >>> >>>Here is the ouput from bugr: >>> >>>FREESURFER_HOME: /trumpet/downloads/FreeSurfer/freesurfer >>> >>>Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0 >>> >>>RedHat release: Fedora release 10 (Cambridge) >>> >>>Kernel info: Linux 2.6.27.21-170.2.56.fc10.x86_64 x86_64 >>> >>>I have sets of dicom files such as: >>> >>>[jdr...@trumpet orig]$ ls >>>70731171155016_S32496_I63397_0.dcm* >>> 70731171155016_S32496_I63397_25.dcm* >>>70731171155016_S32496_I63397_100.dcm* >>> 70731171155016_S32496_I63397_26.dcm* >>>70731171155016_S32496_I63397_101.dcm* >>> 70731171155016_S32496_I63397_27.dcm* >>>70731171155016_S32496_I63397_102.dcm* >>> 70731171155016_S32496_I63397_28.dcm* >>>70731171155016_S32496_I63397_103.dcm* >>> 70731171155016_S32496_I63397_29.dcm* >>>70731171155016_S32496_I63397_104.dcm* >>> 70731171155016_S32496_I63397_2.dcm* >>>70731171155016_S32496_I63397_105.dcm* >>> 70731171155016_S32496_I63397_30.dcm* >>>70731171155016_S32496_I63397_106.dcm* >>> 70731171155016_S32496_I63397_31.dcm* >>>70731171155016_S32496_I63397_107.dcm* >>> 70731171155016_S32496_I63397_32.dcm* >>>70731171155016_S32496_I63397_108.dcm* >>> 70731171155016_S32496_I63397_33.dcm* >>>70731171155016_S32496_I63397_109.dcm* >>> 70731171155016_S32496_I63397_34.dcm* >>>70731171155016_S32496_I63397_10.dcm* >>>70731171155016_S32496_I63397_35.dcm* >>>70731171155016_S32496_I63397_110.dcm* >>> 70731171155016_S32496_I63397_36.dcm* >>>70731171155016_S32496_I63397_111.dcm* >>> 70731171155016_S32496_I63397_37.dcm* >>>70731171155016_S32496_I63397_112.dcm* >>> 70731171155016_S32
Re: [Freesurfer] Re: zero determinant error in using mri_convert rawavg.mgz orig.mgz --conform
Hello again, I incorrectly used the term intercranial volume in my email below. I meant to type intracranial volume. john On Fri, May 15, 2009 at 7:29 AM, John Drozd wrote: > Hello Bruce and Nick, > > Thank you, Bruce, for the clarification that FreeSurfer when reading > my dicom files, it thinks the slice thickness is 0, and thank you Nick for > your help as well. Just for your information, 3D Slicer was able to read > in > the dicom files successfully. I find this perplexing. > > Anyways, I tried an alternate route with FreeSurfer which seemed to work > reasonably well. The dicom files that I was using were derived from a > nifti .nii file. > So I used the original .nii file and everything worked with FreeSurfer, > except > when I tried to perform non-uniform intensity normalization (the program > gave a segmentation crash) when I typed: > mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 > > So I did the talairach transformation without performing the non-uniform > intensity normalization, and then I was able to calculate the total > intercranial > volume when I typed: > talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm > cp transforms/talairach.auto.xfm transforms/talairach.xfm > mri_segstats --subject subjid --etiv-only > > Now that I am able to calculate the total intercranial volume with > FreeSurfer, > I am interested in the details of the procedure that FreeSurfer uses to > calculate > the intercranial volume. Afterall, the pudding is in the details. > I am interested in what components of the head FreeSurfer includes/excludes > in its calculation of total intercranial volume. I am also interested in > the details of > the mathematical and computer algorithm used to calculate the total > intercranial > volume (as well as for calculating ventricle volume). I am performing > image analysis > for research on Alzheimer's Disease and I need to understand these > calculations > in detail. Can you recommend any good references that would provide me > information on how FreeSurfer calculates the total intracranial volume and > ventricle volume? > Also, please let me know if the source code is available for my viewing if > at all possible, > which would be really handy. > > Thank you, > John Drozd > > PostDoctoral Fellow > Robarts Research Institute, > Imaging Department, > The University of Western Ontario > London, Ontario, Canada > > On Wed, May 13, 2009 at 5:28 PM, Bruce Fischl > wrote: > >> looks like it thinks the slice thickness is 0, which is probably bad >> >> On Wed, 13 May 2009, Nick Schmansky wrote: >> >> John, >>> >>> What does the file look like when its opened in tkmedit? ie >>> >>> tkmedit -f T1.mgz >>> >>> does it look like our sample subject data bert? ie, a full brain t1 >>> anatomical scan? >>> >>> Nick >>> >>> On Wed, 2009-05-13 at 16:41 -0400, John Drozd wrote: >>> >>>> >>>>Hello, >>>> >>>>Here is the ouput from bugr: >>>> >>>>FREESURFER_HOME: /trumpet/downloads/FreeSurfer/freesurfer >>>> >>>>Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0 >>>> >>>>RedHat release: Fedora release 10 (Cambridge) >>>> >>>>Kernel info: Linux 2.6.27.21-170.2.56.fc10.x86_64 x86_64 >>>> >>>>I have sets of dicom files such as: >>>> >>>>[jdr...@trumpet orig]$ ls >>>>70731171155016_S32496_I63397_0.dcm* >>>> 70731171155016_S32496_I63397_25.dcm* >>>>70731171155016_S32496_I63397_100.dcm* >>>> 70731171155016_S32496_I63397_26.dcm* >>>>70731171155016_S32496_I63397_101.dcm* >>>> 70731171155016_S32496_I63397_27.dcm* >>>>70731171155016_S32496_I63397_102.dcm* >>>> 70731171155016_S32496_I63397_28.dcm* >>>>70731171155016_S32496_I63397_103.dcm* >>>> 70731171155016_S32496_I63397_29.dcm* >>>>70731171155016_S32496_I63397_104.dcm* >>>> 70731171155016_S32496_I63397_2.dcm* >>>>70731171155016_S32496_I63397_105.dcm* >>>> 70731171155016_S32496_I63397_30.dcm* >>>>70731171155016_S32496_I63397_106.dcm* >>>> 70731171155016_S32496_I63397_31.dcm* >>>>70731171155016_S32496_I63397_107.dcm* >>>> 70731171155016_S32496_I63397_32.dcm* >>>>
[Freesurfer] licensing question
*Hello, I have a question regarding the second statement in the Clinical Use section of your registration web page. "Clinical Use: This software may not and should never be used for clinical purposes. Software used for clinical purposes may require regulatory documentation and associated filings." Does the statement "**Software used for clinical purposes may require regulatory documentation and associated filings." mean that a version of FreeSurfer can be used for clinical work? Thank you for your time, john drozd * ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] licensing question
Hello, Do you know of any regulations about using FreeSurfer outside of the U.S., specifically in Canada? Thank you, john drozd 2009/5/25 Pedro Paulo de Magalhães Oliveira Junior > Software used for clinical purposes need a FDA approval in US. > FreeSurfer main target is research. If you use it for clinical purposes you > are on your own risk. > > cheers. > > PPJ > --- > Pedro Paulo de M. Oliveira Junior > Diretor de Operações > Netfilter & SpeedComm Telecom > --- Novo Netfilter 3.0 www.netfilter.com.br > > > > 2009/5/25 John Drozd > >> *Hello, >> >> I have a question regarding the second statement in the Clinical Use >> section of your registration web page. >> >> "Clinical Use: This software may not and should never be used for >> clinical purposes. Software used for clinical purposes may require >> regulatory documentation and associated filings." >> >> Does the statement "**Software used for clinical purposes may require >> regulatory documentation and associated filings." mean that a version of >> FreeSurfer can be used for clinical work? >> >> Thank you for your time, >> john drozd >> * >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] segmentation fault when running mris_anatomical_stats
Hello, I am running the reconall steps individually for a firts try. I noticed that I get a segmentation fault when I run mris_anatomical_stats as whown below: [jdr...@trumpet mri]$ mris_anatomical_stats -mgz -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -cf ../label/aparc.annot.ctab convertedfile lh INFO: assuming MGZ format for volumes. computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/mri/wm.mgz... reading input surface /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/surf/lh.white... reading input pial surface /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/surf/lh.pial... reading input white surface /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/surf/lh.white... reading colortable from annotation file... colortable with 35 entries read (originally /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name Segmentation fault john ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: question about eTIV calculation
Hello, I have a question about the eTIV intracranial volume calculation. My question is: Does the eTIV intracranial volume include everything interior to the outer pial surface (excluding the skull, eyes, neck and dura), and does it also include the CSF? That's all. Thank you for your time. john drozd ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: segmentation fault when running mris_anatomical_stats
Hello again, Sorry, I forgot to include the required info: john FREESURFER_HOME: /trumpet/downloads/FreeSurfer/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0 RedHat release: Fedora release 10 (Cambridge) Kernel info: Linux 2.6.27.21-170.2.56.fc10.x86_64 x86_64 - Please include the following additional information in your report: 1) subject name: convertedfile 2) the entire command-line executed: mris_anatomical_stats -mgz -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -cf ../label/aparc.annot.ctab convertedfile lh 3) the error message generated: Segmentation fault 4) optionally include the subject's /script/recon-all.log On Tue, May 26, 2009 at 2:23 PM, John Drozd wrote: > Hello, > > I am running the reconall steps individually for a firts try. > > I noticed that I get a segmentation fault when I run mris_anatomical_stats > as whown below: > > [jdr...@trumpet mri]$ mris_anatomical_stats -mgz -f > ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -cf > ../label/aparc.annot.ctab convertedfile lh > INFO: assuming MGZ format for > volumes. > computing statistics for each annotation in ../label/lh.aparc.annot. > reading volume > /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/mri/wm.mgz... > reading input surface > /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/surf/lh.white... > reading input pial surface > /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/surf/lh.pial... > reading input white surface > /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/surf/lh.white... > reading colortable from annotation file... > colortable with 35 entries read (originally > /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) > Saving annotation colortable ../label/aparc.annot.ctab > > table columns are: > number of vertices > total surface area (mm^2) > total gray matter volume (mm^3) > average cortical thickness +- standard deviation (mm) > integrated rectified mean curvature > integrated rectified Gaussian curvature > folding index > intrinsic curvature index > structure name > > Segmentation fault > > john > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Re: question about eTIV calculation
Hi Doug, Thank you for your clarification. I checked Randy Buckner's paper, and it did include the CSF based on my interpretation of the paper's Fig. 3 images of the manual tracings in atlas space. john On Tue, May 26, 2009 at 3:08 PM, Douglas N Greve wrote: > > The eTIV we report is not based on counting voxels inside the skull. > Instead, it is based on a statistical relationship between the TIV computed > from a manual segmentation and the talairach transfrom (see Randy Buckner's > paper). I don't know whether the original manual segs included CSF (I assume > it did). > > doug > > John Drozd wrote: > >> Hello, >> >> I have a question about the eTIV intracranial volume calculation. >> >> My question is: >> >> Does the eTIV intracranial volume include everything interior to the outer >> pial surface >> (excluding the skull, eyes, neck and dura), and does it also include the >> CSF? >> >> That's all. >> Thank you for your time. >> >> john drozd >> >> >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Re: segmentation fault when running mris_anatomical_stats
Hi Doug, It is writing to the trumpet directory which is not full. It does write out the output file aparc.annot.ctab, but seg faults at the end. Here is the df -h output for the trumpet directory (775Gb are available): [jdr...@trumpet label]$ df -h FilesystemSize Used Avail Use% Mounted on /dev/md2 50G 7.7G 40G 17% / /dev/md3 862G 43G 775G 6% /trumpet /dev/md0 122M 21M 95M 19% /boot tmpfs 3.0G 952K 3.0G 1% /dev/shm nil:/people/j 185G 180G 3.1G 99% /people/j nil:/scratch 62G 60G 1.1G 99% /scratch nil:/irus 40G 38G 2.0G 95% /net/nil/irus nil:/local 40G 38G 2.0G 95% /localaparc.annot.ctab The subject is not an average subject but is part of an Alzheimer's study. I have not done any manual interventions/corrections in freesurfer (maybe I should at this stage). I am just running the commands for a first try. Thanks, john On Tue, May 26, 2009 at 3:13 PM, Douglas N Greve wrote: > Can you verify that the disk it is writing to is not full? > > Is this an average subject? > > doug > > John Drozd wrote: > >> Hello again, >> >> Sorry, I forgot to include the required info: >> >> john >> >> FREESURFER_HOME: /trumpet/downloads/FreeSurfer/freesurfer >> >> Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0 >> >> RedHat release: Fedora release 10 (Cambridge) >> >> Kernel info: Linux 2.6.27.21-170.2.56.fc10.x86_64 x86_64 >> >> - >> Please include the following additional information in your report: >> >> 1) subject name: convertedfile >> >> 2) the entire command-line executed: >> mris_anatomical_stats -mgz -f ../stats/lh.aparc.stats -b -a >> ../label/lh.aparc.annot -cf ../label/aparc.annot.ctab convertedfile lh >> >> 3) the error message generated: >> Segmentation fault >> >> 4) optionally include the subject's /script/recon-all.log >> >> >> On Tue, May 26, 2009 at 2:23 PM, John Drozd > john.dr...@gmail.com>> wrote: >> >>Hello, >> >>I am running the reconall steps individually for a firts try. >> >>I noticed that I get a segmentation fault when I run >>mris_anatomical_stats as whown below: >> >>[jdr...@trumpet mri]$ mris_anatomical_stats -mgz -f >>../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -cf >>../label/aparc.annot.ctab convertedfile lh >> INFO: assuming MGZ format for >>volumes. computing >> statistics for each annotation in ../label/lh.aparc.annot. >>reading volume >> >> >> /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/mri/wm.mgz... >>reading input surface >> >> >> /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/surf/lh.white... >>reading input pial surface >> >> >> /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/surf/lh.pial... >>reading input white surface >> >> >> /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/surf/lh.white... >>reading colortable from annotation file... >>colortable with 35 entries read (originally >> >> /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) >>Saving annotation colortable ../label/aparc.annot.ctab >> >>table columns are: >>number of vertices >>total surface area (mm^2) >>total gray matter volume (mm^3) >>average cortical thickness +- standard deviation (mm) >>integrated rectified mean curvature >>integrated rectified Gaussian curvature >>folding index >>intrinsic curvature index >>structure name >> >>Segmentation fault >> >>john >> >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Re: segmentation fault when running mris_anatomical_stats
Hi Doug, ./stats/lh.aparc.stats does NOT exist, but it still seg faulted when I have chmod'd -R 777 the mri directory recursively. john On Tue, May 26, 2009 at 3:43 PM, Douglas N Greve wrote: > Does ../stats/lh.aparc.stats exist and do you have write perms to the file > and directory? > > John Drozd wrote: > >> Hi Doug, >> >> It is writing to the trumpet directory which is not full. >> It does write out the output file aparc.annot.ctab, but seg faults at the >> end. >> >> Here is the df -h output for the trumpet directory (775Gb are available): >> >> [jdr...@trumpet label]$ df -h >> FilesystemSize Used Avail Use% Mounted on >> /dev/md2 50G 7.7G 40G 17% / >> /dev/md3 862G 43G 775G 6% /trumpet >> /dev/md0 122M 21M 95M 19% /boot >> tmpfs 3.0G 952K 3.0G 1% /dev/shm >> nil:/people/j 185G 180G 3.1G 99% /people/j >> nil:/scratch 62G 60G 1.1G 99% /scratch >> nil:/irus 40G 38G 2.0G 95% /net/nil/irus >> nil:/local 40G 38G 2.0G 95% /localaparc.annot.ctab >> >> The subject is not an average subject but is part of an Alzheimer's study. >> I have not done any manual interventions/corrections in freesurfer (maybe >> I should at this stage). >> I am just running the commands for a first try. >> >> Thanks, >> john >> >> On Tue, May 26, 2009 at 3:13 PM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >>Can you verify that the disk it is writing to is not full? >> >>Is this an average subject? >> >>doug >> >>John Drozd wrote: >> >>Hello again, >> >>Sorry, I forgot to include the required info: >> >>john >> >>FREESURFER_HOME: /trumpet/downloads/FreeSurfer/freesurfer >> >>Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0 >> >>RedHat release: Fedora release 10 (Cambridge) >> >>Kernel info: Linux 2.6.27.21-170.2.56.fc10.x86_64 x86_64 >> >> >> - >>Please include the following additional information in your >>report: >> >> 1) subject name: convertedfile >> >> 2) the entire command-line executed: >> mris_anatomical_stats -mgz -f ../stats/lh.aparc.stats -b >>-a ../label/lh.aparc.annot -cf ../label/aparc.annot.ctab >>convertedfile lh >> >> 3) the error message generated: >> Segmentation fault >> >> 4) optionally include the subject's /script/recon-all.log >> >> >>On Tue, May 26, 2009 at 2:23 PM, John Drozd >>mailto:john.dr...@gmail.com> >><mailto:john.dr...@gmail.com <mailto:john.dr...@gmail.com>>> >> >>wrote: >> >> Hello, >> >> I am running the reconall steps individually for a firts try. >> >> I noticed that I get a segmentation fault when I run >> mris_anatomical_stats as whown below: >> >> [jdr...@trumpet mri]$ mris_anatomical_stats -mgz -f >> ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -cf >> ../label/aparc.annot.ctab convertedfile lh >> INFO: assuming MGZ format for >> volumes. >> computing statistics for each annotation in >>../label/lh.aparc.annot. >> reading volume >> >> /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/mri/wm.mgz... >> reading input surface >> >> /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/surf/lh.white... >> reading input pial surface >> >> /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/surf/lh.pial... >> reading input white surface >> >> /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/surf/lh.white... >> reading colortable from annotation file... >> colortable with 35 entries read (originally >> >> /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) >> Saving annotation colortable ../label/aparc.annot.ctab >> >> table columns are: >>
Re: [Freesurfer] Re: segmentation fault when running mris_anatomical_stats
Hi Doug, I fixed the problem. i had given the path ../stats when I should have used ./stats. Now it works: [jdr...@trumpet mri]$ mris_anatomical_stats -mgz -f ./stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -cf ../label/aparc.annot.ctab convertedfile lh INFO: assuming MGZ format for volumes. computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/mri/wm.mgz... reading input surface /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/surf/lh.white... reading input pial surface /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/surf/lh.pial... reading input white surface /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/surf/lh.white... reading colortable from annotation file... colortable with 35 entries read (originally /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 11531 7108 11411 1.451 1.619 0.114 0.089 36637.0 unknown 1295891 2178 2.425 0.532 0.117 0.028 11 1.6 bankssts 974704 1943 2.590 0.832 0.154 0.042 19 1.8 caudalanteriorcingulate 3260 2212 5748 2.385 0.505 0.125 0.049 55 8.0 caudalmiddlefrontal 1872 1196 2383 1.811 0.445 0.147 0.051 28 4.0 cuneus 693467 2361 3.584 0.791 0.147 0.088 15 2.6 entorhinal 4796 3279 9604 2.589 0.699 0.147 0.053 90 9.8 fusiform 6161 4063 10836 2.339 0.646 0.137 0.052 9211.4 inferiorparietal 5067 3375 10530 2.586 0.756 0.152 0.064 11813.1 inferiortemporal 1081705 1860 2.360 0.767 0.153 0.063 22 2.6 isthmuscingulate 9902 6468 15926 2.218 0.616 0.158 0.063 18423.8 lateraloccipital 3797 2613 7013 2.505 0.749 0.159 0.113 246 9.2 lateralorbitofrontal 3856 2526 5376 1.978 0.679 0.155 0.071 16311.9 lingual 2341 1578 3433 2.080 0.657 0.134 0.038 35 4.0 medialorbitofrontal 4354 2924 9107 2.554 0.666 0.144 0.046 78 8.0 middletemporal 769504 1623 2.774 0.850 0.113 0.0358 1.0 parahippocampal 2055 1262 3268 2.334 0.684 0.112 0.038 31 3.8 paracentral 2055 1402 3801 2.422 0.485 0.125 0.034 25 2.9 parsopercularis 1020701 1920 2.208 0.573 0.177 0.076 25 3.7 parsorbitalis 1792 1213 2899 2.136 0.498 0.126 0.035 23 2.7 parstriangularis 2111 1441 2038 1.504 0.381 0.158 0.067 34 6.2 pericalcarine 6149 3918 7916 1.801 0.569 0.115 0.037 73 9.4 postcentral 1685 1152 3253 2.559 0.744 0.175 0.072 45 5.2 posteriorcingulate 7186 4460 12819 2.523 0.621 0.112 0.040 9110.8 precentral 4656 3134 7658 2.347 0.599 0.141 0.041 63 7.7 precuneus 981704 2271 2.797 0.920 0.174 0.080 25 3.1 rostralanteriorcingulate 8129 5573 13843 2.126 0.559 0.146 0.052 14716.5 rostralmiddlefrontal 10613 7339 19998 2.361 0.608 0.134 0.044 15017.1 superiorfrontal 10405 6830 17061 2.194 0.647 0.133 0.038 13815.6 superiorparietal 5177 3505 10352 2.580 0.610 0.119 0.054 58 6.5 superiortemporal 5240 3516 9413 2.368 0.520 0.136 0.093 293 9.9 supramarginal 342235766 2.442 0.556 0.203 0.082 12 1.3 frontalpole 667458 2300 3.769 0.639 0.143 0.0499 1.4 temporalpole 679385913 2.282 0.333 0.124 0.0477 1.1 transversetemporal Thanks for all your help. john On Tue, May 26, 2009 at 3:43 PM, Douglas N Greve wrote: > Does ../stats/lh.aparc.stats exist and do you have write perms to the file > and directory? > > John Drozd wrote: > >> Hi Doug, >> >> It is writing to the trumpet directory which is not full. >> It does write out the output file aparc.annot.ctab, but seg faults at the >> end. >> >> Here is the df -h output for the trumpet directory (775Gb are available): >> >> [jdr...@trumpet label]$ df -h >> FilesystemSize Used Avail Use% Mounted on >> /dev/md2 50G 7.7G
[Freesurfer] source code for FreeSurfer and comparison with Neuroquant
Hello, I am reviewing the papers outlined in the "FreeSurfer Analysis Pipeline Overview". I would find it helpful if I could download the source code for FreeSurfer. Please let me know if this is at all possible. Also I was wondering how different Cortech's commercial sister program to FreeSurfer called Neuroquant is from FreeSurfer? Other than Neuroquant being able to be used clinically, I was wondering if the functionality is different. Thank you for your time, John Drozd Postdoctoral Fellow Robarts Research Institute Medical Imaging Department The University of Western Ontario London, Ontario, Canada ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Invitation to connect on LinkedIn
LinkedIn Freesurfer, I'd like to add you to my professional network on LinkedIn. - John Confirm that you know John Drozd https://www.linkedin.com/e/isd/1058664165/nSlXVFJx/ -- (c) 2010, LinkedIn Corporation___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] measuring cortical thickness using FreeSurfer
Hi, I am running freesurfer on 64 bit Fedora 10 linux. I am using version: freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0. Can anyone point me to a reference web page listing what steps I need to type to process a series of MRI dicom slices and use FreeSurfer to measure cortical thickness for this dicom series? Thank you, John -- John Drozd Post-Doctoral Fellow, Robarts Research Institute The University of Western Ontario London, ON, Canada http://publish.uwo.ca/~jdrozd2/index.htm ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] measuring cortical thickness using FreeSurfer
Hi Bruce and Pedro, Thank you both for sending me your suggestions. Just to let you know, because my .dcm (dicom) files had a space and two dots in the filenames: (e.g. "2008_12_08.ek -0035-0001-1.dcm" ) (and using quotes around the file name or "\ " within the filename without the quotes did not work with recon-all), recon-all truncated the filename before the space as "2008_12_08.ek" feeding it to an mri_convert command and gave an error message. So I worked around this problem as follows: I converted the .dcm series to a nifti .nii volume using 3D Slicer, and then used mri_convert to convert the .nii format to .mgz format. Then I ran recon-all on the .mgz formatted file and it is now running successfully. I see on the online tutorials and slides, that this process takes about 20 hours. Is there a way to only run partial steps pertaining only to the cortical thickness? Pedro also suggested that I go through the FreeSurferBeginnersGuide wiki which I am doing now. Also, reading some mailing lists emails, I noticed that matlab can be used to analyze the cortical thickness statistiics, and also freesurfer comes with matlab scripts. I will try these tools out as well. Thank you for your time, John On Tue, Jul 5, 2011 at 1:18 PM, Bruce Fischl wrote: > recon-all \ >-i \ >-s \ >-sd \ >-all > > > cheers > Bruce > > > > On Tue, 5 Jul 2011, John Drozd wrote: > > Hi, >> >> I am running freesurfer on 64 bit Fedora 10 linux. >> I am using version: freesurfer-Linux-centos4_x86_**64-stable-pub-v4.3.0. >> Can anyone point me to a reference web page listing what steps I need to >> type to process >> a series of MRI dicom slices and use FreeSurfer to measure cortical >> thickness for this dicom series? >> >> Thank you, >> John >> >> -- >> John Drozd >> Post-Doctoral Fellow, Robarts Research Institute >> The University of Western Ontario >> London, ON, Canada >> http://publish.uwo.ca/~**jdrozd2/index.htm<http://publish.uwo.ca/%7Ejdrozd2/index.htm> >> >> >> >> > ___ > Freesurfer mailing list > Freesurfer@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. > > -- John Drozd Post-Doctoral Fellow, Robarts Research Institute The University of Western Ontario London, ON, Canada http://publish.uwo.ca/~jdrozd2/index.htm ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] measuring cortical thickness using FreeSurfer
Hi Bruce, Okay, thank you. I understand and can see that to do an accurate job, the pipeline must be complicated. I have eight processors on my linux desktop computer. Maybe some parts of recon-all are multi-threaded which could speed things up for me :-) Thank you, John 2011/7/5 Bruce Fischl > sorry, but the majority of the time is required. We're working to speed > things up, but it is complicated software with multiple nonlinear warps, > segmentation procedures, etc > > > Bruce > > > > On Tue, 5 Jul 2011, John Drozd wrote: > > Hi Bruce and Pedro, >> >> Thank you both for sending me your suggestions. >> Just to let you know, because my .dcm (dicom) files had a space and two >> dots >> in the filenames: >> (e.g. "2008_12_08.ek -0035-0001-1.dcm" ) >> (and using quotes around the file name or "\ " within the filename without >> the quotes did not work with recon-all), recon-all truncated the filename >> before the space as "2008_12_08.ek" feeding it to an mri_convert command >> and >> gave an error message. >> >> So I worked around this problem as follows: I converted the .dcm series to >> a >> nifti .nii volume using 3D Slicer, and then used mri_convert to convert >> the >> .nii format to .mgz format. Then I ran recon-all on the .mgz formatted >> file >> and it is now running successfully. >> >> I see on the online tutorials and slides, that this process takes about 20 >> hours. Is there a way to only run partial steps pertaining only to the >> cortical thickness? >> >> Pedro also suggested that I go through the FreeSurferBeginnersGuide wiki >> which I am doing now. >> >> Also, reading some mailing lists emails, I noticed that matlab can be used >> to analyze the cortical thickness statistiics, and also freesurfer comes >> with matlab scripts. I will try these tools out as well. >> >> Thank you for your time, >> John >> >> On Tue, Jul 5, 2011 at 1:18 PM, Bruce Fischl >> wrote: >> recon-all \ >> -i \ >> -s \ >> -sd \ >> -all >> >> >> cheers >> Bruce >> >> >> >> On Tue, 5 Jul 2011, John Drozd wrote: >> >> Hi, >> >> I am running freesurfer on 64 bit Fedora 10 linux. >> I am using version: >> freesurfer-Linux-centos4_x86_**64-stable-pub-v4.3.0. >> Can anyone point me to a reference web page listing what >> steps I need to >> type to process >> a series of MRI dicom slices and use FreeSurfer to measure >> cortical >> thickness for this dicom series? >> >> Thank you, >> John >> >> -- >> John Drozd >> Post-Doctoral Fellow, Robarts Research Institute >> The University of Western Ontario >> London, ON, Canada >> >> http://publish.uwo.ca/~**jdrozd2/index.htm<http://publish.uwo.ca/%7Ejdrozd2/index.htm> >> >> >> >> >> __**_ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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. >> >> >> >> >> -- >> John Drozd >> Post-Doctoral Fellow, Robarts Research Institute >> The University of Western Ontario >> London, ON, Canada >> http://publish.uwo.ca/~**jdrozd2/index.htm<http://publish.uwo.ca/%7Ejdrozd2/index.htm> >> >> >> >> -- John Drozd Post-Doctoral Fellow, Robarts Research Institute The University of Western Ontario London, ON, Canada http://publish.uwo.ca/~jdrozd2/index.htm ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] measuring cortical thickness using FreeSurfer
Hi Bruce, Thanks for the suggestion, Bruce. I'll run 8 different subjects at once. Take care, John 2011/7/5 Bruce Fischl > Sorry, that won't help a single subject much, although there are options to > run the hemis in parallel. You can run multiple subjects at the same time, > which is what we usually do. Or you can use cuss > > > > On Jul 5, 2011, at 5:11 PM, John Drozd wrote: > > Hi Bruce, > > Okay, thank you. I understand and can see that to do an accurate job, the > pipeline must be complicated. > I have eight processors on my linux desktop computer. > Maybe some parts of recon-all are multi-threaded which could speed things > up for me :-) > > Thank you, > John > > 2011/7/5 Bruce Fischl < > fis...@nmr.mgh.harvard.edu> > >> sorry, but the majority of the time is required. We're working to speed >> things up, but it is complicated software with multiple nonlinear warps, >> segmentation procedures, etc >> >> >> Bruce >> >> >> >> On Tue, 5 Jul 2011, John Drozd wrote: >> >> Hi Bruce and Pedro, >>> >>> Thank you both for sending me your suggestions. >>> Just to let you know, because my .dcm (dicom) files had a space and two >>> dots >>> in the filenames: >>> (e.g. "2008_12_08.ek -0035-0001-1.dcm" ) >>> (and using quotes around the file name or "\ " within the filename >>> without >>> the quotes did not work with recon-all), recon-all truncated the filename >>> before the space as "2008_12_08.ek" feeding it to an mri_convert command >>> and >>> gave an error message. >>> >>> So I worked around this problem as follows: I converted the .dcm series >>> to a >>> nifti .nii volume using 3D Slicer, and then used mri_convert to convert >>> the >>> .nii format to .mgz format. Then I ran recon-all on the .mgz formatted >>> file >>> and it is now running successfully. >>> >>> I see on the online tutorials and slides, that this process takes about >>> 20 >>> hours. Is there a way to only run partial steps pertaining only to the >>> cortical thickness? >>> >>> Pedro also suggested that I go through the FreeSurferBeginnersGuide wiki >>> which I am doing now. >>> >>> Also, reading some mailing lists emails, I noticed that matlab can be >>> used >>> to analyze the cortical thickness statistiics, and also freesurfer comes >>> with matlab scripts. I will try these tools out as well. >>> >>> Thank you for your time, >>> John >>> >>> On Tue, Jul 5, 2011 at 1:18 PM, Bruce Fischl < >>> fis...@nmr.mgh.harvard.edu> >>> wrote: >>> recon-all \ >>> -i \ >>> -s \ >>> -sd \ >>> -all >>> >>> >>> cheers >>> Bruce >>> >>> >>> >>> On Tue, 5 Jul 2011, John Drozd wrote: >>> >>> Hi, >>> >>> I am running freesurfer on 64 bit Fedora 10 linux. >>> I am using version: >>> freesurfer-Linux-centos4_x86_**64-stable-pub-v4.3.0. >>> Can anyone point me to a reference web page listing what >>> steps I need to >>> type to process >>> a series of MRI dicom slices and use FreeSurfer to measure >>> cortical >>> thickness for this dicom series? >>> >>> Thank you, >>> John >>> >>> -- >>> John Drozd >>> Post-Doctoral Fellow, Robarts Research Institute >>> The University of Western Ontario >>> London, ON, Canada >>> <http://publish.uwo.ca/%7Ejdrozd2/index.htm> >>> http://publish.uwo.ca/~**jdrozd2/index.htm >>> >>> >>> >>> >>> __**_ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> 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 >>> >>>
