Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

A personal invitation from binod
by binod (binod.thapachhetry＠gmail.com) via Shop It To Me 18 Dec '12

18 Dec '12

I got you on the list for Shop It To Me, and a spot is open. You should sign up now. BTW, I signed up for 'Daily.' Go here: http://www.shopittome.com/expiring_invitation/abv5a1d7feb -binod This private invitation will expire in 24 hours. binod (binod.thapachhetry(a)gmail.com) has sent you this email. If you do not want to receive these messages, paste the following link into your browser: http://www.shopittome.com/blocked_email/ZnJlZXN1cmZlckBubXIubWdoLmhhcnZhcmQ… Shop It To Me, Inc. 410 Townsend Street #150 San Francisco, CA 94107, USA.

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Re: [Freesurfer] WM-hypointensities
by Gabriel Gonzalez Escamilla 17 Dec '12

17 Dec '12

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Chunks of missing WM
by Jonathan Holt 17 Dec '12

17 Dec '12

I've had this happen a handful of times and I'm wondering what I can do about it. For reference using Freesurfer 5.0.0. Edited a brain and ran "recon-all -autorecon2 -autorecon3 -s subj_id" which completed without error. The resulting brain had chunks of missing auxiliary volume in areas that I had not touched at all. This is bizarre and I am not sure what to do about it. Images of said issue attached of both main and auxiliary volumes.

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Bus error in mri_ca_normalize w/ high-res data
by Fred Dick 17 Dec '12

17 Dec '12

Dear all I have been trying to recon a high-res (.75 isotropic) volume, which goes along fine until it hits a certain bit of mri_ca_normalize. I've run this 4 times and it always dies at the same point. There was also a previous unanswered post about 8 months ago showing an error at the same place http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21685.html ## Recon-all command: recon-all -all -cm -subjid dancar-750um2 # I checked the Talairach transform, which was OK. ## The mri_ca_normalize command as run by recon-all mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /Applications/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz ## The tail end of the log with the error Right_Cerebellum_White_Matter: limiting intensities to 98.0 --> 125.0 0 of 38 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (154, 160, 124) --> (194, 241, 166) Bus error Darwin rancate.lan 12.2.0 Darwin Kernel Version 12.2.0: Sat Aug 25 00:48:52 PDT 2012; root:xnu-2050.18.24~1/RELEASE_X86_64 x86_64 ## freesurfer install specifics: Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Kernel info: Darwin 12.2.0 x86_64 Thanks for any assistance, Fred

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Re: [Freesurfer] WM-hypointensities
by Douglas N Greve 17 Dec '12

17 Dec '12

The PV is done based on intensities. For each voxel an the boundary of an ROI, the voxel intensity is assumed to be a weighted summation of the the average intensities in each ROI. Knowing the average intensities in the ROIs and the actual intensity of the voxel, the PV can be computed. doug On 12/17/2012 09:59 AM, Gabriel Gonzalez Escamilla wrote: > Thanks Doug, > > In my case I did as you said but as Bruce recommend use the wmparc, so > the voxels less than 4000, and = 5001 were left , and more than or > equal to 4000, and =5002 were right. > > So different approach but I think would be the same, isn't it? > > Can you explain to me how FS makes the PV correction on the output > volumes in aseg.stats? > > > Best Regards, > Gabriel. > > > El 13/12/12, *Douglas N Greve * <greve(a)nmr.mgh.harvard.edu> escribió: >> >> Gabriel, the way I've done it is to just assign WMSA to left or right >> based on the column number of the WMSA voxel. If it is less than 128, >> then it is right (78) if it is greater than 128 it is left (79). It's >> not perfect, but it is correct in the vast majority of cases. >> doug >> >> >> On 12/12/2012 01:56 PM, Gabriel Gonzalez Escamilla wrote: >> >Thanks Bruce, >> > >> >The problem is that for this set of subjects I only have the T1s, >> anyways I would like to give a try onto the tools for WMSA, since I >> have T2 from some subjects. >> > >> >On the other hand, If I'm right the way to do the assignment on >> matlab, would be something like opening the mgz, finding their >> positions and look which are the neighbors right? >> >If so, I would like to not assign just the neighbor voxel, as this >> might bias the assignment, I'm guessing that something like the >> assignment done during the aparc+aseg.mgz creation (using GM >> parcelation to map GM labels to the wm voxels - mri_aparc2aseg) >> should be a correct way to do so. Can you point me to an article or >> explain to me how this works indeed, and how the decision to the >> belonging voxel is made, I think I know the basis, but not enough to >> make my own script. >> > >> >If I do not understand bad, is something like, you take a voxel a >> look to some contiguous voxels till you get into a point where all >> the contiguous voxels are too far from the seed, and are surrounded >> by lots of voxels belonging to other areas. I'm not quite sure about >> the decision about when to stop the search. I really think that the >> method like the implemented in the mri_apar2aseg is the perfect solution. >> > >> >Regards, >> >Gabriel >> > >> > >> > >> > >> >El 12/12/12, *Bruce Fischl * <fischl(a)nmr.mgh.harvard.edu> escribió: >> >>then I would either use TRACULA (if you have DWI) or the wmparc to >> generate ROIs. I meant that you could count whether there are more lh >> or rh wm labels neighboring each one to figure out which hemi they are in >> >> >> >>cheers >> >>Bruce >> >> >> >> >> >>On Wed, 12 Dec 2012, Gabriel Gonzalez Escamilla wrote: >> >> >> >>>Yes I did loo at the total WH-hypointensities(77), and substract >> them without a problem. >> >>> >> >>>What do you mean with lateralize them based on neighboring labels? >> How can I perform such thing on FS? >> >>> >> >>>Actually I'm interested in knowing to wich specific label o region >> they are. >> >>> >> >>>Bests, >> >>>Gabriel >> >>> >> >>> >> >>>El 12/12/12, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> escribió: >> >>> Hi Gabriel >> >>> >> >>> we don't lateralize them by default, so look for >> WM_hypointensities (77) instead. It would be pretty easy to >> >>> lateralize them based on neighboring labels. >> >>> >> >>> cheers >> >>> Bruce >> >>> >> >>> >> >>> On Wed, 12 Dec 2012, Gabriel Gonzalez Escamilla wrote: >> >>> >> >>> > >> >>> >Dear Freesurfers, >> >>> > >> >>> >I'm looking for a way to compute the left and right >> WM-hypointensities, as volume values or images. They always >> >>> appear empty in >> >>> >the aseg.stats, and the corresponding segs No 78 & 79 do >> not appear in the aseg.mgz, and I'm a bit lost with it. >> >>> > >> >>> >Can any one help me? >> >>> > >> >>> >Best Regards, >> >>> >Gabriel. >> >>> > >> >>> > >> >>> >> >>> >> >>> 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. >> >>> >> >>> >> >>>-- >> >>>-------------------------- >> >>>PhD. student Gabriel González-Escamilla >> >>>Laboratory of Functional Neuroscience >> >>>Department of Physiology, Anatomy, and Cell Biology >> >>>University Pablo de Olavide >> >>>Ctra. de Utrera, Km.1 >> >>>41013 - Seville >> >>>- Spain - >> >>> >> >>>Email: ggonesc(a)upo.es >> >>>http://www.upo.es/neuroaging/es/ >> >>> >> > >> >-- >> >-------------------------- >> >PhD. student Gabriel González-Escamilla >> >Laboratory of Functional Neuroscience >> >Department of Physiology, Anatomy, and Cell Biology >> >University Pablo de Olavide >> >Ctra. de Utrera, Km.1 >> >41013 - Seville >> >- Spain - >> > >> >Email: ggonesc(a)upo.es >> >http://www.upo.es/neuroaging/es/ >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)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/ >> > > -- > -------------------------- > PhD. student Gabriel González-Escamilla > Laboratory of Functional Neuroscience > Department of Physiology, Anatomy, and Cell Biology > University Pablo de Olavide > Ctra. de Utrera, Km.1 > 41013 - Seville > - Spain - > > Email: ggonesc(a)upo.es > http://www.upo.es/neuroaging/es/ -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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/

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what image should I finally work with?
by Prasanna M 17 Dec '12

17 Dec '12

I ran Freesurfer on OASIS longitudinal data with the longitudinal pipeline. I want to work with the full brain image (with gray level intensities) which is intensity normalized and skull stripped and all the timepoints of a subject are rigidly registered to the 1st time point. There were many brain mgz files created during the processing. What is the best final image which I should be working with? Thanks, Prasanna -- -- Let there be peace on earth... And let it begin with me.

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Re: [Freesurfer] Import % crop
by Douglas N Greve 17 Dec '12

17 Dec '12

yes, it should doug On 12/14/2012 07:43 PM, octavian lie wrote: > Dear Doug, > Thank you for your suggestions, > to be more clear, the original preresection volume was in old analyze > format (hdr/img), and was already processed through freesurfer, so I > have pre.mgz instead of pre.img. I do not have the pre.img any more, > but pre.mgz. Do the formulas still apply (with changing nii to img)? > Also, the postresection volume is .img. > Thank you, > Octavian. > > On Thu, Dec 13, 2012 at 11:52 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > On 12/12/2012 09:42 AM, octavian lie wrote: > > Dear All, > > Excuse the basic nature of these quetions. I coregistered 2 analyze > > volumes in SPM (pre and post resection MR scans for same > patient) with > > cost function masking. I imported the preresection scan in > Freesurfer, > > and processed it with recon -all. > > 1) What transform matrices should I multiply the postresection > scan to > > get it in the FS space in alignment with the processed preresection > > MR, and where do I find them? > If the two volumes are in alignment, then you can run > mri_vol2vol --mov post.nii --targ pre.nii --regheader --o > post-in-pre.nii > > To check that FS thinks that they are in alignment, you can run > tkregister2 --mov post.nii --targ pre.nii --regheader --reg junk.dat > > > > 2) Once in FS, how do I crop/mask the posteresection volume using > > saggittal, coronal or axial planes of my choosing? (I am > interested in > > generating a small cube containing the posteresection volume, then > > extracting the postresection volume itself by intensity > threshold (CSF > > vs surronding cavity wall brain) and masking with preresection > MR pial > > surface laterally). > You can use --crop and --cropsize options in tkmedit > mri_convert --crop 1 2 3 --cropsize 100 120 130 input.nii output.nii > > Please advise, > > Octavian. > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto: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. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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/

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about the ROI
by xiangbo_2010 17 Dec '12

17 Dec '12

Dear experts I had obtained the ROI label from Freesurfer, the following I want to obtain the FA value from DTI in this ROI, what should I do? Thanks! Bo Xiang

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regarding use-mritotal
by Eric Cunningham 17 Dec '12

17 Dec '12

Hi, this link: http://surfer.nmr.mgh.harvard.edu/fswiki/TalFailV5.1 discusses a solution to bad talairach.xfm transforms, the -use-mritotal flag. this link: http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV mentions that the talairach.xfm is used to calculate the total intracranial volume. is using mritotal likely to result in significantly different intracranial volumes even if the talairach.xfm does not appear to be very different when viewed? thanks much, -eric

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Areal measures: Winkler method
by Jürgen Hänggi 15 Dec '12

15 Dec '12

Dear FS and SD experts I tried to run the Winkler method for measuring surface area. I followed the instruction on http://brainder.org/download/areal/ and on https://sites.google.com/site/yeoyeo02/software/sphericaldemonsrelease. When I try to run the SphericalDemons (SD) example delivered with SD, the following error occurred: >> CoregisterSurfaces Read Uniform Meshes ??? Undefined function or method 'MARS_convertFaces2FacesOfVert' for input arguments of type 'int32'. Error in ==> MARS_readUniformMesh at 55 vertexFaces = MARS_convertFaces2FacesOfVert(faces, int32(size(vertices, 1))); Error in ==> CoregisterSurfaces at 197 reg_parms.meshes{1} = MARS_readUniformMesh(SD_atlas.parms.uniform_mesh_dir, 'ic4.tri'); Any idea what is wrong here? I use MATLAB 7.9.0 on Mac OS X Intel. Thanks in advance Regards Jürgen Hänggi ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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