Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30086 discussions

Surface file coordinate system
by John Schulman 14 Sep '10

14 Sep '10

I'm looking at an ascii version of a surface file generated by freesurfer. #!ascii version of patch ./lh.orig. The 1st index is not a vertex number 150463 299577 1 vno=0 27.392525 -134.276505 -66.754089 2 vno=1 27.100813 -134.257095 -66.985382 3 vno=2 26.631136 -134.229446 -67.306076 4 vno=3 29.255196 -134.120728 -65.788467 etc. In what coordinate system are these vertices? I want to convert to ijk index from the anatomical volume used to make the surface.

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Re: [Freesurfer] problem of mri_vol2surf
by Douglas N Greve 13 Sep '10

13 Sep '10

The 27307 x 6 was originally done to be able to store data in nifti and analyze formats. They can be reshaped into a single vector of length 163842. When you load it into tksurfer, do you set the threshold to something very close to 0 to see if your values are just too small? Is everything 0 in matlab? Did you check the registration? doug Jing Ming wrote: > Hi Doug: > > what I meant here is when we load output file on fsaverage surface, > we can see nothing. And I have a question, why the mri_vol2surf need > to reshape the whole vertex vector into 27307 x 6 dimention? > > Reshaping 6 (nvertices = 163842) > > > Writing to ./sig-rh.mgh > > > Dim: 27307 1 6 > > I have been able to load this mgh file into matlab, and should I > just need to concatenate the six row of data to reconstruct a complete > vector corresponding to the suface template? > > Thanks much for your help! > > Jing > > > > > > > Date: Mon, 13 Sep 2010 13:19:40 -0400 > > From: greve(a)nmr.mgh.harvard.edu > > To: mj_coming(a)hotmail.com > > CC: freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] problem of mri_vol2surf > > > > what do you mean that you were not able to overlay it on the surface? > > What is actually going wrong? It looks like mri_vol2surf complete > > succesffully. > > > > doug > > > > Jing Ming wrote: > > > Hi surfers: > > > > > > I was trying to convert a volume dataset from PET to fs surface > > > template. The command I used is the following: > > > > > > mri_vol2surf --src pet2t1.mgz --srcreg register.dat --hemi rh --o > > > ./sig-rh.mgh --out_type mgh --float2int round --trgsubject ico > > > --icoorder 7 > > > > > > The output file here is .mgh format. I also tried paint format. > > > However, I was not able overlay the surface file (.mgh or .w) using > > > freesufer. Is there anythign wrong with the command line? > > > > > > Here is the the output log: > > > ************************************************** > > > IcoOrder = 7, nIcoVtxs = 163842 > > > srcvol = pet2t1.mgz > > > srcreg = register.dat > > > srcregold = 0 > > > srcwarp unspecified > > > surf = white > > > hemi = rh > > > trgsubject = ico > > > surfreg = sphere.reg > > > interp = nearest > > > float2int = round > > > GetProjMax = 0 > > > INFO: float2int code = 0 > > > Done loading volume > > > Reading surface > /project/ADNI/PET/127_S_1210X1a_63646/127_S_1210X1a_63646/surf/rh.white > > > Done reading source surface > > > Mapping Source Volume onto Source Subject Surface > > > 1 0 0 0 > > > vol2surf_linear: nhits = 152282/152282 > > > Done mapping volume to surface > > > Number of source voxels hit = 94326 > > > Reading source surface registration > > > > /project/ADNI/PET/127_S_1210X1a_63646/127_S_1210X1a_63646/surf/rh.sphere.reg > > > Done loading source registration surface > > > Reading icosahedron, order = 7, radius = 100 > > > Reading icosahedron /pkg/brainmap/freesurfer/lib/bem/ic7.tri > > > Done loading target registration surface > > > Mapping Surfaces (127_S_1210X1a_63646 -> ico) > > > surf2surf_nnfr: building source hash (res=16). > > > Surf2Surf: Forward Loop (163842) > > > > > > surf2surf_nnfr: building target hash (res=16). > > > Surf2Surf: Reverse Loop (152282) > > > Reverse Loop had 34160 hits > > > Surf2Surf: Dividing by number of hits (163842) > > > INFO: nSrcLost = 0 > > > Done mapping surfaces > > > nSrc121 = 116454, nSrcLost = 0, nSrcMulti = 35828, MnSrcMultiHits > = 2.2761 > > > nTrg121 = 138122, nTrgMulti = 25720, MnTrgMultiHits = 2.32815 > > > Reshaping 6 (nvertices = 163842) > > > Writing to ./sig-rh.mgh > > > Dim: 27307 1 6 > > > ************************************************** > > > > > > Thanks > > > Jing Ming > > > Northwestern University > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)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 > > 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 > > > > _______________________________________________ > > 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. > > -- 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

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Re: [Freesurfer] Re-run FreeSurfer with V.5.0
by Gina Caetano 13 Sep '10

13 Sep '10

Hello, Version 4.2.0 was used to start processing data for a 3-years project. We are still acquiring data for the project, and would like to start using version 5.0. For some of the subjects already processed, manual talairach alignment was performed with tkregister2, and as I understood when recon-all -autorecon1 is run it will not overwrite this alignment. Former processing also contains manual edits to the brainmsak.mgz, wm.mgz as well as control points, and as I understood when re-running autorecon2 the manual edits will be saved by default. Thus, I am thinking to re-run all the recon-all steps when changing from v4.2 to v.5.0. Would you advise it? Thank you all in advance, Gina

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problem of mri_vol2surf
by Jing Ming 13 Sep '10

13 Sep '10

Hi surfers: I was trying to convert a volume dataset from PET to fs surface template. The command I used is the following: mri_vol2surf --src pet2t1.mgz --srcreg register.dat --hemi rh --o ./sig-rh.mgh --out_type mgh --float2int round --trgsubject ico --icoorder 7 The output file here is .mgh format. I also tried paint format. However, I was not able overlay the surface file (.mgh or .w) using freesufer. Is there anythign wrong with the command line? Here is the the output log: ************************************************** IcoOrder = 7, nIcoVtxs = 163842 srcvol = pet2t1.mgz srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = ico surfreg = sphere.reg interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Reading surface /project/ADNI/PET/127_S_1210X1a_63646/127_S_1210X1a_63646/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 vol2surf_linear: nhits = 152282/152282 Done mapping volume to surface Number of source voxels hit = 94326 Reading source surface registration /project/ADNI/PET/127_S_1210X1a_63646/127_S_1210X1a_63646/surf/rh.sphere.reg Done loading source registration surface Reading icosahedron, order = 7, radius = 100 Reading icosahedron /pkg/brainmap/freesurfer/lib/bem/ic7.tri Done loading target registration surface Mapping Surfaces (127_S_1210X1a_63646 -> ico) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (152282) Reverse Loop had 34160 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 116454, nSrcLost = 0, nSrcMulti = 35828, MnSrcMultiHits = 2.2761 nTrg121 = 138122, nTrgMulti = 25720, MnTrgMultiHits = 2.32815 Reshaping 6 (nvertices = 163842) Writing to ./sig-rh.mgh Dim: 27307 1 6 ************************************************** Thanks Jing Ming Northwestern University

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Missing structures lh.aparc.stats
by Jordi Delgado 13 Sep '10

13 Sep '10

Dear FS experts, We are using the 4.3.1 version of FreeSurfer, and we have noticed that in the lh.aparc.stats/rh.aparc.stats file there are 35 structures calculated and not 36 structures, only corpuscallosum is missing. We have also compared it with an old subject processing (using 4.0.2 version of FreeSurfer) where corpuscallosum structure has been calculated... Is this a known bug or maybe have we an error in our FS configuration or recon-all parameters? Thank you in advance, /Jordi.

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problem with mri_vol2surf
by ythomas 13 Sep '10

13 Sep '10

Hi, I am trying to sample a volume of integers in subject's anatomical space to fsaverage surf. However, the output does not seem to be integer valued anymore even though I specify nearest neighbor for interpolation type. I tried both stable4 and the dev version and used the following command: mri_vol2surf --regheader 090425_QF86JB_FS --mov /autofs/cluster/ con_003/users/ythomas/test_mri_vol2surf/090425_QF86JB_FS/data/ 090425_QF86JB_vol2vol.nii.gz --hemi lh --projfrac .5 --trgsubject fsaverage --o /autofs/cluster/con_003/users/ythomas/test_mri_vol2surf/ 090425_QF86JB_FS/data/lh.090425_QF86JB_vol2surf.nii.gz --reshape -- interp nearest You can replicate the results, by going to /autofs/cluster/con_003/users/ythomas/test_mri_vol2surf/ and running "test_script.csh" Interestingly, if I replace "fsaverage" in the trgsubject with the subject as the trgsubject (projection onto the same subject's surface), the output remained integer valued. I am not sure how mri_vol2surf works, but perhaps the step from the subject's surface to the fsaverage's surface is messed up? Thanks, Thomas

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Using freesurfer over NoMachine connection
by Christopher deCharms 13 Sep '10

13 Sep '10

We are hoping to view a Freesurfer session running on Fedora 13 using NoMachine. So far, we have not succeeded. Freesurfer runs fine locally, and NoMachine is otherwise working fine to display output. However, when running qdec (for example), we get the following error: ERROR: In /usr/pubsw/packages/vtk/5.6.0/src/Rendering/vtkXOpenGLRenderWindow.cxx, line 405 vtkXOpenGLRenderWindow ()xc30a6d0): Could not find a decent visual. Using tkmedit and tksurfer produces similar errors involving GLUT. Looking through the other user posts, it appears that it is possible to use freesurfer over NoMachine, and that there is something about setting it up for OpenGL required, but we have not succeeded. We are using the current, free version of NoMachine. We have minimal linux configuration ability, so significant detail/explanation regarding any configuration required would be very helpful. Thanks very much for your help CdC

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wm edits to fix memory error
by Mishkin Derakhshan 12 Sep '10

12 Sep '10

I don't think this made it through to the list the first time... Hi, Like others on the list I got the ran out of memory error, which seems to be the result of a gross error somewhere: CORRECTING DEFECT 1 (vertices=109084, convex hull=14490) Excessive topologic defect encountered: could not allocate 649386741 edges for retessellation Cannot allocate memory Linux bach 2.6.24-27-server #1 SMP Fri Mar 12 01:23:09 UTC 2010 x86_64 GNU/Linux recon-all -s freesurfer_results exited with ERRORS at Thu Sep 9 22:15:45 EDT 2010 Anyway, it looks like my skull strip is okay, but my wm.mgz and thus my filled.mgz files are where I have the gross errors. It looks like a lot of WM voxels are missing, and not just due to lesions. Skull: http://imgur.com/hJO5U.jpg WM: http://imgur.com/r6nGT.jpg Filled: http://imgur.com/LanJS.jpg My questions is, should I just fix the WM using this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits, or is this a problem at the normalization step, or is there something else I can try? thanks, mishkin p.s i tired using 4.5.0 and 5.0.0

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FW: error messages in skull strip
by Zoltick, Brad (NIH/NIMH) [E] 10 Sep '10

10 Sep '10

Hi, I have been running subjects in Version 5, and notice there are consistently weird error messages in the skull strip section of recon-all.log. These look like: IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 006: -log(p) = 10319.2 tol 0.000010 Despite the log containing a few of these warnings, recon-all itself almost always completes “without errors, ” and the subjects appear to be fully processed. However, I have noticed a greater prevalence of bad skull strips compared to version 4.5. Does anyone know what this error means? Thanks, Brad Zoltick and Aaron Goldman

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two questions about freesurfer
by Dai Dai 10 Sep '10

10 Sep '10

Hi, all I am a new user of freesurfer and now I have two questions. 1. For my work, the number of vertex in surface data is too much to process. How can I downsample the surface mesh as well as the curvation file (e.g. thickness)? The vertex number of fsaverage template is ~160,000, normally more than that of every subject. Can I construct an average surface of less vertexes or downsample the fsaverage surface to that of ~20000 vertexes and then transform all the subjects using these templates with less vertexes (using recon-all -qcache)? 2. How can I convert the freesurfer surface format to gifti, with two hemisphere surfaces in one gifti file. And how can I write the parcellation of surface to another gifti file which is corresponding to the gifti of surface data? Many thanks. 2010-09-10 Neural Imaging Computation and Analysis Group, Key Lab of Complex Systems and Intelligent Science, Institute of Automation, Chinese Academy of Sciences(CASIA) Beijing, China

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Freesurfer