Freesurfer December 2012

freesurfer@nmr.mgh.harvard.edu

101 participants
161 discussions

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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ooops deleted fsaverage
by Joshua Lee 14 Dec '12

14 Dec '12

do I need to download the whole freesurfer package again to get it? - Josh

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Re: [Freesurfer] Contents of SUBJECTS_DIR
by Douglas N Greve 14 Dec '12

14 Dec '12

On 12/14/2012 04:51 PM, Tudor Popescu wrote: > Thanks Doug! I tried figuring out how to create symlinks manually (as > I think recon-all has already been run in the case of the group > analysis tutorial, therefore they were not generated automatically) > but could not find anything helpful on the wiki. cd $SUBJECTS_DIR ln -s $FREESURFER_HOME/fsaverage > > I also looked for a tutorial on how to run recon-all on raw NIFTI > files (which I guess first have to be converted to MGZ), as I'd first > have to do this step to my own data before starting to follow the > steps described in the group analysis tutorial. You can just spec the nifti file as input (--i file.nii), you do not need to convert doug > > Tudor > > On 14 December 2012 21:23, Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > Hi Tudor, you can create a symbolic link to fsaverage rather than > copying it. > doug > > > On 12/14/2012 04:18 PM, Tudor Popescu wrote: > > Hello everyone, > > > > I'm following the group analysis tutorial, but have difficulty > getting > > all files in the right folders. I have my tutorial data set in > > //media/Dell/_FS/buckner_data// (a folder that is shared in my > > VirtualBox), and my original subjects folder in the default path of > > //home/virtualuser/freesurfer/subjects/. > > > > The tutorial page > > <http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data> suggests > > that the data set should be inside /$FREESURFER_HOME/subjects/, > > however I have no room in my virtual drive to copy over the > whole data > > set, and VirtualBox is making it difficult for me to extend its > size. > > I have thus defined SUBJECTS_DIR to > be//media/Dell/_FS/buckner_data//, > > but then the first command of the analysis (mris_preproc) says it > > can't find fsaverage! > > > > The command only works if I create a new folder and copy the > following > > in there: > > > > * the contents of //group_analysis_tutorial/ (i.e. folders of the > > type /004/, /008/, ..), and > > * the contents of//home/virtualuser/freesurfer/subjects/ (i.e. > > folders such as /bert/, /fsaverage/, ..) > > > > ..and then run the command from there -- however, this seems very > > cumbersome and takes a lot of time. > > > > My question: does one always have to copy the fsaverage folder > > manually at the same level as the data folders, or does it have > to be > > the other way around (i.e. data set copied into default //subjects/ > > folder)? Can't there be two environment variables, one for > fsaverages > > and one for the data set, so that no moving/copying is necessary? > > > > Many thanks for any help! > > Tudor > > > > > > _______________________________________________ > > 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 > Fax: 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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Contents of SUBJECTS_DIR
by Tudor Popescu 14 Dec '12

14 Dec '12

Hello everyone, I'm following the group analysis tutorial, but have difficulty getting all files in the right folders. I have my tutorial data set in * /media/Dell/_FS/buckner_data/* (a folder that is shared in my VirtualBox), and my original subjects folder in the default path of * /home/virtualuser/freesurfer/subjects*. The tutorial page <http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data>suggests that the data set should be inside *$FREESURFER_HOME/subjects*, however I have no room in my virtual drive to copy over the whole data set, and VirtualBox is making it difficult for me to extend its size. I have thus defined SUBJECTS_DIR to be*/media/Dell/_FS/buckner_data/ *, but then the first command of the analysis (mris_preproc) says it can't find fsaverage! The command only works if I create a new folder and copy the following in there: - the contents of */group_analysis_tutorial* (i.e. folders of the type * 004*, *008*, ..), and - the contents of* /home/virtualuser/freesurfer/subjects* (i.e. folders such as *bert*, *fsaverage*, ..) ..and then run the command from there -- however, this seems very cumbersome and takes a lot of time. My question: does one always have to copy the fsaverage folder manually at the same level as the data folders, or does it have to be the other way around (i.e. data set copied into default */subjects* folder)? Can't there be two environment variables, one for fsaverages and one for the data set, so that no moving/copying is necessary? Many thanks for any help! Tudor

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Freesurfer December 2012