Freesurfer June 2005

freesurfer@nmr.mgh.harvard.edu

35 participants
66 discussions

RE: [Freesurfer] vertex correspondance
by Fornito, Alexander 22 Jun '05

22 Jun '05

Is there some kind of correspondance between them that is specified in any of the files? I'm thinking of trying to use something like the link method (desrcibed in the Lerch & Evans, 2005 paper) for estimating thickness, but as I understand it, there needs to be some kind of established link between the points on each surface. -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 6/22/2005 9:20 PM To: Fornito, Alexander Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] vertex correspondance Hi Alex, yes, all the surfaces of a hemisphere (except qsphere) have the same # of vertices/edges and faces. I think Doug has something that will sample the mask. mri_vol2label or something like that? Bruce On Wed, 22 Jun 2005, Fornito, Alexander wrote: > Hi again, > > So many questions!! > > Is there some sort of correspondence between vertices on the inner (wm) > and outer (pial) surfaces? Ie., for every vertex on the inner surface, > is there a point on the outer surface, and if so, does Freesurfer retain > this information in any of the files? > > > > Also, I have some binary masks that I have manually traced using another > program that I would like to apply to the surfaces to get regional > measures of thickness. The mask images are in analyze format. Is there > any way that I can do this? > > Thanks as always, > > Alex > > > > > > Alexander Fornito > > M.psych (Clin. Neuro.)/PhD candidate > > Melbourne Neuropsychiatry Centre and Department of Psychology > > The University of Melbourne > > alexander.fornito(a)wh.org.au > > > >

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vertex correspondance
by Fornito, Alexander 22 Jun '05

22 Jun '05

Hi again, So many questions!! Is there some sort of correspondence between vertices on the inner (wm) and outer (pial) surfaces? Ie., for every vertex on the inner surface, is there a point on the outer surface, and if so, does Freesurfer retain this information in any of the files? Also, I have some binary masks that I have manually traced using another program that I would like to apply to the surfaces to get regional measures of thickness. The mask images are in analyze format. Is there any way that I can do this? Thanks as always, Alex Alexander Fornito M.psych (Clin. Neuro.)/PhD candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito(a)wh.org.au

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some data for FreeSurfer presentation
by Renat Yakupov 21 Jun '05

21 Jun '05

Hello. I was wondering if you could help me with the following. I need to prepare a short ~30 min presentation on FreeSurfer to medium-to-advanced level MRI (e.g. research coordinators and people actually acquiring, processing and analyzing MR data). Are there any resources, in addition to FreeSurfer homepage, on FreeSurfer techniques, data processing, etc? I also need to mention any other software packages that can calculate and analyze cortical thickness and maybe do sub-cortical grey matter segmentation. Is there any other software available for free out there? Any input would be appreciated! Thank you. Regards, Renat.

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RE: [Freesurfer] mris_glm
by Fornito, Alexander 21 Jun '05

21 Jun '05

Fantastic. I really appreciate all your help!! -----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Tuesday, June 21, 2005 11:00 PM To: Fornito, Alexander Cc: Freesurfer Mailing List; Bruce Fischl Subject: RE: [Freesurfer] mris_glm Alex, Attached is the make_average_surface script. Copy it to the freesurfer/bin directory, and be sure to make it executable (run 'chmod 755 make_average_surface' in the freesurfer/bin directory). Type 'make_average_surface' to get help. Basically, just the subject names are required. By default, a 'subject' named 'average' will be created from your set of subjects (a name instead of 'average' can be specified on the command line). Nick ps. I am working on the mris_surface seg-fault problem using the rh.orig file that you sent. On Tue, 2005-06-21 at 08:23 -0400, Bruce Fischl wrote: > Hi Alex, > > you're better off using the make_average_surfaces.csh script to make an > average of your subjects. Nick: can you send Alex a copy? > > thanks, > Bruce > On Tue, 21 Jun > 2005, Fornito, Alexander wrote: > > > Def. sounds worth doing then! I'll give it a try. > > My other question is, where can I get my hands on the average7? It's > > used as the target in the mris_glm examples, but I haven't been able to > > find the actual average7 surface in any of the freesurfer directories. > > Am I missing something? > > Thanks again, > > Alex > > > > -----Original Message----- > > From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] > > Sent: Tuesday, June 21, 2005 4:11 PM > > To: Fornito, Alexander > > Cc: freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] mris_glm > > > > > > You can run with just the design matrix, but you won't be able to use > > the cool fsgdf stuff in tksurfer (Load->FSGDF). The fsgdf is a way to > > specify how to build the des mtx. The fsgdf keeps track of what the > > regressors mean (eg, Age, Class, IQ, etc). When you save the > > preprocessed data with --y, you'll see that there will be an fsgdf > > file saved with it. Load this in tksurfer, click on a point, and you > > will be able to make a scatter plot of, say, thickness vs age, with > > each class (eg, Male, Female) having a different color dot in the > > scatter plot. When you mouse-over the dot, it tells you the subject > > name. Click on a new point and you'll see the scatter plot for that > > point. If you use --xmat, you can save the design matrix (in matlab-4 > > format). > > > > doug > > > > > > On Tue, 21 Jun 2005, Fornito, Alexander wrote: > > > >> Hi, > >> > >> I was seeking some clarification re: the relationship between the > > fsgdf > >> and design matrix file for use with mris_glm. It seems to me that the > >> two contain very similar info, the examples in the -help don't use the > >> fsdf at all. Is it necessary to create one, or can you just run an > >> analysis with the desmtx? > >> > >> Thanks, > >> > >> Alex > >> > >> > >> > >> Alexander Fornito > >> > >> M.psych (Clin. Neuro.)/PhD candidate > >> > >> Melbourne Neuropsychiatry Centre and Department of Psychology > >> > >> The University of Melbourne > >> > >> alexander.fornito(a)wh.org.au > >> > >> > >> > >> > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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RE: [Freesurfer] mris_glm
by Fornito, Alexander 21 Jun '05

21 Jun '05

Def. sounds worth doing then! I'll give it a try. My other question is, where can I get my hands on the average7? It's used as the target in the mris_glm examples, but I haven't been able to find the actual average7 surface in any of the freesurfer directories. Am I missing something? Thanks again, Alex -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Tuesday, June 21, 2005 4:11 PM To: Fornito, Alexander Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_glm You can run with just the design matrix, but you won't be able to use the cool fsgdf stuff in tksurfer (Load->FSGDF). The fsgdf is a way to specify how to build the des mtx. The fsgdf keeps track of what the regressors mean (eg, Age, Class, IQ, etc). When you save the preprocessed data with --y, you'll see that there will be an fsgdf file saved with it. Load this in tksurfer, click on a point, and you will be able to make a scatter plot of, say, thickness vs age, with each class (eg, Male, Female) having a different color dot in the scatter plot. When you mouse-over the dot, it tells you the subject name. Click on a new point and you'll see the scatter plot for that point. If you use --xmat, you can save the design matrix (in matlab-4 format). doug On Tue, 21 Jun 2005, Fornito, Alexander wrote: > Hi, > > I was seeking some clarification re: the relationship between the fsgdf > and design matrix file for use with mris_glm. It seems to me that the > two contain very similar info, the examples in the -help don't use the > fsdf at all. Is it necessary to create one, or can you just run an > analysis with the desmtx? > > Thanks, > > Alex > > > > Alexander Fornito > > M.psych (Clin. Neuro.)/PhD candidate > > Melbourne Neuropsychiatry Centre and Department of Psychology > > The University of Melbourne > > alexander.fornito(a)wh.org.au > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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mris_glm
by Fornito, Alexander 21 Jun '05

21 Jun '05

Hi, I was seeking some clarification re: the relationship between the fsgdf and design matrix file for use with mris_glm. It seems to me that the two contain very similar info, the examples in the -help don't use the fsdf at all. Is it necessary to create one, or can you just run an analysis with the desmtx? Thanks, Alex Alexander Fornito M.psych (Clin. Neuro.)/PhD candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito(a)wh.org.au

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ERROR: nu_correct
by Margaret Duff 17 Jun '05

17 Jun '05

Hi, I have just recently gotten an error when running recon-all-nmr. I am on the computer troy and my command line is recon-all-nmr -stage1 -subjid SM2S2 and my SUBJECTS_DIR is /space/troy/1/users/FREESURFER. I tried resetting my LANG to C and en_US and neither made a difference. It seems like it can't find a start up file, which I found in /usr/lib/perl5/5.8.5/MNI, but this doesn't seem to be one of the paths its looking in. Is there anything I can do to prevent this error? I have attached the error file from the terminal window below. Thanks, Margaret (nmr-std-env) recon-all-nmr -stage1 -subjid SM2S2 ######################################## program versions used $Id: recon-all-nmr,v 1.53 2004/12/08 20:45:06 greve Exp $ $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ mri_convert --version stable2 minctracc.c $Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $ mri_convert --version stable2 # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ # $Id: nu_estimate.in,v 1.1 2003/04/16 14:29:34 bert Exp $ stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 stable2 ####################################### INFO: SUBJECTS_DIR is /autofs/space/troy_001/users/FREESURFER WARNING: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer/beta Previous: /usr/local/freesurfer/dev --------------------------------------------- MotionCor Fri Jun 17 16:16:50 EDT 2005 /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig mri_motion_correct2 -o . -i 001 -i 002 tmpdir is ./tmp-mri_motion_correct2-27002 -------------------------------------------------------------- mri_motion_correct2 logfile is ./mri_motion_correct2.log -------------------------------------------------------------- ----------------------------------------- Converting 001 Fri Jun 17 16:16:54 EDT 2005 mri_convert 001 /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-1.mnc ^[[B^[[A^[[B^[[B^[[B^[[Breading from 001... TR=2730000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -0) j_ras = (-0, 0, -1) k_ras = (-0, 1, -0) writing to /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-1.mnc... ----------------------------------------- Converting 002 Fri Jun 17 16:17:06 EDT 2005 mri_convert 002 /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc reading from 002... TR=2730000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -0) j_ras = (-0, 0, -1) k_ras = (-0, 1, -0) writing to /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc... ----------------------------------------- Motion Correcting /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc Fri Jun 17 16:17:17 EDT 2005 COG of v1: 4.496311 15.253652 -23.867643 COG of v2: 4.493972 15.296473 -24.011532 [trans] = -0.002339 0.042821 -0.143888 Initial objective function val = 0.01666989 Final objective function value = 0.01148322 successful write ----------------------------------------- Resampling /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/cor-2.mnc Fri Jun 17 16:18:21 EDT 2005 Transforming slices:................................................................................................................................................................................................................................................................Done ----------------------------------------- Averaging Fri Jun 17 16:18:27 EDT 2005 Processing:................................................................................................................................................................................................................................................................Done ----------------------------------------- Converting Average to output Fri Jun 17 16:18:32 EDT 2005 mri_convert /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/avgvol.mnc . -tr 2.73e+06 -te 0 -TI 0 -flip_angle 0 reading from /autofs/space/troy_001/users/FREESURFER/SM2S2/mri/orig/tmp-mri_motion_correct2-27002/avgvol.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -0) j_ras = (-0, 0, -1) k_ras = (-0, 1, -0) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions writing to .... Started at: Fri Jun 17 16:16:54 EDT 2005 Ended at: Fri Jun 17 16:18:41 EDT 2005 mri_motion_correct2: done --------------------------------------------- Nu Intensity Correction Fri Jun 17 16:18:41 EDT 2005 mri_convert orig nu0.mnc mri_convert orig nu0.mnc reading from orig... TR=2730000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -0) j_ras = (-0, 0, -1) k_ras = (-0, 1, -0) writing to nu0.mnc... nu_correct -clobber nu0.mnc nu1.mnc Can't locate MNI/Startup.pm in @INC (@INC contains: /usr/lib/perl5/5.8.5/i386-linux-thread-multi /usr/lib/perl5/5.8.5 /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl/5.8.4 /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl/5.8.4 /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 /usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at /usr/pubsw/packages/mni/current/bin/nu_correct line 37. BEGIN failed--compilation aborted at /usr/pubsw/packages/mni/current/bin/nu_correct line 37. ERROR: nu_correct ------------------------------------------ Filesystem 1K-blocks Used Available Use% Mounted on troy:/local_mount/space/troy/1 201855952 169100440 32755512 84% /autofs/space/troy_001 ------------------------------------------ recon-all exited with errors at Fri Jun 17 16:18:53 EDT 2005

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skull-stripping hi-res monkey data
by florent segonne 16 Jun '05

16 Jun '05

Hello, mri_watershed was specifically designed for the skull-stripping of human brain data. Not surprisingly, it might fail on hi-res monkey data. However, here is a short watershed trouble shooting guide that might help you find a valid set of options to successfully skull-strip your images. Good Luck, Best, Florent ----------------------------------------------------------- WATERSHED TROUBLESHOUTING GUIDE: I am putting below some suggestions about how to find the correct set of parameters without spending too much time on it. I think that there are sufficient options to get a correct skull-stripping on almost every sca ns. Before getting into the details, you have to know that mri_watershed is a pipelined process, composed of two main steps. The first one ends with the first template smoothing and is composed of 3 substeps (watershed segmentation, post-processing and first template smoothing). The second step corresponds to a fine template deformation. HOW TO PROCEED TO OBTAIN A VALID SKULL-STRIPPING (when it fails with the default options): * If the skull-stripping fails, my first suggestion is to try to understand why it is failling. Rerun the mri_watershed program with the -surf_debug option, which writes out two surfaces into the output volume (first template smoothing and fine template deformation). V * Looking at the output, there are two possibilities: either the first step fails (this corresponds to the first template smoothing, which is the exterior surface into the output volume), or the second step fails (the fine template deformation = the interior surface). Let's analyze the two cases separately: 1) Failing of the first segmentation step. This first step is the result of 3 pipelined sub-steps: watershed segmentation, post-processing and first template smoothing. In order to fix the problem, there are a few choices about how to proceed. 1-1) "I-am-feeling-lucky" choice: you might want to go down this path, if the skull-stripping removed a few brain regions. The best option is probably to try to add seed points in the excluded brain regions (with the -s option), even though you could increase the preflooding height (-h option). In my experience, there is no point in trying thousand of values for the preflooding height. A couple of tries are sufficient. If it does not work for these, then, try with more seed points... 1-2) "what-is-failling" approach: since the program fails during the first step, it could come either from the watershed segmentation, or the post-processing step, or the first template smoothing. One way to find out is to first run the program with the option -wat and -n: this will stop the program right after the watershed segmentation before the post-processing. If the segmentation is already failing, try adding seed points with the option -s or play with the preflooding height -h. In my experience, the best way to quickly find the right set of parameters is to use seed points (potentially lots of them). In order to find the right set of parameters, just run the program with the options "-wat -n". This will be much faster. nce the right set of parameters have been found, run the program with the "-n" option, as the postprocessing step should be useless... If the program fails after the watershed processing, then this means that the post-processing is probably producing the errors. This is often resulting in too much tissue being included. Simply run the program with the "-n" option. 2) In case of failure during the second step (fine surface deformation), you have several option (most failures come from the first step). 2-1) if you think that the first step produced a correct segmentation, you can directly stop the segmentation at this point with the -wat+temp option. 2-2) you think that the first step produced a good intialization for the brain surface and that it needs to be refined a little: use the -first_temp option. 2-3) try the -atlas option that will incorporate shape information into the deformation process and should give some correct results! IN SUMMARY: 1) Try to understand what's happening with the option "-surf_debug" 2) Try the option "-atlas" if the program advises you to do so, or try it too if you have time for it (~10 minutes)! "I usually skip this step". 3) Depending on what you see with the surf_debug option, you may try to correct the watershed segmentation or the fine segmentation. * To correct the watershed segmentation, you can: - play with the preflooding height (use the -wat option to visualize the result quickly, without having to run all the program). - modify or suppress the post-watershed analysis mode (-n to suppress the post_watershed analysis, -t to change the threshold used in the merging of the basins). - use some (lots of) seed points... THIS IS WHAT WORKS BEST AND QUICKLY. IMPORTANT: In order to experiment with the options -n, -h, -s, don't forget to run the program with the option -wat. (no need to run all the program). SOME OTHER MODE ADVANCED TIPS: o You can set the global parameters manually, if you think that the ones found during the process are incorrect: this is the -man option. You would have to precise the csf max, the transition intensity, and the gray matter intensity. o The difference between -first_temp and -wat+temp is that the first option will use the first surface to compute the local intensity values at the border of the brain and then try to shrink it a bit. The second option -wat_temp will only use the first surface and immediately segment the brain out. PARTIAL LIST OF OPTIONS (command line: "mri_watershed -option") Option -wat : option that stops the algorithm after the initial watershed segmentation (the post-analyze segmentation is included). Option -h hpf , with hpf an integer: modification of the preflooding height used in the watershed segmentation. A typical value for hpf is 25 (corresponding to 25% of the maximal intensity); lower values tend to decrease the size of the main basin (which could be infirmed by the post-analyze process) and higher values increase its size. However, for any given image, the preflooding height hpf can be varied over a certain range without significantly changing the output. Option -n : the post-analyze is not used with this option. Option -t th, with th an integer: that option specifies the threshold used in the post-watershed analysis. The default value is 100 (100%, meaning that the threshold is exactly the cubic root of the size of the ambiguous basin). A value of 0 will result in a post-watershed analysis that will merge any ambiguous basin with the main one. Option -wat+temp : with this option, only the watershed segmentation and the first template deformation is used. This option could be typically used when the image contains a lot of artifacts, resulting in a fine surface segmentation that shaves some part of the cortex; in that extreme case, the watershed segmentation may still lead to successful results and the first template deformation to a valid brain segmentation. Options -less or -more: option designed to increase or decrease the transition threshold used in the fine surface. The result is respectively a shrunk or expanded surface compared to the typical surface. Option -surf_debug: this option will write out, into the output volume, the localization of the different surfaces used during the algorithm; it will enable the user to visualize the results of the different template deformations, and eventually to detect, understand and correct some errors. Option -s int_i int_j int_k : this option allows the user to add some new seed points for the watershed process. This option is very useful when the cerebellum is removed by the watershed segmentation, since a seed point inside the removed cerebellum may be added, leading to the merging of the corresponding basin with the main one. However, the atlas-based validation-correction step should be sufficient to correct the segmentation. Option -man int_CSF int_transition int_GM: this option allows the user to manually set the parameters used in the fine surface deformation. Option -surf surface_name: this option is used to generate tessellated surfaces of the brain, inner and outer skull, and outer scalp from the T1-weighted image. The brain surface is the one produced by the fine surface deformatio n described. The outer scalp surface is generated by another surface deformation. However, the MRI-based force is quite simple, since the scalp appears bright on T1-weighted images. The deformation is initialized with a radius set to include the whole head, and a series of iterative deformation matches the surface onto the head scalp-skin. The outer and inner skull surfaces are much harder to find, since the skull and the cerebrospinal fluid look the same in these type of images (dark intensity). Besides, the skull may contain some fat tissue that makes the border between the scalp and the outer skull difficult to localize. For these reasons, the two surfaces, outer skull and inner skull, are respectively interpolated from the outer scalp and brain surface. They are a smoothed version of the corresponding surface that has been respectively shrunk or expanded a few millimeters inwards or outwards (3 mm). Option -brainsurf surface_name: that option writes out the final tessellated brain surface. Option -shk_br_surf hshk surface_name: this option writes out the final tessellated brain surface that has been shrunk hshk mm inwards. Option -LABEL: this option enables the user to obtain a labeled volume into 5 classes: scalp, skull, csf, gray and white matter. First the whole algorithm is run and the surfaces corresponding to the brain, outer scalp, outer skull, inner skull are estimated. Based on the localization of these surfaces, we label the volume into brain, scalp, skull, and csf ; then, the brain segment is divided into gray an white matter based on the intensity statistics calculated during the template deformation process. Option -atlas: with that option, the program uses an atlas, compiled from successfully segmented brains, in order to detect the rightness of the surface, and to eventually correct it. That should solve some of the problems, especially those when the cerebellum is removed (or part of it!). Option -first_temp: with that option, the final deformation uses the first template deformation as a starting point. ------------------------------------- Florent Segonne PhD Candidate Stata Center 32-D430 CSAIL MIT 1 617 253 2986 http://people.csail.mit.edu/~fsegonne ------------------------------------- On Thu, 5 May 2005, Bruce Fischl wrote: > Hi Flo, > > could you send your watershed troubleshooting guide to the BWH folks (ccd) so > they can include it in the manual? > > thanks, > Bruce > >

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skullstripping hi-res monkey data
by Bell, Andrew (NIH/NIMH) 15 Jun '05

15 Jun '05

Greetings Fellow FreeSurfers, I've been having some trouble skull stripping some hi-res monkey data and was wondering if anyone had some tips for a newbie: The data is 256*256*256, 0.5mm3 I've normalized using the following: mri_normalize -no1d -f ../tmp/control.dat -n 1 orig T1 and it yields a very nice set of brain images (good contrast between wm and gm). there is some very intense areas outside the brain (muscles) - i don't know whether that has an effect. When I try "mri_watershed T1 brain", it runs (and takes a LONG time) to completion but the images are essentially untouched from the T1 images. There are several warnings (e.g., mean intensity may be too low) which it looks like it tries to adjust for but again... no success. Any help is greatly appreciated!!! Andy Andrew H. Bell, PhD Laboratory of Brain and Cognition National Institute of Mental Health Bethesda Maryland USA

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RE: [Freesurfer] recon-all stage3
by Fornito, Alexander 15 Jun '05

15 Jun '05

I'll keep an eye one it. As an aside, I tried to run freesurfer on an image acquired at 3T (I converted it to 8 bit first), and got an error during stage1 of recon-all. I've included the relevant bits below. Any ideas? Transforming slices:...............................................................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:..........................................................................................................................................................................................................................................................................................................................................Done mri_convert nu/nu4.mnc nu mri_convert nu/nu4.mnc nu reading from nu/nu4.mnc... DimSizes: 3, 330, 330, 330, 1 DataType: 1 MINC Linear Transform -1.0000 0.0000 0.0000 165.0000 0.0000 0.0000 1.0000 -165.0000 0.0000 -1.0000 0.0000 165.0000 0.0000 0.0000 0.0000 1.0000 Done reading minc TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) Original Data has (1, 1, 1) mm size and (330, 330, 330) voxels. Data is conformed to 1 mm size and 330 voxels for all directions writing to nu... non-standard value for imnr1 (330, usually 256) in volume structure non-standard value for width (330, usually 256) in volume structure non-standard value for height (330, usually 256) in volume structure ... #it then seems to proceed as normal until I get this: --------------------------------------------- Tessellate rh Tue Jun 14 18:34:47 EST 2005 mri_tessellate /data/flanders/work/alex/freesurfer/subjects/mw_3T/mri/filled 127 /data/flanders/work/alex/freesurfer/subjects/mw_3T/surf/rh.orig /data/flanders/work/alex/freesurfer/subjects/mw_3T/scripts warning: non-standard value for imnr1 (330, usually 256) in file /data/flanders/work/alex/freesurfer/subjects/mw_3T/mri/filled/COR-.info warning: non-standard value for x (330, usually 256) in file /data/flanders/work/alex/freesurfer/subjects/mw_3T/mri/filled/COR-.info warning: non-standard value for y (330, usually 256) in file /data/flanders/work/alex/freesurfer/subjects/mw_3T/mri/filled/COR-.info slice 80: 25 vertices, 35 faces slice 90: 2235 vertices, 2414 faces slice 100: 7950 vertices, 8225 faces slice 110: 14980 vertices, 15343 faces slice 120: 24760 vertices, 25210 faces slice 130: 35948 vertices, 36485 faces slice 140: 47251 vertices, 47791 faces slice 150: 59398 vertices, 59994 faces slice 160: 69840 vertices, 70396 faces slice 170: 79968 vertices, 80513 faces slice 180: 89126 vertices, 89647 faces slice 190: 97517 vertices, 98045 faces slice 200: 104180 vertices, 104653 faces slice 210: 110417 vertices, 110849 faces slice 220: 115639 vertices, 116067 faces slice 230: 120291 vertices, 120699 faces slice 240: 123600 vertices, 123982 faces slice 250: 125319 vertices, 125574 faces slice 260: 125319 vertices, 125574 faces slice 270: 125319 vertices, 125574 faces slice 280: 125319 vertices, 125574 faces slice 290: 125319 vertices, 125574 faces slice 300: 125319 vertices, 125574 faces slice 310: 125319 vertices, 125574 faces slice 320: 125319 vertices, 125574 faces slice 330: 125319 vertices, 125574 faces using the conformed surface RAS to save vertex points... writing /data/flanders/work/alex/freesurfer/subjects/mw_3T/surf/rh.orig --------------------------------------------- Smooth1 rh Tue Jun 14 18:35:32 EST 2005 mris_smooth /data/flanders/work/alex/freesurfer/subjects/mw_3T/surf/rh.orig /data/flanders/work/alex/freesurfer/subjects/mw_3T/surf/rh.smoothwm /data/flanders/work/alex/freesurfer/subjects/mw_3T/scripts Segmentation fault ------------------------------------------ Filesystem 1k-blocks Used Available Use% Mounted on /dev/hda9 130282400 12524220 111140208 11% /data/flanders ------------------------------------------ recon-all exited with errors at Tue Jun 14 18:35:33 EST 2005 -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 6/15/2005 12:33 PM To: Fornito, Alexander Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] recon-all stage3 then you should just run the rest of the analysis I guess and see if it works. In general all the surfaces of a hemisphere should have the same # of edges/faces/vertices *except* the ?h.qsphere surface. They should have all have an euler number of 2. cheers, Bruce On Wed, 15 Jun 2005, Fornito, Alexander wrote: > > Hi Bruce, > I ran the topology fixer again and it seemed to work. Unfortunately, silly me just wrote over the original files, so all I have is the euler number from the orig surface that is output in the recon-all log. > > > Euler Number lh Sat Jun 11 04:20:04 EST 2005 > /data/flanders/work/alex/freesurfer/subjects/1000192 > mris_euler_number /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.orig > euler # = v-e+f = 2g-2: 179761 - 539277 + 359518 = 2 --> 0 holes > F =2V-4: 359518 = 359522-4 (0) > 2E=3F: 1078554 = 1078554 (0) > > total defect index = 0 > Euler: NHoles = 0 > > > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Tue 6/14/2005 10:12 PM > To: Fornito, Alexander > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] recon-all stage3 > Hi Alex, > > that's a starnge one. Did the partition run out of space? Can you do an ls > -l in the surf dir and send it along? Also, run mris_euler_number on > lh.orig, lh.smoothwm, lh.inflated and lh.qsphere. > > > > On Tue, 14 Jun 2005, Fornito, > Alexander wrote: > >> Hi, >> I got an error when running recon-all -stage3.I've included the relevant part of the log below. Any ideas as to what went wrong? >> Thanks, >> alex >> >> writing spherical brain to /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.qsphere >> spherical transformation took 0.91 hours >> navgs=32 and tol=1.000e-01 >> integrating with navgs=32 and tol=1.000e-01 >> integrating with navgs=8 and tol=1.000e-01 >> taking momentum steps... >> integrating with navgs=8 and tol=1.000e-01 >> integrating with navgs=8 and tol=1.000e-01 >> integrating with navgs=2 and tol=1.000e-01 >> taking momentum steps... >> integrating with navgs=2 and tol=1.000e-01 >> integrating with navgs=2 and tol=1.000e-01 >> integrating with navgs=0 and tol=1.000e-01 >> pass 1 complete, delta sse/iter = 0.16/60 = 0.00 >> final distance error %31.34 >> optimization complete. >> unfolding took 0.81 hours >> --------------------------------------------- >> Fix Topology lh Sat Jun 11 04:24:54 EST 2005 >> /data/flanders/work/alex/freesurfer/subjects/1000192/scripts >> mris_fix_topology 1000192 lh >> reading input surface /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.qsphere... >> before topology correction, eno=-301 (nv=188932, nf=378516, ne=567749, g=151) >> mrisReadTriangleFile(/data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.orig): surface doesn't match /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.qsphere >> >> No such file or directory >> mrisReadTriangleFile failed. >> >> No such file or directory >> MRISreadOriginalProperties: could not read surface file orig >> No such file or directory >> mris_fix_topology: could not read original surface orig >> No such file or directory >> reading T1 volume from T1... >> reading wm segmentation from wm... >> >> recon-all exited with errors at Sat Jun 11 04:24:58 EST 2005 >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > > >

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Freesurfer June 2005