Freesurfer

freesurfer@nmr.mgh.harvard.edu

1 participants
30076 discussions

pial editing
by Derin Cobia 14 Feb '07

14 Feb '07

I have a question regarding editing the pial surface. Many times it includes bright spots, such as fat or vessels. Should I be editing this out? I'm pretty clear on getting rid of included dura, but if I spent the time to edit out every little bright spot, it would be pretty time intensive. Would leaving these little "extras" skew my data? Is there some balance I can strike when editing? Thanks! -Derin

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WM vol
by Nurunisa Neyzi 14 Feb '07

14 Feb '07

Hi, when I use mri_anatomical stats - I get a total WM value 503450 for left and right hemispheres that's the same number in the stats file in the stats folder. but when I use mris_wm_volume - I get 174896 and 178464 which one is the accurate one? also, is the GM volume I get from mris_anatomical_stats accurate? thanks, n. 174896 17464

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average thickness overlay per group
by Marie Schaer 14 Feb '07

14 Feb '07

Hello, I have a two groups comparison design, and I was wondering if there is any easy way to compute an average thickness file per group (in order to be able to overlay mean thickness values on my average subject). Is there an existing command or matlab function to do it? If yes, would I also be able to do a standard deviation file using the same command? Many thanks, Marie Schaer

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Reconstruction problems
by Fornito, Alexander 13 Feb '07

13 Feb '07

Hi, I'm having problems reconstructing the surface for one individual on an older version of recon-all (v. 1.104). It always seems to exit with no error message during mris_fix_topology. I've tried to re-run this subject several times, and even starting from scratch does not seem to help. I'm not sure why this is happening, as I've used this version of recon-all on hundreds of other images without any problem. There's no obvious difference between this image and any of the others that I can see by looking at the T1 (e.g., no apparent artifacts, etc.). I've attached recon-all.log. Any suggestions? Thanks, Alex Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1861 Fax: +61 3 9348 0469 email: alexander.fornito(a)wh.org.au

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(no subject)
by Nurunisa Neyzi 13 Feb '07

13 Feb '07

Hi, I am trying to color code my labels according to the stats associated with each label. I was playing with the colortable but that did not work. I will appreciate any guidance/ help on that. How can I give to a given label the color I want to? thanks, Nurunisa

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smoothing with mris_preproc
by Lars M. Rimol 12 Feb '07

12 Feb '07

Hi, If I don't specify any smoothing level when running mris_preproc, with --fwhm or --niters, does that mean that it won't apply any smoothing or is there a default smoothing level? -- yours, LMR

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display bilateral pial surface by tksurfer
by tulu 11 Feb '07

11 Feb '07

Dear freesurfer experts, Can I use tksurfer to display two surface volume ? how to display bilateral pial surface from same subject under tksurfer ? Thanks replay Sincerely Kl chen

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error with mri_ca_register
by Binyam Nardos 09 Feb '07

09 Feb '07

Hi Nick, I keep getting the same error with mri_ca_register. I have now tried this with two different subjects and they both fail at about the same stage. I have checked both brainmask.mgz files in tkmedit for any skull stripping or talairach registration errors and they look fine. Like you had recommended, I have also checked the messages in the /var/log directory but found nothing to suggest that the system was running out of memory. I'm fresh out of ideas. Please let me know if there's any other thing that comes to mind. I've attached the logs again for reference. Binyam Binyam Nardos Cognitive Rehabilitation Research Group Washington University School of Medicine Box # 8505 4444 Forest Park Blvd St. Louis, MO 63108 Office: (314) 454-7795 Fax: (314) 286-1601 The contents of this e-mail message and any attachments are intended solely for the addressee(s) named in this message. This communication is intended to be and to remain confidential and may be subject to applicable physician/patient and/or work product privileges. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message and its attachments. -----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Thu 2/8/2007 3:31 PM To: Binyam Nardos Subject: RE: [Freesurfer] error with mri_ca_register Binyam, My run of mri_ca_register using the stable rh9 build of freesurfer also completed successfully, so I was not able to recreate the segfault problem you are seeing. One thing I just learned is that you can view the file: /var/log/messages and check it for messages that say "Out of Memory". This sort of message would appear if a freesurfer binary (or any other) is unable to allocate memory. You will need root or sudo access to read the file on your system. Nick On Wed, 2007-02-07 at 16:46 -0600, Binyam Nardos wrote: > Nick, > upgrading my RAM is definitely on top of my list. As far as the > documentation that I mentioned, I don't think it's something you can > update. I just remembered that I had seen that on the > Dale/Fischl/Sereno 1999 paper (Cortical Surface-Based Analysis I), > which, I know is pretty old, vis-a-vis all the time-consuming changes > that I'm sure have been implemented since then. In any case, I think > the paper reads "The entire procedure, from intensity normalization, > through segmentation, tessellation, and inflation, runs completely > automatically in about 1.5h on current PC architectures ..." > > Binyam > > Binyam Nardos > Cognitive Rehabilitation Research Group > Washington University School of Medicine Box # 8505 > 4444 Forest Park Blvd > St. Louis, MO 63108 > Office: (314) 454-7795 > Fax: (314) 286-1601 > > > > The contents of this e-mail message and any attachments are intended solely for the addressee(s) named in this message. This communication is intended to be and to remain confidential and may be subject to applicable physician/patient and/or work product privileges. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message and its attachments. > > > ______________________________________________________________________ > From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > Sent: Wed 2/7/2007 4:35 PM > To: Binyam Nardos > Subject: RE: [Freesurfer] error with mri_ca_register > > > > The mri_ca_register step typically takes about 10 hours to complete. > It > took 9 hours 37 minutes on the 2GHz machine I ran it on yesterday. > > Also, 1GB of RAM is pretty low. All of our machines have at least 2GB > (our minimum recommended), most 4GB. This might actually be the > source > of your problem, as our code does not check when it runs out of memory > (very bad, I know). I'll know more when this second run completes. > But > if it is at all possible to upgrade to 2GB or 4GB of RAM, I *highly* > recommend it. I know with certainty that when someone on the mailing > list upgraded from 512MB to 2GB, these sorts of problems disappeared. > > Can you point me to the documentation that says the segmentation takes > 2-3 hours to complete? I'd like to update that. > > > On Wed, 2007-02-07 at 16:20 -0600, Binyam Nardos wrote: > > thanks Nick, > > I tried processing another subject yesterday and again got stuck > > somewhere around mri_ca_register, I believe it said (segmentation > > error ... sorry I dont' have the details because I'm in windows > world > > right now.) In any case, I had another quick question for you: > > I am running Freesurfer on ubuntu, which is installed on a separate > HD > > on my computer. Some of my specs are 1GB RAM, 3.2GHz dual processor. > > In some of the documetation that I've read, a typical pc takes about > > 2-3 hours for complete segmentation. It's been taking me about 3 > times > > that (i'm actually yet to fully segment a subject successfuly ). But > > is this normal? > > > > thanks again, > > Binyam > > > > Binyam Nardos > > Cognitive Rehabilitation Research Group > > Washington University School of Medicine Box # 8505 > > 4444 Forest Park Blvd > > St. Louis, MO 63108 > > Office: (314) 454-7795 > > Fax: (314) 286-1601 > > > > > > > > The contents of this e-mail message and any attachments are intended > solely for the addressee(s) named in this message. This communication > is intended to be and to remain confidential and may be subject to > applicable physician/patient and/or work product privileges. If you > are not the intended recipient of this message, or if this message has > been addressed to you in error, please immediately alert the sender by > reply e-mail and then delete this message and its attachments. > > > > > > > ______________________________________________________________________ > > From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > > Sent: Wed 2/7/2007 4:10 PM > > To: Binyam Nardos > > Subject: RE: [Freesurfer] error with mri_ca_register > > > > > > > > Binyam, > > > > I was able to run mri_ca_register successfully with this subject, > but > > I > > was using a 'development' build (not the one used publicly), and I > was > > running on a 64bit system. So this problem is not a blatant bug in > > the > > code. > > > > I am going to re-run mri_ca_register again, this time using the rh9 > > stable build (which is what you used) to see if I can get it to > > segfault > > (the problem that you are encountering). > > > > Nick > > > > > > On Tue, 2007-02-06 at 12:01 -0600, Binyam Nardos wrote: > > > thanks Nick > > > > > > Binyam > > > > > > Binyam Nardos > > > Cognitive Rehabilitation Research Group > > > Washington University School of Medicine Box # 8505 > > > 4444 Forest Park Blvd > > > St. Louis, MO 63108 > > > Office: (314) 454-7795 > > > Fax: (314) 286-1601 > > > > > > > > > > > > The contents of this e-mail message and any attachments are > intended > > > solely for the addressee(s) named in this message. This > > communication > > > is intended to be and to remain confidential and may be subject to > > > applicable physician/patient and/or work product privileges. If > you > > > are not the intended recipient of this message, or if this message > > has > > > been addressed to you in error, please immediately alert the > sender > > by > > > reply e-mail and then delete this message and its attachments. > > > > > > > > > > > > -----Original Message----- > > > From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > > > Sent: Tue 2/6/2007 11:41 AM > > > To: Binyam Nardos > > > Subject: RE: [Freesurfer] error with mri_ca_register > > > > > > Binyam > > > > > > I've received the files and will have a look at them today. > > > > > > Nick > > > > > > > > > On Tue, 2007-02-06 at 11:32 -0600, Binyam Nardos wrote: > > > > Hi Nick, > > > > I have just uploaded the 4 mgz files for the subject. I hope > > that's > > > > what you were looking for. I checked the skull-strip and > talairach > > > > registration and it looks fine. > > > > > > > > > > > > > > > > thanks, > > > > Binyam > > > > > > > > Binyam Nardos > > > > Cognitive Rehabilitation Research Group > > > > Washington University School of Medicine Box # 8505 > > > > 4444 Forest Park Blvd > > > > St. Louis, MO 63108 > > > > Office: (314) 454-7795 > > > > Fax: (314) 286-1601 > > > > > > > > > > > > > > > > The contents of this e-mail message and any attachments are > > intended > > > > solely for the addressee(s) named in this message. This > > > communication > > > > is intended to be and to remain confidential and may be subject > to > > > > applicable physician/patient and/or work product privileges. If > > you > > > > are not the intended recipient of this message, or if this > message > > > has > > > > been addressed to you in error, please immediately alert the > > sender > > > by > > > > reply e-mail and then delete this message and its attachments. > > > > > > > > > > > > > > > > -----Original Message----- > > > > From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > > > > Sent: Tue 2/6/2007 11:18 AM > > > > To: Binyam Nardos > > > > Cc: Freesurfer Mailing List > > > > Subject: Re: [Freesurfer] error with mri_ca_register > > > > > > > > Binyam, > > > > > > > > The recon-all.log indicates that mri_ca_register hit a > > segmentation > > > > fault, which is bad. Can you send me the subject data so that I > > can > > > > try > > > > to recreate this segfault in a debugger? You can upload to me > via > > > the > > > > filedrop: > > > > > > > > https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > > > In the meantime, also look at the brainmask.mgz file with > tkmedit > > > and > > > > confirm that it is skull-stripped and that the cerebellum is > > > attached. > > > > Also check the talairach registration with tkregister2. > > > > > > > > Nick > > > > > > > > > > > > On Tue, 2007-02-06 at 10:39 -0600, Binyam Nardos wrote: > > > > > hi all, > > > > > I just ran autorecon2 on one of our subjects (for the second > > time, > > > > > after getting a similar error, i.e. ERROR: mri_ca_register > with > > > non- > > > > > zero status. I just rerun recon-all with -autorecon2 without > > > > > removing/changing anything produced by the previous > autorecon2). > > > Is > > > > > there any logical place to start to fix the problem or do I > have > > > to > > > > > rerun mri_ca_register as shown below: > > > > > > > > > > mri_ca_register -align -nobigventricles -mask brainmask.mgz -T > > > > > transforms/talairach.lta > > > > > norm.mgz /usr/local/freesurfer//average/RB_all_2006-02-15.gca > > > > > transforms/talairach.m3z > > > > > > > > > > I have attached the recon-all log for reference. > > > > > Please advise, > > > > > > > > > > thanks, > > > > > Binyam > > > > > > > > > > > > > > > Binyam Nardos > > > > > Cognitive Rehabilitation Research Group > > > > > Washington University School of Medicine Box # 8505 > > > > > 4444 Forest Park Blvd > > > > > St. Louis, MO 63108 > > > > > Office: (314) 454-7795 > > > > > Fax: (314) 286-1601 > > > > > > > > > > > > > > > > > > > > The contents of this e-mail message and any attachments are > > > intended > > > > > solely for the addressee(s) named in this message. This > > > > communication > > > > > is intended to be and to remain confidential and may be > subject > > to > > > > > applicable physician/patient and/or work product privileges. > If > > > you > > > > > are not the intended recipient of this message, or if this > > message > > > > has > > > > > been addressed to you in error, please immediately alert the > > > sender > > > > by > > > > > reply e-mail and then delete this message and its attachments. > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >

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labels in matlab
by Nurunisa Neyzi 09 Feb '07

09 Feb '07

Hi, just a quick question, I am reading my annotation files into matlab following: [v, L, ct] = read_annotation(annotation_filename); Suppose N is the number of vertices. Then, (1) v = N x 1 vector, v(i) = i-1 (you can usually ignore v) (2) L = N x 1 vector, L(i) = label of ith vertex of mesh (3) ct = colortable structure But I cannot interpret the L vector. For example if the lable of a vertex is 126465, what's the label? Going back to the color table, we have R G B , is there are relationship between these L's and the R G B's?

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[Fwd: Re: [Freesurfer] total brain volume]
by Derin Cobia 06 Feb '07

06 Feb '07

Not sure if this went through the first time yesterday, here it is again. Thanks. I've noticed that the gray matter volume output from mris_anatomical_stats (lh) vs. mris_volume (lh.pial) differs. Am I missing something? Do I need to run mris_volume for a different surface? Thanks. -Derin

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Freesurfer