Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30096 discussions

Spherical morphometry
by Chacko Cherian 13 Jul '06

13 Jul '06

Hello everyone, In spherical morphometry,to create the spherical surfaces,Im using the step 8.1 in the Wiki tutorial. Could someone please explain what the colors stand for? DOING "tksurfer subj001 rh sphere" gives me a sphere on the display.But I'm not able to map it and provide the overlay info rh.curv. the command "tksurfer -subjid subj001 -morph" gives me the error "Flag unrecognized".. THanks in advance. Chacko. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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problem with mri_em_register
by Abdel Douiri 13 Jul '06

13 Jul '06

Hi all, I want to try Freesurfer in object with a physical sizes are (310.00 mm, 310.00 mm, 310.00 mm) but I have a segmentation fault when running the recon-all, precisely, in stage 2 when running: mri_em_register -mask brainmask.mgz nu.mgz /home/samba/user/douiri/dev/freesurfer/average/RB_all_2006-02-15.gca transforms/talairach.lta the out put is : using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/home/samba/user/douiri/dev/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type average std = 7.4 using min determinant for regularization = 5.5 0 singular and 1662 ill-conditioned covariance matrices regularized reading 'nu.mgz'... Segmentation fault I have done an mri_info on nu.mgz (Fov: 310) and brainmask.mgz (Fov: 256) and I found that brainmask.mgz ((256.00 mm, 256.00 mm, 256.00 mm)) has a size smaller of nu.mgz. I would be gratefully if you can tell me what going wrong with my data. Regards A

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question about h_NNN.dat volumes
by Sebastian Moeller 12 Jul '06

12 Jul '06

Hi Doug, hi List, I got a question regarding the h volumes inside the analysis sub directories. The content of those file are the regression coefficients for each voxel (XY planes) for each condition (Z stack). Supposedly those estimates are corrected for the noise and would make really nice descriptors of the overall activation of voxels/rois for the given conditions. Now, here is my question, what is the unit of the values in the maps? And is there a way to transform those values into something ala percent change? Would dividing a XY voxel of a slice though the matching voxel value from the h-offset volume result in percent of total? ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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Cortical gray matter volume
by derin＠conte.wustl.edu 12 Jul '06

12 Jul '06

Hi, I am attempting to assess (& compare) total cortical gray matter volume in a series of subjects (schiz vs. control), and was wondering if the tabular mris_anatomical_stats gm output consisted of only cortical gm, or included subcortical and other nuclei as well. I've searched the wiki, articles, and listserve archive with not much success; I get the sense that it is, but want to make sure. Additionally, what is shown in the ?h.ribbon.mgz files appears to be exactly what I am looking for. Is there any way to run the mris_anatomical_stats command on these files (use mris_convert maybe)? Thanks in advance. -Derin

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stripping MP-RAGEs from Allegra
by Russell Poldrack 10 Jul '06

10 Jul '06

hi - I've been trying to run a set of MP-RAGE images collected on our allegra through the first part of the autorecon process, and I've run into somewhat of a problem with the skull-stripping. In all 8 of the brains that I have tried, there is a substantial amount of scalp left over after stripping (primarily on the dorsal posterior surface of the skull). I have tried the recommendations from the wiki (reducing the wsthresh to 5, and using -wsatlas) to no avail, there is still skull left over. Short of editing out the scalp by hand, are there any other tricks I might try to get the automated stripping to work? for what it's worth, we have found these Allegra MP-RAGE images to wreak havoc on BSE and BET as well. Any suggestions would be most appreciated! cheers russ --- Russell A. Poldrack, Ph.d. Associate Professor UCLA Department of Psychology Franz Hall, Box 951563 Los Angeles, CA 90095-1563 phone: 310-794-1224 fax: 310-206-5895 email: poldrack(a)ucla.edu web: www.poldracklab.org

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mri_normalize
by Don Hagler 10 Jul '06

10 Jul '06

I am getting an error running mri_normalize (as part of recon-all) on a particular subject's volume. Here is the command from recon-all: mri_normalize -g 1 nu.mgz T1.mgz Here is the output: WM removal version using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 0.860 -0.007 -0.123 -96.500; -0.087 0.643 -0.647 -17.669; 0.096 0.653 0.636 -156.251; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize: could not find any valid peaks mri_normalize: normalization failed nu.mgz looks fine, so I wonder what could be the problem. Any ideas?

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details on subcortical segmentation
by Sasha Wolosin 10 Jul '06

10 Jul '06

Dear all, I am interested in learning more about the details of subcortical segmentation, in particular how the basal ganglia structure boundaries are determined. Is there any literature I may refer to? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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old_freesurfer question
by Stefano Pellegrini 10 Jul '06

10 Jul '06

Hi everybody, I have a small problem with an old version of freesurfer. I am studing some data that someone analyzed some months ago using the old version of freesurfer. I am looking for the mean cortical thickness of each hemisphere, but I have found only the thickness af each single area of the segmented cortex in a txt file in the label directory. Can anybody please tell me where I can find the information about the average cortical thickness of each hemisphere? Should I recalculate it averaging all the cortical labeled areas (each weighted on the extention of its surface)? thank you, -stefano

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vertices for mri_label2label using volume registration
by Darren Weber 10 Jul '06

10 Jul '06

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Doug et al., when using mri_label2label with the --regmethod volume, there are no vertices output in the .label file. When loading the .label file into tksurfer, it crashes tksurfer without any error message. It is possible to obtain vertices and to visualize them for the results of mri_label2label when using the volume regmethod? Best, Darren - -- Darren L. Weber, Ph.D. Postdoctoral Scholar Dynamic Neuroimaging Laboratory, UCSF Department of Radiology, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber "To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." Thomas Willis (The Anatomy of the Brain and Nerves, 1664) -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.3 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFEra33xaCYN7qs0v4RAkgGAKCNxkYDcQDFCPbu2HCxhSyJPrywDgCfeEua 7Yqo15X8Brb7w5hYssPII5I= =99Kz -----END PGP SIGNATURE-----

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trouble using inorm-sess
by Sebastian Moeller 10 Jul '06

10 Jul '06

Hi List, we have some problems with inorm-sess and some data sets. No matter how we set -tresh (well, 0.1, 0.5, 0.75 or 1.0) some of our functional runs produce errors/warnings. (and the "INFO: no voxels found under thershold" messages, but they look benign). The warning are mostly divides by zero, but they still result in inorm-sess exiting SUCCESSFULLY, they coincide with the INFO... lines so they might be expected. But some of the runs are weirder, they give "??? Subscripted assignment dimension mismatch. \n Error in ==> fast_inorm at 88 \n twf_under(nthslice,:) = mean(y2(iunder,:));" Unfortunatelly looking inside fast_inorm.m does not give me any clue, what is going on. If there is anything I can do to help debug this problem, let me know. BTW the same data can be safely normalized after smoothing (using spatialsmooth-sess). freesurfer 3.0.3 Linux-centos4_x86_64-pub, Matlab 7.1 x86_64, running suse Linux 10.1 ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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