Freesurfer

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mgh format wiki doc: Error; additions
by Graham Wideman 13 Jul '06

13 Jul '06

Folks: (Probably Nick S?) Comments on the MghFormat wiki doc page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial_2fMghFormat 1. Width/Height/Depth confusion. -------------------------------- Doc says... width integer first dimension of the image buffer (slowest) height integer second dimension of the image buffer (2nd slowest) depth integer fastest dimension when reading the buffer ... yet mriio mghWrite(...) source code says... for (frame = start_frame ; frame <= end_frame ; frame++) { for (z = 0 ; z < depth ; z++) { for (y = 0 ; y < height ; y++) { [...] for (x = 0 ; x < width ; x++) Ie: width should be fastest, and depth slowest, contrary to doc. Further, the statement "the bytes being read in the order Z --> Y --> X" is either incorrect or doesn't have any meaning. 2. "image data starts at specified offset, which is currently ???". -------------------------------------------------------------------- Looks like from the source code that the header is padded to 24 + 256, which means image starting at byte 280 (counting from zero). 3. Other Data -------------- In the doc, the Other Data section ends at "FoV". Actually the source code shows that mghWrite writes out other stuff beyond that, which in the examples I looked at appears to be a history of commands performed on the image so far, for example (abbreviated [...] and wrapped by me): =========================== [...] mri_convert /data/[...]/39174a/mri/rawavg.mgz [output filepath] --conform ProgramVersion: $Name: stable3 $ TimeStamp: 06/06/07-04:10:32-GMT CVS: $Id: mri_convert.c,v 1.121 2006/02/22 05:39:36 greve Exp $ User: graham Machine: gwlin[...] CompilerName: GCC Compile[...] mri_ca_normalize -mask brainmask.mgz nu.mgz [...] norm.mgz ProgramVersion: $Name: stable3 $ TimeStamp: 06/06/11-05:41:45-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: graham Machine: gwlin[...] GCC CompilerVersion: [...] =========================== (Plus the source code suggests that if a Talairach transform has been applied it appears here in some form). ----------------------------- Graham

2 1

mri_label2label validation failed
by Darren Weber 13 Jul '06

13 Jul '06

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Doug et al., I'm trying to test mri_label2label because we've observed some strange results in the download for: freesurfer-Linux-rh9-stable-pub-v3.0.2 To test the program, I thought it would be sensible to map a label of one subject onto itself, with a different label filename for the output. So I created a large label in a subject rh inflated surface and saved it to X.label file. I then tried to run mri_label2label using the same srcsubject and target subject, with a different name for the target label, ie: mri_label2label \ - --srclabel $SUBJECTS_DIR/${srcsubject}/label/$label \ - --trglabel $SUBJECTS_DIR/${srcsubject}/label/$newlabel \ - --srcsubject ${srcsubject} \ - --trgsubject ${srcsubject} \ - --regmethod surface --hemi $hemi --trgsurf pial In effect, this should be equivalent to: cd $SUBJECTS_DIR/${srcsubject}/label/ cp $label $newlabel That is, the label mapping onto the same subject surface should be identical. It is not. Can you please try to replicate this result? I would like to know if it is particular to the setup here. If you find a bug in mri_label2label, please forward a fix ASAP, as we are trying to complete some analysis that depends on mapping labels across subjects. Thanks, 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 iD8DBQFEtDeZxaCYN7qs0v4RApcvAKCBTkFl5dOPIaAVD0Qv5vejQ7E+3wCglb2U LXK6ke2GQGjDITqafbLtVGk= =5OcG -----END PGP SIGNATURE-----

3 7

cortical thickness table.
by Chacko Cherian 13 Jul '06

13 Jul '06

Hello all, The cortical thickness table which is located in the stats folder..i am currently opening it with my vi editor.Is there any way to open it directly as a spreadsheet to print it out?? THanks Chacko. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

3 2

read_surf
by Satrajit Ghosh 13 Jul '06

13 Jul '06

Hi Doug, I'm using the matlab routine 'read_surf' from the 3.0.3 distribution to read a surface generated by mri_tessellate. The magic number for the surface is: 16777213, which does not match either the QUAD or the TRI magic numbers listed in read_surf and hence does not read it. Is there an updated version of read_surf available? Thanks, Satra

3 3

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

2 1

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

4 9

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

2 3

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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