Freesurfer January 2008

freesurfer@nmr.mgh.harvard.edu

54 participants
69 discussions

midline errors in pial and white matter boundary
by nima＠nmr.mgh.harvard.edu 29 Jan '08

29 Jan '08

Hi Guys, In few recons, I noitced that in the midline, pial and white matter boundaries are not the way they are supposed to be; i.e., they sometimes diverge toward the ventricles instead of following the midline and these divergences are not symmetrical either. I thought maybe I should add some cp...but that does not make sense because in actuality there is not white matter there as it is underneath the cortical gray matter... Any suggestion? The new version of the freesurfer fills the 3rd ventricle adjacent to the fornices. Should I leave the fornices in? or I should clean it up like old versions? ps. is there any way to add control points for pial surface? cheers nima

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Creating average overlays for time-varying data (MEG)
by Pádraig Kitterick 29 Jan '08

29 Jan '08

Dear list, I am trying to use freesurfer to visualise MEG data (minimum norm) overlayed on the cortical surface, both at an individual and group level. I have successfully processed all of the participants MRIs using recon-all, and have decimated the cortical surface (white) to compute the MEG solution. I would be grateful if anyone could help with the following issues I have run into: 1) I would like to know how to view the time-varying solution over the cortex using tksurfer. I have successfully exported the overlay for a single sample to a .w file (using matlab), and then smoothed it (mri_surf2surf) and viewed it on the cortical surface, which works great. But I am aware that .w format only supports a single 'frame' of data. Some previous posts on the list suggest that exporting the data in .mgh format as a nverts x 1 x 1 x nsamples volume would allow visualisation of the timecourse in tksurfer. My question is: is there a way to only write out the data for the vertices with values (i.e. left after decimation) when using the mgh format, and not a matrix of the total vertices in the original cortex? For example, if the surface has N vertices, and after decimation I have M vertices left, using the .w format I only need to write out data for the M vertices, along with a list of the vertex numbers to place them on the original surface. Can I do this with .mgh? It is difficult to get matlab to write out an mgh file with a 140000x1x1x500 volume! 2) I wish to view the average data across several subjects, mapped onto the fsaverage subject template. I have seen that mris_preproc can warp one or more overlays onto a single subject. My question is: will mris_preproc work with the type of .mgh files I described above, i.e. containing multiple frames of data overlay? Or am I better trying to do the whole operation with .w files, with one per timepoint? Many thanks in advance, Padraig -- Pádraig Kitterick Graduate Student Department of Psychology University of York Heslington York YO10 5DD UK Tel: +44 (0) 1904 43 3170 Email: p.kitterick(a)psych.york.ac.uk

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source code of freesurfer
by Defeng WANG 29 Jan '08

29 Jan '08

Dear FS users and experts, It seems that freesurfer is open source, could anybody here tell me where I can download the souce code of freesurfer? Thanks, Vincent

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recon-all times
by Thomas Doering 28 Jan '08

28 Jan '08

Dear freesurfers, as a suggestion of Mishkin, i would like to expand the freesurfer wiki page and add some infos about typical reconstruction times of freesurfer. For this reason, i would like to ask everybody to write me a message including following informations of your computer: ex: CPU-MODEL: 2 x Intel(R) Xeon(R) CPU X5355 CPU-FREQ: 2.66GHz RAM: 16GB FREESURFER-VERSION TIME: freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.1 TIME: 20.5 h Thanks in advance for your contribution, Thomas

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mris_wm_volume
by Gallo, Antonio (NIH/NINDS) [F] 28 Jan '08

28 Jan '08

Hello All, We are trying to obtain an accurate measurement of the total WM volume (cerebral WM + WM hypointensities) in a group of patients with multiple sclerosis. As per Bruce's suggestion, we are using mris_wm_volume that should give more accurate measures than aseg.stats. When looking at our data we have noticed that within the WM surface (yellow line) there are many voxels labeled as ?h-Cerebral-Cortex, and some juxtacortical lesions labeled as None Upon manual editing of these mislabeled voxels on the aseg.mgz (i.e. relabeling them as WM), we have noticed that WM volume actually change. Since mris_wm_volume computes the WM volume using the WM surface and subtracting all non WM structures, we were wondering if there is any way to capture and correct for all these mislabeled voxels in a more automated manner (i.e. automatically considering them as WM instead of subtracting them from WM). In this way it should be possible to get more accurate measures of WM volumes as well as save a lot of time in manual editing. Thanks a lot in advance, Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5C203B Bethesda, MD, 20892 - USA ph #: 001-301-496.7368 fax #: 001-301-402.0373 ***********************

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CC q's
by Juranek, Jenifer 27 Jan '08

27 Jan '08

Hi, I'm running FSv4.0.1 on a 64bit linux platform and had a few questions about the new added feature wrt the corpus callosum segmentation added as early as v4.0.0...details were not readily returned in Wiki searches...so please point me in the correct direction? 1) The 5 separate regions of the CC...how are the boundaries determined? In equal subdivisions (20%) from the genu through the splenium? 2) Although the LUT.txt contains entries for the CC subdivisions, I have been unsuccessful with attempts to display either the aseg.auto_CCseg.mgz or wmparc.mgz files in tkmedit such that the boundaries between subdivisions are easy to visualize...do I need to modify the LUT.txt file with different entries in the last 4 columns than those already present to make it more obvious? EXAMPLE of current entries in LUT.txt... 251 CC_Posterior 0 0 64 0 252 CC_Mid_Posterior 0 0 112 0 253 CC_Central 0 0 160 0 254 CC_Mid_Anterior 0 0 208 0 255 CC_Anterior 0 0 255 0 3) The aseg.stats file contains data for each subdivision...do the values represent area (mm2)? On the midsagittal slice? Many Thanks for any info you can provide! Jenifer

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Labelling Results on Tksurfer
by cthornto＠uci.edu 26 Jan '08

26 Jan '08

Hi I am using Freesurfer version 3.0.5 via Linux and I am trying to label my results on tksurfer. I have already loaded the group descriptor file and the overlay. I can visualize my results but when I click on these specific reasons, it does not tell me where these areas lie. How do I go about labellingmy results so that everytime I click on any one of these regions it will automatically tell me the name of the area? Any feedback is greatly appreciated. Christine Thornton

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recon-all error, COR-.info...
by Cameron Ellis 26 Jan '08

26 Jan '08

Hi, I keep getting an error when I submit jobs to seychelles that a COR-.info file cannot be found. Do you know why this would be? I pasted the full command and error log below. Thanks! Cameron recon-all -i /space/grouch/4/users/ponce/ponce_002d2/3danat/003 -i /space/grouch/4/users/ponce/ponce_002d2/3danat/004 -all -subjid Ponce_002d2 -force INFO: /autofs/space/grouch_004/users/ponce/Ponce_002d2 exists with -i, but -force specified. Deleting any previous source volumes INFO: SUBJECTS_DIR is /autofs/space/grouch_004/users/ponce Actual FREESURFER_HOME /autofs/space/freesurfer/centos4.0/stable4 -rw-rw-r-- 1 cameo zenuwgp 12297 Jan 26 10:00 /autofs/space/grouch_004/users/ponce/Ponce_002d2/scripts/recon-all.log Linux node0081 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT 2006 i686 i686 i386 GNU/Linux /autofs/space/grouch_004/users/ponce/Ponce_002d2 mri_convert /autofs/space/grouch_004/users/ponce/ponce_002d2/3danat/003 /autofs/space/grouch_004/users/ponce/Ponce_002d2/mri/orig/001.mgz mri_convert /autofs/space/grouch_004/users/ponce/ponce_002d2/3danat/003 /autofs/space/grouch_004/users/ponce/Ponce_002d2/mri/orig/001.mgz corRead(): can't open file /autofs/space/grouch_004/users/ponce/ponce_002d2/3danat/003/COR-.info $Id: mri_convert.c,v 1.146.2.1 2007/11/30 23:18:44 greve Exp $ reading from /autofs/space/grouch_004/users/ponce/ponce_002d2/3danat/003... Linux node0081 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT 2006 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Sat Jan 26 10:14:40 EST 2008

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slice thickness
by Brian C. Schweinsburg, Ph.D. 26 Jan '08

26 Jan '08

I have an older dataset with .938 x .938 x 2mm resolution but good contrast and SNR. In previous posts, I have seen recommendations to not exceed 1.5 mm thickness for z-plane. I was wondering if this resolution was equally problematic for volume (aseg) labeling, similar to the surface path. Thanks, Brian

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Recon-all failing at CA Reg
by Caroline Chapman 25 Jan '08

25 Jan '08

Hello, I am having trouble with one subject during the recon-all process. It has failed twice at CA Reg: status file for recon-all Thu Nov 8 15:11:20 EST 2007 #@# MotionCor Thu Nov 8 15:11:20 EST 2007 #@# Nu Intensity Correction Thu Nov 8 15:18:50 EST 2007 #@# Talairach Thu Nov 8 15:21:26 EST 2007 #@# Intensity Normalization Thu Nov 8 15:23:01 EST 2007 #@# Skull Stripping Thu Nov 8 15:30:05 EST 2007 #@# EM Registration Thu Nov 8 15:33:05 EST 2007 #@# CA Normalize Thu Nov 8 15:42:54 EST 2007 #@# CA Reg Thu Nov 8 15:45:14 EST 2007 Linux node0052 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT 2006 i686 athlon i386 GNU/Linux The brainmask, orig, and talairach look okay. Any ideas why this might be failing? Thanks! Caroline -- Caroline Chapman Research Technician Massachessetts General Hospital Geriatric Research, Education and Clinical Center VA Boston Healthcare System (857)364-2093 chapman(a)nmr.mgh.harvard.edu

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Freesurfer January 2008