Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30083 discussions

MEMPR sequence for freesurfer analyses
by Juranek, Jenifer 15 Jan '09

15 Jan '09

Has anyone attempted an MEMPR-like sequence as described by van der Kouwe et al (2008 NeuroImage 40: 559-569) on a 3T Philips Intera? The paper utilized a 3T Siemens TRIO. Are the published sequence parameters directly transferable to a 3T Philips Intera with an 8 channel head coil and SENSE? Or is some "translation" between Siemens & Philips needed to get it to work as well as published for the Siemens? Many Thanks for any info, Jenifer

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thickness value
by Feng-Xian 15 Jan '09

15 Jan '09

Hi, I gain the cortical thickness value and other information of all ROIs for all my subjects (found in $FREESURFER_HOME/subjects/filename/stats). But, can I gain the cortical thickness value and other information of all vertices for all my subjects? I want to gain the values, not maps. Thank you in advance! Feng-Xian ------------------------------------------------- Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)

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mri_convert failure
by Ian Malone 15 Jan '09

15 Jan '09

Hi, I'm finding that mri_convert produces a read error when trying to convert some short analyze files to mgz, invoked as the following: mri_convert -it analyze -i `pwd`/reslice/00125-003-1.img -o reslice/mni.mgz The output contains (the dimensions shown are correct): ERROR: premature end of file ERROR: Success (0) frame = 0, slice = 219, k=219, row = 155 nread = 171, nexpected = 172 fname = height = 156 width = 172 depth = 220 and: analyzeRead2(): error reading from file reslice/00125-003-1.img The file in question is 11806080 bytes. Using strace I can see that when the .img file is opened 1 byte is read from it before reading in blocks of 1024, and a final read of 383 bytes. Trying another short file (which works) this initial 1 byte read does not happen. Is this is bug? I can provide the files in question if needed. Build stamp: freesurfer-Linux-rh9-stable-pub-v4.0.3 Kernel info: Linux 2.6.21.5-smp i686 Thanks, Ian Malone

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tksurfer error
by Joshua Grant 14 Jan '09

14 Jan '09

Hello, I've run into a problem when trying to view surfaces. tkmedit works fine but tksurfer gives an error saying "Window type not found". I see that others have had this problem in the past but the solution didn't work, i.e. setenv doublebufferflag 1 tksurfer ... Also see: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00010.html I'm using a brand new quad-core machine with independent graphic memory, running Ubuntu and the CentOS 4 x86_64 V4.1.0. version of Freesurfer. Any help would be most appreciated. Joshua

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RE: [Freesurfer] reg-feat2anat failed
by Wang, Xin 14 Jan '09

14 Jan '09

Hello, Dr. Greve, I followed the steps in the tkregister2 --help: converted both example_func and orig.mgz to .img of ANALYZE format and ran the tkregister2 use -- fsl example_func2highres.mat of fsl/FEAT. The two brains are in the different views (i.e., axial view of example_func overlay on the coronal view of orig). I am still struggle with same questions as before. I appreciate any suggestion. Thank you, Xin Wang ________________________________ From: Wang, Xin Sent: Tue 1/13/2009 4:36 PM To: Douglas N Greve Cc: freesurfer Subject: RE: [Freesurfer] reg-feat2anat failed Sorry for the confusion. Let me rephase my questions. question 1: I want to use the example_func2highres.mat created by fsl/FEAT registration to register example_func and orig.mgz. Can the flag --fslregout or --fsl do it? Question 2: These numbers appear in the terminal whenever I click a point in tkregister2? What do these numbers mean? Screen: 256 257 (113,113,113), inorm = 1, mov_frame = 0 Anat: (128 126 127) ( 0.0 -1.0 2.0) 25.0000 32.7 Func: ( 31 32 21) ( 4.2 3.1 1.4) 756.0000 112.5 question 3: I can only see the middle portion of the brain in tkregister2 when I zoomed in. How can I see other parts of the target and movable pictures? Thank you, Xin Wang ________________________________ From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Tue 1/13/2009 4:19 PM To: Wang, Xin Subject: Re: [Freesurfer] reg-feat2anat failed 1) I don't know what you mean. The fslmatout is for creating an fsl mat file from a freesurfer register.dat 2. I don't know what you mean. 3. What do you mean by "moving the two images together"?

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Average subject
by Kelly Silva 14 Jan '09

14 Jan '09

Hi, When the average subject is built, is it used for the analyses or only to visualize? I want to understand how freesurfer makes the average subject. Thanks, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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mri_label2vol aliasing problem
by Ian Malone 14 Jan '09

14 Jan '09

Hi, I'm trying to use mri_label2voxel to produce an image of a segmented region in the original image voxel space and am seeing black lines through the output region, these are oriented parallel to the voxel axes. In the attached image you can see three of them: two parallel horizontal lines and one vertical one just cutting through the right hand side of the region. This appears to be some kind of aliasing artefact; if I move all the labels by adding 0.2 to each of the location values in the labels file then the lines are shifted to different voxels (not the immediately adjacent ones). Using the 1mm^3 voxel registered volume as the template does not show this problem, neither does viewing the label overlaid on orig.mgz in tkmedit. Is there anything I can adjust to avoid this while still outputting a volume in the original image dimensions? Thanks, Ian Malone

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Doubt pial segmentation
by Kelly Silva 14 Jan '09

14 Jan '09

Hello, Thanks por the answers! Now I´m sending 3 images: 1) no segmentation, 2) segmentation with separation of cortex and cerebellum with radius 1, 3) segmentation with separation of cortex and cerebellum with radius 2. Wich image is the best way and use of radius to separate cerebellum from cortex? Thanks, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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Doubt pial segmentation
by Kelly Silva 14 Jan '09

14 Jan '09

Hello, Thanks por the answers! Now I´m sending 3 images: 1) no segmentation, 2) segmentation with separation of cortex and cerebellum with radius 1, 3) segmentation with separation of cortex and cerebellum with radius 2. Wich image is the best way and use of radius to separate cerebellum from cortex? Thanks, Kelly ________________________________ Veja quais são os assuntos do momento no Yahoo! + Buscados: Top 10 - Celebridades - Música - Esportes Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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map label to subjects failed?
by David Qixiang Chen 13 Jan '09

13 Jan '09

Hi, I'm running Qdec to gather cortical thickness in specific regions based on the scalar visuals. when I've drawn ROIs over certain areas, I've found "Mapping labels to subjects" would return an error message for certain subjects. There error is as follows: ERROR: srcvtxno = -1 < 0 trgvtxno = 111070, dmin = 1000 trgregxyz = 0, 0, 0 This means that a vertex in the target surface could not be mapped to a vertex in the source surface because the xyz of the target is outside of the range of the hash table. command failed: mri_label2label --srclabel rh.pos.orbitalfrontal --srcsubject fsaverage --trgsubject DI_April08_filtered --trglabel rh.pos.orbitalfrontal --regmethod surface --hemi rh Why would this error occur if the surface data in Qdec is based on the averaging of all the subjects? And how can I best go about fixing this problem? Thanks! - David Qixiang Chen Neurosurgical Research Assistant Toronto Western Hospital

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Freesurfer