Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30129 discussions

stage1
by Timothy O'Keefe 18 Jul '05

18 Jul '05

I ran recon-all stage1 and it took a very long time. Well, at least longer than people document. I didn't time it, but it must have taken close to 10 hours. Also I received this error during mri_fill(): ... using +/- offset search region where offset is 39..... using +/- offset search region where offset is 42..... using +/- offset search region where offset is 45..... using +/- offset search region where offset is 48..... mri_fill: could not find pons No such file or directory INFO: Modifying dst c_(r,a,s), using the transform dst INFO: Modifying dst c_(r,a,s), using the transform dst INFO: Modifying dst c_(r,a,s), using the transform dst talairach cc position changed to (0.90, -7.51, 23.75) INFO: Modifying dst c_(r,a,s), using the transform dst INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in structure! Searching neighborhood... find_cutting_plane:seed point not in structure! Searching neighborhood... ERROR: mri_fill exited with non-zero status recon-all exited with errors at Sat Jul 16 01:13:52 EDT 2005 Are there any suggestions? I am using a single T1 (1x1x1) image acquired from a Siemens 1.5T machine. I realize I should use multiple images for averaging, however I am just trying to get a feel for the software. -T

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.mat matrix format for cosine info in mri_convert
by Glenn Lawyer 18 Jul '05

18 Jul '05

Hi, We are also seeing the segmentation fault when running mri_convert on our dicom files. As a work-around, I have written a script that uses xmedcon to batch convert dicom to analyze. I'm planning on posting the script to this list, but want to resolve one little issue first. When I run mri_convert on the resulting analyze files, the COR images are in axial orientation. This is probably because the command"$mri_convert 001/001.img ." "Could not find the direction cosine information. Will use the HORIZONTAL orientation. If not suitable, please provide the information in 001/001.mat file". I want to modify my script so that it creates the .mat file, but do not know the format. I can extract the directional cosine information using dicom2 (dicom2 -t1 001/IMAGE_1.dcm | grep Orientation), giving me Image Orientation (Patient) (0020,0037) 6 DS [0.999848\0.00778219\0.0156255\0.0156255\0.00012207\-0.999878] Could you kindly send me the appropriate 001.mat file for this subject/aquisition? +glenn -- I want to go farther, farther! A. E. L. > Glenn Lawyer < > +352 061 967 244 < > Instituttgruppe for psykiatri < > Postboks 1130 Blindern < > 0318 Oslo < < http://folk.uio.no/davidgl > <><><><><><><><><><><><><><><><><:)

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Vertex number
by Sarah Rugheimer 15 Jul '05

15 Jul '05

Hello, Does anybody know if there is a file with or a way to obtain a mapping of the vertex number with say the RAS coordinate system. I know when you are in the tksurfer window by using the mouse/cursor you can see each vertex number with the corresponding RAS coordinate, but is there a way to output all the vertex numbers with the cooresponding RAS coordinates to a file or matrix or some such thing. Thank you very much for any help. Sarah Rugheimer

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edit white matter lesion
by Antao Du 15 Jul '05

15 Jul '05

Hi, I am trying to edit the white matter lesion in wm volume. when I open tkmedit subjid wm. There is a white matter lesion that was misclassified. I paint that region with white matter lesion to white color using button 2. Do I need to paint all ventricle? The manual says that the ventricle is autofilled. But I can't see it and can't find a function to do it. Any helps there? Thanks, Antao

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recon-all issue
by Timothy O'Keefe 15 Jul '05

15 Jul '05

First, I am a newcomer to the FreeSurfer community so bear with me. I have installed a snapshot of FreeSurfer for OSX: freesurfer-Darwin- tiger-full.dmg I seem to have everything working fine in terms of environment settings etc. I created a subject directory and populated it with some T1 data using mksubjdirs and mri_convert (from an AFNI BRIK). Now, upon running recon-all -sid <whatever> -stage1 I receive this output: INFO: SUBJECTS_DIR is /blah/blah/blah ######################################## program versions used $Id: recon-all-nmr,v 1.68 2005/07/07 04:59:34 greve Exp $ $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ mri_convert --version $ $Header: /software/source/minc/progs/rawtominc/rawtominc.c,v 6.13.2.2 2005/03/16 19:02:52 bert Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/ minctracc.c,v 96.11 2004/02/12 05:54:22 rotor Exp $ !p$Header: /software/source/minc/progs/mincresample/mincresample.c,v 6.12.2.1 2005/03/16 19:02:51 bert Exp $ $Header: /software/source/minc/progs/mincaverage/mincaverage.c,v 6.4.2.2 2005/03/16 19:02:49 bert Exp $ $Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ # $Id: nu_estimate.in,v 1.1 2003/04/16 14:29:34 bert Exp $ $ $ $ $ ####################################### ERROR: cannot determine format of input So, I decided maybe I should just write my own script to run the commands visible through the csurf GUI logfile. I was able to script up everything except when I hit the mri_fill() point, I receive this error: .... using +/- offset search region where offset is 33..... using +/- offset search region where offset is 36..... using +/- offset search region where offset is 39..... using +/- offset search region where offset is 42..... using +/- offset search region where offset is 45..... using +/- offset search region where offset is 48..... mri_fill: could not find pons No such file or directory Does anyone have any suggestions? -T

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Skull stripping
by Fornito, Alexander 15 Jul '05

15 Jul '05

Hi, recon-all stage1 overstrips some of my images during the skull-stripping stage. I've played with the different options, but they don't seem to make any difference at all. Any suggestions? I've tried feeding in a pre-stripped brain (stripped using BET), but the intensity normalization doesn't seem to do to well (ie., although it finishes without error, the wm values are not very uniform, and the segmentation misses large portions of wm). Thanks, Alex

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Tksurfer: Unable to view .orig file
by Arvind Gururajan 14 Jul '05

14 Jul '05

Hi, I have trouble viewing .orig files in Tksurfer. I used mris_convert to generate .orig files from .ascii( with number of vertices and triangles for each hemisphere). Any quick thoughts on what could be wrong ? No error messages. Help would be appreciated. Arvind Gururajan

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Center and radius of qsphere surface
by Ngo Trung Thanh 14 Jul '05

14 Jul '05

Hi, How can we know the center and radius of the sphere surface in qsphere files? I guess that the center is (0,0,0) (RAS), what about the radius? Thanks. Best, ntt __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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RE: [Freesurfer] Anatomical stats for labels
by Fornito, Alexander 13 Jul '05

13 Jul '05

Right, so if vertex 'i' is labelled on the white surface, then vertex 'i' will be labelled on the pial surface, and no additional vertices will be labelled on the pial surface (ie., no new ones that are not labelled on the wm surface?). In that case differences is in surface area between the white and pial come about as a result of shearing forces as the wm surface is deformed outward. Is that correct? -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thu 7/14/2005 8:04 AM To: Fornito, Alexander Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Anatomical stats for labels the label is identified by the vertex indices, which allow it to be projected onto any surface. On Thu, 14 Jul 2005, Fornito, Alexander wrote: > Makes sense. If the lable is only defined along the wm surface, how are the pial surface vertices defined/identified? > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Wed 7/13/2005 9:32 PM > To: Fornito, Alexander > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] Anatomical stats for labels > > > > yes, if you specify pial it will be the pial surface area. > > On Wed, 13 Jul > 2005, Fornito, Alexander wrote: > > > Cool, thanks. > > On this issue, I've noticed that lables are defined along the wm surface (eg., when you load them in tkmedit, they do not appear long the pial surface). As such, when I assume that "total surface area" in mris_anatomical_stats corresponds to the area of this specified wm surface when white is specified as the surface in the command line. If pial is specified, does "total surface area" refer to the surface area of the pial surface defined by the vertices linked to those on the wm surface label (ie., those that were deformed out from the wm), or does it refer to a surface selected by some other means? I have some manually delineated labels (obtained from 3D overlays) that cover the wm surface of the area I'm interested in, but am unsure of the extent to which I need to worry about what parts of the pial surface (or intermediate gm) is included. > > Hope this makes sense! > > Thanks, > > Alex > > > > > > -----Original Message----- > > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > > Sent: Tue 7/12/2005 1:09 AM > > To: Fornito, Alexander > > Cc: freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] Anatomical stats for labels > > Hi Alex, > > > > that's a bug - the volume is the total of the surface area of each > > triangle times the average thickness there, so the pial will be different > > from the white (should just take the average of the two) > > > > Bruce > > > > On Mon, 11 Jul 2005, Fornito, Alexander wrote: > > > >> Hi, > >> I've noticed that when I run mris_anatomical stats on a label, I get a different value for "total gray matter volume" if I run it on the pial surface, compared to if I run it on the white surface. Just wondering why this is, how the total gray matter volume is calculated, and which one represents the true gray matter volume? > >> Thanks, > >> Alex > >> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> > > > > > > > > > > > > > > > > >

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RE: [Freesurfer] Anatomical stats for labels
by Fornito, Alexander 13 Jul '05

13 Jul '05

Makes sense. If the lable is only defined along the wm surface, how are the pial surface vertices defined/identified? -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 7/13/2005 9:32 PM To: Fornito, Alexander Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Anatomical stats for labels yes, if you specify pial it will be the pial surface area. On Wed, 13 Jul 2005, Fornito, Alexander wrote: > Cool, thanks. > On this issue, I've noticed that lables are defined along the wm surface (eg., when you load them in tkmedit, they do not appear long the pial surface). As such, when I assume that "total surface area" in mris_anatomical_stats corresponds to the area of this specified wm surface when white is specified as the surface in the command line. If pial is specified, does "total surface area" refer to the surface area of the pial surface defined by the vertices linked to those on the wm surface label (ie., those that were deformed out from the wm), or does it refer to a surface selected by some other means? I have some manually delineated labels (obtained from 3D overlays) that cover the wm surface of the area I'm interested in, but am unsure of the extent to which I need to worry about what parts of the pial surface (or intermediate gm) is included. > Hope this makes sense! > Thanks, > Alex > > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Tue 7/12/2005 1:09 AM > To: Fornito, Alexander > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Anatomical stats for labels > Hi Alex, > > that's a bug - the volume is the total of the surface area of each > triangle times the average thickness there, so the pial will be different > from the white (should just take the average of the two) > > Bruce > > On Mon, 11 Jul 2005, Fornito, Alexander wrote: > >> Hi, >> I've noticed that when I run mris_anatomical stats on a label, I get a different value for "total gray matter volume" if I run it on the pial surface, compared to if I run it on the white surface. Just wondering why this is, how the total gray matter volume is calculated, and which one represents the true gray matter volume? >> Thanks, >> Alex >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > > > > >

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