Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30076 discussions

Cerebellum Segmentation
by Pedro Paulo Oliveira Jr 26 Oct '07

26 Oct '07

Yesterday I gave a course on FreeSurfer basics + usage for our Radiology department in São Paulo University. Two questions that I was not able to answer was: 1) When will the source code of FreeSurfer be released? 2) Is there some plan to include the cerebellum in the automatic parcellation/segmentation? I think last question about this in this list was in 2005. Thanks Pedro Paulo Jr.

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skull strip problem
by Michael Harms 25 Oct '07

25 Oct '07

Hello, We have a subject processed in V4 for which T1.mgz looks fine (white matter ~ 110; no obvious artifacts), but the brainmask.mgz is basically all zeros (except for a section of the background in slices 200-255 of the coronal view). The recon-all.log file is attached. I don't know if the problem is with the derivation of talairach_with_skull.lta that is used in 'mri_watershed' in V4, or if the issue occurs in 'mri_watershed' itself. (NB: There are a lot of "ambiguous basin" messages as part of the 'mri_watershed' output). How do you check the accuracy of talairach_with_skull.lta? Any other suggestions (particular options to change for the watershed...)? thanks, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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talairach failure detection
by Michael Harms 25 Oct '07

25 Oct '07

Hello, Thought that this might be of interest: We've found a case for which the talairach.xfm is grossly wrong (checked using tkregister2) but the automatic-failure detection of version 4.0.1 indicated no problems. #-------------------------------------------- #@# Talairach Failure Detection Thu Oct 25 12:29:08 CDT 2007 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/010502_61774/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.2262, pval=0.0169 >= threshold=0.0050) #------------------------------------------ Is this something that anyone else has noticed so far? thanks, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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Re: [Freesurfer]thickness difference map
by Nick Schmansky 25 Oct '07

25 Oct '07

Support for the curv format as a target was added to mri_surf2surf in freesurfer v4.0. For your version, you can just exclude the -tfmt curv parameter. On Wed, 2007-10-24 at 21:19 -0400, Wang, Xin wrote: > ERROR: Cannot select curv as target format. > > Thank you, Nick. > > Xin Wang > > > ______________________________________________________________________ > From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > Sent: 2007-10-24 (星期三) 21:16 > To: Wang, Xin > Cc: Doug Greve; Freesurfer Mailing List > Subject: Re: {Spam?} 答复: [Freesurfer]thickness difference map > > > > Can you send along the output text that shows the error? > > On Wed, 2007-10-24 at 21:10 -0400, Wang, Xin wrote: > > Thank you for your response, Doug. I attached all the commends I > > modified from Han's note. I worked through step1 & 2. But the step3 > is > > the problem now. step4 hasn't been tried. I look forward to hearing > > your suggestions. > > > > Thank you again, > > > > Xin > > > > > > > ______________________________________________________________________ > > From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] > > Sent: 2007-10-24 (星期三) 19:12 > > To: Wang, Xin > > Cc: Nick Schmansky; Freesurfer Mailing List > > Subject: RE: [Freesurfer] thickness difference map > > > > > > > > > > > > What is your cmd line and what is the terminal output? > > > > > > > > On Wed, 24 Oct 2007, Wang, Xin wrote: > > > > > Thank you very much, Nick. I ran into a problem when I ran the > step > > 3 of Han's note of thickness repeatability. The --tfmt of > > mri_surf2surf is curv. The step can not be completed. > > > > > > Please help me. > > > > > > Thank you again, > > > > > > Xin > > > > > > ________________________________ > > > > > > From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > > > Sent: Sat 10/20/2007 5:34 PM > > > To: Wang, Xin > > > Cc: Freesurfer Mailing List > > > Subject: Re: [Freesurfer] thickness difference map > > > > > > > > > > > > Xin, > > > > > > Have a look at this wiki page written by Xiao (the author of the > > paper): > > > > > > http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility > > > > > > It describes the procedure for how Figure 2 was created. > > > > > > Nick > > > > > > On Fri, 2007-10-19 at 15:42 -0400, Wang, Xin wrote: > > >> Hello, Group, > > >> > > >> We want to make a figure as Fig2 in Han X et al. 2006 reliability > > >> paper. Does anyone kindly share his/her way to make a map of > > >> difference in average thickness between two groups? > > >> > > >> Thank you in advance, > > >> > > >> Xin Wang > > >> _______________________________________________ > > >> Freesurfer mailing list > > >> Freesurfer(a)nmr.mgh.harvard.edu > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve(a)nmr.mgh.harvard.edu > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > In order to help us help you, please follow the steps in: > > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > > > > > > >

2 2

stats for average subject...
by Cameron Ellis 25 Oct '07

25 Oct '07

Hi, Does anyone know if it is possible to generate an aparc.stats file for an average subject? mris_anatomical stats does not seem like it will work because it requires wm.mgz which is not generated in the make_average_subject process. I would like to find the number of vertices and the surface area of each hemisphere. I think the average surface area can be found in the make_average_subject log file but I cannot find the number of vertices there. Any suggestions? Thanks, Cameron

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Incorrect results after re-run.
by zheng.hui＠singhealth.com.sg 25 Oct '07

25 Oct '07

Hi, I did some editing, add in control points and edit pial surface on one set of our data on the left hand side of the screenshot attached, and re-run recon-all -autorecon2 -autorecon3 -s subjID The result turned out to be wrong as shown in the right hand side of the screenshot. The algorithm worked well at the temporal lobe where control points were added, but it failed at the superior part. Can you suggest why it is so? Thanks Zheng Hui

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Re: {Spam?} 答复: [Freesurfer] thickness difference map
by Nick Schmansky 24 Oct '07

24 Oct '07

Can you send along the output text that shows the error? On Wed, 2007-10-24 at 21:10 -0400, Wang, Xin wrote: > Thank you for your response, Doug. I attached all the commends I > modified from Han's note. I worked through step1 & 2. But the step3 is > the problem now. step4 hasn't been tried. I look forward to hearing > your suggestions. > > Thank you again, > > Xin > > > ______________________________________________________________________ > From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] > Sent: 2007-10-24 (星期三) 19:12 > To: Wang, Xin > Cc: Nick Schmansky; Freesurfer Mailing List > Subject: RE: [Freesurfer] thickness difference map > > > > > > What is your cmd line and what is the terminal output? > > > > On Wed, 24 Oct 2007, Wang, Xin wrote: > > > Thank you very much, Nick. I ran into a problem when I ran the step > 3 of Han's note of thickness repeatability. The --tfmt of > mri_surf2surf is curv. The step can not be completed. > > > > Please help me. > > > > Thank you again, > > > > Xin > > > > ________________________________ > > > > From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > > Sent: Sat 10/20/2007 5:34 PM > > To: Wang, Xin > > Cc: Freesurfer Mailing List > > Subject: Re: [Freesurfer] thickness difference map > > > > > > > > Xin, > > > > Have a look at this wiki page written by Xiao (the author of the > paper): > > > > http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility > > > > It describes the procedure for how Figure 2 was created. > > > > Nick > > > > On Fri, 2007-10-19 at 15:42 -0400, Wang, Xin wrote: > >> Hello, Group, > >> > >> We want to make a figure as Fig2 in Han X et al. 2006 reliability > >> paper. Does anyone kindly share his/her way to make a map of > >> difference in average thickness between two groups? > >> > >> Thank you in advance, > >> > >> Xin Wang > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > >

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thickness difference map
by Wang, Xin 24 Oct '07

24 Oct '07

Hello, Group, We want to make a figure as Fig2 in Han X et al. 2006 reliability paper. Does anyone kindly share his/her way to make a map of difference in average thickness between two groups? Thank you in advance, Xin Wang

3 3

orientation
by Nurunisa Neyzi 24 Oct '07

24 Oct '07

Hi, I have these analyze files with wrong orientation I can change their orientation using fslswapdim but when I convert them to mgz files using mri_convert, the orientation is wrong again. i tried the following reading from 001.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, 0, -1) j_ras = (1, 0, 0) k_ras = (0, -1, 0) reordering axes... MRIreorder: incorrect dst width error reordering axes so not sure what i should do, can you please help me on this?

3 2

Brodman areas using tksurfer/tkmedit
by Pratap Kunwar 24 Oct '07

24 Oct '07

Hi, Can tksurfer/tkmedit have Brodman arreas as well as talairach coordinates displayed? thanks pratap

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