Freesurfer April 2011

freesurfer@nmr.mgh.harvard.edu

121 participants
166 discussions

preproc-sess OSX bug fix getrunlist
by Juli Dolzhenko 01 Apr '11

01 Apr '11

Hello, I am running into an issue with running preproc-sess on OSX as outlined here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15896.html I saw Doug posted a bug fix that should solve this problem, however, I am unable to access it from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/getrunlist Is there a way I can download this new version of getrunlist? Thanks so much, Juli

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Where can I find long_mris_slopes
by lan lin 01 Apr '11

01 Apr '11

I installed freesurfer 5.0 and want to use long_mris_slopes to prepare the longitudinal data but couldn't find the command. Where can I find it? thanks Lan

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problems with loading a pial surface
by Iris Steinmann 01 Apr '11

01 Apr '11

Hello Freesurfers I still have the problem using a tcl script that should load the pial surface on a patch in tksurfer. I tried to use the following three commands: 1. set gaLinkedVars(vertexset) 3 SendLinkedVarGroup view redraw 2. read_pial_vertex_coordinates redraw 3. read_surface_vertex_set 3 lh.pial redraw But none of them loaded the pial surface. I would be very thankful for a solution ore a hint. Iris

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Re: [Freesurfer] incorrect GM/WM surfaces
by Daniel G Wakeman 01 Apr '11

01 Apr '11

Hi Mayuresh, I assume you are talking about the area in the posterior midline, where the pial surface seems to go 'squiggly'. You also seem to have a problem with the right hemisphere (left visually: I hate radiology ;)), where some dura seems incorrectly labeled as pial surface (although the grey matter is very difficult to see on this sequence/ at this setting). To fix these I recommend this wiki page: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits Good Luck! Dan On 2011 Apr 1, at 05:08 , <freesurfer-request(a)nmr.mgh.harvard.edu> <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. incorrect GM/WM surfaces (Mayuresh K) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 1 Apr 2011 15:21:18 +1100 > From: Mayuresh K <mayureshk.82(a)gmail.com> > Subject: [Freesurfer] incorrect GM/WM surfaces > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <AANLkTi=BLTOKkZngtH5SxhsQvmFrUHakzG9u07Xzworn(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello freesurfer experts, > > I have successfully finished running the recon-all analysis without any > errors for a dataset scanned on the 1.5T GE scanner. The output GM/WM > surfaces however look incorrect and I am not sure what may have gone wrong. > See attached screenshot from tkmedit. > Any suggestions how to fix this would be helpful. > > I have processed other datasets collected from the same scanner using the > same sequence which seem to have correctly identified the pial and > grey-white boundaries. I am using > freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.1. > > Thanks, > Mayuresh >

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incorrect GM/WM surfaces
by Mayuresh K 01 Apr '11

01 Apr '11

Hello freesurfer experts, I have successfully finished running the recon-all analysis without any errors for a dataset scanned on the 1.5T GE scanner. The output GM/WM surfaces however look incorrect and I am not sure what may have gone wrong. See attached screenshot from tkmedit. Any suggestions how to fix this would be helpful. I have processed other datasets collected from the same scanner using the same sequence which seem to have correctly identified the pial and grey-white boundaries. I am using freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.1. Thanks, Mayuresh

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Re: [Freesurfer] A question about make_average_subject
by Douglas Greve 31 Mar '11

31 Mar '11

Hi Lijie, we have a default surface template that we use. When you create an average subject from a group, a template based on those subjects is created at the same time. This can be used as a registration target. doug On 3/31/11 9:03 PM, soft.join Huang wrote: > Thanks for your reply, Douglas. > I also have something unclear, that which target is used when we > register one subject's surface to a 'template', a default surface in > the FreeSurfer or something else, like one surface selected randomly > from my specified subjects. > Best Regards, > Lijie Huang > > On Fri, Apr 1, 2011 at 5:34 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi Lijie, yes, for the volume averages that is the process (uses > the linear 12 DOF registration to the MNI305). For surfaces, the > average surfaces are created based on the non-linear surface > transformation (not from the average volume). > doug > > soft.join Huang wrote: > > Hi all: > Recently, I have a question about some details of the > function make_average_subject, which creates some average > surfaces and volumes based on the specified subjects' files. > And I'm wondering how it make an average one. > In my opinion, every specified subject's volume and surface > register to a existed template( something like fsaverage) and > we can acquire a transform matrix or something like it. > According to the transformation, we can register them roughly. > And then we can average them to a mean one. > I don't know whether my thought right or not. Can anyone give > me some tips? :) > Thanks in advance > Lijie Huang > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > >

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Freesurfer April 2011