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add subject to group but cannot find brain for 049
by Knut J Bjuland 01 Apr '11

01 Apr '11

I have added a subject to the to the groups of subject that was available for the qdec tutorials. with this in mind I have used make_average_subject and I have now 41 subject. But when I run this command there is always a subject for which it can not find brain. I am positive that the necessary files are available. The subject that I have add is anonymous mri picture that i have imported into freesurf, and the subject is 20 years old female. Knut J

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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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Visualizing SPM Results on Template FreeSurfer Brain
by Andrew Jahn 31 Mar '11

31 Mar '11

Hello, I have second-level results in .img/.hdr format that I have just run through SPM. I was wondering whether there is a way to visualize these results onto a template FreeSurfer surface model in MNI space. Is this possible, or can you only visualize second-levels which have been processed through FreeSurfer? Thanks, -Andrew

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A question about make_average_subject
by soft.join Huang 31 Mar '11

31 Mar '11

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

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Longitudinal comparison of thickness data
by Jonathan DuBois 31 Mar '11

31 Mar '11

Hi Freesurfer users, I have been working from the list posting below for vertex comparison of longitudinal thickness data, although there are a couple issues I was hoping someone could help with. Using FS v5.0 with the fixed binaries, I have put together the following steps for data comparison following the third step of the longitudinal stream with their associated commands and questions (highlighted in bold). I am sorry if it is a lot of information, although I thought it might be useful for other users working with longitudinal analysis. Thanks Jonathan ------------------------------ Martin Reuter mreuter at nmr.mgh.harvard.edu <freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20Longitudinal%20processing&In-Reply-To=%3C1277843000.24825.221.camel%40riemann.nmr.mgh.harvard.edu%3E> Tue Jun 29 16:23:20 EDT 2010 Hi Sandra, (and the list, I think this might be interesting for others) 1. the longitudinal ?h.thickness files are in registration (within subject) so in order to compute the difference or the rate you can simply use: mris_calc -o lh.outdiff sdir2/surf/lh.thickness sdir1/surf/lh.thickness and for the rate, you can divide by time 1 thickness or by the average thickness. If the time points are not equally spaced across subjects, you can also divide by difference in time. It is best to smooth the thickness files before you do all this (i.e. within time point smooth the ?h.thickness files with mri_surf2surf). 2. then map everything to your template (e.g. fsaverage) with mri_surf2surf 3. there you can stack the thick-differences or thick-rates with mri_concat 4. do the glm Best Gruesse, Martin ------------------------------ 1. Smooth surface data: mri_surf2surf --s subj1_tp1.long.template --sval subj1_tp1.long.template/surf/lh.thickness --tval subj1_tp1.long.template/surf/lh.thickness.fwhm10.mgh --fwhm-src 10 --hemi lh mri_surf2surf: could not read surface /space/mdeh2/1/halgdev/emcbkp/1/halgdev/projects/nyuproj/subjects/subj1_tp1.long.template/surf/lh.sphere.reg No such file or directory *--The longitudinal processing does not create a ?h.sphere.reg or a ?h.sphere for running mri_register. While, the registration is specific to the longitudinal analysis, could I simply copy over the ?h.sphere.reg from the original subject, since it is the same brain? If not, how should this be generated?* ** 2. Compare time point differences within subjects using mris_calc and one of the three options: a. divide tp2 by tp1 - [mris_calc -o lh.NC024_thick_diff_fwhm10.mgh subj1_tp2.long.template/surf/lh.thickness.fwhm10.mgh div subj1_tp1.long.template/surf/lh.thickness.fwhm10.mgh] b. divide by average thickness c. divide by between scan time difference *--Option (a) is straight forward, although option (c) would be ideal given that our subjects vary in time between scans. How would option (b) or © be set up with mris_calc? Would mris_calc work for more than two time points?* 3. Register subjects' between scan difference map to fsaverage mri_surf2surf --s lh.NC024_thickness_diff_fwhm10.mgh --trgsubject fsaverage --tval lh.NC024_thickness_diff_fsaverage.fwhm10.mgh --fwhm-src 10 --hemi lh *--I haven't gotten to this step yet, but I'm not sure that it will work given that there is only a .mgh file without an associated subject? Also, similar problem to question one (no sphere.reg).* ** 4. Stack subjects' difference maps using mri_concat 5. Run GLM using mri_glmfit

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