Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Pial Surfaces Cutting off Gyri
by Sherri Novis 07 Apr '10

07 Apr '10

Hello brilliant and generous FS people, I have introduced a problem I cannot solve. I am simply trying to capture as much gray matter as possible. We have some very bad constrast images (ghostly edeges where the gray matter should be). I'm adding control points to try to capture - however, now when I run AR2-cp, the pial surfaces go haywire on the superior borders of the slices. Attached are two images displaying the problem. I have edited wm.mgz to fill in the ventricles because I was getting islands, and I manually edited the brainmask to remove some vasculature that was being included in the pial surfaces. Can you tell me where I introduced this instability? Best Regards, Sherri

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2005 vs 2009 parcellations
by Frida Polli 07 Apr '10

07 Apr '10

hi aside from new ROIS (i.e. the cingulate being divided into 3 parts), the 2009 looks like it has smoother/different boundaries than the 2005 one, even for ROIs that remain the same as the 2005. what is that a result of? thanks, frida -- Frida E. Polli, PhD Postdoctoral Fellow Brain & Cognitive Sciences, MIT 43 Vassar St., Room 46-4033 Cambridge, MA 02139 email: fpolli(a)mit.edu tel: (617) 324 2897

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Re: [Freesurfer] Optseq2 - Incorporate sequential order of trials as a factor
by Gaber, Tilman 07 Apr '10

07 Apr '10

Thank you for your quick response. Initially I had the same idea. Unfortunately, this easy solution does not work. All trials are successor of the previous and predecessor of the following trial. Therefore we can't just randomly distribute pairs of trials. The whole chain of trials has to be in proper order. ([A-B-A-A-B-B-B-A-...] = [AB BA AA AB BB BA ...]) My thinking was to somehow add these restrictions to the initial part of optseq2 algorithm and fix for null event interuptions afterwards... Tilman --------------------------------------------------------------------------------- Tilman J. Gaber, Dipl.Psych. Translational Neuroscience in Psychiatry and Neurology Dpt. of Child and Adolescent Psychiatry and Psychotherapy RWTH Aachen University Neuenhofer Weg 21 52074 Aachen Germany PHONE: +49-(0)241-80.85347 FAX: +49-(0)241-80.3335070 Email: tgaber(a)ukaachen.de ________________________________________ Von: Douglas N Greve [greve(a)nmr.mgh.harvard.edu] Gesendet: Freitag, 26. Februar 2010 18:56 An: Gaber, Tilman Cc: freesurfer(a)nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Optseq2 - Incorporate sequential order of trials as a factor You can specify that there are 4 trial types (AA, AB, BA, BB), and give the duration twice that of the individual. doug Gaber, Tilman wrote: > Dear mailinglist recipients, > > I am currently planning an optimized experiment using optseq2 and a 2x2 factors behavioral response task (Simon-task). > The task consists of a pseudo-randomized series of two kinds of trials (congruent and incongruent). > In addition there is a sequential factor, i.e. it is of interest whether a trial follows a trial of the same or the opposite kind. In other words there are (2x2) four different conditions where trials relate to precedent trials (AA,AB,BB,BA). > Would it be possible to incorporate this sequential factor into the optseq2? > I am aware that null events will fall between trials and thus interrupt trial sequences. Trials following null events would therefore be treated separately (i.e. for data analysis). In order to obtain an equal number of trials per condition, this would require increasing the number of trials depending on the number and order of null events. > Currently I am able to produce a randomized order of equally balanced trials regarding trial type and sequential order (AA,AB,BB,BA). > Any thoughts or suggestions are more than welcome! > > Best, > Tilman > _______________________________________________ > 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 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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flattening occipital lobe results in closed patch
by Vadim Axel 07 Apr '10

07 Apr '10

Dear all, For one of my brains I fail to flatten correctly occipital lobe neither for rh, nor for lh (I get 'closed' patch). I tried to make several cut planes with different calcarine cut lines, but the result was the same. I attach a screenshot of rh with three of my attempts and the reconstructed full brain (resized it a little to fit the screenshot).I run: mris_flatten -w 0 -distances 20 20 command. Any idea what exactly might have gone wrong? How crucial is to have the calcarine cut and cut plane to be exactly on its place in order to achieve successful flattening procedure? I am using Ubuntu VirtualBox FreeSurfer v4.5 version. Thanks a lot, Vadim

2 1

Rawavg wrong
by Janani Dhinakaran 07 Apr '10

07 Apr '10

Hello, I was wondering whether you could help me wit this. I had reported a talairach error during recon and was asked to check what the rawavg looked like. Sagital is shown instead of Coronal, and upside down at that! Clearly, there is some formatting error. Is there a way to fix this within Freesurfer or would you recommend I use Analyze to reformat, flip and then introduce the newly saved copy as the subject files? Are there any other options? Thank you for your help Jan -- I am the Sun, I know no darkness.

2 1

scripting get label form talirach point
by Ben Hamida Cammoun Leila Faiza 07 Apr '10

07 Apr '10

Hello, I am trying to check if some talairach coordinates of AI (auditory primary) (from paper) are in the transverstamporal label, on am subjects. To do this, and thanks to your answers I used the commands line in tksurfer: select_talairach_coordinate x y z mark_vertex $select 1 and I can read: the vertex number and the label but I have to get the vertex number and the label for 5 points and 40 subjects, do you know how to get the vertex number and the label in a script? I tried func_select_label which gives me the label in the command line but I don't know how to get it in a file. Thanks a lot for this help

2 1

Using own atlas - file conversion
by Pernille Iversen 07 Apr '10

07 Apr '10

Dear all, We have created our own atlas based on several subjects. We have the atlas in analyze volume files and would like to know if we can somehow convert these files into the .gcs format without having to go through all the manual steps of creating a template and labels. Thanks, Pernille Iversen

2 1

Is this longitudinal result correct
by Guang Zeng 06 Apr '10

06 Apr '10

Hi, there, I ran the freesurfer longitudinal stream to analysis scans from two tps. I attached the segmentation results of one time-point to its orig.mgz and the longitudinal brainmask, I can see part of the brainmask are not labeled, I understood that it is because of the brainmask is the mean or median of the norm.mgz from different time points. Just wanna double check that the results is ok. Thanks! Guang _________________________________________________________________ The New Busy is not the too busy. Combine all your e-mail accounts with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28…

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How to convert a cortical thickness map to a NIFTY file
by Xiaojing Long 06 Apr '10

06 Apr '10

Hi, I have a question regarding how to convert a cortical thickness map (i.e. lh.thickness) to a NIFTY file. I have a subject called 'subjid' and I run recon-all on it. So I got the ?h.thickness files. Does freesurfer provide a tool to convert the surface file to a nifty file? I tried using the command 'mri_surf2vol' as follows: mri_surf2vol --surfval lh.thickness --hemi lh --template orig.mgz --volregidentity subjid \ --outvol /path/to/lh.thickness.nii The thickness values of the output lh.thickness.nii are integers between 1 and 3. But the original thickness values are between 0~5 and not all of them are integers. Could someone know what's wrong or suggest another tool? Thanks in advance. Best, Xiaojing

1 0

radiologic convention ?
by ridatta＠mail.med.upenn.edu 06 Apr '10

06 Apr '10

Hello All, If my input images are in Analyze format in Radiologic convention, does FreeSurfer "know" that the MPRAGE images are in radiologic convention (right side of the brain on the left side of the image)? How do we confirm this? Thanks Rito

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