Freesurfer

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30059 discussions

label outputs for mri_surfcluster
by Doug Greve 09 Jul '04

09 Jul '04

mri_surfcluster, which does clustering on the surface, can now output each cluster as a label file. I've updated the --help with info on how to use it, but basically you just need to add --olab labelbase, and it will save the label for the Nth cluster as labelbase-000N.label. For those in the Martinos Center, the new version is already on line. For those on outside who just can't wait for a snapshot, you can download the new version from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surfclust… mri_surfcluster does not assign p-values to clusters, but I'm working on that as part of a new version of mris_glm. doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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Remote tksurfer
by Daniel Goldenholz 08 Jul '04

08 Jul '04

I am trying to view images from tksurfer remotely. My computer at work has everything all set up fine, and my computer at home has no linux, and therefore no freesurfer. I wanted to look at a particular surface and overlay, but I had not previously viewed it. So I called up tksurfer from my VNC terminal, and was told that some graphics routines needed for tksurfer were not there. I don't mind so much - it's annoying, but if I could find a workaround it wouldn't bug me too much. I was hoping I could simply use a tcl script to draw the image on my work computer, save it, and then view it remotely. For reasons that are not clear to me, this didn't work either. So. What I want to do is given a particular view that I set up in a tcl script, I would like to get an RGB file of that, without drawing it locally. Any ideas or creative workarounds? Thanks -- Daniel Goldenholz ----------------------------------------------------- Cell: 617-935-9421 http://people.bu.edu/danielg/

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(no subject)
by Chekema Nayasha Prince 08 Jul '04

08 Jul '04

I am trying to load the thickness overlay on the inflated brain but when I select the h.thickness surface it doesn't overlay anything. The inflated brain just refreshes but no overlay appear. Is there another way to get the overlay loaded? -Keyma

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ROI labels from clusters on surface .w
by Daniel Goldenholz 08 Jul '04

08 Jul '04

The problem: I have some areas in MEG I would like to track as "ROI"s. To do this, I need labels for those areas which are active clusters. In MEG, I can convert an activity map into a .w file, which is the "paint" format used for overlays in tksurfer. So the new problem: I have a .w file, which contains clusters of areas which are above a threshold value. I want label files for each cluster. mri_surfcluster, which seems similar to what I need, does not output labels, or anything like it, so far as I can tell. Does a method exist, or should I invent one? (an example of this would be: do a vision experiment in MEG. primary visual areas will be active, so a blob shows up over there in MEG. If I want to see the behavior of that blob vs. time, I need a label. I am hoping there exists a way to send the image of the blob (or blobs) from MEG to surfer as .w files, and then figure out automatically where clusters (blobs) appear, and then create a label file for each one) Daniel Goldenholz ----------------------------------------------------- Cell: 617-935-9421 http://people.bu.edu/danielg/

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RE: Making own template for registration
by Hämäläinen Janne 05 Jul '04

05 Jul '04

Hi, The problem was found. Apparently you have to specify the extension '.tif' for the template file, otherwise you get the error shown in the message below. So to make a template of the right hemisphere from, for example, the Freesurfer example data 'bert', the following command seems to be working: mris_make_template rh sphere bert template.tif Cheers, Janne -----Original Message----- From: Hämäläinen Janne To: 'freesurfer(a)nmr.mgh.harvard.edu' Sent: 7/5/2004 10:46 AM Subject: Making own template for registration Hi, I asked about these things earlier (see http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2004-June/000134.ht ml), but we're still having troubles. We're trying to create our own template for the registration procedure. The idea was to make the template by first registering all the other template surfaces to one single surface and proceed from there. We've tried the method 'mris_make_template', which we've interpreted to be the one intended for the procedure. However, we're getting an error when, for example, attempting to create a template from the Freesurfer example data 'bert': > mris_make_template rh sphere bert template_test <OUTPUT> creating new parameterization... processing subject bert reading spherical surface /data/hamalja/freesurfer/subjects/bert/surf/rh.sphere... computing parameterization for surface /data/hamalja/freesurfer/subjects/bert/surf/rh.inflated... computing parameterization for surface /data/hamalja/freesurfer/subjects/bert/surf/rh.sulc... computing parameterization for surface /data/hamalja/freesurfer/subjects/bert/surf/rh.smoothwm... writing updated template to template_test... HIPS unsupported </OUTPUT> So, are we doing something wrong, or could there perhaps be something wrong with our installation? Any help would be appreciated. Thanks in advance, -Janne Hämäläinen -- Janne Hämäläinen Researcher Helsinki University Central Hospital Department of Radiology janne dot hamalainen at hus dot fi

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Making own template for registration
by Hämäläinen Janne 05 Jul '04

05 Jul '04

Hi, I asked about these things earlier (see http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2004-June/000134.html) but we're still having troubles. We're trying to create our own template for the registration procedure. The idea was to make the template by first registering all the other template surfaces to one single surface and proceed from there. We've tried the method 'mris_make_template', which we've interpreted to be the one intended for the procedure. However, we're getting an error when, for example, attempting to create a template from the Freesurfer example data 'bert': > mris_make_template rh sphere bert template_test <OUTPUT> creating new parameterization... processing subject bert reading spherical surface /data/hamalja/freesurfer/subjects/bert/surf/rh.sphere... computing parameterization for surface /data/hamalja/freesurfer/subjects/bert/surf/rh.inflated... computing parameterization for surface /data/hamalja/freesurfer/subjects/bert/surf/rh.sulc... computing parameterization for surface /data/hamalja/freesurfer/subjects/bert/surf/rh.smoothwm... writing updated template to template_test... HIPS unsupported </OUTPUT> So, are we doing something wrong, or could there perhaps be something wrong with our installation? Any help would be appreciated. Thanks in advance, -Janne Hämäläinen -- Janne Hämäläinen Researcher Helsinki University Central Hospital Department of Radiology janne dot hamalainen at hus dot fi

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parcellation file format
by Darren Weber 03 Jul '04

03 Jul '04

Dear Bruce, can we read the parcellation annotation file into matlab? Essentially, how can we obtain a list of all the vertex indices and their classification? Best, Darren -- Darren L. Weber, Visiting Postdoctoral Fellow, China Basin Landing, Dynamic Neuroimaging Laboratory, Department of Radiology, University of California, San Francisco 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94143-0946 Address for express mail/deliveries: 185 Berry Street, Suite 350, San Francisco, CA 94107 voice:(1) 415 353-9444 fax: (1) 415 353-9421 www: http://dnl.ucsf.edu/users/dweber "People travel to wonder at the height of the mountains, at the huge waves of the seas, at the long courses of the rivers, at the vast compass of the ocean, at the circular motion of the stars; and they pass by themselves without wondering." --St. Augustine (b. 354, d. 430) "A good traveler has no fixed plan and is not intent on arriving." --Lao Tzu

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inflation<-> area
by L.Scheef＠uni-bonn.de 01 Jul '04

01 Jul '04

Dear list members, I wonder if during the inflation process "areas" are preserved. Or does inflation induces local deformations? Best wishes, Lukas Lukas Scheef, MD, MSc MR-Tomography Department of Radiology University of Bonn Sigmund-Freud-Straße 25 D-53105 Bonn Fax: +49-228-287-5598 Phone:+49-228-287-4496 E-mail: L.Scheef(a)uni-bonn.de

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Parcellate_subject
by Chekema Nayasha Prince 30 Jun '04

30 Jun '04

I ran parcellate subject and I overlayed the annotation on the inflated surface. The medial wall segmentation looks incorrect. The medial wall area section is very large and is also spreading into the frontal regions. I looked at the T1 image with the lh.white surface loaded in tkmedit and the outline around the wm and gm look ok. This is the first time I have seen the medial wall appear so wide spread in the parcellated inflate brain. Is there a way to either fix the problem or investigate what is causing it? -Keyma

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non-primate brains
by Geoffrey Aguirre 29 Jun '04

29 Jun '04

Free surfers -- I am collecting data from dogs. Any advice regarding passing this data through the system? I have a couple of specific questions: 1) Should I acquire data with voxel sizes smaller than 1mm, given that the brain is much smaller? How would I tell free-surfer to operate with this higher resolution data? 2) So far, automated skull stripping has been a failure, even with definition of a "seed point" in the white matter. The routine strips away the brain around the seed point, leaving a large chunk of scalp and muscle with a bit of cortex attached. Any thoughts on how to get this going? Thanks in advance for any help, Geoff -- Geoffrey Karl Aguirre, M.D., Ph.D. University of Pennsylvania Center for Cognitive Neuroscience 3815 Walnut Street Fax: (215) 898-1982 Philadelphia, PA 19104-6196 mailto:aguirre@neuro.med.upenn.edu http://ccn.upenn.edu/~aguirre

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