Freesurfer July 2004

freesurfer@nmr.mgh.harvard.edu

16 participants
23 discussions

overlay problems
by Nguyen, Thang Q 19 Jul '04

19 Jul '04

Hello all, I have been trying to overlay PET data. When I open tkregister2, it shows the data as a gigantic white block. However, when I open my PET images in SPM, they look fine. I have tried searching the email archives and have not found an answer. What could this possibly be? Thanks, Thang ------------------------ Thang Nguyen Psychiatry and Human Behavior - Brain Imaging Center University of California, Irvine Email: thangqn(a)uci.edu This e-mail/fax message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail/fax and destroy all copies of the original message.

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moving a label in tkmedit
by Chekema Nayasha Prince 14 Jul '04

14 Jul '04

Can you move a label to a new location that has already been drawn in tkmedit without redrawing the label ? -Keyma

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new segmentation error
by Chekema Nayasha Prince 14 Jul '04

14 Jul '04

I used the new segmentation in tkmedit to draw labels in the orig volume. When I went to "File-> Save segmentation As" and tried to same it in a new directory I got the following error: "Error:Invalid Command Name "Save Segmentation"" Is there another way to save the segmentation volume? -Keyma

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drawing labels in tkmedit
by Chekema Nayasha Prince 13 Jul '04

13 Jul '04

i'm using the "Select Voxels Tool" to make labels in tkemdit. Each time I draw a label I save it and I have to close tkmedit it and open it again to save a new label. Is there another way to draw all the labels at the same time and save them under different names? -Keyma

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mri_cor2label
by Chekema Nayasha Prince 12 Jul '04

12 Jul '04

I would like to create a label in the orig volume and copy this label to the another scan of the same subject in order to measure SNR values. I drew the label using tkmedit on the orig volume and saved it. Is mri_cor2label the correct function to use in order to copy this label to the other scan? -Keyma

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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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Freesurfer July 2004