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30070 discussions

Cannot view average curvature after make_average_subject
by Johannes Klein 11 Sep '06

11 Sep '06

Hi all, I'm setting up a small study where I want to compare a subject to some matched controls. I've been following the Group analysis tutorial and I've run make_average_subject on my controls. Now, I'd like to check my data and view averaged curvature and thickness measurements. When I try to load the lh.avg_curv onto lh white in tksurfer, I get the following error: ERROR: number of vertices in XX/lh.avg_curv does not match surface (173612,163842)surfer: error reading curvature file The same applies to lh.avg_thickness However, there is a file called lh.curv that I can load. What am I doing wrong here? How can I view the average curvature and thickness measurements? Thanks a lot everyone, Johannes

4 5

Re: [Freesurfer] aseg total volumes
by Graham Wideman 09 Sep '06

09 Sep '06

Bruce: That's pretty interesting... >this is probably due to the partial volume correction we do when >computing the volumes. Is this algorithm described somewhere? I can see the intent, but your description doesn't completely illuminate how you decide which input voxels contribute to which output voxels, and how much. Graham >Basically we assume that each voxel is a linear >combination of the tissue at that voxel and the next most likely label that >neighbors that voxel. The weighting is computed as mixture weight for the >local class mean for each class that explains the voxel intensity. Our >internal studies show that this improves test-retest reliability and >presumably also accuracy. > >cheers, >Bruce

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FS using uncompressed (not mgz) MRI files?
by Graham Wideman 06 Sep '06

06 Sep '06

Folks -- probably Nick? I'd like to be able to work with some FS sessions using uncompressed data, ie: not using mgz files. (Why? So that I can conveniently use some other tools for troubleshooting and inspection, tools that don't know how to uncompress mgz files). Questions: 1. If I just try to gunzip mgz files, some of their names collide with the directories that mksubjdirs has set up. Historically, most of these dirs used to act as containers for per-slice COR files, so they don't seem useful anymore. Can they just be deleted without consequence? 2. I'm assuming that the uncompressed files should be given the extension ".mgh". Do the FS pipeline scripts and programs automatically adapt to uncompressed files? Thanks, Graham

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nan issue
by Derin Cobia 06 Sep '06

06 Sep '06

Bruce, I worked my way backwards through the stream on each .mgz file. The aseg.mgz (and aseg.auto.mgz) file came up in pieces, some parts were there, others weren't; brain.mgz was blank, there was nothing there, as well as the values being 0; the same for norm.mgz. However, both brainmask & nu.mgz appeared normal, which makes me suspect the talairach.lta file. Is this bad output because of the talairach registration? -Derin

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tkmedit problem, crash on loading aseg
by Johannes Klein 05 Sep '06

05 Sep '06

Hi everyone, I have a rather obscure problem. There are some subjects whose aseg subcortical parcellations will not load up in tkmedit, causing it to crash. This happens when using a Mac with X11 to view them, not on my Linux machine. Interestingly though, this does not happen for all subjects, some do get displayed correctly on the Mac, too. Here's what I do: tkmedit mysubj T1.mgz Then, use tkmedit's File-Load Segmentation There, select aseg.mgz and tkmeditColorsCMA tkmedit then crashes, producing the following log: tkmedit started: Tue Sep 5 17:26:20 2006 tkmedit PAT_XXXX T1.mgz lh.white -aux-surface rh.white $Id: tkmedit.c,v 1.274.2.1 2006/03/06 19:52:48 kteich Exp $ $Name: stable3 $ Set user home dir to /Volumes/JalapenoSAN/Scratch/XXXXXX/fs Set subject home dir to /Scratch/XXXXXX/fs/PAT_XXXX Using interface file /usr/local/freesurfer/lib/tcl/tkmedit.tcl Tcl: Successfully parsed tkmedit.tcl Tcl: Successfully parsed tkm_functional.tcl Error 1 in CLUT_GetLabel: Invalid pointer to object. I wonder if this is a known problem for Macs? Thanks, Johannes

2 1

newbie, white matter volumes
by Romke Rouw 05 Sep '06

05 Sep '06

Hi all, I would like to compare two groups of human subjects on volumetric measures of cerebral white matter. Does anyone know how to get more detailed information on white matter volumes ? (per brain region, or per white matter structure). Thanks! Romke

2 1

transform back to origin coordination ?
by tulu 05 Sep '06

05 Sep '06

Dear Freesurfer experts, I use freesurfer and when I finish recon-all autorecon1, I would like to transform Brainmask.mgz image back to origin coordination. How to do it ? Thank replay Kl chen

4 7

Mri convert
by Lee HL 04 Sep '06

04 Sep '06

Hi Bruce and all, I wish to convert the MGZ format image into ANALYZE format image. I used the command line to convert the MGZ format image: "mri_convert -i brainmask.mgz -o brainmask.img --out_type spm". When I display the image using SPM, the coordinate (0, 0, 0) appears at the posterior commissure. However, when I display the mgz format image using tkmedit, the coordinate (0, 0, 0) appears at the anterior commissure. Was I using the correct command line to convert the image? Thanks! Cheers, HweeLing

2 3

func2tal-sess question
by Cameron Ellis 01 Sep '06

01 Sep '06

Hi, Quick simple question I hope: does running func2tal-sess with two groups at once with a sessid that includes them both and running func2tal with each group separately result in any difference? And if you do need to resample your groups separately do you need to do this under 2 different analyses? Thanks, Cameron

2 1

Hardware/Distro Gottchas?
by Grant McAuley 31 Aug '06

31 Aug '06

Hello, We are about to install Free Surfer on a machine with Intel Core 2 Duo E6400, 2Gb DDR2 and Nvidia Geforce 7300GT video using an Ubuntu or Fedora Core distribution. Are there any 'gottchas' I should know about with this hardware or Linux distros (I will be using the latest drivers and distros)? -- Grant McAuley Research Affairs IS Support Loma Linda University 909-558-1000 Ext 87750 gmcauley(a)llu.edu

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