Freesurfer February 2005

freesurfer@nmr.mgh.harvard.edu

19 participants
22 discussions

Preparing cortical surface for EEG source localization
by Alex Wade 14 Feb '05

14 Feb '05

I have recently started to use FS to generate cortical surfaces for boundary element modelling in EEG source localization. In particular I would like to use the pial surface generated by FS. I have three problems: 1: I can only get FS to generate individual hemispheres. For the BEM, I need a single, connected, mesh for the entire brain. Is there a way to get this (perhaps by fooling FS into not disconnecting the hemispheres early in the segmentation process)? 2: The white/gray boundary mesh is topologically correct (no bridges / handles / holes etc..). Is the pial surface mesh also correct? 3: Is there a way to generate the volume inside the pial surface? That is - can I flood fill the pial surface in some way to extract the voxels that lie inside it as 3d volume? Many thanks Alex A.R. Wade Ph.D. Associate Scientist The Smith-Kettlewell Eye Research Institute 2318 Fillmore Street San Francisco, CA 94115 tel. 415 345 2083 fax. 309 416 6533

4 3

new binaries for tkmedit and tksurfer
by Wan Park 14 Feb '05

14 Feb '05

hi teich, i went to this place: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/ tkmedit_tksurfer-20050211-Darwin.tar.gz and I Unziped it in a temp directory, then move bin/tkmedit and bin/tksurfer into your freesurfer/bin/Darwin directory, and the lib/tcl/* files into freesurfer/lib/tcl. now when i put: $tksurfer i receive this new message: dyld: tksurfer can't open library: /sw/lib/libBLT.2.dylib (No such file or directory, errno = 2) Trace/BPT trap [ogden:freesurfer_package/freesurfer/subjects] wpark% how can i solve this problem? thanks wan

2 1

Freesurfer MAC OSX Installlation
by willcott＠pop.ruf.rice.edu 11 Feb '05

11 Feb '05

I have downloaded and installed freesurfer-20040218-Darwin.tar.gz with no seeming problems. I modified my .tcshrc file, checked directories and think all is in order. I operate in X11 windows. I still can not find csurf or any work-around. Does anyone have any ideas about my problem? -- M. Robert Willcott 1807 Orchard Country Lane Houston, TX 77062 713.302.5148

4 3

MNI align
by Wan Park 11 Feb '05

11 Feb '05

I think I need to do the MNI align. Could someone teach me how to do this? Thanks, Wan

1 0

about tkmedit
by Wan Park 10 Feb '05

10 Feb '05

after processing the volume, when i try to see the images (orig, T1, brain, wm) with the tkmedit tools, i press coronal view but i see horizontal and when i press horizontal i see the coronal view. when i press sagittal, i see the brain "looking" (face) down. interestingly, after doing the talairach, the coordinates seems to keep the coronal, horizontal and sagittal order as i was in correct order (i discovered this when i try to go to a point where it is supposed to be amygdala and it seemed over the place, but if you "draw o mark" that point in the coronal view on my monitor and change to coronal to sagittal view seems to be correct). any solution? thanks a lot, wan ps: any news with the new binaries for OSX endian issue for the visualization of the parcellation? thanks!

1 0

mri_convert
by Joongnam Yang 07 Feb '05

07 Feb '05

Hi I tried to convert *.img functional data into *.mnc file, using "mri_convert" and when I checked the *.mnc file for functional using "mincinfo", it gave me some "unknowns" for the time dimension. image: signed__ short 0 to 1131 image dimensions: xspace yspace zspace time dimension name length step start -------------- ------ ---- ----- xspace 64 3.8 -121.6 yspace 64 3.8 -121.6 zspace 23 5 -57.5 time 240 unknown unknown Does anyone know a way to specify the time dimension during the conversion using "mri_convert"? Thanks. Nam.

1 0

Re: [Freesurfer] talairaching functional data
by Joongnam Yang 04 Feb '05

04 Feb '05

Thanks, Doug, For some reason, mri_vol2vol is missing on my system. (everything else is there). Is there any way that I can download the binary alone from you without reinstalling everything...? Nam. >>> Doug Greve <greve(a)nmr.mgh.harvard.edu> 02/03/05 10:36 AM >>> You're better off using mri_vol2vol. There are lots of docs with --help, including how to convert a volume into talairach space. doug Joongnam Yang wrote: > > Hi, > > I ran "func2tal" with functional data (*.img) and got > > INFO: autodetected functype raw > ERROR: only selxavg, selavg, and sfa functypes are currently supported > > How can I change *.img functional data into the above functypes? > > Thanks. > > Nam. > _______________________________________________ > 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

1 0

error in the visualization of the parcellation
by Wan Park 03 Feb '05

03 Feb '05

hi, i am using a mac G5. after successfully doing the talairach (thanks tosa and quinn) i went through and i did the parcellation: (last part) labeling surface... relabeling using gibbs priors... 000: 12553 changed, 169800 examined... 001: 3181 changed, 48112 examined... 002: 1021 changed, 16263 examined... 003: 473 changed, 5771 examined... 004: 281 changed, 2658 examined... 005: 157 changed, 1570 examined... 006: 69 changed, 848 examined... 007: 34 changed, 397 examined... 008: 19 changed, 211 examined... 009: 9 changed, 120 examined... 010: 8 changed, 47 examined... 011: 8 changed, 49 examined... 012: 2 changed, 44 examined... 013: 0 changed, 11 examined... 000: 538 total segments, 417 labels (5917 vertices) changed 001: 158 total segments, 44 labels (399 vertices) changed 002: 116 total segments, 2 labels (13 vertices) changed 003: 114 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 172 changed) writing output to /usr/local/freesurfer_package/freesurfer/subjects/22970/label/ rh.aparc.annot... writing colortable into annotation file... classification took 4 minutes and 49 seconds. i tried to see it and wrote: tksurfer 22970 rh inflated en then file> label> import annot> /usr/local/freesurfer_package/freesurfer/subjects/22970/label/ rh.aparc.annot but i receive this message: [ogden:freesurfer_package/freesurfer/subjects] wpark% tksurfer 22970 rh inflated surfer: current subjects dir: /usr/local/freesurfer_package/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer_package/freesurfer/subjects surfer: /usr/local/freesurfer_package/freesurfer/subjects/22970/mri/T1/COR- .info INFO: Src volume /tmp/mritotal_4912/orig_8_dxyz.mnc INFO: Target volume /usr/local/mni/share/mni_autoreg/average_305_8_dxyz.mnc INFO: Volume /tmp/mritotal_4912/orig_8_dxyz.mnc cannot be found. ncopen: filename "/usr/local/mni/share/mni_autoreg/average_305_8_dxyz.mnc": Invalid dimension id or name miopen: MINC package entry point Error opening /usr/local/mni/share/mni_autoreg/average_305_8_dxyz.mnc mincRead(): error reading volume from file /usr/local/mni/share/mni_autoreg/average_305_8_dxyz.mnc surfer: vertices=169800, faces=339596 surfer: using interface /usr/local/freesurfer_package/freesurfer/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer_package/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer_package/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer_package/freesurfer/lib/tcl/fsgdfPlot.tcl Couldn't load libtclfsgdf.dylib. Reading /usr/local/freesurfer_package/freesurfer/lib/tcl/tkUtils.tcl Read /usr/local/freesurfer_package/freesurfer/surface_labels.txt, found 95 structures Successfully parsed tksurfer.tcl % reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) reading colortable from annotation file... *** malloc_zone_calloc[11526]: arguments too large: 3221210976,520 CTABreadFrom: could not allocate -1073756320 bin table Cannot allocate memory Bus error [ogden:freesurfer_package/freesurfer/subjects] wpark% could you please help me with this? thanks, wan

2 1

averaging brains over two sessions
by Margaret Duff 03 Feb '05

03 Feb '05

Hello, I am trying to reconstruct brains of patients who had one structural scan during each of 2 visits, a month apart. I averaged the two images together, but since they are from different visits, they look very badly lined up. It looks like there is one image and another image overlaid and shifted by a cm or so. These are clearly wrong and will not work but I was wondering if it was OK to run freesurfer with only one of the images, or if there was a way to line these two images up better so they can be combined? Thanks, Margaret

5 10

talairaching functional data
by Joongnam Yang 03 Feb '05

03 Feb '05

Hi, I ran "func2tal" with functional data (*.img) and got INFO: autodetected functype raw ERROR: only selxavg, selavg, and sfa functypes are currently supported How can I change *.img functional data into the above functypes? Thanks. Nam.

2 1

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer February 2005