Freesurfer November 2005

freesurfer@nmr.mgh.harvard.edu

49 participants
73 discussions

automated parcellation
by Goulven Josse 04 Nov '05

04 Nov '05

Dear Freesurfers, We have used the automated parcellation (Fischl et al, 2004) in several subjects and noticed in some cases labeling of the lateral part of a gyrus (i mean the part that's visible on the folded surface), as belonging to a sulcus. The example I have in mind is the labeling of a gyrus that could be the middle temporal or the angular gyrus as the posterior part of the superior temporal sulcus (STS). I figured the program could not find the correspondence between that particular gyrus and any labels and, since it happened to be close and, sometimes, between two branches of STS, it was labeled as such. Or we made a mistake somewhere ... ? Could anyone please comment on this ? thanks ! Goulven Josse (U of Chicago)

4 9

area file
by Marie Schaer 03 Nov '05

03 Nov '05

Hello everybody! I have one question about how surface areas are calculated by mris_anatomical stats (release2004). I noticed that the ?h.area file may contain the portion of area corresponding to each different vertex. Actually, the sum of all these areas is around 7'500mm^2 for one hemisphere, which is approximately (but not exactely) the result given by mris_anatomical_stats. However, when I converted the pial surface in matlab, and calculated the sum of the area of each triangle using the following equation http://mathworld.wolfram.com/TriangleArea.html, I obtained a very higher result (~10'000mm^2). Perhaps because the triangles are too big to calculate an accurate area at this stage? So my question was, on which basis is calculated the information contained in lh.area? Does the first row of ?h.area correspond to the piece of area attributable to the first vertice, and so on? Thank you very much for your response! Marie Schaer

4 5

freesurfer tutorial
by peggy christidis 03 Nov '05

03 Nov '05

Would you consider providing a .pdf version of the web document "FreeSurfer Tutorial: Morphometry and Reconstruction" that could be easily downloaded and printed out? We occasionally teach a FS class here at the NIH and I know it helps to have a paper-version of the manual to refer to (which is very nice by the way, well-written). Thanks! Peggy

2 1

coordinate transform functional -> COR-anatomy (fwd)
by Claus Tempelmann 03 Nov '05

03 Nov '05

Hello, on behalf of a collegue who has not yet registered for the freesurfer mailing list I want to send you the questions below. Thanks for your help Claus ----------------------------------------------------------------------- Hi, we are currently trying to spatially transform functional data into the anatomical 256*256*256 1mm isovoxel COR-anatomy. We already have a register.dat and therefore a rotation-translation matrix. Our functional data are in a 128*128*24 bshorts file (1.406*1.406*2mm voxels). Slice orientation is approximately orthogonal to the calcarine sulcus Our problem is that the functional data do not fall on the correct location in the anatomical volume. Our approach so far is: We built a datacube from the anatomical COR* files and oriented it with respect to the RAS system so that: R corresponds to -X (the inverted first coordinate direction in our data cube) A corresponds to Y S corresponds to Z >From the functional data (in bshort format) we reconstruct a similar volume and orient it the same way. We assume the origin of the two coordinate system (the anatomical and the functional) in the center voxel of the two volumes Whe now calculate [xAnat, yAnat, zAnat,1]'=[4*4-matrix from register.dat]*[xFunctional, yFunctional, zFunctional,1]' The x*, y* and z*s are in millimeters. An example: we choose the voxel in the center of gravity of the functional volume [0,0,0,1]' and multiply it at the right of the matrix in register.dat. Shouldn't this give us the location of that voxel in the anatomical volume ? Our qusestions: Can the register.dat be used to transform the functional data onto the COR-anatomy ? If yes how ? How does the coordinate system look like in both volumes especially the functional? The *.bhdr file related to the functional bshorts contains RAS-coordinates of the corners of the (first ?) slice. What is the corresponding coordinate system ? Scanner, COR-anatomy ...? We already checked the wiki-site that describes the coordinate systems and transforms but this did not solve our problem. Thank you very much for your help. PS. The 4*4 transformation matrix we are using: 1.081372e+00 5.667235e-02 0.000000e+00 8.327621e+00 3.764737e-02 -7.183544e-01 -6.946586e-01 -6.509724e+01 3.635561e-02 -6.937064e-01 7.193404e-01 -4.349084e+01 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00

2 1

freesurfer + fsl
by Peter Soros 02 Nov '05

02 Nov '05

Hi All, I have installed Freesurfer for Mac OS X (2 Oct 2005) on my system (running 10.4.2) - thanks for the OS X release! Unfortunately, fsl doesn't work after the installation of Freesurfer. This is the error message I get when I try to open the fsl GUI: Error in startup script: no suitable image found. Did find: /Applications/freesurfer/lib/tcltktixblt/lib/ libtix8.1.8.4.a: unknown fi le type, first eight bytes: 0x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A while executing "load /Applications/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a Tix" ("package ifneeded" script) invoked from within "package require Tix" invoked from within "if { [ string first tclsh [ file tail [ info nameofexecutable ] ] ] ! = 0 } { package require Tix tix configure -scheme TixGray option add ..." (file "/usr/local/fsl/tcl/fslstart.tcl" line 3) invoked from within "source [ file dirname [ info script ] ]/fslstart.tcl" (file "/usr/local/fsl/tcl/fsl.tcl" line 71) invoked from within "source ${FSLDIR}/tcl/${origname}.tcl" (file "/usr/local/fsl/bin/fsl" line 19) FSL was installed in the recommended directory /usr/local/fsl/ and worked well before. Any help to get FSL working again is highly appreciated!! Peter

1 0

(no subject)
by Goldman, Aaron (NIH/NIMH) 02 Nov '05

02 Nov '05

Hi, I have a script that basically opens up tksurfer and tkmedit for manual editing, and then runs recon-all stage2 once you're done editing. We recently tried to run the script on a different computer with the same freesurfer distribution, and got an error I'm not used to seeing. It says: WARNING: Couldn't not load orig volume from /????//surf/../mri/orig.mgz Talairach coords will be incorrect. (the '????' was edited in by me) I was just wondering if this error will create problems, either with correct manual editing or with running stage2. Thanks, -Aaron- Aaron L. Goldman Post-Bacc IRTA Genes, Cognition and Psychosis Program, NIMH Building 10, Room 3C108 Phone: (301) 435-0944 Email: aarong(a)mail.nih.gov

2 1

Re: Freesurfer Digest, Vol 21, Issue 3
by Sasha Wolosin 02 Nov '05

02 Nov '05

Regarding this issue with the old version of mris_anatomical_stats, will problems with rh.area effect any of the other results? Or are there any bugs effecting other anatomical stats besides rh.area? Message: 2 Date: Wed, 02 Nov 2005 12:58:06 -0500 From: Doug Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] area file To: Marie Schaer <marie.schaer(a)medecine.unige.ch> Cc: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <4368FE2E.2020503(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=us-ascii; format=flowed We found a problem with this computation about a year ago (11/12/2004 to be specific). I think I sent an email about it to the list. Any releases prior to that date will have this error in the area computations. Can you try it with a more recent release? Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin(a)kennedykrieger.org Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

1 0

Re: [Freesurfer] help with mris_ca_label
by Sasha Wolosin 02 Nov '05

02 Nov '05

thanks, I created a label directory and that solved the problem. It looks like all our subjects are missing a label directory. Do you know why that might happen? Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin(a)kennedykrieger.org >>> Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 11/02/05 1:46 PM >>> Hi Sasha, it gets written into the label dir by default. Are you sure that directory exists (should be at the same level as surf) Bruce On Wed, 2 Nov 2005, Sasha Wolosin wrote: > I'm having trouble specifying the output file when running > mris_ca_label- should it be in the surf folder or somewhere else? > (output below) > Thanks, > Sasha > > [root@localhost surf]$ pwd > /home/wolosin/subjects/dec1877J_prac/surf > [root@localhost surf]$ mris_ca_label dec1877J_prac rh rh.sphere.reg > /freesurfer/ average/rh.atlas2002_simple.gcs rh.aparc.annot > reading atlas from /freesurfer/average/rh.atlas2002_simple.gcs... > reading color table from GCSA file.... > input 1: CURVATURE FILE, flags 0, avgs 0, name sulc > input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature > labeling surface... > relabeling using gibbs priors... > 000: 9230 changed, 125897 examined... > 001: 2224 changed, 34779 examined... > 002: 681 changed, 11344 examined... > 003: 275 changed, 3817 examined... > 004: 160 changed, 1602 examined... > 005: 76 changed, 937 examined... > 006: 31 changed, 434 examined... > 007: 18 changed, 193 examined... > 008: 15 changed, 103 examined... > 009: 7 changed, 86 examined... > 010: 2 changed, 46 examined... > 011: 3 changed, 16 examined... > 012: 0 changed, 10 examined... > 000: 286 total segments, 189 labels (2604 vertices) changed > 001: 107 total segments, 12 labels (195 vertices) changed > 002: 95 total segments, 0 labels (0 vertices) changed > 10 filter iterations complete (10 requested, 121 changed) > writing output to rh.aparc.annot... > could not write annot file > /home/wolosin/subjects/dec1877J_prac/surf/../label/rh .aparc.annot > No such file or directory > mris_ca_label: could not write annot file rh.aparc.annot for > dec1877J_prac > No such file or directory > [root@localhost surf]$ > > Sasha Wolosin > Research Assistant > Developmental Cognitive Neurology > Kennedy Krieger Institute > 707 N. Broadway > Baltimore, MD 21205 > ph: (443) 923-9270 > wolosin(a)kennedykrieger.org > > > > Disclaimer: > The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. > > >

2 1

Re: [Freesurfer] help with mris_ca_label
by Sasha Wolosin 02 Nov '05

02 Nov '05

I'm having trouble specifying the output file when running mris_ca_label- should it be in the surf folder or somewhere else? (output below) Thanks, Sasha [root@localhost surf]$ pwd /home/wolosin/subjects/dec1877J_prac/surf [root@localhost surf]$ mris_ca_label dec1877J_prac rh rh.sphere.reg /freesurfer/ average/rh.atlas2002_simple.gcs rh.aparc.annot reading atlas from /freesurfer/average/rh.atlas2002_simple.gcs... reading color table from GCSA file.... input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... relabeling using gibbs priors... 000: 9230 changed, 125897 examined... 001: 2224 changed, 34779 examined... 002: 681 changed, 11344 examined... 003: 275 changed, 3817 examined... 004: 160 changed, 1602 examined... 005: 76 changed, 937 examined... 006: 31 changed, 434 examined... 007: 18 changed, 193 examined... 008: 15 changed, 103 examined... 009: 7 changed, 86 examined... 010: 2 changed, 46 examined... 011: 3 changed, 16 examined... 012: 0 changed, 10 examined... 000: 286 total segments, 189 labels (2604 vertices) changed 001: 107 total segments, 12 labels (195 vertices) changed 002: 95 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 121 changed) writing output to rh.aparc.annot... could not write annot file /home/wolosin/subjects/dec1877J_prac/surf/../label/rh .aparc.annot No such file or directory mris_ca_label: could not write annot file rh.aparc.annot for dec1877J_prac No such file or directory [root@localhost surf]$ Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin(a)kennedykrieger.org Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

2 1

subcortical segmentation
by Eliezer Kahn 02 Nov '05

02 Nov '05

Hi, As mentioned in a previous message, running the subcortical segmentation takes 10-15 hours, primarily because of the Cannonical Registration (mri_ca_register) step. However, one the freesurfer papers (Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain) states on the very first page that it takes only 30 minutes to label the brain. How essential is the Cannonical Registration part? Can one leave it out and still get a good subcortical segmentation? Thanks, Eli

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 November 2005