Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

amygdala segmentation
by Karen E Murphy 08 Sep '10

08 Sep '10

Does anyone know whether subcortical segmentation of the amygdala includes the "extended amygdala" (i.e. bed nucleus of the stria terminalis)? Thanks, Karen Karen Blackmon, Ph.D. Clinical Coordinator New York University Department of Psychology email: keb217(a)nyu.edu phone: 646-302-4466

2 1

adding control points
by Paola Valsasina 08 Sep '10

08 Sep '10

Dear FS experts, we have run autorecon2 on a set of subjects and now we are in the process of manual editing adding control points. We read the tutorial about the manual editing; however, sometimes we have some doubts about adding or not adding control points in some regions. We had a look at the subject "bert" (included in FS distribution) to have a reference on what can be considered a "good" output and what is necessary to be edited. Can this subject be considered as a good one and used as reference, or do you have any additional reference subjects to look at? Thank you in advance Kind regards, Paola ------------------------------------------------------------- DAI IL TUO 5 X MILLE AL SAN RAFFAELE. BASTA UNA FIRMA. SE FIRMI PER LA RICERCA SANITARIA DEL SAN RAFFAELE DI MILANO, FIRMI PER TUTTI. C.F. 03 06 42 80 153 INFO: 5permille(a)hsr.it - www.5xmille.org

1 0

issues about pial and wm edit
by Daniel Ferreira Padilla 08 Sep '10

08 Sep '10

Dear all, I will really appreciate if you can help me with some issues about editing the pial surface. I have carefully followed the information on the web and looked up the mailing list but I still have the same doubts: 1) I have noticed that pial surface usually includes more than GM (dura, vessels...). My first question is if should we edit this kind of error. Sometimes I am completely sure what I need to correct, but I don't want to put human error in it. Moreover, we will spend to much time with big samples. 2) I have tried to edit the pial surface following the tutorial. After re-running -autorecon2-pial nothing seems to change. The voxels I deleted before are still there and the pial surface looks the same. What could be happening? 3) I have had the same problem with WM edit. After -autorecon2-wm everything remain as before edit. 4) I have read about regenerate the new pial surface with "make_final_surfaces" or from inside recon-all with -finalsurfs. The command could be something like this? recon-all -s <mysubjectname> -finalsurfs 5) If I need to fix pial and wm lesions in the same subject, do I need to run autorecon2-pial and -autorecon2-wm separately? Can I do it at the same time? And if I could, what command do I have to use? I hope these are not too much questions. Thank you very much in advance. Daniel Ferreira

1 0

Longitudinal pial editing
by Derin Cobia 07 Sep '10

07 Sep '10

Based on our understanding of the longitudinal pipeline for 4.5, image edits for the -long runs come mostly from the template/base subj (with an optional flag for CPs to be copied from the template; http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg13256.html, http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12895.html) In addition, our assumption is that pial edits will come via the template, as the -long brainmask, is a result of masking the -long T1.mgz by the template brainmask.mgz (which itself is the norm_template.mgz, a combination of every time point's norm.mgz [which is pre-edit stage]). We've run into an issue where our -long runs are still in need of pial editing, despite edits having been done to both the cross sectional and template runs (see attached). However, it's also our understanding that we should not edit the -long runs and try to re-run (using -autorecon2-pial -autorecon3), as this will pollute the correction for intrasubject variation (per communication from Martin). How would you recommend to proceed? Thanks. -Derin

2 3

Saving multiple control points
by Musen, Gail 07 Sep '10

07 Sep '10

Hi, We have been trying to replicate the manual cortical surface-volume tracing method for the enthorinal cortex described in Feczko et al. (2009) and Dickerson et al. (2009). In this method, points selected on the coronal MRI slices (in the tkmedit) are matched to points along the surface of the reconstructed cortical surface model (in tksurfer). These points are used to define anatomical landmarks and they serve as connection points in the surface volume for tracing. We are running into problems with loading multiple control points on the surface volume. That is, when we place control points on the MRI data and then Go To Saved Point in the surface volume then we only get a single most recent placed point while the other points specified in the MRI slice are "lost". Is there a way we can load all these points simultaneously on the surface so that we can demarcate borders as described in these papers? Thanks -Gail Musen

2 1

new rawavg in fs5 and reprocessing
by k.b.walhovd＠psykologi.uio.no 07 Sep '10

07 Sep '10

Hi, I see there's a new motion correction procedure in fs5, meaning that the rawavg is created differently. When reprocessing data, should we then do everything over, including remaking the rawavg and all edits? I'm asking esp. w/ regards to edits - can they possibly be slightly wrong if kept? And with regard to reprocessing data that have been run w/ the previous versions together with data that have not been previously processed- will such a mix be problematic? I'd highly appreciate your recommendations! Best, Kristine -- Kristine B Walhovd Professor University of Oslo Center for the Study of Human Cognition Department of Psychology PB 1094 Blindern 0317 Oslo Norway

3 2

CVS/Source distribution
by Yaroslav Halchenko 07 Sep '10

07 Sep '10

Dear FreeSurfer Developers, Thank you very much for providing source code exposed under CVS. I wonder if there are any plans to either switch to another version control system and/or provide source distribution in versioned tarballs? N.B. I was asking about vcs change, because rich history of freesurfer development since 1996 is not really accessible with CVS any longer (at least to me with cvs 1:1.12.13-12 on Debian). For instance if I do > cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -D 1996/02/26 dev it fails with an error ... U dev/utils/matfile.c cvs [checkout aborted]: invalid change text in /usr/fscvsroot/dev/utils/matrix.c,v are you observing similar behavior? -- Yaroslav O. Halchenko Postdoctoral Fellow, Department of Psychological and Brain Sciences Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik

1 0

Visualizing Brodmann's areas
by Walimuni, Indika S 07 Sep '10

07 Sep '10

Hi FreeSurfer list Please apologize me if this has been already answered. Is their a way that I can visualize Brodmann's areas on a FreeSurfer subject ? If this is not possible, then is there a standard Brodmann template/atlas so that I can register my volume to it and then visualize ? Thanks, Truly, Indika Walimuni, PhD Post-doctoral Research Associate University of Texas Health Science Center Houston, TX.

2 4

corpuscallosum missing in lh.aparc.stats/rh.aparc.stats
by Yolanda Vives 07 Sep '10

07 Sep '10

Hi all, We have a problem with Freesurfer v4.3.1. The output files "lh.aparc.stat/rh.aparc.stat" don't contain the results corpuscallosum (there are only 35 entries in the file and corpuscallosum is missing). Is it a known bug? Thank you for your time, Yolanda

1 0

Re: [Freesurfer] control points
by Ali Radaideh 07 Sep '10

07 Sep '10

Hi Bruce, Catting the file shows something like cat control.dat info numpoints 0 useRealRAS 0 The version of freesurfer is freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 Unfortunately, I repeated hat you suggested in your previous email (-make all) to another subject but failed at some point although this subject's data have been proceed month ago successfully ( the data from the first subject still running), the error is: second estimation of the COG coord: x=129,y=120, z=120, r=9758 iterations GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=32 , nb = 22554 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=24 , nb = 1548 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=23 , nb = 1656 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=33 , nb = 9459 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=32 , nb = 9819 OTHER CSF_MIN=0, CSF_intensity=18, CSF_MAX=39 , nb = 72 mri_watershed Error: GLOBAL region of the brain empty ! Linux comp13 2.6.22.17-0.1-default #1 SMP 2008/02/10 20:01:04 UTC x86_64 x86_64 x86_64 GNU/Linu x recon-all exited with ERRORS at Mon Sep 6 15:03:10 BST 2010 Thanks Ali -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, September 06, 2010 3:30 PM To: Ali Radaideh Subject: RE: [Freesurfer] control points Hi Ali, can you post your responses to the list? Try catting that file to see what's in it. Also, what version are you running? cheers Bruce On Mon, 6 Sep 2010, Ali Radaideh wrote: > Hi Bruce, > > control.dat file is there (size=75). > > Actually I finished running this subject before and checked that. > > Now I am running the recon-all with -make all flag as you suggested and > it is working fine. > > But not sure if 'reading 0 control points' means that there will be no > improvement after running the recon-all !! > > Thanks > Ali > > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce > Fischl > Sent: Monday, September 06, 2010 2:03 PM > To: Ali Radaideh > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] control points > > Hi Ali, > > the control points are saved in the subject's directory under > > <subject id>/tmp/control.dat > > does that file exist? It also looks like you hadn't finished running > this > subject previously. Try running -make all in recon-alll which will rerun > > only what it needs to. > > cheers > Bruce > > > On Mon, 6 Sep > 2010, Ali Radaideh wrote: > >> Dear Freesurfer experts, >> >> >> >> One more question for today please. I have edited the wm in tkmedit > and >> saved the control points then ran >> >> >> >> Recon-all -autorecon2-cp -autorecon3 -s mySubjectName >> >> >> >> But unfortunately I got the following message after 5min of running. I >> tried to use a different subject but I got the same message again. >> >> >> >> It was displaying a message that it is 'reading 0 control points'. Is >> this message related to the error below? >> >> >> >> mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta >> -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz >> >> >> >> logging cutting plane coordinates to ../scripts/ponscc.cut.log... >> >> INFO: Using transforms/talairach.lta and its offset for Talairach > volume >> ... >> >> using segmentation aseg.auto_noCCseg.mgz... >> >> reading input volume...done. >> >> searching for cutting planes...voxel to talairach voxel transform >> >> 1.047 0.006 0.067 -14.718; >> >> 0.005 1.161 0.015 -27.233; >> >> -0.083 -0.006 1.022 -2.059; >> >> 0.000 0.000 0.000 1.000; >> >> mri_fill: could not read segmentation from aseg.auto_noCCseg.mgz >> >> reading segmented volume aseg.auto_noCCseg.mgz... >> >> ERROR: cannot find >> /data_local/ali/freesurfer/subjects/ali1/mri/aseg.auto_noCCseg.mgz >> >> No such file or directory >> >> Linux comp07 2.6.22.17-0.1-default #1 SMP 2008/02/10 20:01:04 UTC > x86_64 >> x86_64 x86_64 GNU /Linux >> >> >> >> recon-all exited with ERRORS at Mon Sep 6 13:00:12 BST 2010 >> >> >> >> >> >> >> >> Many thanks >> >> Ali >> >> This message and any attachment are intended solely for the addressee > and may contain confidential information. If you have received this > message in error, please send it back to me, and immediately delete it. > Please do not use, copy or disclose the information contained in this > message or in any attachment. Any views or opinions expressed by the > author of this email do not necessarily reflect the views of the > University of Nottingham. >> >> This message has been checked for viruses but the contents of an > attachment >> may still contain software viruses which could damage your computer > system: >> you are advised to perform your own checks. Email communications with > the >> University of Nottingham may be monitored as permitted by UK > legislation. > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom > it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > >

2 5

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer