Freesurfer June 2012

freesurfer@nmr.mgh.harvard.edu

124 participants
195 discussions

trac-all -bedp terminated job
by stobyne＠nmr.mgh.harvard.edu 04 Jun '12

04 Jun '12

Hello, I'm running bedpostx_seychelles from the seychelles prompt (via trac-all -bedp -c $SUBJECTSDIR/[dmrircfile]) with vers. v5.1.0-20110514. The processes are generated and run correctly, as far as I can see, until the post-processing job. I receive and email stating: PBS Job Id: 1535470.seychelles.nmr.mgh.harvard.edu Job Name: bedpostx_post Execution terminated Exit_status=0 resources_used.cput=00:00:00 resources_used.mem=0kb resources_used.vmem=0kb resources_used.walltime=00:00:00 Why might the process be terminated? -Sean

3 4

Re: [Freesurfer] Concatenating Transforms
by Clark Fisher 04 Jun '12

04 Jun '12

Hi Doug, I do plan to manually align the functionals to the structural as a final step, but our epi scans look different enough from our T1s that I want to use this as a starting point. Also, combining transforms is something I've wanted to be able to do a few times now as I explore different ways of looking at my data, so I think it could be useful for the future. One thing that seems to have worked for my current case is to convert my registrations to the xfm format, add a final row to make a 4x4 matrix, multiply them in matlab, and make a new xfm file with the resulting matrix. Is there a better way to do this? -Clark

2 1

Assertion failed at line 827
by Kiley Seymour 04 Jun '12

04 Jun '12

Dear Freesurfers, I have previously had no trouble using recon-all to process my structural scans. However, today I encountered the problem below. I have looked at postings on this mailing list and it seems this issue is not a freesurfer one. During my last functional analysis of retinotopy data in freesurfer, I came across a problem that required me to install a full version of FSL on my ubuntu machine. Do you think this could be the source of the problem somehow? Otherwise, I am not sure what could have changed since the last time I processed my data with recon-all. Your input would be very much appreciated. Thanks Kiley Assertion failed at line 827 in file templates/CachedArray.cc nu_estimate_np_and_em: crashed while running volume_stats (termination status=256) nu_correct: crashed while running nu_estimate_np_and_em (termination status=256) ERROR: nu_correct Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux Dr Kiley Seymour Alexander von Humboldt Postdoctoral Fellow Klinik für Psychiatrie und Psychotherapie Charité Campus Mitte Charitéplatz 1 D-10117 Berlin tel: 0049-(0)30-450 517131

2 1

Anatomic Inferences
by Govindarajan, Koushik Athreya 04 Jun '12

04 Jun '12

Dear Freesurfers, I had a question about interpreting the results of the Monte-Carlo simulation. It is my understanding that the clusters are labeled based on the value of the maximum significant vertex in a cluster. So, assuming that a cluster kind of borders or extends over 2 adjacent regions, it could well be labeled as a single region whereas anatomically, it would actually be 2 separate regions. Are there any suggestions for an atlas that could help me make my inferences more meaningful? Sorry if this is a naive question, my knowledge of anatomic labelling is less than impressive :-) Thanks Koushik

2 3

when are uncorrected 0, 001 results permitted instead of FWE?
by Daniel Ferreira 04 Jun '12

04 Jun '12

Dear all, I have heard that the FWE correction sometimes could be demanding and kill very subtle differences, overall for example in aging studies with normal people and narrow-age intervals, or young people, where changes are supposed to be not very big. So, do you know when uncorrected results are justified or at least permitted instead of FWE? Any paper or information about this specific FWE disadvantages in aid of p<0,001 uncorrected results? Thank you very much in advance Daniel Ferreira

2 1

Couldn't download rtview
by Michael Bannert 04 Jun '12

04 Jun '12

Dear freesurfer community, I tried to download rtview but it didn't work. I used the following URL: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/rtview ... as described here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21560.html I need this function to interpret retinotopic mapping data. I followed the instructions for running retinotopic mapping using Freesurfer 5 I found here ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis ) and everything seems to work fine but I find it hard to interpret the results and to determine the boundaries between visual areas. Could you please tell me where the file can be found? (Or is there a more elegant way to get a nice color wheel in Freesurfer 5?) Thank you very much! Michael PS: The URL for the FsFast tutorial data still seems to be incorrect as well. See also http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23019.html -- Michael Bannert, Dipl.-Psych. Vision & Cognition Lab, Centre for Integrative Neuroscience, Univ. of Tübingen & BCCN Tübingen Otfried-Müller-Str. 25, 72076 Tübingen, Germany Phone: +49 - (0)7071 / 29 - 89031

2 1

qdec table file
by Laura M. Tully 04 Jun '12

04 Jun '12

Hi Doug, Attached is the qdec table file and associated levels files. It's strange that qdec won't let me select more than one continuous variable. What's even more strange is that I have been able to do that last month when I originally looked at these data before doing manual edits and quality control. I don't think that I have changed anything since then, but I'm not sure what to look for. Any help you have would be most appreciated! Best, Laura. -- Laura Tully Social Neuroscience & Psychopathology Harvard University 840 William James Hall 33 Kirkland St Cambridge, MA 02138 ltully(a)fas.harvard.edu -- My musings as a young clinical scientist: http://theclinicalbrain.blogspot.com/ Follow me on Twitter: @tully_laura -- Laura Tully Social Neuroscience & Psychopathology Harvard University 840 William James Hall 33 Kirkland St Cambridge, MA 02138 ltully(a)fas.harvard.edu -- My musings as a young clinical scientist: http://theclinicalbrain.blogspot.com/ Follow me on Twitter: @tully_laura

2 1

Re: [Freesurfer] Inter-hemispheric registration issue
by Douglas N Greve 04 Jun '12

04 Jun '12

Irene, this is a problem with the script. The work-around is to run xhemireg before running surfreg with the --xhemi option. doug On 05/16/2012 01:56 AM, Irene Altarelli wrote: > Dear Doug, > > here is what I get. > > First, I ran surfreg --s aa_tris --t fsaverage_sym --lh and got the > attached log file. Here is the terminal output: > > setenv SUBJECTS_DIR /home/ialtarelli/DATABASE/Karla5/ > cd /home/ialtarelli > /home/ialtarelli/freesurfer/bin/surfreg --s aa_tris --t fsaverage_sym > --lh > > Linux lscp-iao1 2.6.32-5-amd64 #1 SMP Mon Jan 16 16:22:28 UTC 2012 > x86_64 GNU/Linux > #@# lh mardi 15 mai 2012, 19:23:56 (UTC+0200) > #CMD# mris_register -curv -annot > aparc.annot /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.sphere /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.fsaverage_sym.sphere.reg > using smoothwm curvature for final alignment > zeroing medial wall in aparc.annot > $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $ > $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ > reading surface > from /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.sphere... > reading colortable from annotation file... > colortable with 36 entries read > (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > reading template parameterization > from /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif... > ripping medial wall... > writing registered surface > to /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.fsaverage_sym.sphere.reg... > curvature mean = 0.007, std = 0.603 > curvature mean = 0.030, std = 0.806 > curvature mean = 0.024, std = 0.853 > curvature mean = 0.009, std = 0.826 > curvature mean = 0.011, std = 0.936 > curvature mean = 0.003, std = 0.836 > curvature mean = 0.005, std = 0.972 > curvature mean = 0.001, std = 0.837 > curvature mean = 0.001, std = 0.988 > curvature mean = -0.032, std = 0.312 > curvature mean = 0.032, std = 0.124 > curvature mean = 0.079, std = 0.315 > curvature mean = 0.031, std = 0.151 > curvature mean = 0.049, std = 0.489 > curvature mean = 0.031, std = 0.165 > curvature mean = 0.028, std = 0.631 > curvature mean = 0.031, std = 0.171 > curvature mean = 0.011, std = 0.749 > 159: 0 negative triangles > surfreg-Run-Time-Hours aa_tris lh 0 0,90 > mardi 15 mai 2012, 20:17:58 (UTC+0200) > surfreg done > > Then, I ran surfreg --s aa_tris --t fsaverage_sym --lh --xhemi and the > terminal output is just: > > ERROR: cannot > find /home/ialtarelli/DATABASE/Karla5//aa_tris/xhemi/surf/lh.sphere > > without any log file, at least I can't find any modified file in the > subject's folder. > > > Hope this helps make things clearer. > Many thanks in advance! > Irene > > > Le mardi 15 mai 2012 à 15:19 -0400, Douglas N Greve a écrit : >> Can you send me the command line and terminal output? Did you run >> xhemireg first? Should not have had to ... >> >> On 05/15/2012 03:02 PM, Irene.Altarelli(a)ens.fr wrote: >>> Dear Doug, >>> >>> where would that log file be? As the /subject/xhemi fails to be created the log >>> normally appearing in there cannot be found.. Sorry if I misunderstood >>> something. >>> >>> Thanks, >>> Irene >>> >>> >>> Selon Douglas N Greve<greve(a)nmr.mgh.harvard.edu>: >>> >>>> Hi Irene, can you send the log file for the command that is failing? >>>> doug >>>> >>>> On 05/15/2012 01:28 PM, Irene Altarelli wrote: >>>>> Dear all, >>>>> >>>>> I'm trying to use the new script for the inter-hemisphere analysis, in >>>>> Fs version 5.0. I have downloaded the files as suggested >>>>> (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21706.html) >>>>> >>>>> Surfreg seems to be running fine (surfreg --s subject --t fsaverage_sym >>>>> --lh), but I have problems then with the --xhemi option. Some files >>>>> appear to be missing, I get the following error messages: >>>>> >>>>> ERROR: cannot find /path/subject/xhemi/surf/lh.sphere >>>>> ERROR: cannot find /path/subject/xhemi/surf/lh.smoothwm >>>>> ERROR: cannot find /path/subject/xhemi/surf/lh.sphere >>>>> ERROR: cannot find /path/subject/xhemi/label/lh.aparc.annot >>>>> >>>>> lh.fsaverage_sym.sphere.reg is created in $subject as it should (please >>>>> find the surfreg log below). >>>>> >>>>> Thank you in advance, >>>>> Irene >>>>> >>>>> >>>>> Log file for surfreg >>>>> samedi 12 mai 2012, 17:36:31 (UTC+0200) >>>>> >>>>> setenv SUBJECTS_DIR /home/ialtarelli/DATABASE/Karla5/ >>>>> cd /home/ialtarelli >>>>> /home/ialtarelli/freesurfer/bin/surfreg --s aa_copie --t fsaverage_sym >>>>> --lh >>>>> >>>>> Linux lscp-iao1 2.6.32-5-amd64 #1 SMP Mon Jan 16 16:22:28 UTC 2012 >>>>> x86_64 GNU/Linux >>>>> #@# lh samedi 12 mai 2012, 17:36:31 (UTC+0200) >>>>> #CMD# mris_register -curv -annot >>>>> aparc.annot /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.sphere >>>> /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif >>>> /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.fsaverage_sym.sphere.reg >>>>> using smoothwm curvature for final alignment >>>>> zeroing medial wall in aparc.annot >>>>> $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $ >>>>> $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ >>>>> reading surface >>>>> from /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.sphere... >>>>> reading colortable from annotation file... >>>>> colortable with 36 entries read >>>>> (originally >>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>>> reading template parameterization >>>>> from /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif... >>>>> ripping medial wall... >>>>> writing registered surface >>>>> to >>>> /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.fsaverage_sym.sphere.reg... >>>>> curvature mean = 0.007, std = 0.603 >>>>> curvature mean = 0.030, std = 0.806 >>>>> curvature mean = 0.024, std = 0.853 >>>>> curvature mean = 0.009, std = 0.826 >>>>> curvature mean = 0.011, std = 0.936 >>>>> curvature mean = 0.003, std = 0.836 >>>>> curvature mean = 0.005, std = 0.972 >>>>> curvature mean = 0.001, std = 0.837 >>>>> curvature mean = 0.001, std = 0.988 >>>>> curvature mean = -0.032, std = 0.312 >>>>> curvature mean = 0.032, std = 0.124 >>>>> curvature mean = 0.079, std = 0.315 >>>>> curvature mean = 0.031, std = 0.151 >>>>> curvature mean = 0.049, std = 0.489 >>>>> curvature mean = 0.031, std = 0.165 >>>>> curvature mean = 0.028, std = 0.631 >>>>> curvature mean = 0.031, std = 0.171 >>>>> curvature mean = 0.011, std = 0.749 >>>>> 159: 0 negative triangles >>>>> surfreg-Run-Time-Hours aa_copie lh 0 0,84 >>>>> samedi 12 mai 2012, 18:26:49 (UTC+0200) >>>>> surfreg done >>>>> >>>>> >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve(a)nmr.mgh.harvard.edu >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> >>>> _______________________________________________ >>>> 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. >>>> >>>> >>>> >>> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

3 6

freeview RAS
by Oya, Hiroyuki (UI Health Care) 04 Jun '12

04 Jun '12

Dear Sir, When I view a brain volume (e.x., orig.mgz) with freeview and tkmedit, RAS coordinate differs. Why? Thank you. Hiroyuki ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________

2 1

Re: [Freesurfer] tkregister question
by Shay Ohayon 04 Jun '12

04 Jun '12

Dear Doug, Following up on tkregister (lets see if my logic make sense). So, if I use --regheader, the actual transformation that will be written to register.dat will be this one ? T* = Tk_vox2ras(B) * inv(vox2rasB) * T * vox2rasA * inv(tkvox2rasA) where T maps X,Y,Z of volume A (in mm) to X,Y,Z of volume B (in mm) when mm space was obtained using vox2ras. This way, things will be compatible when I call tkregister again without the regheader? What bothered me was that if you use vox2ras to map things you get transformation T, which is actually different than the transformation you would get if you use tkvox2ras (i.e., T*). If this is the case, then I think I finally understand whats going on :) -- Shay Date: Fri, 01 Jun 2012 12:03:13 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] tkregister question To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <4FC8E7C1.6060806(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed When you use --regheader, then it uses the vox2ras transform in the header. If you pass it a register.dat file as input, then vox2ras is ignored. doug On 05/31/2012 06:39 PM, Shay Ohayon wrote: > Hi, > > Bump? > > Can someone please explain to me the puzzle described below regarding > tkregister2 and vox2ras0 (which I thought should be ignored for > registration purposes?) > > Thanks! > > -- Shay > > > On Sat, May 26, 2012 at 2:23 PM, Shay Ohayon <shay.ohayon(a)gmail.com > <mailto:shay.ohayon@gmail.com>> wrote: > > Hi, > > Here's a question to Doug / anyone else who mastered the intricate > way of volume transformations: > > I'm a bit puzzled. > According to Free surfer's documentation (fscoordinates.pdf), the > way two volumes are registered to each other using tkregister is > always using > the fixed transformation (tkvox2ras) (see page 6). > > However, when I do the following little experiment (using matlab's > freesurfer API) > > A = '001.nii'; > B = '002.nii'; > X=MRIread(A); > X.vox2ras0(1,4) = 40; > MRIwrite(X,B); > > tkregister2 --targ 001.nii --mov 002.nii --regheader -reg R.reg > > The two volumes are not in alignment when they are loaded into > tkregister. > Now, what am I missing here? > If both were loaded using the fixed transform, they should still > be in alignment (i.e., vox2ras should be ignored for registration > purposes). > > Thanks in advance, > > -- Shay > Tsao lab > Caltech > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

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 June 2012