Freesurfer July 2013

freesurfer@nmr.mgh.harvard.edu

165 participants
332 discussions

Error "Cannot allocate memory"
by Annemarie Brandhofe 29 Jul '13

29 Jul '13

Dear freesurfer community, we are conducting cortical-thickness analysis using freesurfer-5.1.0 and have been experiencing some problems with the automatic recognition of the control points. For several subjects, we run the recon-all command and after about 40 hours of computations, we receive the error message “Excessive topologic defect encountered: could not allocate 171060256 edges for retessellation Cannot allocate memory”. After the occurrence of the error message, the computation is stopped. Below, we provide the details of our setup and the exact error message for one subject. Feel free to ask for more information. Thank you very much for your help! Yours sincerely, Annemarie $ bugr FREESURFER_HOME: /apps/prod/i486/freesurfer-5.1.0 Build stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 Debian version: 5.0.6 Kernel info: Linux 2.6.27.39-1-ql-beowulf i686 $ which freesurfer -> /apps/prod/i486/freesurfer-5.1.0/bin/freesurfer Used command: recon-all –autorecon2-cp –subjid IB34_mdeft. Error message: CORRECTING DEFECT 0 (vertices=72621, convex hull=6983) Excessive topologic defect encountered: could not allocate 171060256 edges for retessellation Cannot allocate memory Linux beo-08 2.6.27.39-1-ql-beowulf #1 SMP Mon Nov 23 10:55:10 CET 2009 i686 GNU/Linux recon-all -s IB34_mdeft. exited with ERRORS at Sat Jul 27 00:01:52 CEST 2013

2 1

Re: [Freesurfer] infant atlas segmentation
by Mark Plantz 29 Jul '13

29 Jul '13

I guess the problem is that those regions should not be out of bounds. Maybe I need to create a new Lookup Table for the infant mri's? Is that possible to do? On Wed, Jul 24, 2013 at 2:21 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu>wrote: > Hi Mark, please post to the list and not to me. > thanks > doug > > On 07/24/2013 03:21 PM, Mark Plantz wrote: > >> I guess the problem is that those regions should not be out of bounds. >> Maybe I need to create a new Lookup Table for the infant mri's? Is that >> possible to do? >> >> >> On Wed, Jul 24, 2013 at 2:15 PM, Douglas N Greve < >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu>>> >> wrote: >> >> >> what is the problem exactly? The fact that there are red regions >> or that that the red regions are labeled as "Out of Bounds"? If >> the latter, you will need to create a LUT that matches your >> regions. the out of bounds means that the index in the volume does >> not match an index in the LUT. >> doug >> >> >> >> On 07/24/2013 01:26 PM, Mark Plantz wrote: >> >> Finally got the registration to work. However, it looks like >> the out of bounds regions (in red) are still present (even >> though the regions are well within our boundaries). Is that >> expected since they were labeled in the original segmentation >> volume? Is there anyway to correct those? >> >> Thanks for all of the help! >> >> - Mark >> p.s. I attached a picture of the original brain.mgz file >> viewed with the corrected segmentation volume >> >> >> On Wed, Jul 24, 2013 at 12:22 PM, Mark Plantz >> <markplantz2016(a)u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> > >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu>>>> >> wrote: >> >> Finally got the registration to work. However, it looks >> like the >> out of bound regions (in red) are still prevalent. Is that >> expected since they were present in the original segmentation >> volume? Would there be anyway to correct those? >> >> Thanks for all the help! >> >> - MP >> >> >> On Wed, Jul 24, 2013 at 11:11 AM, Mark Plantz >> <markplantz2016(a)u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> > >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu>>>> >> wrote: >> >> Nevermind, it turned out to be a permissions issue. >> Thanks! >> >> >> On Wed, Jul 24, 2013 at 10:12 AM, Mark Plantz >> <markplantz2016(a)u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> > >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu>>>> >> wrote: >> >> Thanks for the reply Doug. I recently ran the >> bbregister >> command and attempted to view the results using >> tkregister2. I received the following error: >> >> dhcp-165-124-23-232 <tel:165-124-23-232> >> <tel:165-124-23-232 <tel:165-124-23-232>>:Desktop >> >> >> IngvalsonLab$ tkregister2 --mov >> /Volumes/Wong_Lab/**CochlearImplant/UNC_NiFTI/ >> **infant-1yr-mgz/mri/avgseg.mgz >> --reg /Users/IngvalsonLab/Desktop/**register.dat >> --surf >> >> tkregister_tcl >> /Applications/freesurfer/**tktools/tkregister2.tcl >> INFO: no target volume specified, assuming >> FreeSurfer orig >> volume. >> target volume orig >> movable volume >> /Volumes/Wong_Lab/**CochlearImplant/UNC_NiFTI/ >> **infant-1yr-mgz/mri/avgseg.mgz >> reg file /Users/IngvalsonLab/Desktop/**register.dat >> LoadVol 1 >> ZeroCRAS 0 >> $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 >> greve Exp $ >> Diagnostic Level -1 >> regio_read_register(): Undefined error: 0 >> Error reading subject from >> /Users/IngvalsonLab/Desktop/**register.dat >> ERROR: reading >> /Users/IngvalsonLab/Desktop/**register.dat >> dhcp-165-124-23-232 <tel:165-124-23-232> >> <tel:165-124-23-232 <tel:165-124-23-232>>:Desktop >> >> >> IngvalsonLab$ >> >> I do not believe it is a permissions issue? >> >> Could it simply be that the register was bad? Is >> there an >> easy way to open up the register.dat.mincost file >> to check >> the registration? >> >> Thanks again, >> >> MP >> >> >> On Tue, Jul 23, 2013 at 9:32 PM, Douglas Greve >> <greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>>> >> wrote: >> >> >> You can try using bbregister. Normally, you >> don't use >> bbregister on a segmentation, but the segmentation >> index numbers just happen to be "T1-weighted". >> doug >> ps. Please remember to copy the list when >> responding. >> thanks! >> >> >> >> On 7/23/13 9:51 AM, Mark Plantz wrote: >> >> Hi Doug, >> >> Sorry about that vague explanation. So >> I received >> a series of infant brain atlases from a >> UNC medical >> research group >> (http://www.med.unc.edu/bric/** >> ideagroup/free-softwares/unc-**infant-0-1-2-atlases<http://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2-atlas…> >> ). >> I have a series of infant MRI's that I >> would like to >> segment (using the infant atlases, instead >> of the >> default adult atlas in FreeSurfer). >> >> As a preliminary step, I was attempting >> to check >> the alignment of one of the atlas files >> ('avgseg.mgz') with one of the input brains >> ('brain.mgz'). [I attached these two >> files, just in >> case]. >> >> So my command line would be: >> >> tkmedit $Subject brain.mgz -segmentation >> avgseg.mgz >> $FREESURFER_HOME/**FreeSurferColorLUT.txt >> >> The result was the previously attached >> image. I was >> just wondering if there is any way to >> shift the two >> images manually so the alignment is >> better? Or maybe >> the two files are simply not compatible >> with one another? >> >> Thanks for all the help! >> >> Best, >> >> Mark >> >> >> >> >> On Mon, Jul 22, 2013 at 3:53 PM, Douglas N >> Greve >> <greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu>>>> >> wrote: >> >> >> Hi Mark, I have no idea what you are >> doing. Can >> you send a command line? >> Are either of the images generated by FS? >> doug >> >> >> >> >> On 07/22/2013 03:56 PM, Mark Plantz wrote: >> > Hello FreeSurfers, >> > >> > I recently obtained a set of infant >> templates. Out of curiousity, >> > I decided to view one of the input >> brains with >> the provided segmented >> > volume file. It appears that there >> is some >> misalignment. I wouldn't >> > expect the alignment to be perfect, >> since I am >> basically overlaying an >> > average of multiple brains onto one. >> However, >> it looks like this >> > misalignment may be caused by >> either: 1.) the >> segmentation volume file >> > being shifted down or 2.) the slices >> not lining >> up properly (i.e. one >> > file starts before the other). >> > >> > Any ideas what could cause a >> problem like >> this? Could it be that >> > the segmented files are simply not >> compatible >> with FreeSurfer? >> > >> > Thanks for the help, >> > >> > Mark >> > >> > >> > >> > >> ______________________________**_________________ >> > Freesurfer mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >> >> >> > >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** >> freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> >> Phone Number: 617-724-2358 >> <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> >> Fax: 617-726-7422 <tel:617-726-7422> >> <tel:617-726-7422 <tel:617-726-7422>> >> >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> <http://surfer.nmr.mgh.** >> harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: >> https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.** >> html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> >> <http://www.nmr.mgh.harvard.** >> edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** >> greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> ______________________________ >> **_________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >> >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** >> freesurfer <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<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 <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> Fax: 617-726-7422 <tel:617-726-7422> >> >> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> >> > -- > 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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > >

3 7

displaying labels from old session onto new session
by Bianca van Kemenade 29 Jul '13

29 Jul '13

Hi Freesurfers, I have some participants of whom I obtained retinotopic polar angle data in a previous session, and scanned eccentricity data in a later session. I used the polar angle data to define V1-3, and would like to display these labels on the eccentricity session to help me define V3A. However, when I load my old V1-3 labels onto the inflated brain based on the new session the labels look very strange. I attached a screenshot of what is supposed to be lh dorsal V1, as you can see it is scattered all over the cortex. When I load the .nii based on the label into MRIcron, the ROI looks fine. Data from the newer session were coregistered to the older session, so that can't be the problem. I looked around on the wiki and found the command mri_label2label that seemed useful. However, this command needs acces to the 'surf' folders of both sessions. Due to a computer crash I only have the labels of the previous session, not the 'surf' folder. Is there a way to display my old labels onto the new session without needing access to 'surf'? Thanks, Bianca

3 17

Processing Multiple Subjects
by Michael Kranz 29 Jul '13

29 Jul '13

Hi all, If I process more subjects than the recommended amount given my number of cores and memory, will this affect the stats/surfaces or just slow the process down? I'm asking due to the sensitivity of workstations and also I seem to be getting slightly different stats sometimes when I re-submit to recon-all but haven't pin pointed the reason yet. Thanks, Mike

2 1

function that do the same step like qcache?
by fatma zribi 29 Jul '13

29 Jul '13

Dear Bruce, Would you mind tell me if there is a function of freesurfer that I can use to do the same step of qcache to smooth and interpolate in the fsaverage one subject with mri_surf2surf I can smooth only or align one subject with an average. thank you for you help. with best regards, Fatma

2 3

Error
by Muhammad Naveed Iqbal Qureshi 29 Jul '13

29 Jul '13

Dear Community, I got the following error every time I try to calculate the cortical thickness of my MRI data: bmssa-desktop:~> recon-all -i /home/bmssa/freesurfer/subjects/CHR/CHR01_PJH/t1/1.3.12.2.1107.5.2.32.35413.2010042817343895747424.dcm -subject sub02 -all -qcache & WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /home/bmssa/freesurfer/subjects Actual FREESURFER_HOME /home/bmssa/freesurfer Linux bmssa-desktop 3.5.0-36-generic #57~precise1-Ubuntu SMP Thu Jun 20 18:21:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /home/bmssa/freesurfer/subjects/sub02 mri_convert /home/bmssa/freesurfer/subjects/CHR/CHR01_PJH/t1/1.3.12.2.1107.5.2.32.35413.2010042817343895747424.dcm /home/bmssa/freesurfer/subjects/sub02/mri/orig/001.mgz mri_convert /home/bmssa/freesurfer/subjects/CHR/CHR01_PJH/t1/1.3.12.2.1107.5.2.32.35413.2010042817343895747424.dcm /home/bmssa/freesurfer/subjects/sub02/mri/orig/001.mgz ERROR: cannot determine file type for /home/bmssa/freesurfer/subjects/CHR/CHR01_PJH/t1/1.3.12.2.1107.5.2.32.35413.2010042817343895747424.dcm Linux bmssa-desktop 3.5.0-36-generic #57~precise1-Ubuntu SMP Thu Jun 20 18:21:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub02 exited with ERRORS at Mon Jul 29 14:10:40 KST 2013 For more details, see the log file /home/bmssa/freesurfer/subjects/sub02/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Please guide me how to rectify this error. I have used the same command for another dataset and it was working perfectly fine. Best Regards, Muhammad Naveed Iqbal Qureshi Ph.D. Candidate Bio-Medical Signal & System Analysis Laboratory Department of Medical System Engineering Gwangju Institute of Sciences and Technology 123, Cheomdangwagi-ro, Buk-gu, Gwangju, 500-712, Republic of Korea Tel : +82-62-715-3266 Email : mniqureshi(a)hotmail.com URL : http://bmssa.gist.ac.kr P please don't print this e-mail unless you really need to

2 1

dPSD and ev duration
by Ella Hinton 28 Jul '13

28 Jul '13

Hi Quick question - why must the duration of the EVs be an integer multiple of the dPSD, which is also tied to the TR? I have event duration of 3 seconds, but would like to reduce my TR from 3 down to 2.5, but I can't seem to input the correct numbers for optseq to help me. thanks in advance Ella

2 1

A question about coordinates
by jh kim 28 Jul '13

28 Jul '13

Dear experts I have a simple question. To my knowledge, Freesurfer uses Talrairach coordinates. After doing 10000 permutations, I found that the resulting file *.sig.cluster.summary contained MNIX, MNIY, MNIZ coordinates. Are these coordinates in MNI space? Thank you in advance for your answer. Kim

2 2

Combining non accelerated and accelerated MRIs
by Stéphane Poulin 28 Jul '13

28 Jul '13

Dear Freesurfer experts I am using Freesurfer to process part of the ADNI 2 database which includes non accelerated and accelerated images. Images have different voxel sizes. Is there any litterature to guide me what should I do, ie combining or not these scans. Stephane

2 1

FW: VMAC neuroimaging research analyst opening (fwd)
by Bruce Fischl 26 Jul '13

26 Jul '13

FYI From: Jefferson, Angela [mailto:angela.jefferson@Vanderbilt.Edu] Sent: Friday, July 26, 2013 9:36 AM Subject: VMAC neuroimaging research analyst opening Dear colleague, My laboratory at Vanderbilt has a neuroimaging research analyst II opening. If you have students or recent trainees who have 2 years of research experience or a master’s degree equivalent with programming or scientific computing skills who are interested in gaining some research experience in neuroimaging for a couple of years before attending graduate school, this opportunity would be a great fit (especially if they don’t mind relocating to Nashville). If you wouldn’t mind distributing the attached posting to potential candidates, I would very much appreciate it. Best regards, Angela Angela L. Jefferson, PhD Director, Vanderbilt Memory & Alzheimer’s Center Associate Professor of Neurology Vanderbilt University Medical Center 2525 West End Avenue, 12th Floor, Suite 1200 Nashville, TN 37203 www.vanderbiltalzheimers.com www.vanderbiltcognitiveaging.com

1 0

← Newer
1
2
3
4
5
6
7
8
9
...
34
Older →

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 July 2013