Freesurfer January 2012

freesurfer@nmr.mgh.harvard.edu

97 participants
171 discussions

mri_glmfit-sim error
by zhang mingxia 10 Jan '12

10 Jan '12

Hi, every one, I just run the flag mri_glmfit-sim for Surface-based Correction for Multiple Comparisons as below: mri_glmfit-sim \ --glmdir lh.Chinese_fastreading_thickness.glmdir \ --cache neg 1.3 \ --cwpvalthresh .025 lh.Chinese_fastreading_thickness.glmdir is the pre-cached simulation results. There is error:printf: neg: expected a numeric value ERROR: thresh = 0.0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 What is the problem? Thank you in advance. Sincerely, Mingxia Zhang

2 2

trac-all update
by Anastasia Yendiki 09 Jan '12

09 Jan '12

Hi all - There is an updated version of trac-all here that's recommended for all users: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/trac… This version switches on an option in the implementation that had not been fully tested at the time of the release last May, but that we now believe will make better use of the atlas data and thus give you more accurate paths. The change will affect the -prior and -path steps of the analysis. Also the tracula wiki pages have been modified to make some of the information there clearer, hopefully: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula This documentation is still a work in progress. Thank you for understanding and we appreciate your continuing feedback! a.y | Anastasia Yendiki, Ph.D. | Martinos Center for Biomedical Imaging | 149 13th St. Suite 2301 | Charlestown, MA 02129 | Tel: 617-726-9434 | Fax: 617-726-7422

1 0

GLM design question
by Martijn Steenwijk 09 Jan '12

09 Jan '12

Dear all, I'm relatively new with Freesurfer, but slowly getting more and more used to it's great possibilities. To be 'sure', I've a question about the design of a GLM. I want to compare CT in Healthy Controls vs Diseased, and control for age and sex. It appears to me that factors (eg sex) cannot be used as covariate/variable, which forces me to model them as a separate class although I'm not interested in sex differences. This brings me to the following FSGD file: # HcDis.fsgd GroupDescriptorFile 1 Title HcDis Class Hc_Male Class Hc_Female Class Dis_Male Class Dis_Female Variables Age Input subjid1 Hc_Male 35 Input subjid2 Dis_Female 30 .. Then the difference between Hc and Dis, corrected for age and sex is given by the contrast matrix #Hc-vs-Dis.mtx 0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 Is this correct? Best, Martijn

3 5

How to export non spatial normalization fMRI images?
by Long 09 Jan '12

09 Jan '12

Hi, I have run preproc-sess to analyze fMRI images. I'd like to analyze fMRI images in the individual space, but I found that the final output (i.e., fmcpr.up.sm4.fsaverage.lh.nii.gz) were already spatial normalized. So, How to just smooth fMRI images in surface space and export them as the co-registered fMRI images in volume space? I think it could start at "fmcpr.up.nii.gz"? Thank you in advance! Best, Xiangyu Long

2 1

Reviewer request
by Jürgen Hänggi 08 Jan '12

08 Jan '12

Dear FS experts We have the following request from one reviewer: "Provide more detail and more discussion on why the thickness maps produced by FreeSurfer are not limited to the voxel resolution of the image. This is not obvious to everybody who is not an expert in cortical thickness measurements using the free-surfer approach, since it is not so easy to comprehend that differences can be found that are beyond the resolution of the acquisition." I can provide the references that provide this statement, but I do not really have a sound explanation why this is possible. Any idea is welcome and appreciated Thanks in advance Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

2 2

Qdec Issue
by James, Brian 07 Jan '12

07 Jan '12

Hi Guys, So I have Freesurfer running quite well on Ubuntu (thank you to all who helped me on this one). I am going through the testing phase (as described here https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer ) and when I try to run the command 'qdec', I get the following error: Qdec.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory How do I fix this? Brian James The information contained in this electronic transmission is intended for the person(s) or entity to whom it is addressed. Delivery of this message to any person other than the intended recipient(s) is not intended in any way to waive confidentiality. This material may contain confidential or personal information which may be subject to the provisions of Ontario's Personal Health Information Protection Act. Any review, retransmission, dissemination or other use of this information by entities other than the intended recipient is prohibited. If you receive this in error, please contact the sender and delete the material immediately. L'information contenue dans ce message ?lectronique est destin?e uniquement au destinataire ou aux destinataires vis?s. La transmission de ce message ? une personne autre que son destinataire ou ses destinataires vis?s ne supprime en rien l'obligation d'en respecter la confidentialit?. Ce message peut contenir des renseignements de nature confidentielle ou personnelle qui pourraient ?tre soumis aux dispositions de la Loi de 2004 sur la protection des renseignements personnels sur la sant?. L'examen, la retransmission, la diffusion et toute autre utilisation de l'information contenue dans ce message par des personnes autres que le destinataire ou les destinataires vis?s sont interdits. Si vous recevez ce message par erreur, veuillez le supprimer imm?diatement et en avertir l'exp?diteur.

2 2

Qdec: problems
by Cat Chong 07 Jan '12

07 Jan '12

Hi Experts: Sorry, I forgot to attach the following error message I get when I attempt to generate stats data tables: I would be grateful if you tell me what I am doing wrong, catherine asegstats2table --common-segs --meas volume --tablefile /5000_series/5000_series/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 5002_out 5003_out 5005_out 5006_out SUBJECTS_DIR : /5000_series/5000_series Parsing the .stats files ERROR: The stats file /5000_series/5000_series/5002_out/stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files fmris-Mac-Pro-2:qdec fmri$ ERROR: In /usr/pubsw/packages/KWWidgets/CVS-7Aug2010/src/KWWidgets/vtkKWTkUtilities.cxx, line 230 vtkKWQdecApp (0x588e8d0): Script: vtkTemp2 GenerateStatsDataTables Returned Error on line 1: Uncaught exception: command failed: asegstats2table --common-segs --meas volume --tablefile /5000_series/5000_series/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 5002_out 5003_out 5005_out 5006_out Stack trace: Uncaught exception: command failed: asegstats2table --common-segs --meas volume --tablefile /5000_series/5000_series/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 5002_out 5003_out 5005_out 5006_out while executing "vtkTemp2 GenerateStatsDataTables"

2 1

tksurfer only showing a 'corner' of the brain
by Sasha Rayshubskiy 07 Jan '12

07 Jan '12

Hi, I downloaded and installed freesurfer on RHEL5 recently. I'm following instructions for testing the installation for 'tksurfer bert rh pial' to get a surface rendering, and only seeing a corner of the 'brain'. When I click with the mouse in the display area it leaves marks as if there's data behind a veil. I'm new to using freesurfer and wondering what mistake I'm making. Screenshot of what I'm seeing is attached. Thanks, -Sasha -- Sasha Rayshubskiy, M.Eng. Research Assistant Laboratory for Functional Optical Imaging Department of Biomedical Engineering Columbia University New York, NY 10027 Tel: 917 697 3841

2 1

Fw : Re: get_4dfp_dimoe problem
by LAOUCHEDI MAKHLOUF 07 Jan '12

07 Jan '12

--- En date de : Ven 6.1.12, LAOUCHEDI MAKHLOUF <laoumakhl(a)yahoo.fr> a écrit : De: LAOUCHEDI MAKHLOUF <laoumakhl(a)yahoo.fr> Objet: Re: [Freesurfer] get_4dfp_dimoe problem À: "AviSnyder" <avi(a)npg.wustl.edu> Date: Vendredi 6 janvier 2012, 15h28 hi everyone i just remind you of my problem of the file name which was too long on our cloud; you advised us to download the endianio.c module, we did this and we installed it then we've run recon-all but we still have an error message : $Id: imgreg_4dfp.c,v 1.4 2010/02/27 01:41:53 nicks Exp $ Getifh: /var/spool/pbs/tmpdir/171598.gridgate.scg.nuigalway.ie/https_3a_2f_2falbalonga.cnaf.infn.it_3a9000_2ff_5f9HZFcSVMqQu-a5r7O6fQ/ws28210/.tmp/d924f86d-ff81-451c-9d0b-f655f3361f66/systemExecTask5971557784595886118/freesurfer/average/711-2B_as_mni_average_305_mnone.4dfp.ifh read error, imgfile='/var/spool/pbs/tmpdir/171598.gridgate.scg.nuigalway.ie/https_3a_2f_2falbalonga.cnaf.infn.it_3a9000_2ff_5f9HZFcSVMqQu-a5r7O6fQ/ws28210/.tmp/d924f86d-ff81-451c-9d0b-f655f3361f66/systemExecTask5971557784595886118/freesurfer/average/711-2B_as_mni_average_305_mnone.4dfp.img' Segmentation fault ERROR: 'imgreg_4dfp /var/spool/pbs/tmpdir/171598.gridgate.scg.nuigalway.ie/https_3a_2f_2falbalonga.cnaf.infn.it_3a9000_2ff_5f9HZFcSVMqQu-a5r7O6fQ/ws28210/.tmp/d924f86d-ff81-451c-9d0b-f655f3361f66/systemExecTask5971557784595886118/freesurfer/average/711-2C_as_mni_average_305 /var/spool/pbs/tmpdir/171598.gridgate.scg.nuigalway.ie/https_3a_2f_2falbalonga.cnaf.infn.it_3a9000_2ff_5f9HZFcSVMqQu-a5r7O6fQ/ws28210/.tmp/d924f86d-ff81-451c-9d0b-f655f3361f66/systemExecTask5971557784595886118/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 4355' failed! status=139 ERROR: mpr2mni305 execution aborted i've attached the recon-all.log contained in the scripts dir and the log file contained in mri/transforms dir thank you very much --- En date de : Mer 4.1.12, Snyder, Avi <avi(a)npg.wustl.edu> a écrit : De: Snyder, Avi <avi(a)npg.wustl.edu> Objet: Re: [Freesurfer] get_4dfp_dimoe problem À: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> Cc: "LAOUCHEDI MAKHLOUF" <laoumakhl(a)yahoo.fr>, "Freesurfer(a)nmr.mgh.harvard.edu" <Freesurfer(a)nmr.mgh.harvard.edu> Date: Mercredi 4 janvier 2012, 1h31 I don't think there are any special env variables. It may be that the environment in which FreeSurfer is being run simply generates huge pathnames. A few months ago I revised the module containing get_4dfp_dimoe() to double the size of filename buffers. This module (endianio.c) is attached. Theoretically, compiling with this revised source could fix the problem. Avi ----------------------------- On 1/3/12 6:04 PM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: >Hi Avi > >just running recon-all I think. Is there an env variable you use to >specify >a tmp dir or something? > >thanks >Bruce > >On Tue, 3 Jan 2012, Snyder, Avi wrote: > >> It looks like both the command (imgreg_4dfp) and argument >> (.../711-2B_as_mni_average_305_mask.4dfp.img) fields are garbled. >> Evidently, operating system paths have not been correctly set. >> The 4dfp suite of tools is available and probably could be installed but >> I'm not sure that is what is wanted. >> I don't understand what LAOUCHEDI MAKHLOUF is trying to do. >> >> AZS >> ----------------------------------------------------- >> On 1/3/12 10:40 AM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: >> >>> this is actually not part of FreeSurfer proper, but rather something >>>that >>> Avi Synder (ccd) was kind enough to contribute. Avi: can you comment? >>> >>> thanks >>> Bruce >>> On >>> Tue, 3 Jan 2012, LAOUCHEDI MAKHLOUF wrote: >>> >>>> hi everyone >>>> we run recon-all on a cloud and we obtained this error: >>>> >>>> mpr2mni305 failed, see transforms/talairach_avi.log >>>> >>>> The log says the file name is too long perhaps because of the tmp dir >>>> file >>>> names: >>>> >>>> >>>> >>>>get_4dfp_dimoe:/var/spool/pbs/tmpdir/169536.gridgate.scg.nuigalway.ie/h >>>>tt >>>> ps_3a_2f_2fwms01. >>>> >>>> >>>>ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws15158/.tmp/8d3aa62d-5994-4 >>>>7e >>>> 5- >>>> >>>> >>>>ba6d-031806ec9ffb/systemExecTask8201883777111446775/freesurfer/average/ >>>>71 >>>> 1- >>>> 2B_as_mni_average_305_mask.4dfp.img filename too long >>>> ERROR: >>>> >>>>'imgreg_4dfp/var/spool/pbs/tmpdir/169536.gridgate.scg.nuigalway.ie/http >>>>s_ >>>> 3a_2f_2fwms01. >>>> >>>> >>>>ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws15158/.tmp/8d3aa62d-5994-4 >>>>7e >>>> 5- >>>> >>>> >>>>ba6d-031806ec9ffb/systemExecTask8201883777111446775/freesurfer/average/ >>>>71 >>>> 1- >>>> 2C_as_mni_average_305 >>>> /var/spool/pbs/tmpdir/169536.gridgate.scg.nuigalway.i >>>> >>>> >>>>e/https_3a_2f_2fwms01.ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws1515 >>>>8/ >>>> .t >>>> >>>> >>>>mp/8d3aa62d-5994-47e5-ba6d-031806ec9ffb/systemExecTask82018837771114467 >>>>75 >>>> /f >>>> reesurfer/average/711-2B_as_mni_average_305_masktalsrcimg_g11 none >>>> talsrcimg_to_711-2C_as_mni_average_305_t4 4355' failed! status=255 >>>> >>>> >>>> knowing that it is difficult for us to do things differently (to >>>>change >>>> the >>>> path); is it possible to do something in freesurfer to work with >>>>thesse >>>> filenames ? >>>> >>>> thanks for your help >> >> >> >> > > >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 1

SPGR compressed files
by Cat Chong 07 Jan '12

07 Jan '12

Hi Experts, We wanted to run clinical scans that underwent some compression at the scanner through freesurfer. I just wanted to seek confirmation that SPGR sequences that have undergone slight compression can not be run through freesurfer, is that correct? thank you, catherine

2 3

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 January 2012