Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Entorhinal cortex
by Ozioma Okonkwo 10 Jan '12

10 Jan '12

Hi: I understand that information on the accuracy of the entorhinal cortex parcellation, for each subject, may be found in their ?h.entorhinal_exvivo.label file. I reviewed this file but could not tell which column (if any) contains accuracy information. Could someone point me in the right direction, please? I need this for a grant submission. Thanks ozioma

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anterior temporal lobe problems
by Michael Harms 10 Jan '12

10 Jan '12

Hi guys, We have a sample of 150+ pediatric brains that we pumped through FS 5.1, and in an easy majority of them the white/pial surface accuracy in the anterior temporal lobe is poor. I know that this is an area where problems have frequently been reported. What is it about that area in particular that makes it difficult to get accurate surfaces? (Is the contrast and SNR in that area inherently worse?) And, short of a large time commitment of control point and wm.mgz editing, are there any flags/tweaks that we could attempt to fix the problem in a more automatic fashion? thanks, -MH -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6604 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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cvs register mri_aparc2aseg running 22 hours ?
by Gregory Kirk 10 Jan '12

10 Jan '12

im running mri_cvs_register --step2, running it in a shell, not in the background. the process returned but top shows mri_aparc2aseg still running at 100% cpu for 1320 minutes. seems something is not running correctly ? greg

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About ROI edit
by zhang mingxia 10 Jan '12

10 Jan '12

Hi, every one, I have a question about ROI edit. Is there a way with which we can define spherical ROIs with exact radius. Now, I just know the manual method. But I want to define a ROI with exact Talairach Coordinate and radius. Are there bottons when I input Talairach Coordinate and radius in them, the ROI label will come out? Thanks very much! Mingxia Zhang

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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

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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

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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

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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

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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. ----------------------------------------------------------------------------

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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.

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