Freesurfer

freesurfer@nmr.mgh.harvard.edu

1 participants
30089 discussions

nu_correct problem
by rega0026＠umn.edu 10 Jul '12

10 Jul '12

Hello, I am trying to run recon-all using freesurfer 5.1.0. This worked on most of my subjects, but for about 10 subjects, I got an error: nu_correct: Command not found I can see on the archive that several others have run into this problem, but I couldn't figure out from the archives what the solution is. I do have perl installed in usr/bin. Thanks very much, Katie -- Kathryn R. Cullen, M.D. Assistant Professor University of Minnesota Medical School Department of Psychiatry Division of Child and Adolescent Psychiatry (612) 273-9825

4 4

Using SPM transformation matrices as initial guess in talairach_avi
by Baudrexel, Simon 10 Jul '12

10 Jul '12

Hello, since I experienced a high rate of registration errors using talairach_avi in the conventional recon-all processing stream (more than 50% misregistration), I would like to incorporate SPM affine registration parameters (as provided in the seg_inv_sn.mat file obtained from the segmentation routine) as initial guess "to help" talairach-avi. Is there a possibility to do this? How do I have to adjust the transformation matrix that it can be handled by freesurfer? I also tried to circumvent the registration-problem using skull-stripped images, which unfortunately also did not improve the results (I think a template made from skull-stripped images has to be used in that case) Any help would be much appreciated Regards, Simon

2 2

multiple correction
by Meng Li 09 Jul '12

09 Jul '12

Hi, freesurfer expert, I have three questions about the multiple correction. I performed the statistical analysis between two groups first in left hemisphere, and got some regions which showed different. 1) so if I then do multiple correction, i don't need to run the mri_glmfit-sim command, and just press the button of the monte carlo null-z simulation in the qdec interface, am i right? 2) Whether mri_glmfit-sim --cache command line and the mc-z in qdec get the same results, or not? and as to the option --cwpvalthresh, should i choose 0.05 or 0.025? 3) And what is the difference between fdr and mc-z correction? Thanks, Meng

1 0

the color range difference in the scale bar
by Leon 09 Jul '12

09 Jul '12

Hi, FreeSurfer experts I noticed that when I automatically draw the mapped results to the surface using tcl in tksurfer, the color range of the scale bar is not correctly displayed: it has mono blue or red color. This happens only when the range of the overlay is between 0 and 1. I then tested using the same data by opening the overlay in tksurfer GUI interface and then set the min and max in the view -> configure -> overlay, I find the color of the scale bar makes sense in this way (see the right one in the attached figure). I wonder if someone would help me on this. Did I do something wrong? The following is the tcl script I used to draw color bar automatically: I first calculated FS_TKFMAX for the overlay, which is 1 in this case xmax="1" FS_TKFMAX=${xmax} ; export FS_TKFMAX # load the overlay echo " set overlayflag 1 " > ${1}/${fold_base}${net_den}/script.tcl echo " set val ${1}/${fold_base}${net_den}/${hemi}.${meas}.mgh " >> ${1}/${fold_base}${net_den}/script.tcl echo " sclv_read_from_dotw 0" >> ${1}/${fold_base}${net_den}/script.tcl echo " set colscalebarflag 1 " >> ${1}/${fold_base}${net_den}/script.tcl echo " set fthresh 0 " >> ${1}/${fold_base}${net_den}/script.tcl echo "redraw" >> ${1}/${fold_base}${net_den}/script.tcl echo "save_tiff ${1}/${fold_base}${net_den}/${hemi}.${meas}_lateral.tif " >> ${1}/${fold_base}${net_den}/script.tcl tksurfer ${2} ${hemi} inflated -tcl ${1}/${fold_base}${net_den}/script.tcl Thank you very much in advance! Leon

1 0

wm problems
by Nicole Senecal 09 Jul '12

09 Jul '12

Hi all, I've been having two variants of problems with wm.mgz, using version5.1. One can be seen in the attached screenshot FI137 - areas that are not white matter are designated as "white matter hypointensities" on wm.mgz, and create problems with both surfaces. This has happened in a number of our subjects, in multiple locations throughout each brain. Is this something we just need to delete manually on each subject, or is there a more efficient way to deal with this? The second is seen in the screenshots of MP860 wm. An area that is not white matter, and is not designated as white matter on wm.mgz, is still created as a white matter surface. This hasn't happened as often as the above, but we don't know how to get rid of an inaccurate wm surface if it's not on wm.mgz. Thanks for your help, Nicole -- Nicole Senecal Neuroscience Graduate Group Kable Lab 3720 Walnut St., Room C37 Philadelphia, PA 19104 Lab phone: 215-746-4371

2 3

Brainhack 2012
by MCLAREN, Donald 09 Jul '12

09 Jul '12

Dear colleagues, I wanted to draw your attention on the upcoming 2012 Brainhack, 1st edition, to be held from September 1-4 at the Max Plank Institute for Human Cognitive and Brain Sciences, Leipzig, Germany. Brainhack is not a conference or a workshop. It should be closer to one of those exciting conversations you may have had at HBM during cocktail or poster sessions. Except that we will have over three days to build up those conversations into full-fledge collaborations. One should come to brainhack ready to engage into collaborative projects, and with some material (slides, ideas, data, tools) ready to start a project or a discussion panel. Brainhack will build on the successful techniques used in other unconferences<http://en.wikipedia.org/wiki/Unconference> to keep the meeting focussed and productive. It is possible to start a project and build a team as early as today. Please have a look at the website for informations on the conference and a sample of projects (more will be added over the summer): http://brainhack.org/2012/04/06/brainhack-2012-unconference/ The list of confirmed attendees includes F. Xavier Castellanos, Michael Hanke, Michael P. Milham, Tal Yarkoni, Arno Villringer, and many members of the neurobureau <http://www.neurobureau.org/NeuroBureau/Welcome.html>. Brainhack is a satellite of the resting-state connectivity conference<http://www.restingstate.com/>. Although many participants will have an interest in connectivity analysis, there will also be attendees coming from a variety of backgrounds within neuroscience. Registration is now opened: http://www.cbs.mpg.de/events/workshops/brainhack Please do not hesitate to share this invitation with your circles. Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.

1 0

mris_divide_parcellation
by Arnaud Messé 09 Jul '12

09 Jul '12

Dear all, I'm using mris_divide_parcellation to subdivide cortical regions into smaller regions and I've some questions about such process. I would like to transform my new annot file to labelled surface and labelled cortical volume. For the former, there's a 'simple' way to transform annot file to surface? I only found utilities that tranform label2surf.. For the latter, I think that I need to use mris_annot_to_segmentation, however I need a colortable associated with my annot file. So my question is how can I generate a colortable from mris_divide_parcellation output. I would be really greatful for any insights about these. Thanks. -- Arnaud Messé, PhD Laboratoire d'imagerie fonctionnelle (LIF) UMRS 678 Inserm/UPMC CHU Pitié-Salpêtrière 91 boulevard de l'Hôpital F-75634 Paris Cedex 13 +33(0)1538284 03 (fax: 48) Arnaud.Messe(a)imed.jussieu.fr http://www.imed.jussieu.fr

1 0

Hanging during Fix Topology
by Tali Swisher 06 Jul '12

06 Jul '12

Hi all, I'm running FreeSurfer v.4.0.5 (see below) and it keeps hanging during the Fix Topology sequence while correcting defects. The last few lines before it's hanging are included below - any suggestions? -------- freesurfer-Linux-rh9-stable-pub-v4.0.5 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /share/apps/freesurfer4.0.5 FSFAST_HOME /share/apps/freesurfer4.0.5/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/pnlstaff/freesurfer/subjects MNI_DIR /share/apps/freesurfer4.0.5/mni ____________________________________________________________________ CORRECTING DEFECT 67 (vertices=117, convex hull=78) After retessellation of defect 67, euler #=27 (83599,243374,159802) : difference with theory (-19) = -46 CORRECTING DEFECT 68 (vertices=19, convex hull=68) After retessellation of defect 68, euler #=28 (83608,243425,159845) : difference with theory (-18) = -46 CORRECTING DEFECT 69 (vertices=38132, convex hull=10573) Thanks! Tali -- Talis M. Swisher, BA Senior Research Assistant Psychiatry Neuroimaging Laboratory Harvard Medical School, Brigham and Women's Hospital 1249 Boylston St, 3rd Floor Boston, MA 02215 Office: (617) 525-6119 Cell: (336) 577-5071 Fax: (617) 525-6150

2 1

Re: [Freesurfer] multiple correction
by Meng Li 06 Jul '12

06 Jul '12

Hi, professor, I performed the statistical analysis between two groups first in left hemisphere, and got some regions which showed different. 1) so if I then do multiple correction, i don't need to run the mri_glmfit-sim command, and just press the button of the monte carlo null-z simulation in the qdec interface, am i right? 2) Whether mri_glmfit-sim --cache command line and the mc-z in qdec get the same results, or not? and as to the option --cwpvalthresh, should i choose 0.05 or 0.025? 3) And what is the difference between fdr and mc-z correction? Thanks, Meng Hi Meng, if you are doing whole hemisphere correction, it will used already computed values which should only take a few seconds to run. doug On 07/05/2012 11:03 AM, Meng Li wrote: > > Hi, all, > > I have some questions about the multiple correction in qdec. > > I performed group analysis using qdec. There are 5 factors in the > qdec.table.dat file: 1 discrete, 4 continuous variables (covariates). > When I tried to perform the multiple correction, Whether I can choose > one of two ways (the fdr and monte carlo null-z simulation) only. And > if I use monte carlo null-z simulation, I have to pre-run > mri_glmfit-sim 10000? > > Thanks, > > Meng >

1 0

TkSurfer and new color table. Mislabelling
by Pedro Paulo de Magalhães Oliveira Junior 06 Jul '12

06 Jul '12

I'm trying to generate an image to a paper and I have to colorize some areas of the cortex with specific colors. I have edited the FreeSurferColorLUT.txt changing the following lines: 1001 ctx-lh-bankssts 255 42 0 0 1003 ctx-lh-caudalmiddlefrontal 255 14 0 0 1006 ctx-lh-entorhinal 255 17 0 0 1017 ctx-lh-paracentral 255 43 0 0 1020 ctx-lh-parstriangularis 255 15 0 0 1022 ctx-lh-postcentral 255 14 0 0 1028 ctx-lh-superiorfrontal 255 79 0 0 1032 ctx-lh-frontalpole 255 17 0 0 1033 ctx-lh-temporalpole 255 14 0 0 2001 ctx-rh-bankssts 255 18 0 0 2010 ctx-rh-isthmuscingulate 255 39 0 0 2014 ctx-rh-medialorbitofrontal 255 60 0 0 2020 ctx-rh-parstriangularis 255 13 0 0 2026 ctx-rh-rostralanteriorcingulate 255 40 0 0 2029 ctx-rh-superiorparietal 255 48 0 0 2032 ctx-rh-frontalpole 255 106 0 0 all other regions are 127 127 127 0 When I load the surface for some case with: tksurfer bert lh pial -annot aparc -ctab FreeSurferColorLUT.txt I get the usual coloring scheme with the labels correct. TkSurfer seems to be ignoring FreeSurferColorLUT.txt, but the labels are placed in the right spots. When I try to manually force the FreeSurferColorLUT.txt I'm visualizing an all grey image. And the surface is completely mislabeled, there is a 4th ventricle in the surface, putamen in the surface, etc. What am I doing wrong? --------------------------------------------------------------------- Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441

4 6

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