Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

VRML support
by andrei sherstyuk 11 Aug '11

11 Aug '11

Greetings, I have problems exporting the surface data in VRML format. When I load the resulting .wrl file into Blender (a 3D modeling tool), the resulting surface is full of holes (bad/missing polygons) and connectivity of vertices is all wrong -- I see edges where they are not supposed to be. Is is a common problem with VRML export? I used "write_vrml 1" command, tksurfer version 5. Any help will be greatly appreciated. Cheers, Andrei

2 1

Label2label on fsaverage
by Rouhollah Abdollahi 10 Aug '11

10 Aug '11

Dear freesurfer experts I've tried to export my label file from individual space to fsaverage space by using this command: mri_label2label --srclabel rh.V1.label --srcsubject SUB1 --trgsubject SUB1 --trglabel rh.V1_reg.label --regmethod surface --srcsurfreg sphere --trgsurfreg sphere.reg --hemi rh and when I tried to load the output label file on fsaverage surface like inflated one it shows a lot of point looks like it is not deformed properly. Is it related to registration to fsaverage or something esle? The question is how I can register the subjects surfaces to fsaverage surfaces? -- With Best Regards Rouhi

2 1

FSGDF matrix
by Antonella Kis 10 Aug '11

10 Aug '11

Dear Bruce, I am ready to start my GLM group analysis. I am trying to construct the FSGDF by constructing an my_age_fsgd.txt file. I was reading the tutorial and I am not sure if I need to put together my patients and controls in my FSGDF since my group study will be for patients versus controls. Please advise me. Thank you. Antonella

3 3

selxavg-sess outputs
by Yang Liu 10 Aug '11

10 Aug '11

Hi all, I want to plot the hemodynamic response of a voxel after my analysis finishes. I hope I can get the hemodynamic response of each voxel for each session, so I can see the statistics by myself. My analysis.cfg is below: -gammafit 0 8 -gammaexp 0.3 -timewindow 40.0000 -prestim 0 -polyfit 2 -TER 2.0000 -autowhiten 40 -nskip 0 -fwhm 0 -extreg mcextreg -nextreg 3 -rescale 1000 After I ran selxavg-sess, I got the following volumes: h0.nii, h0-offset.nii, h.nii, h-offset.nii, rstd.nii, rvar.nii. How can I get a response from these volumes? Yang

2 10

[freesurfer] FS5.1 talairach issue
by Myriam Siefert 10 Aug '11

10 Aug '11

Hi freesurfers, I'm currently re-processing with FS5.1 some data that i had already processed with FS5.0 and am experiencing some unexpected issues with the linear talairach transform. - While manually checking with Tkregister, I noticed that some off the subjects had quite unsatisfying transforms , while no talairach failure was detected on the log - The transforms looked ok for those subjects in FS 5.0 - I re-run autorecon1 using the -use-mritotal flag - While still no error in the log file, the transforms usually then look acceptable in Tkregister but completely wrong when talairach.xfm is loaded in tkmedit : transformation in the top or bottom left corners, coronal and transversal views interverted, sagittal views rotated by 90 degrees... This happens for a few (not all) of the subjects that I've re-processed with FS5.1 so far. I'm probably doing something wrong but can't figure out what nor what to do about it. Any advice would be highly appreciated. Thanks in advance Myriam Siefert, MD, MS candidate Visiting scholar in SACNlab Northwestern University

1 0

mne_analyze not dispalying surfaces
by Vema Krishnamurthy, Santosh 10 Aug '11

10 Aug '11

Hello, I'm trying to display the inflated surfaces through mne_analyze and all I see is only few pixels of the surfaces. I'm assuming this is a problem with graphics, so I think I have Matrox Graphics (MGA G200ew WPCM450 rev 0a) installed on my host machine and I'm accessing this machine through VNC. Thanks and Regards, --------------------------------------------------- Santosh Vema KrishnaMurthy, M.A.Sc Medical Devices Engineer NRC Institute for Biodiagnostics (Atlantic) Elekta/IWK MEG Research office Ph: (902) 470-3984 ---------------------------------------------------

1 0

FMRI Hemispheric Asymmetry Analyses
by Andy Mayer 09 Aug '11

09 Aug '11

Hello- I would like to directly compare asymmetries in FMRI activation in surface space based on the Greve et al pipeline presented at HBM this year. All of our anatomical data have been processed with FS v4.5, but the FMRI data is in AFNI volumes. I am very new to the freesurfer program so any corrections on how to achieve cross-hemisphere registrations would be greatly appreciated. 1) We transformed the functional data to anatomical space using bbregister. 2) We then registered each subject’s T1 data to the contralateral hemisphere of fsaverage and made templates of the contra (?h.con.sphere.reg ) and ipsilateral (?h.sphere.reg ) registrations Registration step mris_register -curv surf/rh.sphere {$FREESURFER_HOME}/average/lh.average.curvature.filled.buckner40.tif surf/rh.CON.sphere.reg mris_register -curv surf/lh.sphere {$FREESURFER_HOME}/average/rh.average.curvature.filled.buckner40.tif surf/lh.CON.sphere.reg template step make_average_subject --out CON_TEMPLATES --surf-reg CON.sphere.reg --subjects M87150222_20110311 M87138477_20080429 .. make_average_subject --out IPS_TEMPLATES --surf-reg sphere.reg --subjects M87150222_20110311 M87138477_20080429 .. 3) I then re-registered RH data to the new contralateral template (study-specific) and LH data to the new ipsilateral template to get everything in the same sphere space mris_register -curv surf/rh.sphere CON_TEMPLATES/rh.reg.template.tif surf/rh.finalTEM.sphere.reg mris_register -curv surf/lh.sphere IPS_TEMPLATES/lh.reg.template.tif surf/lh.finalTEM.sphere.reg 4) Finally, I apply the final registration template to aux data (thickness, FMRI) to bring everything into a common space that can be directly tested for hemispheric asymmetries mris_preproc --hemi rh --target CON_TEMPLATES --surfreg finalTEM.sphere.reg --meas thickness --out final.thickness.nii --s ${subject} mris_preproc --hemi lh --target IPS_TEMPLATES --surfreg finalTEM.sphere.reg --meas thickness --out final.thickness.nii --s ${subject} Please let me if this pipeline makes sense and follows what was proposed at the HBM meeting. Also are the iterations mentioned in the poster necessary (ie make additional templates and re-reregister) when the sample is relatively large (N = 100)? Thanks! Andrew

1 0

Functional Data Hippocampus
by Sunil Patel 09 Aug '11

09 Aug '11

Hello, I'm wondering how to obtain the functional data for the hippocampus between specific slices. Is there a command I can run to do this? If not, what would be the best course of action? Best, Sunil I Patel

3 2

mri_watershed for generating scalp surfaces
by Vema Krishnamurthy, Santosh 09 Aug '11

09 Aug '11

Hello Everyone, I have an application outside freesurfer where I need the scalp/face surface from the MRI file so I'm trying to use mri_watershed algorithm to generate the scalp surface, but when I read the subject-outer_skin.surf file in matlab using the read_surf command I see that the facial features (nose, eyes, lips, chin) are not clear. But when I viewed the MRI file using mrilab I can see the facial features clearly. So I was wondering if there are parameters I can change while running the mri_watershed alrgorithm so that I can get good face shape. I'm also up for any suggestions/hints. Here is the command I used to run the mri_watershed: mri_watershed -atlas -useSRAS -surf /../../bem/watershed/subject /../..subject/T1.mgz /../../bem/watershed/ws/ Thanks and Regards, --------------------------------------------------- Santosh Vema KrishnaMurthy, M.A.Sc Medical Devices Engineer NRC Institute for Biodiagnostics (Atlantic) Elekta/IWK MEG Research office Ph: (902) 470-3984 ---------------------------------------------------

2 1

Functional Data Hippocampus
by Sunil Patel 09 Aug '11

09 Aug '11

1 0

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