Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

More information about mri_cvs_register
by Joakim Vinberg 15 Nov '10

15 Nov '10

Hi, I had a couple of questions regarding mri_cvs_register (which looks terrific), and couldn't find any answers after a quick search. If I missed an important page or pages, please don't hesitate to send me there. We are interested in using mri_cvs_register on a large body of subjects. Specifically, I am curious if we should choose a single subject to be the template for this analysis, or whether we can use the fsaverage brain as the template? Second, approximately how long can we expect mri_cvs_register to take for a single CVS alignment? We're running a quad-core Athlon Phenom with 4GB total; mri_cvs_register is getting a single core (ish) in this case? Finally, what does the output of this function look like? Can we use it with the typical transform processes, or are their dedicated functions to use after the alignment? Again, I apologize if I missed a critical page somewhere. Thanks! Joakim

2 5

Running multiple GLM analyses together
by Matt Russell 15 Nov '10

15 Nov '10

Hello, I'm currently trying to run an analysis on data that has 1 group and 5 covariates. As each of these covariates of interest independently, I would like to calculate a GLM for each of them using FreeSurfer. Is it possible to run all 5 of these in one glm_fit call? If so, how would I specify a DODS matrix to do this? Thank you, Matthew Russell

2 1

BrainSegVol different in wmparc and aseg
by Jeff Sadino 15 Nov '10

15 Nov '10

Hello, When I look at the BrainSegVol and BrainSegVolNotVent in wmparc.stats, the values are around 200,000 - 300,000. However, when I look at the same measures in aseg.stats, the values are around 1,100,000 - 1,500,000. When I sum up the individual ROIs in wmparc, it comes out to >1L. I am currently using freesurfer 4.3.1. When I look at the aseg.stats files from freesurfer 3.0.5, ran on the same subjects, the values are up around that 1 - 1.5L range. This is consistent across all of our subjects: > 100 and from two different scanners at two locations. >From my wmparc file: # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1774481, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1774481.000000, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 243312.000000, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 275688, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 275688.000000, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1302696.178406, mm^3 My question is why would wmparc so severely underestimate the BrainSegVol measure? If I can not fix it, should I take the BrainSegVol from the aseg.stats file? Thank you! Jeff Sadino

2 2

freeview load overlay error...
by Gonzalo Rojas Costa 15 Nov '10

15 Nov '10

Hi: I generated a surface with: mri_vol2surf --src zstat3.nii.gz --src_type nifti --srcreg ../registro.dat --hemi lh --projfrac 0.5 --out ./zstat3_lh.w --out_type w then I tried to load zstat3_lh.w using freeview, but I got the error: "MRISreadBinaryCurvature: incompatible vertex number in file /home/gonzalorojas/Desktop/rendering_broca_wernicke_paper/diestroBL_cov/zstat3_lh.w could not read overlay data from /home/gonzalorojas/Desktop/rendering_broca_wernicke_paper/diestroBL_cov/zstat3_lh.w" Why ?... How can I solve the problem ?... Sincerely, Gonzalo ROjas Costa

2 1

cortical surface areas
by Ed Gronenschild 15 Nov '10

15 Nov '10

Hi, Is there a tool to derive the cortical surface areas of the cortical structures listed in aseg.stats? Ed

2 1

longitudinal processing of volumetry of same patient different dates...
by Gonzalo Rojas Costa 15 Nov '10

15 Nov '10

Hi: How can I do a comparisson between the volumetry of the same patient but with MRI of different dates (longitudinal study) ?... Sincerely, Gonzalo Rojas Costa

1 0

Cerebellar cortical thickness
by G. Shenhar 14 Nov '10

14 Nov '10

Hello :) Is it possible to perform cortical thickness measurements on cerebellar cortex, as is performed on cerebral cortex? Thanks in advance, Grace Shenhar

2 1

normative sample
by Miguel Burgaleta 14 Nov '10

14 Nov '10

Dear surfers, I was wondering if there is any normative sample available to everyone so that I can have a reference for a single subject's cortical and subcortical segmentations? Thanks, Miguel

1 0

about the xubuntu root password
by Braveheart 13 Nov '10

13 Nov '10

Hello, I downloaded the xubuntu version of freesurfer. Now I hope to install several new application the xubuntu system. But the root password is needed to install any new application. Anyone know what the root password is ? Thank you. Best, Junpeng

1 0

mri_convert left.right question
by XJ Kang 12 Nov '10

12 Nov '10

Hi, I am confused by the L/R of the images from mri_convert. Below are what I have: anat.img: anatomical image from scanner, with brain left-side marker appeared on the image left in SPM. I did the following steps: % mri_convert anat.img 001.mgz 001.mgz: brain left-side marker appeared on the image right in tkmedit, flipped L/R compared to anat.img % rmi_convert 001.mgz anatFS.img anatFS.img: brain left-side marker appeared on the image right in SPM, same as 001.mgz, not as the original anat.img This means I cannot get to the original image orientation by mri_converting twice. I also tried the following: %mri_convert 001.mgz --out_orientation RAS anatR.img %mri_convert 001.mgz --out_orientation LAS anatL.img anatR.img and anatL.img appeared the same orientation in SPM, although they have different Analyze matrices. My question, anyway I can flip the left/right of the mgz images using mri_convert? Thank you for clearing this. XJ Kang

2 1

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