Freesurfer November 2010

freesurfer@nmr.mgh.harvard.edu

92 participants
127 discussions

absolute differences using paired diff?
by Mayuresh 16 Nov '10

16 Nov '10

Hi Doug, Nick and other freesurfer users, I have two groups and each group has a matched pair of subjects. I am keen on identifying cortical areas where the difference between the matched pair in group1 is greater than that in group2. How can I do this in freesurfer? >From the email archive it seems to me that -paired-diff option with mris_preproc should do the trick, however as I understand this will create difference maps such that subject1-matchedsubject2. For my purpose I would be needing the absolute difference between the pairs. How can I acheive this? Thanks for any pointers, Mayuresh

2 1

GPU CUDA on Snow Leopard
by Pedro Paulo de Magalhães Oliveira Junior 16 Nov '10

16 Nov '10

Is there a plan to release the FreeSurfer CUDA Binaries for Snow Leopard? Thanks PPJ --------------------------------------------------------------------- Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile

1 0

Cortical thickness of a Volume-defined ROI: Reshaping dimensions
by Righart, Ruthger Dr. 16 Nov '10

16 Nov '10

Dear Freesurfers, I would like to map my subject thickness data to the fsaverage subject, following ROI analyses, as described under step 4: http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness Before step 4, tksurfer showed me that registration from MNI to Freesurfer space of my ROI went well! After that I would like to get thickness data using mri_segstats (step 5). However, Freesurfer indicates that the dimensions of my segmentation image (23406 x 1 x 7) are different from the dimensions of my input image (27307 x 1 x 6), and using mri_info suggests that sth seems to have gone wrong in step 4. I have searched in the Freesurfer archives and I understood that 23406 x 1 x 7 are the correct dimension values and followed the advise to use --reshape in the fourth step. This does however not change the dimensions (it still indicates in the Freesurfer output: Reshaping 6 (nvertices = 163842) which I guess should be Reshaping 7). Any suggestions to solve this problem of different dimensions are very much appreciated! Best Regards, Ruthger Righart (PhD) Institute for Stroke and Dementia Research (ISD) Klinikum der Universität München Max-Lebsche-Platz 30 81377 Munich | Germany Ruthger.Righart(a)med.uni-muenchen.de

2 1

Mean lGI value extraction
by Prapti Gautam 16 Nov '10

16 Nov '10

dear all, I am trying to extract the mean values of lgi from the cortex from a group of subjects. I found the following command useful in extracting for one subject: mris_anatomical_stats -mgz -f lh.lgi.stats -b -a aparc.annot -c lh.lgi.annot.ctab -t pial_lgi $SUBJECT lh However, I have a lot of subjects I wish to extract this for and I was wondering if there is a command that will extract these values similar to the aparcstats2table command (where all the subjects and the mean values for each parcellation is in one output file) thanks, Prapti

2 1

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

← Newer
1
2
3
4
5
6
7
8
9
...
13
Older →

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer November 2010