Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Transparency surface
by Arnaud Boré 01 Oct '13

01 Oct '13

Dear Freesurfer experts, Using tksurfer I open an inflated surface and I display the pial surface. Then I load an overlay but I'm not able to see it correctly. Is it possible to put a transparency/opacity value for the surface so I can see better my overlay ? Thank you for your help Arnaud Bore

2 1

missing eTIV in asegstats2table
by Daniel Ferreira 01 Oct '13

01 Oct '13

Hi, I just run my first asegstats2table in version 5.3 of FS. Is not eTIV included in the generated file anymore? I know that I can get eTIV with mri_segstats --subject subjid --etiv-only but, is it any way to get the values for all my subjects in a text file as asegstas2table does? Thanks a lot Dani

2 1

(no subject)
by Valentina Ciullo 01 Oct '13

01 Oct '13

-- Dott.ssa Valentina Ciullo Laboratorio di Neuropsichiatria Dipartimento di Neurologia Clinica e Comportamentale IRCCS Fondazione Santa Lucia via Ardeatina 306 - 00179 Roma Tel. +39(0)651501101 Fax +39 (0)6 90280774 web: http://www.neuropsichiatrialab.com<http://www.neuropsichiatrialab.com/it/personale/sabrina-fagioli>

1 0

MNI152 to 305 conversion
by Paul Beach 30 Sep '13

30 Sep '13

Freesurfer experts, I'm attempting to utilize an archived e-mail's contents to resample data in MNI152 to 305. The script I'm using is as follows: *mri_vol2vol \* *--mov /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz \* *--targ FSL_MNI152_FreeSurferConformed_1mm.nii.gz \* *--reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \* *--inv --o FSL_MNI305_2mm.nii.gz* * * * * This series of commands is based on the following suggestion from Doug in a previously archived e-mail exchange from someone attempting to do something similar: *>> To go from mni152 to the MNI305 2mm space, use* *>>* *>> mri_vol2vol --mov mni305.2mm.nii.gz \* *>> --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \* *>> --reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \* *>> --inv --o output.mni305.2mm.nii.gz* *>>* *>> This will resample MNI152_T1_2mm.nii.gz (or anything in that space) to the* *>> mni305 2mm space.* However, this changing the orientation of my data - essentially all images are being rotated 90degrees so the frontal lobe is pointed straight up. Are there any suggestions to ameliorate this problem? Thanks! -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - Bozoki Lab: Neurology/Radiology

2 3

Re: [Freesurfer] Effects of age on different parameters (thickness, lGI...)
by Daniel Klein 30 Sep '13

30 Sep '13

Dear FreeSurfer experts, thanks a lot for your solution. It works fine. I have some further questions to polynomial fitting with qdec, to prevent misunderstandings from my point of view. Only to be sure: 1) Linear effects of age: age as continuus factor. 2) Quadratic effects of age: age (quadratic) as continuus factor and age (linear) as nuisance factor. 3) Cubic effects of age: age (cubic) as continuus factor and age (linear) as nuisance factor. 4) Linear+quadratic+cubic effects together: i will have to use mri_glmfit with FSGD file. Best wishes Daniel...

2 1

Re: [Freesurfer] Problem with downloading Xhemi programs
by Douglas N Greve 30 Sep '13

30 Sep '13

Hi Wen, are you using version 5.3? If so, then you will already have all the programs and atlases doug ps. Please remember to post to the list. thanks! On 09/29/2013 06:08 AM, wen.zhang55 wrote: > Dear Doug: > Sorry to bother you, but i have a trouble to download the programs > acoording to your instruction (Surface-based Interhemispheric > Registration:http://ftp.nmr.mgh.harvard.edu/fswiki/Xhemi) in > Freesurfer wiki. No relevant files in that FTP. So would you > please offer me another download link or kindly attach the program > files in the enclosure by email. Thank you very much! > All the best, > Wen Zhang > 2013-09-29 > ------------------------------------------------------------------------ > wen.zhang55 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

1 0

Binary mask of the pons
by pfotiad＠nmr.mgh.harvard.edu 30 Sep '13

30 Sep '13

Hi FS Community, I was wondering whether there is a way to get a binary mask of the pons. Thanks in advance, Panos

1 0

Total Surface Area
by XJ Kang 30 Sep '13

30 Sep '13

Hi Experts, I am trying to figure out the total surface area of a hemisphere. I found out 3 ways to read the area data: 1. Read the lh.area file directly [A, f]=read_curv('lh.area'); Total surface area: sum(A) = 86905.15mm^2 2. Read from the ~/stats/lh.curv.stats (generated by mris_curvature_stats in recon-all): Raw Total Surface Area: 87347.86719 mm^2 3. Read from the results: % mris_anatomical_stats sub lh white total surface area = 91046 mm^2 First, the total area includes the cutting area (unknown region?), right? Secondly, which total area is more reasonable? Thanks. XJ Kang

2 1

Question about preproc-sess -no-subcort-mask
by Leila Reddy 30 Sep '13

30 Sep '13

Hi, I would like to verify (as a sanity check and to make sure that I'm on the right track in my analysis) that preproc-sess runs with -no-subcort-mask by default in freesurfer-Darwin-lion-stable-pub-v5.2.0, but with -no-subcort-mask turned off by default in stablev5.3.0 on snowleopard. I first did an MNI305 analysis in v5.2.0 (mountain lion) and was able to see my slices very nicely overlaid on the average/mni305.cor.mgz brain. However, the same analysis in v5.3.0 (snowleopard) didn't overlay on the brain in a sensible way, and only after I searched the mailing list did I realize that I needed to use -no-subcort-mask. Using this option gave me the same results as with v.5.2.0. Searching through freesurfer/fsfast/bin/preproc-sess I don't see where this flag is set by default to -no-subcort-mask in v5.2.0 (in fact, it seems that ApplySubCortMask = 1; by default). So I'm pretty confused, and I'm just not sure that I'm doing things the right way... Thanks in advance, Leila

2 2

Post-Surgery Volume Analysis
by Germeyan, Sierra (NIH/NINDS) [F] 30 Sep '13

30 Sep '13

Hi all, A couple questions regarding post-surgery scans. 1. Is there a way to run scans of post-surgical brains that takes resections into account and gives more accurate results than "recon-all -all"? 2. Is it possible to obtain resection volumes with FreeSurfer? I tried to do this indirectly by finding the difference between total intracranial volume that FreeSurfer gave for scans pre- and post- surgery. However, I rarely obtained reasonable numbers with this method. Thanks very much for any advice you can give!

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