Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

Question
by Dulce Maria Magdaleno Arroyo 04 Jul '16

04 Jul '16

Hi, I am doing a research about the uterus, in this research I am trying to define the geometry of this organ, so I want to use freesurfer to mapping the uterus into a sphere; as far as I understand I don't need all the brain image processing. I have already a FEM model of the uterus in matlab, and I was wondering if just the command mris_inflate could be used to this task or if I have to consider some other commands? Other question I have is, Do I need to convert my matlab data to .mgh to use the freesurfer commands? If yes, Could you give me some directions to do this task? In advance, thank you so much for your help. Best, DM

1 0

Re: [Freesurfer] controlling for total gray matter volume
by Harms, Michael 04 Jul '16

04 Jul '16

Hi, Why not use total surface area to control for analyses involving area, and mean cortical thickness to control for thickness? I’ve posted to the list before regarding this, so you should be able to find those posts. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mharms(a)wustl.edu On 7/4/16, 9:12 AM, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Clara Kühn" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of ckuehn(a)cbs.mpg.de> wrote: Do you know, if there are any publications concerning this matter? So far I've found only this http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0148852 that controls for tGM only for area and not CT. Cheers Clara ----- Ursprüngliche Mail ----- Von: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> An: "Freesurfer support list" <freesurfer(a)nmr.mgh.harvard.edu> Gesendet: Montag, 4. Juli 2016 15:37:57 Betreff: Re: [Freesurfer] controlling for total gray matter volume sounds right to me Bruce On Mon, 4 Jul 2016, Clara Kühn wrote: > I have decided now to not control for ICV or total gray matter volume >when looking at cortical thickness but to control for total gray matter >volume when looking at surface area. Does that sound about right? > > Cheers, Clara > > ----- Ursprüngliche Mail ----- > Von: "Arkadiy Maksimovskiy" <arkadiym(a)bu.edu> > An: freesurfer(a)nmr.mgh.harvard.edu > Gesendet: Samstag, 2. Juli 2016 18:36:51 > Betreff: Re: [Freesurfer] controlling for total gray matter volume > > Hi Clara, > > If I am understanding your question correctly, you don't need to control >for brain volume when looking at thickness analyses. > > See quote below from this link: > > http://www.freesurfer.net/fswiki/eTIV > > "Note that this correction is only useful in situations where the >structure scales with head size. Outside of this, correction just adds >noise, or provides inaccurate data. In the case of the measures from >Freesurfer, one would apply correction to the volume measures and not >thickness measures. This is because volume scales with head size which is >mostly due to changes in surface area, whereas thickness alone scales to >a much less degree." > > Best, > Arkadiy > > On Sat, Jul 2, 2016 at 12:00 PM, < >freesurfer-request(a)nmr.mgh.harvard.edu > wrote: > > > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. controlling for total gray matter volume (Clara K?hn) > 2. cotrolling for total gray matter volume (Clara K?hn) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 30 Jun 2016 15:19:43 +0200 (CEST) > From: Clara K?hn < ckuehn(a)cbs.mpg.de > > Subject: [Freesurfer] controlling for total gray matter volume > To: Freesurfer support list < freesurfer(a)nmr.mgh.harvard.edu > > Message-ID: > < 600644700.119350.1467292783757.JavaMail.zimbra(a)cbs.mpg.de > > Content-Type: text/plain; charset=utf-8 > > Dear FreeSurfer experts, > > I would like to look at longitudinal thickness data and want to control >for total gray matter volume. Should I use that information from the >CROSS before anything has been registered and smoothed or from the LONG >after they have been registered to the BASE? > Also I was wondering if it is useful to control for total gray matter >volume when looking at surface area? > > Thanks for your help! > Clara > > > ------------------------------ > > Message: 2 > Date: Thu, 30 Jun 2016 15:01:06 +0200 (CEST) > From: Clara K?hn < ckuehn(a)cbs.mpg.de > > Subject: [Freesurfer] cotrolling for total gray matter volume > To: Freesurfer support list < freesurfer(a)nmr.mgh.harvard.edu > > Message-ID: > < 1473114832.117985.1467291666701.JavaMail.zimbra(a)cbs.mpg.de > > Content-Type: text/plain; charset=utf-8 > > Dear FreeSurfer experts, > > I would like to look at longitudinal thickness data and want to control >for total gray matter volume. Should I use that information from the >CROSS before anything has been registered and smoothed or from the LONG >after they have been registered to the BASE? > Also I was wondering if it is useful to control for total gray matter >volume when looking at surface area? > > Thanks for your help! > Clara > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

2 1

Re: [Freesurfer] controlling for total gray matter volume
by Arkadiy Maksimovskiy 04 Jul '16

04 Jul '16

Hi Clara, If I am understanding your question correctly, you don't need to control for brain volume when looking at thickness analyses. See quote below from this link: http://www.freesurfer.net/fswiki/eTIV "Note that this correction is only useful in situations where the structure scales with head size. Outside of this, correction just adds noise, or provides inaccurate data. In the case of the measures from Freesurfer, one would apply correction to the volume measures and not thickness measures. This is because volume scales with head size which is mostly due to changes in surface area, whereas thickness alone scales to a much less degree." Best, Arkadiy On Sat, Jul 2, 2016 at 12:00 PM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. controlling for total gray matter volume (Clara K?hn) > 2. cotrolling for total gray matter volume (Clara K?hn) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 30 Jun 2016 15:19:43 +0200 (CEST) > From: Clara K?hn <ckuehn(a)cbs.mpg.de> > Subject: [Freesurfer] controlling for total gray matter volume > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <600644700.119350.1467292783757.JavaMail.zimbra(a)cbs.mpg.de> > Content-Type: text/plain; charset=utf-8 > > Dear FreeSurfer experts, > > I would like to look at longitudinal thickness data and want to control > for total gray matter volume. Should I use that information from the CROSS > before anything has been registered and smoothed or from the LONG after > they have been registered to the BASE? > Also I was wondering if it is useful to control for total gray matter > volume when looking at surface area? > > Thanks for your help! > Clara > > > ------------------------------ > > Message: 2 > Date: Thu, 30 Jun 2016 15:01:06 +0200 (CEST) > From: Clara K?hn <ckuehn(a)cbs.mpg.de> > Subject: [Freesurfer] cotrolling for total gray matter volume > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <1473114832.117985.1467291666701.JavaMail.zimbra(a)cbs.mpg.de> > Content-Type: text/plain; charset=utf-8 > > Dear FreeSurfer experts, > > I would like to look at longitudinal thickness data and want to control > for total gray matter volume. Should I use that information from the CROSS > before anything has been registered and smoothed or from the LONG after > they have been registered to the BASE? > Also I was wondering if it is useful to control for total gray matter > volume when looking at surface area? > > Thanks for your help! > Clara > > -- > Clara K?hn, Phd Student > > Max-Planck-Institute for Human Cognitive and Brain Science > Department of Neuropsychology > Stephanstrasse 1A > 04103 Leipzig, Germany > > Phone: +49 341 - 9940 2271 > Fax: +49 341 - 9940 2260 > Web: www.cbs.mpg.de > E-Mail: ckuehn(a)cbs.mpg.de > > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 149, Issue 6 > ****************************************** > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >

3 4

Tissue probability maps from aseg.mgz
by Lee Subin Kristine 04 Jul '16

04 Jul '16

Dear FreeSurfers, Is it possible to get tissue probability maps (for the purpose of using them in spm DARTEL, PVElab, etc) out of aseg.mgz? I did read in a previous post (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2007-October/006384.h…) that you can use mri_ca_label with the option -write_probs, but I could not find a -write_probs option. If not, I'm wondering is there is any other possible way to get tissue probability maps from FreeSurfer? Any help would be much appreciated. Regards, Subin

2 1

trac-all error (bvecs and bvals don't have same number of entries)
by Lars M. Rimol 04 Jul '16

04 Jul '16

Hi, Trying to run trac-all -c dmric_file -prep, I get an error message stating that there are different numbers of entries in the bval and bvec files. I don't understand why, since both have the same number of rows (64). OS = Ubuntu 14.04.4 Software: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0; I have updated Tracula and FSL (v 5.0.9). Error message: #@# Tensor fit fr. 01. juli 19:20:29 +0200 2016 dtifit -k /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dwi.nii.gz -m /media/lmr2/subjects/DTI/tracula_2016/4_FS/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvecs -b /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvals -o /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dtifit Error: bvecs and bvals don't have the same number of entries Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at fr. 01. juli 19:20:30 +0200 2016 ---------- I also tried flipping the bvec/bval files, but got the same error. I don't know if there's anything wrong with the bval/bvec files, or if this error message is indicative of some other problem. Is the updated Tracula version only compatible with the dev version of FS? I have attached the bval/bvec files and the trac-all.log. ------------------------------------------------------------------- The contents of the dmric file is: setenv SUBJECTS_DIR /media/lmr2/subjects/DTI set dtroot = /media/lmr2/subjects/DTI/tracula_2016_nativerows set subjlist = (4_FS) set dcmroot = /media/lmr2/subjects/DTI set dcmlist = ( 4/5/1.dcm ) set bvalfile = /media/lmr2/subjects/DTI/bvals_rows.csv set bvecfile = /media/lmr2/subjects/DTI/bvec_rows.csv Thank you! yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway

3 2

tracula not work
by yangfuxing 04 Jul '16

04 Jul '16

Hi professor， When I finished setting up the configuration file "dmrirc", type "trac-all -c dmrirc"in the terminal ,it return "FSLDIR: Undefined variable", how can I solve it?Thank you. Best, yang

2 1

mapping a surface from fsaverage_sym to the subject's native surface
by Ali-Reza Mohammadi-Nejad 03 Jul '16

03 Jul '16

Dear Freesurfer experts, Based on the FS wiki, I calculated the cortical thickness difference between the lh and rh of a subject. Now, I want to use the “mris_apply_reg” command to map the “left-right difference” from fsaverage_sym back to the subject's native surface. Unfortunately, I did not find the appropriate options of this command to do this. Thanks for any help. Best regards,Ali-Reza Ali-Reza Mohammadi-Nejad Pre-doctoralresearch fellow Radiology and NeurologyResearch HenryFord Health System Detroit,MI 48202, USA

1 0

question about aseg.mgz
by Jasmin Alves 02 Jul '16

02 Jul '16

Dear Freesurfer support, I noticed in previous threads, people have inquired about how to check the quality of the aseg.mgz segmentation using the norm.mgz as a reference. When I did this, there were several mislabeled regions according to the norm.mgz ie. voxels labeled as white matter on the norm.mgz but the hippocampus on the aseg.mgz. Other times the accumbens was labeled as the putamen or the pallidum as the amygdala. This was just in one participant, other participants had several more discrepancies. Are these discrepancies something that requires manual editing? Because I feel like I will have to edit almost every voxel. Your suggestions would be greatly appreciated. Thanks, Jasmin -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves(a)usc.edu

2 3

tksufer got the opposite direction of image
by 李琬 02 Jul '16

02 Jul '16

Dear all, I've been trying to use "tksufer" to check the surface images according to the instruction of "Inspection of Freesurfer Oupt". I could get the images, but the direction is opposite. Like if I typed "tksurfer fsaverage lh inflated ", but I got the right one. What may be wrong? Thank you! [root@server1 subjects]# tksurfer fsaverage lh inflated subject is fsaverage hemi is lh surface is inflated surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer/subjects checking for nofix files in 'inflated' Reading image info (/usr/local/freesurfer/subjects/fsaverage) Reading /usr/local/freesurfer/subjects/fsaverage/mri/orig.mgz surfer: Reading header info from /usr/local/freesurfer/subjects/fsaverage/mri/orig.mgz surfer: vertices=163842, faces=327680 surfer: single buffered window surfer: tkoInitWindow(fsaverage) surfer: using interface /usr/local/freesurfer/tktools/tksurfer.tcl Reading /usr/local/freesurfer/tktools/tkm_common.tcl Reading /usr/local/freesurfer/tktools/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/tktools/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % surfer: loaded inflated into set 1 surfer: curvature read: min=-0.673989 max=0.540227 -- Wan

2 1

Qdec-correction for multiple comparison
by John Anderson 02 Jul '16

02 Jul '16

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