Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

SAG FSPGR BRAVO Sequence
by Ashley Hannah 30 Oct '13

30 Oct '13

Hello, Has anyone processed a SAG FSPGR BRAVO sequence successfully through FreeSurfer? When I run these images the program finishes without error however the output in tksurfer is grossly incorrect. Is there a way to adjust the parameters for reading white and gray matter by freesurfer (because BRAVO has a different contrast, not as defined) so that regions and boundaries are parceled correctly? Thanks, -- *Ashley*

2 9

Issues with rh.white and rh.orig surfaces
by Jonathan Holt 30 Oct '13

30 Oct '13

FS experts, both of these surfaces are incorrect and I’d like to be able to fix them. Rh.orig.nofix is unaffected. WM voxels don’t seem to be an issue, though the problem area is incorrectly segmented as white matter. I’ve removed this segmentation and it’s still not alleviated the problem. How best to proceed? Jon

4 7

Re: [Freesurfer] SAG FSPGR BRAVO Sequence
by Bruce Fischl 30 Oct '13

30 Oct '13

Hi Ashley what format are these in? They don't have an extension thanks Bruce On Wed, 30 Oct 2013, Ashley Hannah wrote: > Here are the tkmedit with overlay images. > > Thank you for your help! > > Ashley > > > On Wed, Oct 30, 2013 at 12:40 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > It's hard to tell anything from those images. We need to see > surfaces over volumes in freeview or tkmedit > Cheers > Bruce > > On Oct 30, 2013, at 12:01 PM, Ashley Hannah <ahannah1510(a)gmail.com> > wrote: > > For some reason the images will not display. > Hopefully this works.... > > > On Wed, Oct 30, 2013 at 11:31 AM, Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Ashley > > if you upload a dataset we'll take a look. I am > surprised to hear that you are having problems. Can > you post an example image? > > Bruce > On Wed, 30 Oct 2013, Ashley Hannah wrote: > > Hello, > Has anyone processed a SAG FSPGR BRAVO > sequence successfully through > FreeSurfer? > > When I run these images the program > finishes without error however the > output in tksurfer is grossly > incorrect. > > Is there a way to adjust the parameters > for reading white and gray matter by > freesurfer (because BRAVO has a > different contrast, not as defined) so > that > regions and boundaries are parceled > correctly? > > Thanks, > -- > Ashley > > > > > 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. > > > > > -- > Ashley M. Hannah > > <SAGBravo2_07.png> > > <SAGBravo1_07.png> > > > > > -- > > >

2 1

Using glmfit with 2 different sequences
by celine＠nmr.mgh.harvard.edu 30 Oct '13

30 Oct '13

Hi freesurfer team, I am wondering if there would be a way to process a glm analysis between 2 surfaces from different modalities within one group of subjects. For example, within one population of patients, we would like to see if there is a spatial relationship between cortical thickness and another metrics (DTI metrics for example). What we have done so far is compute the mean cortical thickness for each parcellation, the mean FA for each parcellation, and we did a linear regression with all the subjects of our group. Would there be a way to do that at the vertex level instead of a whole region level? From what I understood, when we use glmfit, the regressors that we can put are single values like age, group, cognitive testing etc, but maybe not an entire surface? Thanks a lot Best, Celine -- Celine Louapre, MD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129

2 3

Mac issue
by krista kelly 30 Oct '13

30 Oct '13

To all my fellow Freesurfers... Has anyone had any issues with doing recon-all on a Mac. I'm having a problem with the automatically generated labels V1, V2, and MT (when loaded in tksurfer there are holes in the mask) and I've been informed that this may be an issue because of running the program on a mac instead of using linux. I'm concerned that if the labels are incorrect, that there may also be a problem with the atlases and doing any whole brain analyses (although the atlas masks and surfs look fine). If anyone else has encountered this issue and can shed light on it for me, I would appreciate it! Best, Krista

1 0

Re: [Freesurfer] Qdec Questions
by Douglas N Greve 30 Oct '13

30 Oct '13

In your case you have HC listed first, so red/yellow means HC>SAD, blue means SAD>HC doug On 10/29/2013 11:03 PM, Ashley Shurick wrote: > Hi Doug, > > Apologies, but I have a rather easy follow-up question that I can't > figure out: > > How do you interpret the effect in each significant region? A previous > post suggests using ctrl + left mouse click on a blob and examining > the plot of the data. However, for the model I am looking at ("Does > the thickness-ERQ correlation differ between HC and SAD?") I still > can't determine if cortical thinning represents HC<SAD or SAD<HC. I'm > attaching a representative plot here. > > Thank you, > > Ashley > > > On Tue, Oct 29, 2013 at 10:25 AM, Ashley Shurick > <ashley.shurick(a)gmail.com <mailto:ashley.shurick@gmail.com>> wrote: > > Thank you! > > > On Tue, Oct 29, 2013 at 10:19 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > On 10/29/2013 01:10 PM, Ashley Shurick wrote: > > Hi all, > > > > I'm running analyses in Qdec and want to verify a few things: > > > > 1. When comparing two groups (HC vs patients) I am including > mean > > cortical thickness as a covariate, using the following equation: > > > > > > bh.thickness = (lh.thickness*lh.surfarea + > rh.thickness*rh.surfarea) / > > (lh.surfarea + rh.surfarea) > > > > > > Is this the best way to calculate global mean thickness? > Yes > > > > > > 2. I want to regress out any effects of age, therefore I need to > > demean the ages for my groups as a whole, and not perform this > > calculation on each group separately, correct? > Yes, in which case the test of the difference between groups > will be > done at an age equal to the mean of the ages. > > > > 3. I'm including questionnaires as a covariate of interest - > do I need > > to demean these values as well? > When you do a test on a continuous covariate, that test will be > unaffected by demeaning of the covariate. Demeaning will > affect the > difference between groups if you use a separate covariate for each > group. If you have a single covariate across groups, demeaning > will have > no effect. > > doug > > > > > > Thank you in advance for your help! > > > > > > Ashley > > > > > > -- > > Ashley A. Shurick > > Ph.D. Candidate > > Department of Psychology > > Stanford University > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@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. > > > -- 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

Qdec Questions
by Ashley Shurick 29 Oct '13

29 Oct '13

Hi all, I'm running analyses in Qdec and want to verify a few things: 1. When comparing two groups (HC vs patients) I am including mean cortical thickness as a covariate, using the following equation: bh.thickness = (lh.thickness*lh.surfarea + rh.thickness*rh.surfarea) / (lh.surfarea + rh.surfarea) Is this the best way to calculate global mean thickness? 2. I want to regress out any effects of age, therefore I need to demean the ages for my groups as a whole, and not perform this calculation on each group separately, correct? 3. I'm including questionnaires as a covariate of interest - do I need to demean these values as well? Thank you in advance for your help! Ashley -- Ashley A. Shurick Ph.D. Candidate Department of Psychology Stanford University

2 1

tksurfer command for saving multiple view tiff
by Jason Tourville 29 Oct '13

29 Oct '13

Is there a command for the "saving multiple views as TIFFs" function in tksurfer that can be used in a TCL script? Thanks, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755

1 0

Power analysis for Qdec
by amirhossein manzouri 29 Oct '13

29 Oct '13

Hi Would you please let me know if it is possible to calculate the power for a group comparison in cortical thickness? Also, a referee is requesting F-values and T map , are they generated by q-dec? That would be great if I can get an answer in more detail since I have seen the post in FAQ, just need more information in detail regarding calculating the power ! -- Best regards, Amirhossein Manzouri

4 8

fast_selxavg3.m - ERROR: design is ill-conditioned
by preciado＠nmr.mgh.harvard.edu 29 Oct '13

29 Oct '13

I have two sets of identical blocks within each fMRI run, so conditions {1,2,3,4,5,1,2,3,4,5}, and there are three separate runs of the two blocks. If I run the analysis treating each with the contrasts set up with this numbering scheme (e.g. 3 vs 1 has two occurrences) , I get the following output from /usr/local/freesurfer/dev/fsfast/toolbox/fast_selxavg3.m ... ntptot = 687, nX = 136, DOF = 551 Saving X matrix to /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008/bold/improv.sm05.lh/Xtmp.mat XCond = 2926.01 (normalized) However, if I want to treat the two sets of blocks separately, i.e., {1,2,3,4,5,6,7,8,9,10} so I can look at contrasts such as 3 vs 1 as well as 8 vs 6 then fast_selxavg3.m gives: ntptot = 687, nX = 146, DOF = 541 Saving X matrix to /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj008_10block/bold/improv.10blocks.sm05.lh/Xtmp.mat XCond = 4.33238e+08 (normalized) ERROR: design is ill-conditioned 1) why does nX increase by 10 in the 2nd case? 2) why is fast_selxavg3.m unhappy and XCond so large? Can it not handle 10 separate blocks? The entire log file in the 2nd case is attached.

2 5

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