Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Dummy Scans and Paradigm Files
by Dave Brohawn 01 Jul '10

01 Jul '10

Hello, My name is David Brohawn, and I am one of Dr. Roffman's research assistants. We run the SIRP and N-Back memory tests with our subjects. We have specified for 3 dummy scans to take place at the beginning of each of these protocols, which takes 6 seconds of scanning time, respectively. When writing paradigm files in freesurfer, should we include a 6 second period to account for these dummy scans, or do we write the paradigm files not making any reference to the time elapsed during these dummy scans? Thanks, Dave

2 1

Qdec default design
by Dankner, Nathan (NIH/NIMH) [F] 01 Jul '10

01 Jul '10

Hello all, I'm running a cortical thickness group analysis in qdec with two groups and one covariate (age). By default, does qdec use the DODS option, or DOSS?

2 1

writing out a transformed fmri volume
by Hansen, Kathleen (NIH/NIMH) [F] 01 Jul '10

01 Jul '10

Hi, We have had several naive questions about registration recently, and thank you all very much for your patience. Here is another one. We have used mrivol2surf with the output of bbregister to transform an individual subject's fmri data into the coordinates of the anatomical used to generate that subject's surface. We are happy with the accuracy of this process and understand that the registration file records the transformation parameters between the original fmri volume and the anatomical. Is there also a way to write the transformed fmri volume itself to disk? Thank you, Kathleen

2 1

Fwd: postdoctoral imaging position
by Susanna Carmona Cañabate 01 Jul '10

01 Jul '10

Applications are invited for a position at the Unitat de Recerca en Neurociència Cognitiva (http://dpsiquiatria.uab.cat/en/grupRecerca_2.php) at the Fundació IMIM- Hospital del Mar, Barcelona, Spain. (www.imim.es) The position is full-time for 18 months. It entails working mainly on a grant entitled: “MR Structural and functional neuroimaging of cognitive and motivational executive functions in ADHD” (SAF2009- 10901), but also in other neuroimaging projects of the group. The postholder will be responsible for analyzing functional, structural, and diffusion tensor data as well as writing up the results. Essential skills include knowledge of fMRI and/or structural MRI techniques, a proficient management of SPM and other programs, and a strong interest in psychiatric diseases. The position is available for a start as soon as October 1st 2010. Salary will be around and gross annual income of €26,200 (plus social security, health and unemployment benefits). The position will be located in Barcelona city, at the Hospital del Mar. Please send enquiries or applications (which must include a covering letter detailing professional objectives and interests, CV, and the names and email addresses of three references, all together in one pdf file) to Dr. Oscar Vilarroya, (ovilarroya1(a)imim.es) with the subject line "Postdoctoral imaging position".

2 1

how to filp Fa maps
by Morita, Marcia E. 01 Jul '10

01 Jul '10

Hi, I would like to know if there is a way to flip FA maps (the FA.nii.gz file) before running TBSS. Many Thanks, Marcia

1 0

Reenviar: signal dropouts in 7T scanners
by Jose Luis Cantero Lorente 01 Jul '10

01 Jul '10

I would be very grateful to receive your comments. Thanks in advance, --- Jose L. Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/en/

2 1

unsubscribe
by Asaf Kaftory 30 Jun '10

30 Jun '10

please unsubscribe me, thanks. ________________________________ From: "freesurfer-request(a)nmr.mgh.harvard.edu" <freesurfer-request(a)nmr.mgh.harvard.edu> To: freesurfer(a)nmr.mgh.harvard.edu Sent: Thu, July 1, 2010 12:20:58 AM Subject: Freesurfer Digest, Vol 76, Issue 58 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. tksurfer bus error (Nai Ding) 2. Re: Grey Matter Density? (Matthew Ku) ---------------------------------------------------------------------- Message: 1 Date: Wed, 30 Jun 2010 15:37:47 -0400 From: Nai Ding <gahding(a)gmail.com> Subject: [Freesurfer] tksurfer bus error To: freesurfer(a)nmr.mgh.harvard.edu Cc: ccamero2-contact ~ <sepranagw(a)yahoo.com> Message-ID: <AANLkTimFZf6O12yqCEGu6lscO0kYhXZ-Lo2roomwRQor(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hi everyone, We installed Freesurfer on our Mac system. freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0-full Everything works except tksurfer. When we try > tksurfer bert rh pial Freesurfer returns > surfer: current subjects dir: /Applications/freesurfer/subjects > Bus error How could we fix the problem? Thanks a lot, Nai

1 0

Re: [Freesurfer] Grey Matter Density?
by Matthew Ku 30 Jun '10

30 Jun '10

Dear Professor Fischl, Thank you for your support and the support from everyone else. It has been a really pleasant experience so far using Freesurfer and it’s great to know that such a great program has comparatively great support! We have accessed the NIH repository for normal pediatric brains, and have run the normative data through Freesurfer, then compared it to data outputted from the contracted NIH program, MINC. These are the results we have obtained so far: Left Right Calculated Total Frontal Occipital Parietal Temporal Frontal Occipital Parietal Temporal Freesurfer 108531 27381 80714 60177 106584 23498 85577 61030 553492 MINC 136241 35980 71381.4 84373.5 133588 32558.9 72250.5 86489.7 652863 By any chance, would you happen to know of any discrepancies between MINC and Freesurfer? In addition, since the NIH website reports their total through MINC as 820,000 while we summed it to be 652,863, do you know what MINC considers grey matter in comparison to what Freesurfer considers grey matter? Best, Matt From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wednesday, June 23, 2010 5:40 PM To: Schwartz, Carl R.E. Cc: mattku(a)seas.upenn.edu Subject: Re: [Freesurfer] Grey Matter Density? Sure, that would be great On Jun 23, 2010, at 5:21 PM, "Schwartz, Carl R.E." <carl_schwartz(a)hms.harvard.edu> wrote: Bruce, if you want I can answer this with a reference tonight and share a thread between you, me and Kagan re VBM vs. freesurfer that may help. Carl On 6/23/10 5:06 PM, "Matthew Ku" <mattku(a)seas.upenn.edu> wrote: Dear Professor Fischl, Thank you for your suggestions. We have used mri_binarize before with success and we are interested with both the cortical and subcortical volumes. However, we would appreciate it if you could clarify why you suggested for us to consider surface area and thickness independently, and how we should use those values in a reportable method. If possible, could you direct us to any relevant literature that would help us understand why we should use these values independently? Thanks for all the help. Best, Matt -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Wednesday, June 23, 2010 3:47 PM To: Matthew Ku Cc: freesurfer(a)nmr.mgh.harvard.edu; dchinapp(a)seas.upenn.edu Subject: Re: [Freesurfer] Grey Matter Density? Hi Matt, you could use mri_binarize to extract a gray matter binarization then go from there, although we've never put together scripts to do it since the biological intepretation is always hard. Are you interested in subcortical volumes or just cortical? If cortical, why not look at surface area and thickness independently? cheers Bruce On Wed, 23 Jun 2010, Matthew Ku wrote: > Dear Professor Fischl, > > Thanks a lot for your prompt response. > > We are trying to compute the grey matter density because we are > analyzing the maturation of grey matter, as referred to by N. Gogtay > et al. (Dynamic mapping of human cortical development during childhood > though early adulthood). > > From Freesurfer's output, we have only noticed grey matter volume. > However, would there be a way to obtain the grey matter mass through > an ROI mask without having to use SPM or FSL? > > Thanks again, > Matt > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce > Fischl > Sent: Wednesday, June 23, 2010 3:20 PM > To: Matthew Ku > Cc: dchinapp(a)seas.upenn.edu; freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Grey Matter Density? > > Hi Matt, > > density is really just average gray matter per unit volume. Why would > you want to compute such a thing? I think the way SPM/FSL does it is > to take a binary segmentation and smooth it, but you can check with them. > > cheers > Bruce > On Wed, 23 > Jun 2010, Matthew Ku wrote: > >> Hi Freesurfer Experts, >> >> >> >> I have been running Freesurfer to calculate the grey matter volume of >> pediatric brains but I was wondering if there was a method to >> determine grey matter density using Freesurfer? I have read a >> question previously posted asking a similar question, but there had >> been no replies or answers. If there is no command to calculate the >> density of grey matter, is there any alternate method to determine >> the density from > the volume data? >> >> >> >> Thanks, >> >> Matt >> >> _________________________________________ >> >> Matthew Ku >> >> University of Pennsylvania >> >> School of Engineering Class of 2013 >> >> (845) 596-3840 >> >> mattku(a)seas.upenn.edu >> >> >> >> > _______________________________________________ > 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 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 2

tksurfer bus error
by Nai Ding 30 Jun '10

30 Jun '10

Hi everyone, We installed Freesurfer on our Mac system. freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0-full Everything works except tksurfer. When we try > tksurfer bert rh pial Freesurfer returns > surfer: current subjects dir: /Applications/freesurfer/subjects > Bus error How could we fix the problem? Thanks a lot, Nai

1 0

mri_glmfit-sim of qdec
by Joana Braga Pereira 30 Jun '10

30 Jun '10

Dear all, I'm running the mri_glmfit script that has been automatically generated in qdec: mri_glmfit-sim \ --glmdir /home/joana/subjects/qdec/results_2sample \ --sim mc-z 10000 2 mc-z.abs.2 \ --sim-sign abs \ --overwrite Because i want to get the clusters, area size and hopefully z or p values of my results. I made a comparison of cortical thickness between 2 groups, with 2 covariates and in qdec this analysis shows that there are some clusters corrected at FDR. Is the script that i'm using correct? It has been running for a week now, which is the average time that it takes? Many thanks for your help, Joana

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