Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] ICV
by Douglas N Greve 08 May '13

08 May '13

Hi Alejandra, I don't work with children, so I'll let someone else (Lilla? Rudolph?) answer. doug ps. Please remember to copy the list on responses. Thanks! On 05/08/2013 01:19 AM, Alejandra Infante wrote: > Thank you! I might have asked this at the training, but I am still not > clear on whether the estimated ICV (from freesurfer) is reliable if > your population of interest are children? Or would you recommend > manual edits (when needed) after checking the quality of the talairach > registration file using tkregister2 --s subjid --fstal --surfs? > > > On Tue, May 7, 2013 at 7:52 PM, Douglas Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > It is neither:) See http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV > and/or Buckner et al. (2004) NeuroImage > <https://surfer.nmr.mgh.harvard.edu/fswiki/NeuroImage> 23:724-738. > > "Basically, total intracranial volume is found to correlate with > the determinant of the transform matrix used to align an image > with an atlas. The work demonstrates that a one-parameter scaling > factor provides a reasonable TIV estimation. This method uses an > atlas based spatial normalization procedure, and requires that the > *talairach.xfm* is correct. " > > This performs the talairach registration for a subject. Then, > based only on the numbers in the matrix, it estimates the ICV > based on subjects that had similar matrices. > > doug > > > > On 5/7/13 9:42 PM, Alejandra Infante wrote: >> Hi, >> I understand that ICV is an estimated measure based on a standard >> talairach transformation; however, I want to know how freesurfer >> is defining intracranial volume (i.e., is this a representation >> of everything within the cranium as the name implies or is it an >> estimate of total brain volume, which would not include space >> between skull and dura)?. We are using fs vesion 5.1 >> >> >> -- >> M. Alejandra Infante >> Doctoral Student >> SDSU/UCSD Joint Doctoral Program in Clinical Psychology >> Phone: (858) 449-2950 <tel:%28858%29%20449-2950> >> E-Mail: infante.alejandra.m(a)gmail.com >> <mailto:infante.alejandra.m@gmail.com> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > 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. > > > > > -- > M. Alejandra Infante > Doctoral Student > SDSU/UCSD Joint Doctoral Program in Clinical Psychology > Phone: (858) 449-2950 > E-Mail: infante.alejandra.m(a)gmail.com > <mailto:infante.alejandra.m@gmail.com> > -- 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/

4 4

Re: [Freesurfer] Using FSL matrix for Talairach transform
by Johannes Klein 08 May '13

08 May '13

Hi Doug, Thanks for your reply! I'm getting closer to a solution now, with tkregister2's display showing a correctly transformed mni305 file, but I still cannot get a valid talairach.xfm file out of this. Here's what I tried: tkregister2 --mov /usr/local/freesurfer/average/mni305.cor.mgz --targ orig.mgz --fsl mni2sub.mat --reg test_mni.mgz.reg works fine. Next, to obtain a suitable .xfm file, I ran tkregister2 --mov /usr/local/freesurfer/average/mni305.cor.mgz --targ orig.mgz --fsl mni2sub.mat --reg test_mni.mgz.reg --xfmout testtal.xfm --noedit and copied the output (testtal.xfm) into mri/transforms/talairach.xfm Now, when I view the result with tkregister2 --s test --fstal --mgz the transform is way off again. Apparently, tkregister2 reads and interprets the FSL matrix correctly, but the output transform that I get is not in the right format for transforms/talairach.xfm. I wonder if I'm using the wrong output switch now - but looking at tkregister2's documentation, it seems to be the one to use? Thanks, Johannes Date: Tue, 07 May 2013 14:11:27 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Using FSL matrix for Talairach transform To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <518943CF.7050801(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Johannes, try using the --xfmout option of tkregister2. I'm not sure what regdat2xfm is doing. doug On 05/07/2013 12:42 PM, Johannes Klein wrote: > Dear all, > I have some tricky subjects that I cannot get to register properly with the standard Talairach process, or even the use-mritotal option. However, with some fiddling, I've produced a reasonable registration matrix with FSL's FLIRT. > > I'm now looking to convert my FSL registration matrix, and use it as Freesurfer's Talairach transform. From the documentation, I gathered that I need to get it into Freesurfer's xfm format, and I suppose this is a two step process. > > I converted the FLIRT-provided matrix cor2raw.xfm like so: > tkregister2 --mov /usr/local/freesurfer/average/mni305.cor.mgz --fslreg cor2raw.xfm --s mysubject --noedit --reg register.dat > > I then converted register.dat to the xfm data format: > regdat2xfm /usr/local/freesurfer/average/mni305.cor.mgz rawavg.mgz register.dat tal.xfm > > and finally replaced talairach.xfm in the transforms directory with the output of the last command. Unfortunately, this doesn't work, and the transform is very much off target when I view it in tkregister2. > Obviously, I've made a mistake when converting between the different transforms - could anybody point me in the right direction? > Thanks all, > Johannes > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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 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/

2 1

Normalization Errors?
by Gonzalo Iribarne 08 May '13

08 May '13

Hello Freesurfers, There are some areas of grey and white matter that are rendered with similar brainmask values ranging from 100 - 122 for some of my participants. I have added control points in order to identify which voxels are white matter, but they are excluded from wm.mgz, as well as the white and grey matter boundaries. Is this a normalization error? Are the motion artifacts visible in the T1 a factor? -Gonzalo [image: Inline image 1]

2 2

Segstats
by Varghese Chikku 08 May '13

08 May '13

Dear FS team, Could any tell me what this numbers stands for in segstats. 31 53 Right-Hippocampus 2953 2953 32 54 Right-Amygdala 969 969 45 251 CC_Posterior 191 191 46 252 CC_Mid_Posterior 200 200 I am referring to this 31 53,32 54,45 251 etc is this the slice range? Many Thanks Chikku

2 1

Re: [Freesurfer] Issues with Cluster generation
by Douglas N Greve 08 May '13

08 May '13

Hi Joshua, have you looked at the help (ie, run it with --help). doug ps. Please remember to copy the list instead of sending replies directly to me. Thanks! On 05/08/2013 01:49 AM, Joshua deSouza wrote: > Hi Doug, > > Thank you for your help. > > Just a request, > Could you just guide me on how to use the --qache function for this > particular situation? > > Thank you > Joshua > > On Wed, May 8, 2013 at 1:58 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > Hi Joshua, there are several issues. First, you are using a > threshold of p<.0001 which is pretty severe. It works for the > tutorial, but you need to understand what this threshold is and > pick one appropriate for your data. Second, you are only doing 5 > iterations. You need to be doing something like 10000. If you are > doing a whole cortex analysis, you can use the cached table > instead of doing a simulation (with --qache). Running your own > simulation will take a long time. The smoothing level is a little > high, I usually run at 10 or 15. There's nothing wrong, it is just > a little high. > doug > > > > On 05/05/2013 03:39 AM, Joshua deSouza wrote: > > Hi Doug, > > The image has undergone fwhm 20 smoothing. > > The final glmdir file is given in the attachments. RC.txt was > the contrast name and folder in which the cluster correction > files are kept. > > The glmdir creation command line : mri_glmfir --y > lh.thomasR.20.mgh --fsgd R.txt dods --C RC.txt --surf > fsaverage lh --cortex --glmdir lh.thomasR.glmdir > > The glmfit-sim command line is : mri_glmfit-sim --glmdir > lh.thomasR.glmdir --sim mc-z 5 4 mc-z.negative --sim-sign neg > --cwpvalthresh 0.999 --overwrite > > The command line to view the image is : tksurfer fsaverage lh > inflated -annot > lh.thomasR.glmdir/RC.txt/mz-z.negative.sig.ocn.annot fthresh 1 > -curv -gray > > The version of freesufrer i'm using is 1.379.2.17 > > Thank you helping me out with this. > > > On Sat, May 4, 2013 at 12:12 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > Can you send the command line and terminal output and the > version > of FS > you are using? > doug > On 05/03/2013 09:01 AM, Joshua deSouza wrote: > > Hello all, > > > > I am facing a problem whereby after running GLMfit and > cluserwise > > correction for multiple comparisons using the > monte-carlo method, I > > was unable to generate any clusters. I do have > significant images > > produced for the glmfit. > > > > All procedures were done according to the tutorial to > match the > > effects under FSGD. > > > > There are no clusters available even when I set the > cwpvalthresh to > > .999 which is supposed to show all clusters. What is the > cluster > > generation dependent upon? As my glmfit does show > significant areas. > > > > Please advise > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@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> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://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> > <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> > <mailto:Freesurfer@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 <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/ > > -- 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

How to show the result with more color by using tksurfer?
by yufeng huang 08 May '13

08 May '13

In my study, I have to show more than 10 functional condition with different colour, I want to know how to define a certain colour in a certain functional condition, and show it using tksurfer.

2 1

(no subject)
by Shani Ben Amitay 08 May '13

08 May '13

Hello Freesurfer I would like to extract the stream for surface-based analysis on the output of an in-house segmentation process. Is this possible?How? Thanks Shani

2 5

mri_convert Segmentation fault
by Oscar Esteban 08 May '13

08 May '13

Dear all, I am experiencing segfaults when trying to convert from nifti to mgz. Ubuntu 13.04 Freesurfer 5.1, 5.2 and 5.3-BETA. I tried to find the problem using ldd, gdb, etc. but there is no debug information. I tried to compile 5.3-BETA but it does not find libminc-dev (while it is installed)... I think this is the same problem (related to the new libc in ubuntu 13.04) that those posted in https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-May/029581.html , https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-January/027532.h… and https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-May/029679.html. I'm looking forward to helping, but since there is no debug information in the binaries and I'm stucked with compilation... I don't know what to do. Best, Oscar Esteban -- Oscar Esteban PhD Student / Researcher Biomedical Image Technologies (BIT), UPM ETSI Telecomunicación Lab. C203, Av. Complutense s/n - E-28040 Madrid (Spain) +34 915 495 700 ext.4234 Signal Processing Laboratory (LTS5), EPFL-STI-IEL-LTS5 ELD 224 (Bâtiment ELD), Station 11, CH-1015 Lausanne, Switzerland

2 1

Issues in version 5.2
by stdp82＠virgilio.it 08 May '13

08 May '13

I apologize for the trivial question, but for me is urgent to understand if the issues that affect the version 5.2 are referred also to TRACULA and hippo-subfield.Do you advice me to cancel my analysis performed by 5.2. and re-run it by new version 5.3? Are the results obtained with version 5.2 reliable? Thank you very much for reply and for your work. Stefano

2 1

Google Talk 使用邀请
by Google Talk 08 May '13

08 May '13

----------------------------------------------------------------------- yufeng huang邀请您使用 Google Talk。如果您已经拥有 Google 帐户，请登录 Gmail 并接受此聊天邀请： http://mail.google.com/mail/b-60fdfa524c-703f0dba08-8eKfT6qRXAGCd7RaLzjh4b7… 要注册 Google 帐户并开始使用 Google Talk，您可以访问： http://mail.google.com/mail/a-60fdfa524c-703f0dba08-8eKfT6qRXAGCd7RaLzjh4b7… 要了解详情，请访问： http://www.google.com/intl/zh-CN/landing/accounts/ 此致， Google 小组敬上

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