Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30096 discussions

Look-up table for aparc+aseg
by Chang, Yishin 08 May '13

08 May '13

Hi, Sorry if this is a duplicate question, but I can't find the answer anywhere. Where can I find a comprehensive look-up table for the indices in aparc+aseg? I'm using version 5.1.0. If a comprehensive one does not exist, I only need the cortical labels. Thanks, Shin

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Subcortical Choi 17 networks ROIs
by Mario Ortega 08 May '13

08 May '13

HI Everyone, I have a question about how to "write out" ROIs for these networks. I realize I can transform the mni template and Masks using mri_vol2vol to create a new "aseg_choi-17" file. But in order to do stats or use them as regions of interest in FSfast, they need to be included in the defaiult FreeSurferColorLUT.txt? So should I overwrite the first 17 seg ids? or can I use a custom (CHOI_7 netwroks Look upTable? Im using FS5.1, as I would imagine FS5.2 may already do these by default, but there are bugs in that version from what I understand. I want to recreate the subcortically defined regions to the cortical functional scan. Thanks, Mario

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T2/FLAIR images longitudinal stream
by MCLAREN, Donald 08 May '13

08 May '13

Martin and others, As the T2/FLAIR image is only available for cross-sectional processing; if we are doing a longitudinal study, is there any advantage of using the T2/FLAIR image? Will the improved pial surface can transferred to the base and long surfaces? Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.

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version 5.2 white surface bug
by Luigi Angelo Maglanoc 08 May '13

08 May '13

Dear Freesurfer experts, I have recently read the thread about issues with version 5.2 concerning white surface and pial surface http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28340.html All of the structural data has been through the longitudinal processing stream using freesurfer version 5.2. I am wondering if it is sufficient to run recon-all -s <subjid> \ -white \ -autorecon3 \ -nosphere \ -nosurfreg for the base data and the final longitudinal data? Or do I have to rerun the whole longitudinal processing and redo any corrections that have been made? Thank you in advance! Sincerely Luigi Maglanoc

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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/

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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/

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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]

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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

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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/

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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.

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