Freesurfer May 2013

freesurfer@nmr.mgh.harvard.edu

174 participants
299 discussions

Working with MEMPRAGE
by Jonathan Holt 09 May '13

09 May '13

Hi all, combed through the mail archives to figure out how to work with multi echo mprage, found what I need but I wanted to confirm which of these two commands is the appropriate mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? jon

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Labels and parcellations
by Tudor Popescu 09 May '13

09 May '13

Hello all, I have some more burning questions, for which I thank you in advance!! 1) I expected that "mri_annotation2label --subject 01 --hemi lh --outdir $SUBJECTS_DIR/myLabels" would give me labels corresponding to structures of the standard FreeSurfer atlas (Destrieux), instead it produced labels with completely different names, e.g. "lh.postcentral.label" instead of the Destrieux name "lh_S_postcentral". Exactly how different are they, and which ones should be used in mri_glmfit for ROI analyses? 2) Does it make sense to use mri_glmfit with volumetric masks, or should it only be used with labels? 3) Say I want to do a ROI analysis for a particular brain structure; how much is there to gain by manually (visually) creating a label/mask for that structure in each subject (i.e. taking into account individual anatomy), as opposed to just using an atlas to create a single label/mask for use with all subjects? 4) I used the command "tkmedit 01 aparc+aseg.mgz" (I also tried adding " -aux brainmask.mgz -surfs –aseg"), thinking that it would display an image like this<http://brainybehavior.com/neuroimaging/wp-content/uploads/2010/05/jt_rh_pia…>, i.e. with all the main cortical structures displayed in different colours. Does aparc+aseg.mgz not contain all the necessary information to produce such an image? 5) Which mask file corresponds to the brain extraction procedure of recon-all? I see that a subject's /mri/brainmask.mgz is not a binary map, as expectd, but instead a BETted (skull-stripped) version of that subject's structural. Thank you so much for your help! Tudor

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Qdec error and design problem
by Sinead Kelly 09 May '13

09 May '13

Dear all, I am trying to run statistical analysis on cortical thickness data using Qdec. I have one group of control subjects that are split into three genotype groups. I want to investigate if cortical thickness significantly between the three genotype groups. Is it possible to look at differences between three groups using Qdec? I am getting the following error when I try to analyse - ERROR: QdecGlmDesign::Create: zero factors! I would really appreciate if anyone could shed some light on this for me as this is the first time I have used Qdec and I don't know what is causing this error. Thank you for your help. Sinead -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8

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Why does smoothing make non-zero intensity to zero in many vertices?
by Glen Lee 08 May '13

08 May '13

Hello freesurfer experts, I'm a newbie for freesurfer and would like to ask a naive question. I've just applied smoothing onto a single surface mgh file using mri_surf2surf (with fwhm ==4) and examined the values in the output map. As it turns out, values become 0 in a number of vertices after smoothing while those in many other vertices look normal (i.e., more or less similar to the values in the vertex of unsmoothed map). I'm not sure why this happened as smoothing average values locally within the kernel (4mm). Any helpful answers would be greatly appreciated. Glen p.s) fyi, the original EPI is a slap data covering only the temporal & occipital cortex.

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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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Freesurfer May 2013