Freesurfer October 2012

freesurfer@nmr.mgh.harvard.edu

119 participants
191 discussions

Talairach Failure Detection
by Daniel Ferreira 17 Oct '12

17 Oct '12

Dear experts, Please, I'm getting the Talairach Failure Detection problem in one of my subjects (message enclosed below). I tried to follow the tutorial to fix a bad Talairach with: 1) tkregister2 --mgz -s <id> --fstal --> not green lines appear, I attach a screenshot. Both the standard and my MRI are slided down to the bottom of the window. See also attached tkmedit file. 2) Anyway, I tried also -notal-check to see if something changed in spite Talairach failed, but it fails also (off course). 3) I used -use-mritotal but I still get the same. However, this time processing finishes without errors, but my MRI is still at the bottom of the window and output cut all what is between middle temporal regions and neck. Please, any idea? Thanks a lot Daniel #@# Talairach Failure Detection Wed Oct 10 09:08:27 CEST 2012 /home/daniel/FreeSurfer/subjects/N001511_d2/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux siv 2.6.32-33-generic #72-Ubuntu SMP Fri Jul 29 21:07:13 UTC 2011 x86_64 GNU/Linux recon-all -s N001511_d2 exited with ERRORS at Wed Oct 10 09:08:27 CEST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Changes to Sub-cortical Structures after adding WM control points
by Mark Fletcher 17 Oct '12

17 Oct '12

Dear FreeSurfers, After adding WMCP to a number of my subjects (which corrected the problem), I retrieved to cortical and subcortical volumes from my subjects using the "aparcstats2table". I had used "aparcstats2table" before and after adding the control points. Accurately, the regions I wanted to change, did change in volume. However, the subcortical volumes post WMCP changed a lot as well? Some regions changed more than 20% after adding WMCP to other regions? Is this normal? Should I go with the original "subcortical" segmentation volumes, or the new ones? Is this part of the known bug in version 5.1.0 mentioned in the release notes about "running recon-all" a second time? Please advise? Sincerely , Mark Fletcher

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Supratentorial volume vs brain segmentation volume
by Kwan, Justin 17 Oct '12

17 Oct '12

Dear Freesurfer experts, What is the difference between the supratentorial volume and brain segmentation volume? Does the supratentorial volume include CSF and ventricle volume? Thank you very much for your help. Best, Justin Justin Kwan, MD Assistant Professor Department of Neurology University of Maryland School of Medicine 110 South Paca Street, 3rd Floor Baltimore, MD 21201

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Functional labels from freesurfer
by ffmpeg ffmpeg 17 Oct '12

17 Oct '12

Hello! I was told that Freesurfer should generate labels for functional areas of the brain (for example, visual zones - V1, V2, etc.) when doing reconstruction (recon-all -autorecon-all). But the the label/ directory in output contains only these files: aparc.annot.a2009s.ctab aparc.annot.ctab lh.aparc.a2009s.annot lh.aparc.annot lh.cortex.label rh.aparc.a2009s.annot rh.aparc.annot rh.cortex.label which contain only anatomical labels. What could be wrong? If freesurfer does not generate those labels, is there some way to obtain them? (Obviously, I could create such labels by hand, but the result would be probably messy and imprecise.) Best wishes, Platon Pronko

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Problem with cortical GM vol (complete)
by Gabriel Gonzalez Escamilla 17 Oct '12

17 Oct '12

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Problem with cortical GM vol
by Gabriel Gonzalez Escamilla 17 Oct '12

17 Oct '12

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Re: [Freesurfer] DODS and group age interaction
by MAHINDA YOGARAJAH 17 Oct '12

17 Oct '12

Dear Doug, Many thanks for reply. Given the age-group interaction, and the fact that even when age is demeaned it simply means a difference in thickness will be tested for at age=mean age (as opposed to age=0) can I at least interpret the findings when using DODS model with age as a nuisance factor by saying that the difference in thickness between groups represents the difference between groups at the mean age across both groups. Beyond that limited interpretation, is there any other way to analyse the data ? Is there a another model I could use ? My age-group interactions are in a different location to the group differences - does this make any interpretation of group differences more robust ? Thanks. Mahinda

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Re: [Freesurfer] Control point edits adversely affect cortical surfaces using FS 5.1
by Vanessa Louise Cropley 16 Oct '12

16 Oct '12

Dear Bruce/freesurfer community, Thank-you for offering to take a look at our data. I have uploaded two files to the ftp. They are called Subject_Before_CP.zip and Subject_After_Cpedit.zip. Please let me know if you haven't received them. I uploaded these last Friday but haven't as yet had a reply. I did this as a test as I assumed that a single ctrl point in WM would have no effect on the surfaces. The 1 ctrl point was added to the LH WM in temporal cortex (slice 120). Thank-you for your help, it would be great if we could find a solution to this problem. - Vanessa On 12/10/12 1:24 AM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Vanessa > > if you can upload an example (the entire subject dir) before adding the > single control point you refer to, and after adding it we'll track it down. > > thanks > Bruce > > > > On Thu, 11 Oct 2012, Vanessa Louise Cropley wrote: > >> Hi all, >> >> I have seen others post a similar problem on the freesurfer mailing list but >> I could not find a solution. >> >> When I edit a volume using control points, I am noticing that the use of CP >> edits adversely effects the wm/gm surfaces in the resulting re-processed >> image. Like others have reported, the surfaces are adversely affected in >> locations distant from the CP edits. The temporal lobes are particularly >> affected. >> >> We are using freesurfer 5.1. >> I have noticed the following things: >> >> 1. The problem occurs irrespective of the number of control points added, >> i.e. whether >100 or <10 control points added >> 2. The problem occurred when only one CP was added in a voxel that was >> clearly wm >> 3. The problem did not occur after reprocessing with FS 4.5 >> 4. I have tried the flag to disable mri_ca_normalize when reprocessing with >> ?autorecon2. This did not seem to help. I used the command: recon-all >> ?nocanorm ?autorecon2-cp ?subjid $SUBJ >> >> I have screenshots available that illustrate the changes in the surfaces >> after reprocessing. >> >> Could anyone help with this problem? >> >> Thank-you, >> >> Vanessa >> > _______________________________________________ > 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. > > ------ End of Forwarded Message

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DODS and group age interaction
by Mahinda Yogarajah 16 Oct '12

16 Oct '12

Dear Experts, I have 2 groups - controls (22 subjects) and patients (19 subjects) with mean ages that are not significantly different, though ranges/median are. I want to compare cortical thickness between groups while allowing for age (age as nuisance factor) but also want to see if there is an interaction between age and group (age as continuous variable). I have demeaned the age across both controls and patients and then used qdec. 1) Using DODS and demeaned ages I find that there is an age-gp interaction such that patients have quicker thickness decline with age than controls. This survives FDR 0.05 and monte carlo VWP 0.005 CWP 0.05. Is this finding valid given that I used demeaned ages (rather than absolute ages) to look for interaction or does it make no difference ? 2) When I come to look to see whether there is a gp difference in thickness I enter age as a nuisance variable in qdec (as opposed to continuous variable above) and use DODS with demeaned age variable across gp. Am I safe to interpret my findings normally given age-gp interaction or is is not safe - if it is not safe how can I look for gp differences or it ok to interpret results provided gp differences are not in regions where I see an interaction ? Thanks. Mahinda

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Re: [Freesurfer] Freesurfer 1mm Isotropic standard and the Future
by Joshua Lee 16 Oct '12

16 Oct '12

Hi Everyone, Back in May I was very excited to learn that there was some movement toward allowing Freesurfer to utilize the higher than 1mm iso. resolutions of some of our structural images, which could be fantastic help in subcortical segmentations. Is this something that is still in the works for the next release? gratefully, Joshua - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805 On Thu, May 31, 2012 at 5:49 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Joshua > > sorry, I haven't found the time to really work on it. I spent a couple of > hours and found some problems, but haven't found the time to fix them > > Bruce > > On Thu, 31 May 2012, Joshua Lee wrote: > > Hi Bruce, >> >> I'm just checking in to see how it turned out with the subcortical >> segmentation using the high resolution images I sent. >> Best, >> >> Joshua >> >> >> >> >> >> >> - >> Joshua Lee >> Graduate Student >> Center for Mind and Brain & >> Department of Psychology >> University of California, Davis >> 530.747.3805 >> >> >> On Tue, May 15, 2012 at 5:29 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu >> > >> wrote: >> you need to call mris_make_surfaces directly. It's a bit >> complicated as you need to intensity normalize and register the >> hires volume to the surfaces first. I have an example script if >> anyone is interested, but no one has used it yet but me I don't >> think (unless Matt Glasser has gotten his version working, which >> on second thought he probably has) >> >> On Mon, 14 May 2012, Michael Waskom wrote: >> >> Hi Bruce, >> Is there a flag for this on recon-all? áOr do you >> >> need to use >> mri_make_surfaces directly? >> >> Best, >> Michael >> >> On Mon, May 14, 2012 at 2:09 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> á á áHi Joshua >> >> á á áyes, we already have upgraded >> mris_make_surfaces to take higher >> á á áres data >> á á áand refine the surfaces with it. Haven't tried >> it on the aseg >> á á áyet, but if >> á á áyou upload a sample dataset I could see how >> hard it is. >> >> á á ácheers >> á á áBruce >> á á áOn Mon, 14 May 2012, >> á á áJoshua Lee wrote: >> >> á á á> Dear Freesurfers, >> á á á> >> á á á> Over the last years, MR imaging technology >> hasimproved such >> á á áthat sub 1-mm >> á á á> isotropic scans can be obtained with good >> signal to noise >> á á ácharacteristics. >> á á á> For example, our lab uses 0.7mm isotropic >> structural MR >> á á áimages. I understand >> á á á> that the Freesurfer pipeline will up-sample >> these to 1mm >> á á áisotropic, but it >> á á á> seems a shame that so much information is >> left unused which >> á á ácould be used to >> á á á> improve the accuracy of sub-cortical and >> cortical >> á á ásegmentation. My question >> á á á> is whether there are any plans at Freesurfer >> to change the >> á á áreference >> á á á> standard resolution from 1mm isotropic, or >> provide another >> á á ásolution that can >> á á á> help researchers make the most of your >> technology. >> á á á> >> á á á> Sincerely, >> á á á> >> á á á> >> á á á> Joshua >> á á á> - >> á á á> Joshua >> á á á> >> á á á> >> á á á> >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** >> freesurfer <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<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<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<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. >> >> >> >>

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Freesurfer October 2012