Freesurfer June 2014

freesurfer@nmr.mgh.harvard.edu

155 participants
234 discussions

interpreting qdec results
by Emma Thompson 26 Jun '14

26 Jun '14

Hi Freesurfers, I am reposting this as my last email bounced. I have conducted a DODS analysis in qdec with group (controls vs patients) set as my fixed factor and age as a nuisance variable to determine if my groups differ in cortical thickness. Controls were added first in the .levels file followed by patients. When I view the results in the display window for "do controls differ from patients in cortical thickness" I see a significant cluster for the caudal anterior cingulate, denoted by a red-orange blob and a positive t-value. I'm wondering if this simply means that controls had greater cortical thickness compared to patients after controlling for age? The reason I ask is that I'm a little confused since when I created an ROI for this cluster using tksurfer and then extracted the means and sd, I see that the patients actually have larger means than the controls, the opposite of my interpretation of the results presented by the qdec display. Furthermore, if I extract the means and sds for the entire caudal anterior cingulate using the aparc file, I get means that are larger in controls, compared to patients, which seems consistent with qdec. Any ideas? Thanks for all the help.

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free surfer
by Sam Raby 26 Jun '14

26 Jun '14

I have downloaded the following file freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz and have extracted the contained files, and I was wondering where the binary file is so that I can open the freesurfer with? <https://surfer.nmr.mgh.harvard.edu/fswiki/QuickInstall> thanks -S

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meaning of foldind
by kangchengwang0808＠gmail.com 25 Jun '14

25 Jun '14

Dear experts, In the Group stats files, there is a file of lh.a2009s.foldind (or rh.a2009s.foldind). What's the meaning of foldind? Thank you Wang Kangcheng

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Post-Doctoral fellowship available at University of California San Francisco Memory & Aging Center
by Rabinovici, Gil 25 Jun '14

25 Jun '14

Seeking a highly motivated and energetic post-doctoral fellow interested in applying multi-modal neuroimaging to improve diagnostic accuracy and study mechanisms that drive clinical and anatomic heterogeneity in Alzheimer's disease, frontotemporal dementia and related disorders. Imaging techniques acquired include structural MRI, functional connectivity ("resting-state") MRI, DTI, amyloid PET and Tau PET. Candidates must have an MD and/or PhD in Neuroscience related field. Strong quantitative skills and statistical knowledge are a pre-requisite. Previous neuroimaging research experience and programming knowledge are preferred but not required. Interested candidates should send a CV and cover letter to the PI: Gil Rabinovici, MD Associate Professor of Neurology UCSF Memory & Aging Center Email: grabinovici(a)memory.ucsf.edu<mailto:grabinovici@memory.ucsf.edu> http://memory.ucsf.edu/ourcenter/staff/grabinovici

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control points - voxels in wm mask being ignored
by Elissa McIntosh 25 Jun '14

25 Jun '14

Hello freesurfer experts, I have a question. I think some of the gray matter is being underestimated and some white matter isn't being classified in particular areas. I went to add control points and I noticed that sometimes the places I want to put control points in have voxels there in the wm.mgz mask. What does it mean when this happens? Should I still add control points or leave it alone? I've attached an example. Thank you!

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trac-all error (segmentation fault?)
by Durai Arasan 25 Jun '14

25 Jun '14

Hi Freesurfer experts, I tried running trac-all with my config file and received the following error : Segmentation fault Linux 129-x-xx-xxx 3.4.33-2.24-desktop #1 SMP PREEMPT Tue Feb 26 03:34:33 UTC 2013 (5f00a32) x86_64 x86_64 x86_64 GNU/Linux trac-paths exited with ERRORS at Tue Jun 24 11:15:12 EDT 2014 Any help would be greatly appreciated! I am attaching the config file, log and error files. Thank you! Durai

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editing aseg
by Andrea Horváth 25 Jun '14

25 Jun '14

Dear All, After running recon-all and checked all the required steps, some part of the right cerebral white matter was still segmented as right cerebral cortex in the aseg.mgz as seen in the attached pictures (red cross). I would like to edit these two labels in aseg which is OK, but how can I get the correct values in the aseg.stats file? Thank you for your help! Andrea [image: Szövegközi kép 4][image: Szövegközi kép 3]

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hippocampal subfields in young subjects
by Joana Braga Pereira 25 Jun '14

25 Jun '14

Dear all, I'm running the GEMS tool in Freesurfer 5.3 to measure the volumes of hippocampal subfields in subjects between 9 and 14 years of age with 3T T1-weighted MRI scans. I noticed that a blackline is consistently drawn around the surface of the subfields (see attached figure) and was wondering whether this is normal. Since the tool has not been validated in young subjects I would like to know if the black line observed in the figure shows that the segmentation has not been carried out correctly. Any help will be greatly appreciated. Many thanks, Joana

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Extracting the individual or average cortical thickness value of significant cluster after multiple compression correction by FDR.
by Santosh Yadav 25 Jun '14

25 Jun '14

Dear FreeSurfer Experts: I have question regarding extracting the individual or average cortical thickness value of significant cluster after multiple compression correction by FDR. For example I have 100s of subjects in an analysis and several blobs showing significant difference between groups after FDR, how do I export mean or individual subjects cortical thickness values for significant blob? I can click on each data point and copy the terminal readout or create an ROI, map label to subjects and export it out but both approaches are time consuming and prone to human error. Is there a way of using existing QDEC setup files to export all this data out more cleanly? With best Regards, Santosh

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group comparison issue
by melinda dora 25 Jun '14

25 Jun '14

Dear list, I have a question re group comparisons. I have one group factor with three levels. I have done group-wise comparisons with these groups using qdec (ie doing pairwise comparisons, as it only allows group comparisons between two groups as far as I am aware?) as well as using mri glm fit, specifying the contrast as 1 0 -1 to compare two groups without the effect of the other third group being included. I have found that I get different results for these two methods; using mriglmfit I get no vertices surviving multiple comparisons, whilst I get several using qdec. Could this be because of the differences in using FDR/monte carlo simulation or does it point towards a bigger problem, for example me doing something wrong at some stage? Or is there another explanation? Very grateful for prompt response and help, Cheers, Melinda

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Freesurfer June 2014