Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

Re: [Freesurfer] Correcting left-right flip for multiple subjects at the same timepoint
by Chiu, Bryan (PHTH) 26 Jun '14

26 Jun '14

The output brain is that which I see from freeview. I usually check their sulci and gyri to confirm if a scan is good. I resolved the issue by rerunning my PAR/REC files through the same dicom to nifiti converter for all of them. It turns out the person before me used a different tool which resulted in incongruent scans of the same participant through multiple timepoints. Thanks, - Bryan

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Qdec Annotation to Individual
by Tara Ann Miskovich 26 Jun '14

26 Jun '14

Hello, I was hoping someone could help me map with mapping my annotation from my significant qdec clusters into each individual space. Thanks! Tara Tara A. Miskovich, B.A. Affective Neuroscience Laboratory Department of Psychology University of Wisconsin-Milwaukee 334 Garland Hall miskovi2(a)uwm.edu

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mri_segstats question
by Martins, Brad 26 Jun '14

26 Jun '14

Hi everyone, I’m new to Freesurfer and I have a question about the output of mri_segstats. I have created an ROI in which I am measuring cortical thickness. When I run mri_segstats I get a table with 2 rows of segmentation values. What are the 2 rows? The SegId of the two rows are 0 and 1 but I don’t know what segmentations that corresponds to or where to find out. Any help would be greatly appreciated! Thanks, Brad

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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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