Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

memory error and WM edits
by Mishkin Derakhshan 10 Sep '10

10 Sep '10

Hi, Like others on the list I got the ran out of memory error, which seems to be the result of a gross error somewhere: CORRECTING DEFECT 1 (vertices=109084, convex hull=14490) Excessive topologic defect encountered: could not allocate 649386741 edges for retessellation Cannot allocate memory Linux bach 2.6.24-27-server #1 SMP Fri Mar 12 01:23:09 UTC 2010 x86_64 GNU/Linux recon-all -s freesurfer_results exited with ERRORS at Thu Sep 9 22:15:45 EDT 2010 Anyway, it looks like my skull strip is okay (attached brainmask.jpg), but my wm.mgz and thus my filled.mgz files are where I have the gross errors. It looks like a lot of WM voxels are missing, and not just due to lesions. My questions is, should I just fix the WM using this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits, or is this a problem at the normalization step, or is there something else I can try? thanks, mishkin p.s i tired using 4.5.0 and 5.0.0

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Symbol to indicate a missing value for a discrete variable in a qdec data table
by Robustelli, Briana (NIH/NIMH) [F] 09 Sep '10

09 Sep '10

Hello, I am new to freesurfer and have created a qdec data table but have a few missing data points for a discrete variable. When using a continuous variable placeholder zeros are used. What should be typed into the table to indicate a data point is missing for a discrete variable? Thank you. Briana

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setting segmentation brush information from command line in tkmedit
by Mehul Sampat 08 Sep '10

08 Sep '10

Hi Folks, Currently I set the "segmentation brush information" from tkmedit buttons. (For example: Set Segmentation as Use as source and also set the color) I need to do this for a large number of subjects and I was wondering if it was possible to do this from command line ? thanks Mehul

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tksurfer problems
by ckung 08 Sep '10

08 Sep '10

Dear all: I installed Freesurfer, tested it with the recommended commands listed in http://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer and encountered a problem only in tksurfer. When I hit tksurfer yc (or bert) lh pial I get two kinds of error messages: can't find talairach file '/Volumes/Sophomore/ncku_KMU_fMRI/surfaces/yc/surf/../mri/orig/COR-.info/../transforms/talairach.xfm' surfer: single buffered window surfer: tkoInitWindow(yc) surfer: using interface /Applications/freesurfer/lib/tcl/tksurfer.new.tcl Error sourcing /Applications/freesurfer/lib/tcl/tksurfer.new.tcl: can't read "env(MRI_DIR)": no such variable I found both problems have been asked before (one at http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg02372.html another http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00029.html and I tried to mimic the solution provided, but no luck so far. The problem persists. So I wonder if gurus in this forum might be kind enough to suggest some directions? I was baffled by this "small" problems for almost 1 week, so.... many thanks, chun-chia p.s., I checked the .xdebug_tksurfer returned empty files, and I am not sure where is the log file located...

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amygdala segmentation
by Karen E Murphy 08 Sep '10

08 Sep '10

Does anyone know whether subcortical segmentation of the amygdala includes the "extended amygdala" (i.e. bed nucleus of the stria terminalis)? Thanks, Karen Karen Blackmon, Ph.D. Clinical Coordinator New York University Department of Psychology email: keb217(a)nyu.edu phone: 646-302-4466

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adding control points
by Paola Valsasina 08 Sep '10

08 Sep '10

Dear FS experts, we have run autorecon2 on a set of subjects and now we are in the process of manual editing adding control points. We read the tutorial about the manual editing; however, sometimes we have some doubts about adding or not adding control points in some regions. We had a look at the subject "bert" (included in FS distribution) to have a reference on what can be considered a "good" output and what is necessary to be edited. Can this subject be considered as a good one and used as reference, or do you have any additional reference subjects to look at? Thank you in advance Kind regards, Paola ------------------------------------------------------------- DAI IL TUO 5 X MILLE AL SAN RAFFAELE. BASTA UNA FIRMA. SE FIRMI PER LA RICERCA SANITARIA DEL SAN RAFFAELE DI MILANO, FIRMI PER TUTTI. C.F. 03 06 42 80 153 INFO: 5permille(a)hsr.it - www.5xmille.org

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issues about pial and wm edit
by Daniel Ferreira Padilla 08 Sep '10

08 Sep '10

Dear all, I will really appreciate if you can help me with some issues about editing the pial surface. I have carefully followed the information on the web and looked up the mailing list but I still have the same doubts: 1) I have noticed that pial surface usually includes more than GM (dura, vessels...). My first question is if should we edit this kind of error. Sometimes I am completely sure what I need to correct, but I don't want to put human error in it. Moreover, we will spend to much time with big samples. 2) I have tried to edit the pial surface following the tutorial. After re-running -autorecon2-pial nothing seems to change. The voxels I deleted before are still there and the pial surface looks the same. What could be happening? 3) I have had the same problem with WM edit. After -autorecon2-wm everything remain as before edit. 4) I have read about regenerate the new pial surface with "make_final_surfaces" or from inside recon-all with -finalsurfs. The command could be something like this? recon-all -s <mysubjectname> -finalsurfs 5) If I need to fix pial and wm lesions in the same subject, do I need to run autorecon2-pial and -autorecon2-wm separately? Can I do it at the same time? And if I could, what command do I have to use? I hope these are not too much questions. Thank you very much in advance. Daniel Ferreira

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Longitudinal pial editing
by Derin Cobia 07 Sep '10

07 Sep '10

Based on our understanding of the longitudinal pipeline for 4.5, image edits for the -long runs come mostly from the template/base subj (with an optional flag for CPs to be copied from the template; http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg13256.html, http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12895.html) In addition, our assumption is that pial edits will come via the template, as the -long brainmask, is a result of masking the -long T1.mgz by the template brainmask.mgz (which itself is the norm_template.mgz, a combination of every time point's norm.mgz [which is pre-edit stage]). We've run into an issue where our -long runs are still in need of pial editing, despite edits having been done to both the cross sectional and template runs (see attached). However, it's also our understanding that we should not edit the -long runs and try to re-run (using -autorecon2-pial -autorecon3), as this will pollute the correction for intrasubject variation (per communication from Martin). How would you recommend to proceed? Thanks. -Derin

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Saving multiple control points
by Musen, Gail 07 Sep '10

07 Sep '10

Hi, We have been trying to replicate the manual cortical surface-volume tracing method for the enthorinal cortex described in Feczko et al. (2009) and Dickerson et al. (2009). In this method, points selected on the coronal MRI slices (in the tkmedit) are matched to points along the surface of the reconstructed cortical surface model (in tksurfer). These points are used to define anatomical landmarks and they serve as connection points in the surface volume for tracing. We are running into problems with loading multiple control points on the surface volume. That is, when we place control points on the MRI data and then Go To Saved Point in the surface volume then we only get a single most recent placed point while the other points specified in the MRI slice are "lost". Is there a way we can load all these points simultaneously on the surface so that we can demarcate borders as described in these papers? Thanks -Gail Musen

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new rawavg in fs5 and reprocessing
by k.b.walhovd＠psykologi.uio.no 07 Sep '10

07 Sep '10

Hi, I see there's a new motion correction procedure in fs5, meaning that the rawavg is created differently. When reprocessing data, should we then do everything over, including remaking the rawavg and all edits? I'm asking esp. w/ regards to edits - can they possibly be slightly wrong if kept? And with regard to reprocessing data that have been run w/ the previous versions together with data that have not been previously processed- will such a mix be problematic? I'd highly appreciate your recommendations! Best, Kristine -- Kristine B Walhovd Professor University of Oslo Center for the Study of Human Cognition Department of Psychology PB 1094 Blindern 0317 Oslo Norway

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