Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30080 discussions

GE 3T protocol
by Kirk Gregory R. 02 Oct '08

02 Oct '08

Hi, can anyone suggest a 1mm isotropic T1 protocol they feel is fairly well optimized for freesurfer for a pre mr750 GE 3T scanner. seems Andre used to have such a list, or was it just for the siemens scanners. thankx Greg.

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Qdec cannot open a qcache file?
by hranilovich＠ucla.edu 02 Oct '08

02 Oct '08

I've been trying to get Qdec up and running for our lab. With some information from your help archives, I've managed to get it to accept our qdec.table.dat file and open the file, however, when I try to run the "Analyze" feature in the Design tab, I get the following ouptput, then error, and have hit a wall figuring out a way around it: Avg-Intercept-thickness ----------------------- Does the average thickness differ from zero? 1.000 1.000 0.000 0.000; Avg-thickness-LAMYG-Cor ----------------------- Does the correlation between thickness and LAMYG differ from zero? 0.000 0.000 1.000 1.000; Diff-1-0-Intercept-thickness ----------------------- Does the average thickness differ between 1 and 0? 1.000 -1.000 0.000 0.000; Diff-1-0-Cor-thickness-LAMYG ----------------------- Does the thickness--LAMYG correlation differ between 1 and 0? 0.000 0.000 1.000 -1.000; Error in Analyze: Couldn't open file /ifs/edevel/UCLA_SCAN/STRUCT_ANALYSES/JB_DAHL/SUBJECTS/FREESURFER_OUTPUTS/6002/surf/lh.thickness.fwhm10.fsaverage.mg I have attached the file in question. Is there something wrong with my qcache output? Opening it is not a permissions issue... Interestingly, I had the same problem when trying to run through the Qdec tutorial in the Variations on Design exercise, but only when I tried to choose my own Smoothing and Measure Morphometric attributes. Any suggestions are appreciated! Thanks, Jennifer Hranilovich

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surface map for animal
by Wang, Feng 02 Oct '08

02 Oct '08

Is anybody here has experience with generating surface maps for animal using freesurfer? Is it fine for you to share your protocol for doing this? Do we need to generate any template for segmentation on a specific animal? We collected 3D anatomical at 0.5x0.5x0.5 mm on varian 9.4T, could it handle data at this resolution? Your help is highly appreciated. Feng

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Default LGI settings
by Martin Kavec 02 Oct '08

02 Oct '08

Hi, I wonder how are the default FS settings to calculate LGI finetuned? More towards large-scale changes, such as in neonal>pediatric cortex, or would it be possible to study rather focal changes, say on a sulcus/gyrus level? Which parameters should I change to become sensitive to "smaller" LGI changes? Thanks a lot for input, Martin

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localGI exits with error
by j janssen 02 Oct '08

02 Oct '08

Hi, i am using version 4.0.5. for two brains out of a larger study, localGI exits with errors, the error message is similar in both brains and looks like: lGI for vertex number 49901 of the outer mesh is 1.9168 lGI for vertex number 50001 of the outer mesh is 2.4523 ratio saved at 50001 lGI for vertex number 50101 of the outer mesh is 3.2668 ... remeasuring lGI value for vertex iV = 50201. It may take a few minutes. WARNING -- Problem for vertex iV = 50201, lGI value is aberrantly high (lGI=43.3799)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface. mris_euler_number ?h.pial gives 0 defects. i ran localGI on both brains several times and got the same error message at the same vertex number (for lh). empirically, surfaces look reasonable. a similar message was posted some time ago: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07281.html but no reply. any ideas? thanks, -joost

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Remote display problems
by Julien Dubois 01 Oct '08

01 Oct '08

Dear freesurfer list I know similar problems have arisen before and I have read the archives. e.g. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07545.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07324.html however I'm still not sure how to solve my problem so here it is: tksurfer only displays a sliver of the brain (on my windows laptop with NoMachineNX viewer) it displays nothing using a xterm on a Mac G4. here's the output -bash-3.2$ tksurfer atm lh inflated surfer: current subjects dir: /local/jdubois/fMRIdata surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /local/jdubois/freesurfer surfer: Reading header info from /local/jdubois/fMRIdata/atm/mri/T1.mgz surfer: vertices=137024, faces=274044 Loading /opt/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: using interface /opt/freesurfer/lib/tcl/tksurfer.tcl Reading /opt/freesurfer/lib/tcl/tkm_common.tcl Reading /opt/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /opt/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /opt/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... tkmedit works fine however there's nothing in .xdebug_tksurfer Server specifications: Graphics card: ATI Rage XL (<http://ati.amd.com/products/server/ragexl/index.html>) GL library: mesa-libGL*-6.5.1-7.5.el5 It is noticeable that it used to work before an OS upgrade was done on the server. I have the same problem with 2 other servers (Dell PowerEdge with ATI RN50 according to Dell, which is apparently the same as ATI ES1000). Same GL library. WHAT CAN I TRY TO DO? - Julien

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Fwd: [Freesurfer] Fixing WM intensity normalization via control points
by John Sheppard 01 Oct '08

01 Oct '08

Hey Allison, I appreciate you getting back to me. Fortunately I figured out the problem. We have some strange issue with one of our lab computers (it's running Red Hat but we had problems with the FS rh9 distro so we were using CentOS version of FS), and basically it did not show the updated segmentation that had occurred after running autorecon2 (after adding control points). Instead it only showed the control points and the old segmentation. Pretty weird, but there's definitely issues with that computer because tksurfer does not work either. A grad student we work with noticed this discrepancy when he viewed the data on his own machine. So, I was fairly confident in what I was doing but totally confused with what I was seeing, hehe. Right now just trying to get better segmentations from sagittally acquired data and will be looking into FS-Fast for functional analysis -- previously we've used afni. Our segmentations have tended to work out much better with axially-acquired images, but we're getting there.. Anyway, thanks! John ---------- Forwarded message ---------- From: Allison Stevens <astevens(a)nmr.mgh.harvard.edu> Date: Oct 1, 2008 12:39 PM Subject: Re: [Freesurfer] Fixing WM intensity normalization via control points To: John Sheppard <johnsheppard2007(a)u.northwestern.edu> Did anyone answer these questions for you? On Wed, 24 Sep 2008, John Sheppard wrote: Hello, > > I have some basic questions with regards to adding control points to fix > the > WM intensity normalization. I am running some subjects through autorecon 1 > and 2 only (we are not concerned with subcortical structures). The > reconstructed volumes had a lot of missing grey matter in the lateral > temporal lobe, and my intention is to fix this by adding WM control points > (the intensity is also off for WM in places). Long story short, I have the > control points added and saved, and then I run the subjects through > recon-all autorecon2-cp. > > 1) Am I correct that autorecon3 will not be necessary if I am only > including > cortical structures? (I see it is included in the command line on the > control point tutorial.) > > 2) Once I run the subjects through autorecon2-cp, when I open them in > tkmedit the segmentation still has not changed - the control points are > still there as before. Do I need to run the subjects through some other > processing step before I will see the changes? (I am doing tkmdedit SUBJECT > brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white) > > 3) Based on the workflow in > http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction, it > seems > that control points need to be added directly after autorecon1. I am > actually adding the CPs on subjects that have gone through autorecon2 > already. Is this a problem or is it still possibe? (If a problem I can > reprocess the data.) > > Sorry if these are painfully obvious questions, but I seem to be slightly > confused with the processing pipeline. > > Much thanks, > > John Sheppard > >

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convert single-frame dicoms to a multi-frame dicom?
by Qianqian Fang 30 Sep '08

30 Sep '08

hi I know that mri_convert and a few other tools are able to convert a series of dicom files into a 4D (multi-frame?) nifti file. However, is there a way, either using freesurfer or other tools you know, can convert a the dicoms, or a 4D nifti, to a 4D (multi-frame) dicom? thanks Qianqian

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Volume processing question
by Tommaso De Marco 30 Sep '08

30 Sep '08

Hi, I'm a freesurfer user beginner. I need to discretize the gray matter in a cubic mesh. I have extracted the $h.pial and $h.white surfaces, and I would know if it is possible in freesurfer to discretize the volume suttended by these surfaces. I have seen that there are some files called $h.volume; what kind of information is stored in these files? Is it possible to open them in a matlab environment or with tksurfer? Regards Tommaso De Marco

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Re: Fwd: Talairach Failure Detection Help
by Marissa Gorlick 30 Sep '08

30 Sep '08

Hello Everyone, I have tried using both the original dicom files and the renamed brain voyager files and although it fixes the Talairach error for some subjects I keep getting the same error for others (I haven't noticed a pattern here). Error message: #@# Talairach Failure Detection Mon Sep 15 11:03:51 PDT 2008 /Applications/freesurfer/subjects/2824mm/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Darwin guest-wireless-207-151-243-073.usc.edu 8.11.1 Darwin Kernel Version 8.11.1: Wed Oct 10 18:23:28 PDT 2007; root:xnu-792.25.20~1/RELEASE_I386 i386 i386 Any idea what could be the cause? many thanks, Marissa On Wed, Aug 20, 2008 at 9:08 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > yes, try the original dicoms. And post these to the list so others can > answer! > > On Wed, 20 Aug 2008, Marissa Gorlick wrote: > > Hi Bruce, >> >> Thank you for helping me join the mailing list. >> >> My data is in DICOM format. I did change the names of the files using a >> brain voyager function before using freesurfer. Could that have >> eliminated >> the direction cosines from the files? >> >> Thanks again, >> >> Marissa >> >> On Tue, Aug 19, 2008 at 7:35 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu >> >wrote: >> >> Can someone help Marissa get on the FreeSurfer mailing list? Marissa: >>> what >>> format is your input data in? If it was analyze, then it probably does >>> not >>> contain the information necessary to orient the images properly so that >>> we >>> are failing to know which axis is front/back etc... You are *far* better >>> off >>> using a format that retains the direction cosines (such as dicom or >>> nifti). >>> >>> cheers, >>> Bruce >>> >>> >>> >>> On Tue, 19 Aug 2008, Marissa Gorlick wrote: >>> >>> Hello Freesurfer Owner, >>> >>>> >>>> I would like to post to your message board. I attempted to join the >>>> opensubscriber forum, however they never e-mailed me my activation code >>>> to >>>> confirm my e-mail address. I have registered freesurfer and received a >>>> licence (through my e-mail address mgorlick(a)usc.edu) Are there other >>>> steps >>>> I should take to become a part of the online freesurfer community? >>>> >>>> Many thanks, >>>> >>>> Marissa >>>> >>>> ---------- Forwarded message ---------- >>>> From: <freesurfer-owner(a)nmr.mgh.harvard.edu> >>>> Date: Tue, Aug 19, 2008 at 4:38 PM >>>> Subject: Talairach Failure Detection Help >>>> To: cosmiccarrot(a)gmail.com >>>> >>>> >>>> You are not allowed to post to this mailing list, and your message has >>>> been automatically rejected. If you think that your messages are >>>> being rejected in error, contact the mailing list owner at >>>> freesurfer-owner(a)nmr.mgh.harvard.edu. >>>> >>>> >>>> >>>> ---------- Forwarded message ---------- >>>> From: "Marissa Gorlick" <cosmiccarrot(a)gmail.com> >>>> To: freesurfer(a)nmr.mgh.harvard.edu >>>> Date: Tue, 19 Aug 2008 16:37:48 -0700 >>>> Subject: Talairach Failure Detection Help >>>> Hello Freesurfer team, >>>> >>>> My name is Marissa Gorlick and I am new to freesurfer. I am trying to >>>> do >>>> a >>>> cortical thickness analysis but I am having trouble processing my data. >>>> >>>> When I input the command: >>>> >>>> recon-all -s <subjid> -all >>>> >>>> The data processing begins for a few minutes and then spits out the >>>> error >>>> message: >>>> >>>> Tue Aug 19 16:18:54 PDT 2008 >>>> talairach_avi done >>>> #-------------------------------------------- >>>> #@# Talairach Failure Detection Tue Aug 19 16:18:54 PDT 2008 >>>> /Applications/freesurfer/subjects/part_2/mri >>>> \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n >>>> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm >>>> ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) >>>> Darwin ger341-macbk2.usc.edu 8.11.1 Darwin Kernel Version 8.11.1: Wed >>>> Oct >>>> 10 >>>> 18:23:28 PDT 2007; root:xnu-792.25.20~1/RELEASE_I386 i386 i386 >>>> >>>> recon-all exited with ERRORS at Tue Aug 19 16:18:55 PDT 2008 >>>> >>>> I looked in the opensubscriber forum and saw a recommendation to use >>>> the "Fixing >>>> Bad Output From the Talairach Registration" tutorial to remedy the >>>> error. >>>> Following the tutorial I ran: >>>> >>>> tkregister2 --mgz --s <subjid> --fstal >>>> >>>> The resulting output images look strange. The TARGET image has low >>>> contrast and can only be viewed in sagittal slices (which are, oddly, >>>> displayed by clicking the coronal button). >>>> The MOVEABLE view is stranger still displaying a very small squished >>>> blurry image of the brain. (see attached images) >>>> >>>> I would appreciate any advice you may have in how I should proceed >>>> with the analysis. >>>> >>>> Many thanks, >>>> >>>> Marissa Gorlick >>>> >>>> >>>> >>>> >>>> >> >> >> -- Marissa Gorlick Mather Lab Manager Phone: (213) 740 - 9543 Andrus Gerontology 3715 McClintock Ave. Los Angeles, CA 90089-0191

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