Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30083 discussions

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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Subject Averaging
by Richard Frye 30 Sep '08

30 Sep '08

Is there any documentation regarding the specifics of the process of subject averaging. Specifically, I am unclear on how the parcellation and cortical thickness is derived for the average subject. Is this information averaged from the input subjects or is it derived from the newly formed average volumes and surfaces? Thanks Rich -- Best Wishes, Richard E. Frye, M.D., Ph.D., F.A.A.P. Assistant Professor of Pediatrics and Neurology University of Texas Medical School at Houston 7000 Fannin -- UCT 2478 Houston, TX 77030 Office: 713-500-3245 e-mail: richard.frye(a)gmail.com

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About the morphing parameters
by jorge luis 29 Sep '08

29 Sep '08

Hello all I would like to know the values of the metric distortion and deformation parameters (of the spherical registration algorithm) when creating an average subject and when registering the underlying population to the previous average. That is to say: What is the difference in the spherical morphing between the creation of the average subject and the alignment of the individual subjects to that average? In advance thank you Jorge Luis Bernal Rusiel Phd Student Laboratory of Functional Neuroscience University of Pablo de Olavide Seville.Spain

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Error in recon-all -long on Linux
by Juergen Haenggi 26 Sep '08

26 Sep '08

Dear FS experts I run recon-all -long on a MacIntel Leopard and everything worked fine. When using the recon-all -long command on a Linux Machine (CentOS 32 bit) it runs untill the end ("recon-all finished without an error"), but there is an error.log file that is about 2 GB in size and it is too large to open. But I recognized an odd behaviour never seen before (see attachment). This behaviour lasted for minimum half an hour and maybe is responsible for the larger error.log file. Please help Thanks a lot Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

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which computer/server to buy?
by Narly A Golestani 26 Sep '08

26 Sep '08

Dear all, I see from previous posts to the list that it is possible to use servers to run freesurfer. I'm in the process of selecting a machine, and would appreciate any input anyone might have on which machine is optimal. In particular I'm concerned about eventual problems described on the mailing list earlier this month (see thread pasted below), regarding the ES1000 chipset that apparently comes with Dell PowerEdge servers (I am no expert with hardware issues such as these so this is all new to me!). Does this chipset come with all of these types of servers, or is it possible to order one with an NVIDIA card installed? Are there better alternatives wrt to which machine to purchase? thanks in advance for any input you might have, best, Narly. Re: [Freesurfer] tksurfer woes Mark J. Pearrow Fri, 12 Sep 2008 12:52:02 -0700 Hi all, FYI, this same problem has been bugging me for several months. Most ATI chipsets have a nice driver installer bundle that, once installed, will let you run tksurfer without a problem. However, this particular chipset, the ES1000, which is the chipset on Dell PowerEdge servers, is unsupported and seems to have been abandoned by ATI/AMD/whoever they are this week. If you happen to be unlucky enough to have Dell PowerEdge servers with this chipset and the need to run tksurfer, you're out of luck, until you put a slightly "better" graphics card in. I just managed to install an nVidia 8400GS (the x1 PCI-e version - the poweredge PCI-e bus is x8, which means it won't work with any of the most recent cards, but will work with slightly older x1 cards) and tksurfer works fine now. I can provide the gory details if you're in this boat. mjp On Sep 8, 2008, at 9:14 AM, Hoptman, Matthew wrote: Hi all, Im having trouble using freesurfers tksurfer program (I only get a sliver of the brain). Here is the error info I get: [ghidra: subjects]$ tksurfer 77059 lh pial surfer: current subjects dir: /home/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/freesurfer/subjects surfer: Reading header info from /home/freesurfer/subjects/77059/mri/ T1.mgz surfer: vertices=184362, faces=368720 Loading /home/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(77059) surfer: using interface /home/freesurfer/lib/tcl/tksurfer.tcl Reading /home/freesurfer/lib/tcl/tkm_common.tcl Reading /home/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... The driver info (from /etc/X11/xorg.conf) is: Section "Device" BoardName "ES1000 515E" BusID "14:13:0" Driver "radeon" Identifier "Device[0]" Option "GARTSize" "32" Option "usevnc" "yes" Section "DRI" Group "video" Mode 0660 EndSection Im have an onboard ATI ES1000 515E graphics chip. Any ideas?? Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e- mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ==================================== Narly Golestani Institute of Cognitive Neuroscience 17 Queen Square London WC1N 3AR United Kingdom Tel: +44 (0)20 7679 7529 ====================================

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Freesurfer Command in Matlab
by Yigal Agam 25 Sep '08

25 Sep '08

Hi, I'm trying to run the following command in through matlab: system(['mri_surf2surf --srcsubject average7 --trgsubject average7 --srcsurfval /space/schnook/1/users/yigal/projects/dti/data/old_recons/results/control_vs_sch_rh_average7_2mm_ttest.mgz --trgsurfval /space/schnook/1/users/yigal/projects/dti/data/old_recons/results/control_vs_sch_rh_average7_2mm_ttest.mgz --hemi rh --nsmooth-out 3']) And get the following error message mri_surf2surf: /usr/pubsw/common/matlab/7.4/sys/os/glnxa64/libgcc_s.so.1: version `GCC_4.2.0' not found (required by /usr/lib64/libstdc++.so.6) When I run the command from a terminal window, there's no problem. Any ideas? Thanks, Yigal

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mri_convert: DICOM to nifti - multiple frames
by Watson, Christopher 25 Sep '08

25 Sep '08

Hi, I'm interested in getting multiple nifti images for each time point, similar to this old thread: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03317.html i.e., for a scan of 5 minutes and TR = 3, I would like 100 separate nifti images. This works fine when I set --out_type spm, but I'd like to start using the nifti format. The command I use: mri_convert.x86_64.dev -dicomread2 i545236.MRDC.1 -ot nifti1 "$SUBJ_DIR/image" only creates one file - image.nii. Is there a newer version of mri_convert that can do what I'm looking for? Here's the info: $./mri_convert.x86_64.dev --all-info ProgramName: mri_convert.x86_64.dev ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2008/09/25-14:47:29-GMT BuildTimeStamp: Jun 15 2007 11:06:50 CVS: $Id: mri_convert.c,v 1.144 2007/06/14 03:18:56 greve Exp $ User: matlab7 Machine: occipital Platform: Linux PlatformVersion: 2.6.9-55.0.6.ELsmp CompilerName: GCC CompilerVersion: 30300 Thanks, Chris

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-normalization error
by Jeff Sadino 24 Sep '08

24 Sep '08

Hello all, I am receiving an error when trying to run autorecon1. When trying to step through it manually step-by-step, everything is fine up to -nuintensitycor. After running that command and looking at nu.mgz in tkmedit, the picture starts to fade out pretty bad above 120 intensity. When I lower the intensity down to about 30, I can see the picture just fine. Next, I skip -talairach (even though and run -normalization. But it exits with an error: [FSuser@cluster mri]$ recon-all -s 070046_S01 -normalization INFO: SUBJECTS_DIR is /data Actual FREESURFER_HOME /apps/freesurfer -rw-rw-r-- 1 FSuser FSuser 90352 Sep 24 16:10 /data/070046_S01/scripts/recon-all.log Linux cluster.mrilab.net 2.6.9-55.0.2.ELsmp #1 SMP Tue Jun 26 14:14:47 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# Intensity Normalization Wed Sep 24 16:15:19 HST 2008 /data/070046_S01/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize: could not find any valid peaks mri_normalize: normalization failed Linux cluster.mrilab.net 2.6.9-55.0.2.ELsmp #1 SMP Tue Jun 26 14:14:47 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Sep 24 16:15:21 HST 2008 Also, I have some of the -talairach files from a previous run: [FSuser@cluster mri]$ ls transforms/ bak talairach.auto.xfm talairach.log talairach.xfm Any ideas? Thank you. Jeff _________________________________________________________________ Get more out of the Web. Learn 10 hidden secrets of Windows Live. http://windowslive.com/connect/post/jamiethomson.spaces.live.com-Blog-cns!5…

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