Freesurfer October 2008

freesurfer@nmr.mgh.harvard.edu

71 participants
110 discussions

Re: [Freesurfer] Error with mri_convert failing to write orig/001.mgz
by John Sheppard 23 Oct '08

23 Oct '08

Hey Krish, Thanks for your input. Good idea too, never thought about doing that. Tried this in command line and worked without a hitch. Then i realized if you just use command line what I did before works as well. The error must somehow be resulting from issues with tcsh or something. But I found a way to get it to work in tcsh shell script, going off of what you suggested. Here is what works for me in tcsh script: cd $FSsubjDir mkdir $subjID cd $subjID mkdir mri cd mri mkdir orig cd orig mv ../../Volume_ns+orig* ./ mri_convert --in_type brik Volume_ns+orig.BRIK 001.mgz etc etc That's probably a primitive way to write the script, but hey, it works. Thanks for the help! John On Wed, Oct 22, 2008 at 10:34 PM, Krish Subramaniam < krish(a)nmr.mgh.harvard.edu> wrote: > John > > Is orig/ already there ? Otherwise try > > mkdir orig > mri_convert --in_type brik Volume_ns+orig.BRIK 001.mgz > mv 001.mgz orig/ > > Thanks > Krish > > > > On Oct 22, 2008, at 10:01 PM, John Sheppard wrote: > > Hey everyone, >> >> I'm having some issues trying to run the volume pipeline using .BRIK input >> from afni (hence running mri_convert command directly). The problem occurs >> at the end of mri_convert at the very beginning when Freesurfer fails to >> write orig/001.mgz, and I'm not sure if I'm making a mistake without >> realizing it or if something weirder is going on. I've tried this on both a >> Mac and a linux station running RHEL, with the same results. I ran the >> script using sudo in RHEL so I do not think this is a permissions issue. >> >> The error occurs right when it tries to write orig/001.mgz: writing to >> orig/001.mgz... >> sh: orig/001.mgz: No such file or directory >> Broken pipe >> >> I'm not really familiar with working with pipes but I'm guessing I >> shouldn't have to deal with that. >> >> Just curious if anyone has encoutered this before and knows what's going >> on. Didn't find this issue in prior mailing list emails, so I hope this >> isn't a repeat question. >> >> Thanks! >> >> John Sheppard >> >> Recon output below: >> >> mri_convert --in_type brik Volume_ns+orig.BRIK orig/001.mgz >> $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ >> reading from Volume_ns+orig.BRIK... >> AFNI Header Information ============================================ >> DATASET_RANK : spatial dims 3, sub-bricks 1 >> DATASET_DIMENSIONS: (256, 256, 160) >> TYPESTRING : 3DIM_HEAD_ANAT >> SCENE_DATA : view type 0, func type 0, verify 0 >> ORIGIN : (-172.926697, 84.177513, -82.874474) >> DELTA : (1.000000, -1.000000, 1.000000) >> IDCODE_STRING : XYZ_FSWwmSca-raNtz0oRbtKow >> BYTEORDER_STRING : LSB_FIRST >> BRICK_STATS : min 0.000000 max 950.000000 >> BRICK_TYPES : short >> BRICK_FLOAT_FACS : 0.000000 >> ==================================================================== >> BRICK_STATS min = 0.000000 <--> actual min = 0.000000 >> BRICK_STATS max = 950.000000 <--> actual max = 950.000000 >> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 >> i_ras = (0, -1, 0) >> j_ras = (0, 0, -1) >> k_ras = (-1, 0, 0) >> writing to orig/001.mgz... >> sh: orig/001.mgz: No such file or directory >> Broken pipe >> Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.1.0 >> Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.1.0 >> INFO: SUBJECTS_DIR is /mnt/win/MTLD1/autorecon >> Actual FREESURFER_HOME /usr/local/freesurfer >> Linux SLR10.soc.northwestern.edu 2.6.18-92.1.13.el5 #1 SMP Thu Sep 4 >> 03:51:01 EDT 2008 i686 i686 i386 GNU/Linux >> #-------------------------------------------- >> #@# MotionCor Wed Oct 22 20:45:32 CDT 2008 >> ERROR: no run data found in >> /mnt/win/MTLD1/autorecon/E-05-010-2-afni-test/mri. Make sure to >> have a volume called 001.mgz in >> /mnt/win/MTLD1/autorecon/E-05-010-2-afni-test/mri/orig. >> >> >> -- >> John Sheppard >> Undergraduate Student (Class of 2010) >> Department of Biomedical Engineering >> Northwestern University >> >> Phone: (630) 957-8321 >> E-mail: john-sheppard(a)northwestern.edu >> Address: 1927 Orrington Ave. Rm 8203 >> Evanston, IL 60201 >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > -- John Sheppard Undergraduate Student (Class of 2010) Department of Biomedical Engineering Northwestern University Phone: (630) 957-8321 E-mail: john-sheppard(a)northwestern.edu Address: 1927 Orrington Ave. Rm 8203 Evanston, IL 60201

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mesh size question
by Tommaso De Marco 23 Oct '08

23 Oct '08

Hi all, I'm using the mri_watershed instruction to extract the skull and skin mesh, because I'm using them in a boundary element method, but the dimensions of these meshes are too big for my application (20480 faces and 10242 vertices for each ones). Do you know if there is a way to define a maximum mesh size for the mri_watershed instruction (or at least an equivalent instruction in which is possible to do it) ? I need of very coarse meshes ( 1000 faces for each ones for example). Thanks!

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Rat template creation: MRIstripskull failed
by Mark Bouts 23 Oct '08

23 Oct '08

Hi, I'm trying to set up a rat brain template for analysis using the freesurfer tool. Before setting up the complete template I have to process a representable rat dataset with the available human template. With some much appreciated help I managed to get to the skull strip procedure . But the application ceases its operations at this point with the message: "White matter intensity 0 is lower than CSF intensity 21. Please examine input images. Will terminate ..." Evaluation using tkmedit does not show something a proper segmentation of the rat brain, however it does show a proper outline of the brain. Since a rat brain and a human brain are very dissimilar I'm not surprised by the fact that the segmentation is incorrect. However the brain is outlined ok. It is also known that the WM intensity values in the rat dataset is somewhat reduced to the GM structure. Which is not expected by the freesurfer tool, which expects WM to be highest intensity value. My question is: is there a way of circumventing this problem. For instance by defining the mean intensity values of each tissue class or.. Hope someone can help me? Thanks! Mark

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Error with mri_convert failing to write orig/001.mgz
by John Sheppard 22 Oct '08

22 Oct '08

Hey everyone, I'm having some issues trying to run the volume pipeline using .BRIK input from afni (hence running mri_convert command directly). The problem occurs at the end of mri_convert at the very beginning when Freesurfer fails to write orig/001.mgz, and I'm not sure if I'm making a mistake without realizing it or if something weirder is going on. I've tried this on both a Mac and a linux station running RHEL, with the same results. I ran the script using sudo in RHEL so I do not think this is a permissions issue. The error occurs right when it tries to write orig/001.mgz: writing to orig/001.mgz... sh: orig/001.mgz: No such file or directory Broken pipe I'm not really familiar with working with pipes but I'm guessing I shouldn't have to deal with that. Just curious if anyone has encoutered this before and knows what's going on. Didn't find this issue in prior mailing list emails, so I hope this isn't a repeat question. Thanks! John Sheppard Recon output below: mri_convert --in_type brik Volume_ns+orig.BRIK orig/001.mgz $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from Volume_ns+orig.BRIK... AFNI Header Information ============================================ DATASET_RANK : spatial dims 3, sub-bricks 1 DATASET_DIMENSIONS: (256, 256, 160) TYPESTRING : 3DIM_HEAD_ANAT SCENE_DATA : view type 0, func type 0, verify 0 ORIGIN : (-172.926697, 84.177513, -82.874474) DELTA : (1.000000, -1.000000, 1.000000) IDCODE_STRING : XYZ_FSWwmSca-raNtz0oRbtKow BYTEORDER_STRING : LSB_FIRST BRICK_STATS : min 0.000000 max 950.000000 BRICK_TYPES : short BRICK_FLOAT_FACS : 0.000000 ==================================================================== BRICK_STATS min = 0.000000 <--> actual min = 0.000000 BRICK_STATS max = 950.000000 <--> actual max = 950.000000 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (-1, 0, 0) writing to orig/001.mgz... sh: orig/001.mgz: No such file or directory Broken pipe Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.1.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.1.0 INFO: SUBJECTS_DIR is /mnt/win/MTLD1/autorecon Actual FREESURFER_HOME /usr/local/freesurfer Linux SLR10.soc.northwestern.edu 2.6.18-92.1.13.el5 #1 SMP Thu Sep 4 03:51:01 EDT 2008 i686 i686 i386 GNU/Linux #-------------------------------------------- #@# MotionCor Wed Oct 22 20:45:32 CDT 2008 ERROR: no run data found in /mnt/win/MTLD1/autorecon/E-05-010-2-afni-test/mri. Make sure to have a volume called 001.mgz in /mnt/win/MTLD1/autorecon/E-05-010-2-afni-test/mri/orig. -- John Sheppard Undergraduate Student (Class of 2010) Department of Biomedical Engineering Northwestern University Phone: (630) 957-8321 E-mail: john-sheppard(a)northwestern.edu Address: 1927 Orrington Ave. Rm 8203 Evanston, IL 60201

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sulc
by david felps 22 Oct '08

22 Oct '08

Dear freesurfers, i m running an analysis using qdec trying to find the group difference between healthy subjects and MCIs according to their sulc parameter. My question is, is there an output file with the statistics results as text file and if so can u please tell me where is it located?? my other question is, are the Folding index and sulc in a way correleted? Best regards _________________________________________________________________ MSN Toolbar: Alle Infos sehen, ohne die Website auf der Sie gerade sind zu verlassen. http://www.msn.de/toolbar

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failure of qdec
by lan lin 22 Oct '08

22 Oct '08

I'm running stable version of freesurfer 4.05 on 64 bit ubuntu 7.10. Every time when I tried to run the qdec, it generated the error message below. Reading /apps/freesurfer/freesurfer/lib/tcl/tkUtils.tcl Using /apps/freesurfer/freesurfer/lib/tcl/fsgdfPlot.tcl X Error of failed request: BadMatch (invalid parameter attributes) Major opcode of failed request: 66 (X_PolySegment) Serial number of failed request: 6022 Current serial number in output stream: 6025 [1] Exit 1 qdec anyone know what's the problem? thanks Lan

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Repost-Segfault Error
by Wilson, Benjamin 21 Oct '08

21 Oct '08

Hi All, I reposted this a little earlier but I thought I would repost with all the information that I have I am running freesurfer on a 64 bit linux machine with 2 quad core Intel Xeon processors and 16 GB of RAM I have run the recon-all command on all of my images without any problems but when I got to view the final output in tkmedit I get the following error ------------- ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to analysis-bugs(a)nmr.mgh.harvard.edu : : Now exiting... ------------------------------- Below is the output of the debug file -------------------- tkmedit started: Mon Oct 20 17:47:56 2008 tkmedit.bin anon1 brainmask.mgz -aux T1.mgz $Id: tkmedit.c,v 1.320.2.5 2008/03/10 14:02:35 nicks Exp $ $Name: stable4 $ Set user home dir to /usr/local/freesurfer/subjects Set subject home dir to /usr/local/freesurfer/subjects/anon1 Using interface file /usr/local/freesurfer/lib/tcl/tkmedit.tcl Tcl: Successfully parsed tkmedit.tcl Tcl: Successfully parsed tkm_functional.tcl Segfault Entering main loop xDebug stack (length: 2) 01: main() 01: Entering main loop 00: 00: ------------------------ Any help would be appreciated Thanks. Sincerely, Ben Wilson

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retinotopy analysis document?
by Xu Cui 20 Oct '08

20 Oct '08

Hi, Freesurfer experts: I was told freesurfer can do retinotopy analysis and I was referred to webpage: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis As I am new to freesurfer, I wonder if there is a more detailed document or tutorial (official or not) on retinotopy analysis. Thanks, Xu -- ---------------------------------------------------------------- Xu Cui Department of Psychiatry and Behavioral Sciences Stanford University ----------------------------------------------------------------

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Recurring issue with poor gray/white distinction - easy fix?
by Laluz, Victor 20 Oct '08

20 Oct '08

Hello everyone, I have many scans taken just under 10 years ago on a 1.5T Siemens scanner. For some reason, the images from this time period have consistent problems with gray matter / white matter contrast; consistently, Freesurfer measures almost all cerebral brain tissue as being white. I have experimented with mri_ca_normalize (turning -p down to 0.25 or so helps), with mri_normalize (using -prune helped somewhat,) but all of these trials are experimental and I haven't gotten a solid script written that handles these special cases for me in an efficient way. My question: has anyone else dealt with this problem regularly, and come up with a good way to either use recon-all to take care of it (I can't find any useful flags, or workflow tutorials for dealing with this on the wiki) or written a handy script to do recon-all with several of these "less wm" options built in? I have seen people ask about issues relating to mri_ca_normalize on the mailing list in the past, but the conversations usually end with "send us some of your data and we'll take a look at it." Or, am I missing something here? Did someone already discuss this in detail? Sorry if this seems obvious. Thanks in advance for any help... Victor Laluz UCSF Memory and Aging Center

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Segfault Error
by Wilson, Benjamin 20 Oct '08

20 Oct '08

Hello all, I am hoping that somebody may be able to help me out with this problem. I am new to freesurfer so please excuse if this is a newbie question. I have run recon-all on my subjects to create the appropriate .mgz files needed for analysis, but now when I try and view these files using tkmedit I get the following error ----------- A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. ---------- Can anybody shed some light on the issue? Thanks. Ben

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Freesurfer October 2008