Freesurfer August 2009

freesurfer@nmr.mgh.harvard.edu

86 participants
143 discussions

Re: [Freesurfer] Freesurfer Digest, Vol 66, Issue 9
by Sebastian Moeller 24 Aug '09

24 Aug '09

Hi Guang, if I recall correctly "the sliver problem" stems from the use of an incompatible libGL. I did the following that a colleague found out: add the following line to ${FREESURFER_HOME}/bin/tksurfer (that is the script that calls tksurfer.bin): setenv LD_PRELOAD ${FREESURFER_HOME}bin/libGL.so.1 Also unpack the following to reside in your ${FREESURFER_HOME}/bin directory: (Those are GL libraries from a redhat 4 / centos 4 system that seem to work with tksurfer). Nick, do you think it would be possible to make this change for the distribution (it was inspired by your inclusion of libGlut to begin with). ahoi & good luck Sebastian On Aug 5, 2009, at 7:22 AM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Date: Wed, 5 Aug 2009 08:49:15 -0500 > From: Guang Zeng <freesurfer_zg(a)hotmail.com> > Subject: [Freesurfer] "redraw failed: no gl window open" problem > To: <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <SNT112-W300BF5F653E2F82B84CEA29C0D0(a)phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > > Hi, there, > > I am running the tksurfer command to view the cortical surface data > as tksurfer bert lh inflated. But I met a problem. > I only can view a sliver part of the brain. This sliver portion can > rotate and do everything that tksurfer is supposed to do, > but I can't view any more of the brain than a tiny piece. Tkmedit > works fine. > > When I run the command, it gave me something like this: > > surfer: current subjects dir: /home/m047599/freesurfer-install/ > freesurfer/subjects > surfer: not in "scripts" dir ==> using cwd for session root > surfer: session root data dir ($session) set to: > surfer: /home/m047599/freesurfer-install/freesurfer > surfer: Reading header info from /home/m047599/freesurfer-install/ > freesurfer/subjects/bert/mri/T1.mgz > surfer: vertices=131369, faces=262734 > Loading /home/m047599/freesurfer-install/freesurfer/surface_labels.txt > surfer: ### redraw failed: no gl window open > surfer: single buffered window > surfer: tkoInitWindow(bert) > surfer: using interface /home/m047599/freesurfer-install/freesurfer/ > lib/tcl/tksurfer.tcl > Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/ > tkm_common.tcl > Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/ > tkm_wrappers.tcl > Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/ > fsgdfPlot.tcl > Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/ > tkUtils.tcl > Successfully parsed tksurfer.tcl > reading white matter vertex locations... > > > I searched the previous posts, it looks like somebody have the same > problem. > There is no NVidia and native Linux system on my computer. I run > tksurfer on a virtual Linux machine using NX 3. 3. 0. 6. > I ran the xdpyinfo | grep GL, it shows that I have GLX and SGI-GLX. > I ran the glxgrears, it works, although very slow. > > So, how can I solve this problem, any suggestions are highly > appreciated. > > Thanks a lot!

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Conversion of wmparc.mgz to Original Volume Space without Resampling
by Matt Glasser 23 Aug '09

23 Aug '09

I am curious about how to use mri_convert to convert wmparc.mgz back to the space that the original nii.gz volume that I gave FreeSurfer was in without resampling for further analysis with FSL. The volume I imported was 176x208x176, and oriented xorient: Left to Right, yorient: Posterior to Anterior, and zorient: Inferior to Superior. When I run mri_convert wmparc.mgz wmparc.nii.gz I get a file that is 256x256x256, and oriented xorient: Right to Left, yorient: Superior to Inverior, and zorient: Posterior to Anterior. How do I use mri_convert to convert wmparc to the original space without resampling? Thanks, Matt.

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Reliability of gyral measures
by Dankner, Nathan (NIH/NIMH) [F] 22 Aug '09

22 Aug '09

Hi all, Have there been any published reports of the reliability of the gyral-based measures in FreeSurfer? I've seen several papers assessing reliability but have been unable to find one that looked at reliability of cortical thickness, volumes, etc associated with the gyral based parcellations. Nathan

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a question about mri_convert
by Guang Zeng 21 Aug '09

21 Aug '09

Hi, there, I got a question about mri_convert. I have a brainmask.nii file, (max intensity value is 64, and minimum intensity is 0), it shows good intensity contrast. Now I want to use mri_convert to convert it to mgz file, my command line is mri_convert A.nii --conform A.mgz Now, I open A.mgz using Tkmedit, I can not see those significant intensity contrast now, and the max intensity value is 255, and minimum intensity is 0 It looks like mri_convert do something like histogram equalization or normalization. Will mri_convert actually change the intensity value of each voxel? Can I keep my original intensity value for each voxel? Use the mri_convert -sc? Thanks a lot! Guang _________________________________________________________________ Windows Live: Keep your friends up to date with what you do online. http://windowslive.com/Campaign/SocialNetworking?ocid=PID23285::T:WLMTAGL:O…

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vertex number
by Feng-Xian Yan 21 Aug '09

21 Aug '09

Hi, I know Freesurfer has a function which can label ROI by us. But, I want to know how many vertices do the labeled ROI has. Would you teach me how to obtain the vertex of the labeled ROI ? Thank you in advance! Feng-Xian

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-randomness flag for recon-all
by Pernille Iversen 21 Aug '09

21 Aug '09

Hi, In the release notes for version 4.4.0 it says that "The -randomness flag can be used to allow usage of a random seed", however, running the following command: recon-all -all -nowmsa -randomness -subjid f4168_1r gives the following error: ERROR: Flag -randomness unrecognized. Is there another way to reintroduce the randomness? I am using the following version: v 1.133.2.51 2009/06/11 Thanks, Pernille

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bbregister question
by Guang Zeng 20 Aug '09

20 Aug '09

Hi, there, Sorry, I asked the same question yesterday, but I think I didn't explain it clear. I have the two scans (001.mgz and 002.mgz) of the same subject, 001.mgz is used as the input of recon-all .... -autorecon1, and I only run -autorecon1. now I have a brainmask.mgz using 001.mgz, I want to register 002.mgz using brainmask.mgz as reference volume. Dr. Greve mentioned that I can use bbregister, but I got a problem now, becuase I only run autorecon1, I do not have lh.white which will be acquired after autorecon2. The bbregister command stopped in the middel. My command line is bbregister --s data_2 --mov 002.mgz --init-fsl --t1 --reg brainreg.dat --o brainmaskReg.mgz I got a error as, Loading mov Loading lh.white surf No such file or directory Is there an option that I do not use lh.white, just use the information I got after autorecon1 to do the registration, or I need use other commands? Thanks a lot! Guang _________________________________________________________________ Windows Live: Make it easier for your friends to see what you’re up to on Facebook. http://windowslive.com/Campaign/SocialNetworking?ocid=PID23285::T:WLMTAGL:O…

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Re: [Freesurfer] mri_compute_seg_overlap
by jentis＠nmr.mgh.harvard.edu 20 Aug '09

20 Aug '09

> Hi Nick, > > I can't get the script to work but that might be due to my inexperience > with matlab. I copied the script into my matlab directory, and tried to > run > dice_labels > (/autofs/space/phrenic_007/users/jon/hires_amy/Round_1/HRDEV150/whole_amygdala.label, > /autofs/space/phrenic_007/users/jon/hires_amy/Round_2/HRDEV150/whole_amygdala.label) > > But the error message said unexpected matlab operator. > > I then tried altering the script by substituting the actual labels for > 'label1' and 'label2' but that didn't work either, and it gave me the same > error message. > > Running the command alone, dice_labels, the error reads >>> dice_labels > ??? Input argument "lname1" is undefined. > > Error in ==> dice_labels at 29 > label1 = read_label('',lname1); > > > I'm sure I'm doing something wrong, but no one in my group knows matlab > well enough to figure it out. > >> Jon, >> >> Do the matlab scripts work for you? The approach you are taking with >> the existing tools is the one I was considering myself but decided it >> was too roundabout and probably wouldn't work for you anyway (because >> mri_compute_seg_overlap looks for particular label ids corresponding to >> subcortical structures), compared to the ease of just computing the dice >> directly from the label files, which are just text files listing the >> label coordinates. >> >> Nick >> >> >> On Thu, 2009-08-20 at 14:09 -0400, jentis(a)nmr.mgh.harvard.edu wrote: >>> Hi Nick, >>> >>> I was actually able to convert the label files into volumes using >>> mri_label2vol and then use the mri_segstats to get the total number of >>> pixels from each volume file. But the mri_compute_seg_overlap didn't >>> work as easily. I tried running the following but the results were all >>> zero, which I've included as well: >>> mri_compute_seg_overlap -olog text whole_amygdala_test.mgz >>> ../../Round_2/HRDEV150/whole_amygdala_test2.mgz >>> >>> logging overall Dice to text >>> Jaccard Coefficients: >>> correct ratio for label 2 = 0 >>> correct ratio for label 41 = 0 >>> correct ratio for label 3 = 0 >>> correct ratio for label 42 = 0 >>> correct ratio for label 4 = 0 >>> correct ratio for label 43 = 0 >>> correct ratio for label 17 = 0 >>> correct ratio for label 53 = 0 >>> correct ratio for label 10 = 0 >>> correct ratio for label 49 = 0 >>> correct ratio for label 11 = 0 >>> correct ratio for label 50 = 0 >>> correct ratio for label 12 = 0 >>> correct ratio for label 51 = 0 >>> correct ratio for label 13 = 0 >>> correct ratio for label 52 = 0 >>> correct ratio for label 18 = 0 >>> correct ratio for label 54 = 0 >>> correct ratio for label 26 = 0 >>> correct ratio for label 58 = 0 >>> correct ratio for label 14 = 0 >>> correct ratio for label 15 = 0 >>> correct ratio for label 5 = 0 >>> correct ratio for label 44 = 0 >>> mean +/- std = 0.0000 +/- 0.0000 >>> Dice Coefficients: >>> label 2 = 0 >>> label 41 = 0 >>> label 3 = 0 >>> label 42 = 0 >>> label 4 = 0 >>> label 43 = 0 >>> label 17 = 0 >>> label 53 = 0 >>> label 10 = 0 >>> label 49 = 0 >>> label 11 = 0 >>> label 50 = 0 >>> label 12 = 0 >>> label 51 = 0 >>> label 13 = 0 >>> label 52 = 0 >>> label 18 = 0 >>> label 54 = 0 >>> label 26 = 0 >>> label 58 = 0 >>> label 14 = 0 >>> label 15 = 0 >>> label 5 = 0 >>> label 44 = 0 >>> mean +/- std = 0.0000 +/- 0.0000 >>> Overall subcortical dice = nan >>> >>> Any ideas? >>> >>> Thanks >>> >>> > Jon, >>> > >>> > None of the existing utilities will calculate the Dice of two labels >>> (at >>> > least not in a straightforward manner). However, its easy to do in >>> > matlab. >>> > >>> > Attached is a script to do this. Copy it to your >>> > $FREESURFER_HOME/matlab directory. >>> > >>> > Usage is: >>> > >>> > dice_labels('label1.label','label2.label') >>> > >>> > or just >>> > >>> > dice_labels('label1','label2') >>> > >>> > >>> > this assumes the two labels were created in the same volume. >>> > >>> > Nick >>> > >>> > >>> > >>> > On Thu, 2009-08-20 at 12:21 -0400, jentis(a)nmr.mgh.harvard.edu wrote: >>> >> Hi, >>> >> >>> >> I need to compute the reliability of two manually traced ROIs and >>> I >>> >> was >>> >> told to use the command mri_compute_seg_overlap. However, it seems >>> >> this command needs its input to be in .mgz format, but the ROIs have >>> >> been saved as .label files in Freeview. A simple renaming function >>> >> does not work, so is there another way to make >>> mri_compute_seg_overlap >>> >> work with .label files? Thanks. >>> >> >>> >> Best, >>> >> Jon >>> >> _______________________________________________ >>> >> Freesurfer mailing list >>> >> Freesurfer(a)nmr.mgh.harvard.edu >>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> >>> >> >>> > >>> >>> >> >> >> > >

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mri_compute_seg_overlap
by jentis＠nmr.mgh.harvard.edu 20 Aug '09

20 Aug '09

Hi, I need to compute the reliability of two manually traced ROIs and I was told to use the command mri_compute_seg_overlap. However, it seems this command needs its input to be in .mgz format, but the ROIs have been saved as .label files in Freeview. A simple renaming function does not work, so is there another way to make mri_compute_seg_overlap work with .label files? Thanks. Best, Jon

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Re: [Freesurfer] mris_fix_topology
by Bruce Fischl 20 Aug '09

20 Aug '09

I can't remember. Nick? On Thu, 20 Aug 2009, Falk Lüsebrink wrote: > Thanks, I'll try to do that. > > Are the commands for mris_topo_fixer the same as of mris_fix_topology? I > haven't seen a help for that one. > > Regards, > Falk > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Thursday, August 20, 2009 2:36 PM > To: Falk Lüsebrink > Cc: freesurfer(a)surfer.nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mris_fix_topology > > yes. The only time I've seen this error is when the surface file didn't > finish writing. You can load the defects with something like: > > tksurfer -orig orig.nofix $subject $hemi inflated.nofix > > then load the curvature file $hemi.defect_labels. You should be able to use > save point/goto point in tksurfer and tkmedit to figure out where each > vertex is in the wm.mgz volume and manually correct it (although this is an > acquired skill!). You may need to specifiy -white orig.nofix as well, > although looking at the code I don't think you do. > > cheers, > Bruce > > On Thu, 20 Aug 2009, Falk Lüsebrink wrote: > >> Hi Bruce, >> >> No, there are some hundreds of GB left. >> >> Is the other topology fixer you meant before mris_topo_fixer? >> >> Thanks in advance, >> Falk >> >> -----Original Message----- >> From: freesurfer-bounces(a)nmr.mgh.harvard.edu >> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce >> Fischl >> Sent: Thursday, August 20, 2009 4:44 AM >> To: Falk Lüsebrink >> Cc: freesurfer(a)nmr.mgh.harvard.edu; 'Douglas N Greve' >> Subject: Re: [Freesurfer] mris_fix_topology >> >> are you out of disk space? >> On Thu, 20 Aug 2009, Falk Lüsebrink wrote: >> >>> Hi Doug, >>> >>> I get the following error: >>> >>> rh.orig: face[161898].v[2] = 82472, but face 161898 not in vertex >>> 82472 face list >>> >>> Falk >>> >>> -----Original Message----- >>> From: freesurfer-bounces(a)nmr.mgh.harvard.edu >>> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas >>> N Greve >>> Sent: Thursday, August 20, 2009 12:12 AM >>> To: Falk Lüsebrink >>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] mris_fix_topology >>> >>> >>> It was not mris_fix_topology that failed but mris_euler_number (but >>> that might have failed because of something in the topology fix). >>> What happens if you: >>> >>> cd /home/falk/freesurfer/subjects/yv98_05mm_div >>> mris_euler_number ../surf/rh.orig >>> >>> doug >>> >>> Falk Lüsebrink wrote: >>>> >>>> Hi FreeSurfers, >>>> >>>> >>>> >>>> Attached is a log file containing an error of mris_fix_topology and >>>> I would like to know how to fix that issue if that is possible. Is >>>> it possible to view a defect (in that case #33) in tksurfer or >>>> freeview to identify a possible error in the wm.mgz or filled.mgz to >>>> correct it manually? >>>> >>>> >>>> >>>> Thanks in advance, >>>> >>>> Falk >>>> >>>> -------------------------------------------------------------------- >>>> - >>>> --- >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> >> >> >> > > > >

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Freesurfer August 2009