Freesurfer November 2012

freesurfer@nmr.mgh.harvard.edu

105 participants
177 discussions

Feature request (adding origin info to surface files)
by Luke Bloy 11 Nov '12

11 Nov '12

Hi all, I'm not sure where the best place to make this request is. so I thought I'll put this here. I often use freesurfer generated surfaces and images in other software packages (Slicer, Matlab etc) for various things. The MGZ files include the origin in the file headers, meaning that software can correctly interpret the world spaces of these images, allowing correct overlays with other results computed from the same scans. The problem is that the surface files treat the 128,128,128 voxel ( of the T1.mgz and other images) as the origin. But the world coordinates of this origin are, to my knowledge not in the surface files. This creates the situation that to correctly interpret these surfaces in relation to other coordinates systems, basically I either need to ignore the world coordinates and do some registration, or I need to load both an mgz file (to get the origin) and surface files to learn correct world coordinates of the surfaces. Ideally it seems like this information should be included in the surface files themselves. Hopefully my description of the problem makes some sense. Thanks. Luke

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ASCII .curv format viewing problem
by Sourena Soheili-Nezhad 10 Nov '12

10 Nov '12

Hello Freesurfer expert community I have been analyzing the jacobian values outside freesurfer by exporting it to ascii format. Now, I have come up to vertex-wise statistical values which I wish to project on the study surface. Reading the list, I have created an ascii with each row representing <#vertex> <X> <Y> <Z> <scalar value>. This file is only viewable in tksurfer (not freeview) and the problem is that after using the curv_to_val script in tcl, the values outside [-2,2] (the blue and red colors) don't get updated when I load another file (they "freeze" on the previously loaded values). Any suggestion on a better way to view the ascii .curv format is highly appreciated. Also, does there exist any publicly-available I/O for writing binary .curv format so I can import it to freeview as well? Thanks, Sourena Soheili-Nezhad

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nii -> mgz conversion inaccuracy; slice shifted.
by Uri Hasson 10 Nov '12

10 Nov '12

Dear Freesurfer experts, I'm converting a batch of nifti files to start a FS pipeline. There is 1 structural image per participant. The initial 'reconall -i' step does not give any errors. But, looking at the 'mri/orig/001.mgz' I notice for 1 participant what appears to be an imperfect conversion. Here is the link to the image showing this small bug.. http://goo.gl/jJKgM It shows the same coronal slice in AFNI and FS. The one on the right is how the original brain looks in AFNI, the one on the left is the FS's 001.gmz where there appears to be a 'pixel shift both saggitally and axially.. Any assistance, much appreciated. Thanks, Uri

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Re: [Freesurfer] checking talairach.lta
by Douglas Greve 09 Nov '12

09 Nov '12

OK, I see the problem. I should have told you to put tkregsiter2.bin into /apps/fs510/tktools/ (after making a copy of the one there). doug On 11/5/12 5:00 PM, Eric Cunningham wrote: > [e4fs@cluster bin]$ ls -l `which tkregister2.bin` > -rwxr-xr-- 1 jsadinol fs 21663433 May 22 2011 /apps/fs510/tktools/ > tkregister2.bin > > [e4fs@cluster bin]$ tkregister2 --all-info > ProgramName: tkregister2.in <http://tkregister2.in/> ProgramArguments: > --all-info ProgramVersion: $Name: stable5 $ TimeStamp: > 2012/11/05-21:43:36-GMT BuildtimeStamp: May 22 2011 08:23:31 CVS: > $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $User: > e4fs Machine: cluster.mrilab.net <http://cluster.mrilab.net/> > Playform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC > CompilerVersion: 30400 > > > > fyi: /apps/fs510/ = $FREESURFER_HOME > i tried replacing this file in tktools with the new tkregister2.bin, > and i get a new error: > /lib64/tls/libc.so.6: version GLIBC_2.4 not found > > > > On Mon, Nov 5, 2012 at 11:34 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Can you send me the result of > > ls -l `which tkregister2.bin` > > and > > tkregister2 --all-info > > > doug > > > > > On 11/05/2012 03:54 PM, Eric Cunningham wrote: > > retried it, same error > > new file is .bin, old file is tkregister2, no old > tkregister2.bin file appeared to be in the folder > $FREESURFER_HOME/bin > > On Mon, Nov 5, 2012 at 10:49 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > I'm not sure that was the right thing to do. There should > be two > files: > tkregister2 and tkregister2.bin. tkregister2 is just a > script that > calls > tkregister2.bin after setting up some environment > variables. Try > keeping > the original file name. > doug > > On 11/05/2012 03:43 PM, Eric Cunningham wrote: > > i am sure > > there is one irregularity, namely that the '.bin' > extension is > absent > > from our old file, so i renamed the new file without it (as > > tkregister2) and moved the other one to tkregister2_backup > > > > the command i listed from previous threads was given to > someone else > > from our lab (and probably worked), so it is likely that > the problem > > is somewhere on our side, i was just hoping that it was > known and > > recognizable from the error > > > > > > > > On Mon, Nov 5, 2012 at 10:15 AM, Douglas N Greve > > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > are you sure you are using the new version? > > > > > > On 11/05/2012 02:38 PM, Eric Cunningham wrote: > > > > tried the new version, and it errored out at the > same step > > > > ERROR: Option --lta-inv unknown > > > > thanks again for your help! > > > > On Mon, Nov 5, 2012 at 8:16 AM, Douglas N Greve > > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: > > > > Try using this version > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/tkregister2.b… > > copy it into $FREESURFER_HOME/bin (but make > a back up of > > the existing > > tkregister2.bin first!) > > doug > > > > On 11/02/2012 03:58 PM, Eric Cunningham wrote: > > > Hi folks, > > > In previous threads, the command provided to check the > > talairach.lta is... > > > tkregister2 --mov > $FREESURFER_HOME/average/RB_all_2008-03-26.gca > > \ --targ ../brainmask.mgz --lta-inv > talairach.lta --reg > > talairach.lta.reg.dat \ --surfs --s $subject > > > > > > When I try to run this command, I run into trouble > with the > > --lta-inv > > > portion. (it is an unknown option). I am running > version 5.1. > > > Can anyone help? > > > Thanks, > > > -Eric > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> > > Phone Number: 617-724-2358 > <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>>> > > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>>>> > > > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended > only for the > > person to > > whom it is > > addressed. If you believe this e-mail was > sent to you in > > error and > > the e-mail > > contains patient information, please contact the > Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline . If the e-mail > was sent to > > you in error > > but does not contain patient information, please > contact the > > sender and properly > > dispose of the e-mail. > > > > > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >

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source of recon-all errors?
by Angie Morales 09 Nov '12

09 Nov '12

I'm using Freesurfer version 5.1.0 and recon-all keeps exiting with errors during the intensity correction step. The error reads: Writing to ./tmp.mri_nu_correct.mni.24988/output.mean.dat (standard_in) 1: syntax error mris_calc -o ./tmp.mri_nu_correct.mni.24988/nu2.mnc ./tmp.mri_nu_correct.mni.24988/nu2.mnc mul Linux funcgrid3 3.1.10-1.16-desktop #1 SMP PREEMPT Wed Jun 27 05:21:40 UTC 2012 (d016078) x86_64 x86_64 x86_64 GNU/Linux recon-all -s 402_1 exited with ERRORS at Thu Nov 1 13:19:28 PDT 2012 Any ideas about what might be going wrong? Thanks, Angie

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Re: [Freesurfer] Error in recon-all after updating mri_segstats.
by Douglas N Greve 09 Nov '12

09 Nov '12

Use this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.… doug On 11/08/2012 10:01 PM, Zheng Hui wrote: > Hi Doug, > > After updating the mri_segstats, all our recon-all encounter errors as > follow log suggest. Please advice a work around. > > Thank you, > Zheng Hui > > > mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.4020/ones.mgz --i > orig.mgz --sum ./tmp.mri_nu_correct.mni.4020/sum.junk --avgwf > ./tmp.mri_nu_correct.mni.4020/input.mean.dat > > $Id: mri_segstats.c,v 1.86 2012/07/16 14:39:07 greve Exp $ > cwd > cmdline mri_segstats --id 1 --seg > ./tmp.mri_nu_correct.mni.4020/ones.mgz --i orig.mgz --sum > ./tmp.mri_nu_correct.mni.4020/sum.junk --avgwf > ./tmp.mri_nu_correct.mni.4020/input.mean.dat > sysname Linux > hostname compute-08-00.cbdc.rhhpc.cluster > machine x86_64 > user gmszh > UseRobust 0 > Loading ./tmp.mri_nu_correct.mni.4020/ones.mgz > Loading orig.mgz > Voxel Volume is 1 mm^3 > Generating list of segmentation ids > Found 1 segmentations > Computing statistics for each segmentation > 0 1 0 0 > > Reporting on 0 segmentations > Computing spatial average of each frame > > Writing to ./tmp.mri_nu_correct.mni.4020/input.mean.dat > mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.4020/ones.mgz --i > ./tmp.mri_nu_correct.mni.4020/nu2.mnc --sum > ./tmp.mri_nu_correct.mni.4020/sum.junk --avgwf > ./tmp.mri_nu_correct.mni.4020/output.mean.dat > > $Id: mri_segstats.c,v 1.86 2012/07/16 14:39:07 greve Exp $ > cwd > cmdline mri_segstats --id 1 --seg > ./tmp.mri_nu_correct.mni.4020/ones.mgz --i > ./tmp.mri_nu_correct.mni.4020/nu2.mnc --sum > ./tmp.mri_nu_correct.mni.4020/sum.junk --avgwf > ./tmp.mri_nu_correct.mni.4020/output.mean.dat > sysname Linux > hostname compute-08-00.cbdc.rhhpc.cluster > machine x86_64 > user gmszh > UseRobust 0 > Loading ./tmp.mri_nu_correct.mni.4020/ones.mgz > Loading ./tmp.mri_nu_correct.mni.4020/nu2.mnc > Voxel Volume is 1 mm^3 > Generating list of segmentation ids > Found 1 segmentations > Computing statistics for each segmentation > 0 1 0 0 > > Reporting on 0 segmentations > Computing spatial average of each frame > > Writing to ./tmp.mri_nu_correct.mni.4020/output.mean.dat > (standard_in) 1: parse error > mris_calc -o ./tmp.mri_nu_correct.mni.4020/nu2.mnc > ./tmp.mri_nu_correct.mni.4020/nu2.mnc mul > Linux compute-08-00.cbdc.rhhpc.cluster 2.6.18-164.el5 #1 SMP Tue Aug > 18 15:51:48 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s SS193D_fs exited with ERRORS at Thu Nov 8 16:50:04 SGT 2012 > > For more details, see the log file > /data/research1/cnl/Experiments/SLABS/FS/mempr/SS193D_fs/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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pre-processing functional data error
by Yangmei LUO 09 Nov '12

09 Nov '12

Hi there, I am a newbie and I used data collected from SIEMENS 3T to practice. It works well when I tried to preprocess structural data using freesurfer. However, there is a problem when I tried to convert the functional data in DICOM into NII using freesurfer. The problem I can not solve, so I turn to you. Could you give me some advice on how to solve this problem? Any help is appreciated! The command I run: * export FREESURFER_HOME=/usr/local/freesurfer /usr/local/freesurfer/bin/mri_convert --in_type dicom --out_type nii I0001.dcm s105.run1.nii* and the result in terminal is */usr/local/freesurfer/bin/mri_convert --in_type dicom --out_type nii I0001.dcm ..nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from I0001.dcm... Starting DICOMRead2() dcmfile = /home/fsl/data/emotion/s105/run1/I0001.dcm dcmdir = /home/fsl/data/emotion/s105/run1 Ref Series No = 3 Found 231 files, checking for dicoms Found 228 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 0 Vs: -nan -nan -nan Second Sorting Counting frames nframes = 228 nslices = 1 ndcmfiles = 228 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=2000.00, TE=30.00, TI=0.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.999945, 0.0104718) k_ras = (nan, nan, -nan) Reslicing using trilinear interpolation MRIresample(): error inverting matrix; determinant is -nan, matrix is: -3.000 -0.000 nan nan; -0.000 -3.000 nan nan; 0.000 0.031 -nan -nan; 0.000 0.000 0.000 1.000;* Thank you very much! Best wishes, Yangmei

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pre-processing error?
by Julia Nantes 08 Nov '12

08 Nov '12

Hello, I am having trouble with the pre-processing step. When I enter the recon-all <subject-id> command I get an error: [Lisa-Koskis-iMac:/Applications/freesurfer/subjects] root# recon-all -s ms_018 ERROR: nothing to do When I enter 'recon-all -s ms_018 -qcache' I get a long list of output but I don't think it worked correctly: [Lisa-Koskis-iMac:/Applications/freesurfer/subjects] root# recon-all -s ms_018 -qcache Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 root wheel 87913 Nov 8 10:52 /Applications/freesurfer/subjects/ms_018/scripts/recon-all.log Darwin Lisa-Koskis-iMac.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/freesurfer/ Previous: /Applications/freesurfer /Applications/freesurfer/subjects/ms_018/surf #-------------------------------------------- #@# Qdec Cache lh thickness fsaverage Thu Nov 8 11:46:43 EST 2012 INFO: File lh.thickness does not exist! Skipping creation of smoothed data for lh.thickness #-------------------------------------------- #@# Qdec Cache lh area fsaverage Thu Nov 8 11:46:43 EST 2012 INFO: File lh.area does not exist! Skipping creation of smoothed data for lh.area #-------------------------------------------- #@# Qdec Cache lh area.pial fsaverage Thu Nov 8 11:46:43 EST 2012 INFO: File lh.area.pial does not exist! Skipping creation of smoothed data for lh.area.pial #-------------------------------------------- ....etc recon-all -s ms_018 finished without error at Thu Nov 8 11:46:43 EST 2012 done My goal is to eventually be able to bring up my T1 images with the qdec application and segment the motor cortex. When I use the tkmedit command it works correctly (I have converted my files to .mgz already). Do you know if it is a pre-processing error that is preventing me from getting the qdec application to work with my own brain images? I cannot open files in qdec currently. Many thanks, Julia

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FW: FreeSurfer remote access question
by Li, Hua 08 Nov '12

08 Nov '12

Hello, We recently installed freesurfer on an Ubuntu 12.04 workstation for doctors in Emergency room which will be used for CT scan analysis. In such case, remote access is required for multiple users. No difficulty was encountered when we tested tkmedit bert orig.mgz locally. However, it shows error message "GLUT: Fatal Error in tkmedit.bin: visual with necessary capabilities not found." When it was tried remotely. Is there any way that this can be resolved? Thank you. Best, Hua Li System Administrator 3D Imaging Service Massachusetts General Hospital Tel: 1-(617)-726-9465

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Re: [Freesurfer] Total cerebral volume.
by Douglas N Greve 08 Nov '12

08 Nov '12

Hi Zheng, there is something wrong with your math. When I sum up all the columns in your table from Left-Lateral-Ventricle to CC_Anterior, I get 215952 for the first row (you get only 67548). Can you double check your calculations? doug On 10/28/2012 11:53 PM, Zheng Hui wrote: > Forgot to attach the excel file. Sorry for that. > > From: zhenghui <zheng.hui(a)duke-nus.edu.sg > <mailto:zheng.hui@duke-nus.edu.sg>> > Date: Monday, October 29, 2012 11:52 AM > To: Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Subject: [Freesurfer] Total cerebral volume. > > Hi Doug, > > Thanks for replying. But our datasets do showed that > Sum(all structures (after ICV in the list) except ventricle, CSF, > cerebellum and brainstem) is much smaller SubCortGrayVol. The former > is only about 30-40% of the later. We are using FS 5.1.0 without the > SupraTentorialVol fix.I attached the aseg file for your reference (the > last three columns in the sheet). > > Thanks, > Zheng Hui > > On 10/24/2012 09:01 AM, Zheng Hui wrote: > > > > Hi freesurfer, > > > > We are trying to calculate the total cerebral volume which excludes > cerebellum, brainstem, ventricle and CSF from the aseg.txt. Do we use > > > > CortexVol + CorticalWhiteMatterVol + SubCortGrayVol > > Or > > CortexVol + CorticalWhiteMatterVol + Sum(all structures (after ICV in > the list) except ventricle, CSF, cerebellum and brainstem) > This should give very close to the same value. I don't think it makes a > difference. > > > > > > Also, I saw Doug's post about the bug fixing for SupraTentorialVol. > To re-run the segstats for longitudinal subjects, any extra step other > than "recon-all –long tpN baseID –segstats" and does it affect any > other structure or just SupraTentorialVol? > It should not affect other structures. > doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Freesurfer November 2012