Freesurfer February 2011

freesurfer@nmr.mgh.harvard.edu

103 participants
152 discussions

DCM filename problems with recon-all
by Joakim Vinberg 11 Feb '11

11 Feb '11

Hi everybody, I have several older anatomical series that I would like to run through recon-all. Unfortunately, the DCM files were pulled down with an older filename convention that seems to trip mri_convert immediately, and I'm having some trouble interpreting the error. Can anybody shed any light on this one? The filenames were pulled down from the scanner in the E8846S5I%d.MR format are still in this format, so I'm not immediately sure what's going on. Thanks in advance for all of the help! Joakim /Volumes/192.168.1.10/projects/freesurfer/0029 \n mri_convert /Volumes/192.168.1.10/projects/freesurfer/0029/dcm/E8846S5I1.MR /Volumes/192.168.1.10/projects/freesurfer/0029/mri/orig/001.mgz \n mri_convert /Volumes/192.168.1.10/projects/freesurfer/0029/dcm/E8846S5I1.MR /Volumes/192.168.1.10/projects/freesurfer/0029/mri/orig/001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /Volumes/192.168.1.10/projects/freesurfer/0029/dcm/E8846S5I1.MR... MRIalloc(1229409857, 0, 124): bad parm fname_format : /Volumes/192.168.1.10/projects/freesurfer/0029/dcm/E8846S5I%d.MR fname_format2 : /Volumes/192.168.1.10/projects/freesurfer/0029/dcm/E8846S5I%03d.MR multi-echo genesis file detected (26981 echoes)... No such file or directory Darwin sam 10.5.0 Darwin Kernel Version 10.5.0: Fri Nov 5 23:19:13 PDT 2010; root:xnu-1504.9.17~1/RELEASE_X86_64 x86_64 recon-all -s 0029 exited with ERRORS at Fri Feb 11 12:06:11 PST 2011

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Segmentation problem
by XJ Kang 11 Feb '11

11 Feb '11

Hi, I have a brain segmentation problem. Scanner: Siemens 3T Verio Sequence: MPrage, TR=1900ms, TE=2.45ms, TI=900ms, Voxel: 1x1x1mm, 192 sagittal slices. Problem: The lay of dura mater between brain and skull is bright (See attached brain.jpg). As a result, the segmented brain.mgz has a "cap", and the pial surface and GM/WM surface will "leak" to the dura layer somewhere (see the red dots in surfaces.jpg). This happened to some places and needs a lot of manual work to remove the connection between the brain and dura. I tried to increase the TR to 3000ms. Still some connection somewhere, although the results are much better. Anybody optimized the mprage sequence to minimize the problem? Thank you. XJ Kang

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Memory allocation problem with mri_robust_template
by Mahen 11 Feb '11

11 Feb '11

Hi all, Since upgrading to Freesurfer v5.0, I have been unable to complete the first step of recon-all ('recon-all -autorecon1 -subjid ...') when using 5 anatomical datasets (our typical load for surface reconstruction). The problem seems to come when the third dataset is being registered, at which point recon-all exits with the following error message: ========================= Resolution: 0 Iteration(single-prec): 1 (subsample 200) mri_robust_template(47536) malloc: *** mmap(size=921600) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(480, 480, 248): could not allocate 921600 bytes for 207th slice Cannot allocate memory /Users/mahen/fMRI/Surfaces/cck_kmu \n mri_convert /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz /Users/mahen/fMRI/Surfaces/cck_kmu/mri/orig.mgz --conform \n mri_convert /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz /Users/mahen/fMRI/Surfaces/cck_kmu/mri/orig.mgz --conform mghRead(/Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz, -1): could not open file $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz... Darwin MahenWillEatYourChildren.local 10.6.0 Darwin Kernel Version 10.6.0: Wed Nov 10 18:13:17 PST 2010; root:xnu-1504.9.26~3/RELEASE_I386 i386 recon-all -s cck_kmu exited with ERRORS at Tue Feb 8 20:50:00 CST 2011 ===================== My machine has 4gb of RAM, and I've ssh'd into my advisor's machine (which has 16gb) and had the same problem. I tryed updating the binaries for recon-all and mri_robust_template (from http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-leopard-in…) but the problem remained unsolved. My advisor informs me that it is now running with version 4.5 (all 5 anatomicals); I'd still like to know what's going on. I have tried running it on version 5 with just 2 anatomical datasets, and it works just fine. Here is the output of bugr: FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 Kernel info: Darwin 10.6.0 i386 Thanks in advance, Mahen

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confusion about look up table labels...
by Joe Andreano 11 Feb '11

11 Feb '11

Hi, I'm looking at the list of anatomical regions (found here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurfe…) and I notice that there are two separate sets of coordinates in the same hemisphere for rostral ACC: 1201, G_cingulate-rostral_ACC, and 1206, S_cingulate-rostral_ACC. Can someone tell me the difference, and what the G and S stand for? Thanks, Joe Andreano _________________________________ Joseph M. Andreano, PhD Research Fellow Interdisciplinary Affective Science Lab Massachusetts General Hospital _________________________________

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mapping surface vertices to functional voxels
by James Thompson 11 Feb '11

11 Feb '11

Hi Doug and list, I'm trying to map surface/mesh vertices (e.g. rh.pial) to voxels (cols, rows, slices) in a functional volume in matlab, and just wanted to a) get a check that what I'm doing sounds right and b) share it in case it's useful to anyone else (I searched the mailing list and found most of my answers there, just not all in one post). Of course, mri_surf2vol does all this, probably better, but I want to iterate through many, many times. I've tested it and it seems to work. Functional data has been registered to anatomical (T1.mgz? orig.mgz? w/e) using bbregister. Doug Greve 19 Dec 2008 said: > >if you have the voxel index (col, row, slice) then you can: > >V2R = [ > -1.00000 0.00000 0.00000 128.00000 > 0.00000 0.00000 1.00000 -128.00000 > 0.00000 -1.00000 0.00000 128.00000 > 0.00000 0.00000 0.00000 1.00000 ] > >crs = [col row slice]'; > > >xyz = V2R * [crs+1; 1]; > >then find the vertex whose xyz coords are closest to xyz So: to find CRS from vertex RAS: crs = round(inv(V2R)*[xyz; 1]) %maybe crs -1 to make a closer match? but then this messes with below ------------------------------------------------------------------------------ >From fscoordinates.pdf page 6, plus above... To go from Func CRS to T1 CRS (& vice versa) bbmtx is the transform matrix from register.dat Q = inv(Func_tkrvox2ras)*bbmtx*T1_tkrvox2ras; Q is now the transform from Func_tkrvox2ras to T1tkrvox2ras To find T1 CRS from Func CRS: T1_crs = inv(Q)*[Func_crs; 1]; To find Tfunc CRS from T1 CRS: Func_crs = Q*[T1_crs; 1]; %T1_crs + 1 if you subtracted 1 above So...to go from vertex RAS to Func CRS: Func_crs = Q*(round(inv(V2R)*[xyz; 1]); This seem right? best, Jim T

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Projecting findings using Freesurfer
by Weisinger, Brian (NIH/NIMH) [F] 11 Feb '11

11 Feb '11

Good Morning, I am attempting to project R squared values that were calculated using Freesurfer volumes for the various automated segmented areas that are calculated in Freesurfer. Is there a way I can can compare two groups in say QDEC and visually see the results? Thank you for your help.

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Contrasts for GLM DODS with both discrete as continues covariates
by Habets P (SP) 11 Feb '11

11 Feb '11

I want to run a GLM DODS in Freesurfer to test whether patients differ from controls with regard to cortical thickness, meanwhile I want to control for several variables, both discrete as continues. This is my manually made fsgd file GroupDescriptorFile 1 Title fsgd pat con.txt MeasurementName Cortical Thickness Class controls Class patients Class female Class male Class mdeft Class adni Variables Age Education Handedness input C002 controls female mdeft 27 6 100 input C003 controls male mdeft 46 5 -89.47368622 input C004 controls female mdeft 43 4 100 input P001 patients male mdeft 32 7 -100 input P003 patients male mdeft 26 6 100 input P004 patients female mdeft 19 6 60 The problem I have is how to specify contrasts, on the Freesurfer website I found that : For DODS, the number of regressors is Nc*(Nv+1) In my case that would be 6* (3+1) = 24 Would the contrast than be: 1 -1 and 22 zero's Does Freesurfer automatically create the correct design matrix using the fsgd file? Because it is not clear to me how I should create the design matrix with some discrete variables as confounders. Bw Petra Habets

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license error
by Pom Sailasuta 10 Feb '11

10 Feb '11

Hello, I just installed freesurfer on my new Fedora 14 desktop following the instruction from the website. Howver when testing for installation, there are errors as follows: [root@pom-PC stable5]# tkmedit bert orig.mgz -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/stable5/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- Cheking .license file , there ia no blank lines at the beginning or end of file [root@pom-PC stable5]# more .license #---------------CUT HERE--------------- pom4pom(a)gmail.com 10301 *CckOVij887CA #---------------CUT HERE--------------- [root@pom-PC stable5]# pwd Also similar error for tksurfer as well but qdec started o.k. Also, according to the instruction freesurfer should be installed in /usr/local/freesurefer directory but SetUpFreeSurfer.csh call for freesurfer/stable5 directory. So I created stable5 dir and move every file up from /usr/loca/freesurfer to /usr/loca/freesufer/stable5. thanks for the help -- Pom

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Questionable T1 sequence
by Scott Sorg 10 Feb '11

10 Feb '11

Hi All, Is the following T1 sequence suitable for surface generation? "T1-weighted 3D SPGR (echo time 5 minimum; repetition time = 24 msec; flip angle = 30; field of view = 24 centimeters; slice thickness = 3 millimeters) collected in the axial plane." It's that 3 mm slice thickness that most concerns me. The sequence was not initially intended for surface reconstruction, but I've run a few volumes through recon-all and they've turned out better than I had expected. We're primarily using the output for automated ROI generation, but I'm wondering if the cortical thickness and volume estimations from such an acquisition are suitable for further analysis (i.e., group comparisons, correlations). -SS

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phase data overlay using fsaverage
by Jason Connolly 10 Feb '11

10 Feb '11

Dear freesurfer experts, I have used the mri.vol and mri.analyzehdr.vol fields to encode my coordinates and phase values using MRIread and MRIwrite (f_LH12.mgz). I then brought these data into freesurfer using the following: bbregister --s fsaverage --mov /Applications/freesurfer/subjects/fsaverage/mri/f_LH12.mgz --reg register12.dat --bold --init-header -t2 mri_vol2surf --mov /Applications/freesurfer/subjects/fsaverage/mri/f_LH12.mgz --reg /Applications/freesurfer/subjects/fsaverage/surf/register12.dat --hemi lh --surf white --o /Applications/freesurfer/subjects/fsaverage/surf/LH12.mgh tksurfer fsaverage lh sphere --overlay /Applications/freesurfer/subjects/fsaverage/surf/LH12.mgh However, I do not see anything on the sphere (or fsaverage for that matter) ... Can you provide any hints? The phase values are normalized and range from 4 - 5 and I have converted to RAS space properly (I hope) ... Any tips would be a big help! Best wishes, Jason.

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Freesurfer February 2011