Freesurfer July 2010

freesurfer@nmr.mgh.harvard.edu

101 participants
140 discussions

question: gray matter segmentation
by Yunjo Lee 16 Jul '10

16 Jul '10

Hi, I am a new user of FreeSurfer and trying to figure out gray matter segmentation. A volume that I extracted from aparc+aseg.mgz using mri_segstats did not match the volume reported in /stats/ text files (for example, aseg.stats, rh.aparc.stats). Even without specifying a mask in mri_segstats, there's always a discrepancy of 100 voxels or something. Where do the numbers in /stats/ files come from? Aren't they from aparc+aseg.mgz? Thanks! Yunjo

3 5

Spatial Smoothing in the processing stream for fMRI-freesurfer integration
by Joonkoo Park 16 Jul '10

16 Jul '10

Dear freesurfers, How is spatial smoothing performed during a conventional fmri processing stream? I used SPM to (1) run the 1st level analysis on each subject, (2) transformed the resulting volumetric statistical parametric map to the surface space, (3) normalized each individual's surface map onto fsaverage (which involves surface-based smoothing), and then (4) ran 2nd level analysis on these data. The question is: 3D-spatial smoothing is normally done (and I believe recommended) at step (1) above when estimating the GLM at the 1st level. However, performing 3D smoothing on raw functional images seems to be detrimental if the data will eventually be projected on to a surface space. I then thought about NOT 3D-smoothing at step (1), that is, estimating GLM on unsmoothed data, and then using 2D smoothing after step (2) when statistical parametric maps are projected onto the surface space. However, this sounds problematic since smoothing followed by model estimation might give different results from model estimation followed by smoothing. The third approach is to convert all the volumetric functional images into surface space, and then start model estimation in the surface space using FreeSurfer. But this means that I won't be able to use SPM or other packages to run model estimation (that might have superior functionality when it comes to fmri data analysis). Is this what's usually done to integrate fmri data with freesurfer procedures? Or, alternatively, is there a better integration protocol between FSL and FS (I don't know much about FSL) to address this issue? I'd be grateful to know how other people are doing this. Thank you! Joon

2 1

overlay registration
by Arslan, Ali 16 Jul '10

16 Jul '10

Hi, I'm trying to use a registration file while overlaying my functional volume on the surface. I'm getting this warning -iMac1-2:~ aarslan$ tksurfer KS02sess1 lh inflated –ovreg $V1/register.dat -overlay $V1/spmT_0001.mgz WARNING: flag –ovreg unrecognized WARNING: flag /Users/aarslan/mypath/register.dat unrecognized surfer: current subjects dir: /path/anat surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/aarslan surfer: Reading header info from /path/anat/KS02sess1/mri/T1.mgz surfer: vertices=142381, faces=284758 surfer: Interpreting overlay volume /Users/aarslan/mypath/spmT_0001.mgz as registered functional volume. surfer: curvature read: min=-1.260472 max=2.154594 I also tried with -overlay-reg flag but got the same warning. The results are the same with or without the registration file, so I'm sure that I'm failing to load it. Loading the registration.dat from gui menus also doesn't make a difference visually. Does this indicate that my registration.dat file is bad or am I making an error in the tksurfer call? Any help would be appreciated. Regards, Ali Arslan

2 1

mri_convert question: converting dicom to mgz
by Kenichiro Tanaka 15 Jul '10

15 Jul '10

Hello, all. I have not been able to convert dicom files to a mgz file using mri_convert. Could you tell me how to use mri_convert to do that and the example? I typed the following command and run: mri_convert -it dicom -ot mgz 001/ 001.mgz Then I got the following message: mri_convert -it dicom -ot mgz 001/ 001.mgz $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from 001/... Starting DICOMRead2() dcmfile = 001 dcmdir = . ERROR: 001 is not a dicom file There are 126 dicom files in the directory "001/". OS is CentOS 4.8(64bit), and the version of the Freesurfer I am using is 4.5. Thank you for all your help. Kenichiro Tanaka.

2 1

Mixing fs 4.3.1 with fs 4.5.0 longitudinally
by Jeff Sadino 15 Jul '10

15 Jul '10

Hello, I processed a 200 subject dataset cross-sectionally using fs 4.3.1 with the intention of running them longitudinally. I now read that the longitudinal stream in 4.3.1 is biased towards the initial timepoint and the 4.5.0 is the recommended version to do longitudinally. Can I just send my 4.3.1 subjects into the 4.5.0 longitudinal stream, or will I have have to redo the cross-sectional reconstruction in 4.5.0? Thank you very much, Jeff Sadino

2 1

A region loss in the ?h.aparc.stats
by liang wang 15 Jul '10

15 Jul '10

Hi, My freesurfer version is v4.5.0. Using tksurfer, I can find the corpus callosum shown in the ?h.aparc.annot (e.g., .. -annot aparc.annot). Moreover in the FreeSurferColorLUT.txt, this region exists (e.g. #No. 1004 ctx-lh-copuscallosum). However, I am surprised when finding its loss in the ?h.aparc.stats file. For all subjects, I did not find any morphometric measures of this region. Also, when using tksurfer to present ?h.aparc.annot, I can not find the insula in the displayed surface, though this region is existing in the ?h.aparc.stats and the FreeSurferColorLUT.txt (e.g. #No. 1035 ctx-lh-insula). I am creating a figure to show all these ROIs. Hence I am curious why there is not the insula shown. I am appreciated if anyone could give me a hand for solving this seemly conflicting information. Thanks so much. Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wanglbit(a)gmail.com

3 4

mri_ca_normalize hanging on a case
by Diandra Lucia 15 Jul '10

15 Jul '10

Hi there, We're processing some new 3T cases in FreeSurfer, and one case has been hanging just after it begins mri_ca_normalize: #@# CA Normalize Wed Jul 14 17:16:05 EDT 2010 /home/pnlstaff/freesurfer/subjects/case01264/mri mri_ca_normalize -mask brainmask.mgz nu.mgz /share/apps/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/share/apps/freesurfer/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=29.9 skull bounding box = (62, 68, 28) --> (193, 185, 208) using (106, 107, 118) as brain centroid... mean wm in atlas = 107, using box (90,93,96) --> (122, 121,140) to find MRI wm before smoothing, mri peak at 164 after smoothing, mri peak at 163, scaling input intensities by 0.656 scaling channel 0 by 0.656442 using 244171 sample points... INFO: compute sample coordinates transform 1.058 0.020 -0.013 -10.456; -0.017 1.106 0.142 -38.892; 0.017 -0.123 0.973 10.525; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (125, 70, 32) --> (190, 174, 202) It doesn't give an error, it just hangs there, using 99.9% of the CPU. I checked the original T1 nifti and the brainmask and they look fine (we actually pre-skullstrip our T1s and copy them to create our brainmasks, and include -noskullstrip when we run autorecon-1). We're running these on freesurfer-Linux-rh9-stable-pub-v4.2.0. We actually had a similar problem about a year ago, and you sent us the CentOS4 build of the mri_ca_normalize script which fixed it, but my colleague who downloaded it from you is on vacation for 2 weeks and then is leaving, and I think it's locked up in her login. So, if this turns out to be a good solution again, I'd need to download the file again. Thanks for your help, Diandra -- Diandra Lucia Research Assistant Project Coordinator INTRuST Neuroimaging Leadership Core Psychiatry Neuroimaging Lab, BWH 1249 Boylston St., Boston, MA 02115 email: diandra(a)bwh.harvard.edu phone: 617-525-6118 cell: 602-332-7013

2 1

FDR Calculations
by James Porter 15 Jul '10

15 Jul '10

Hello- Does the built-in FDR function in tksurfer and QDEC run the calculations upon the actual values in the .mgh files, or does it take the exponent of those -log10(p) values first? -- Jim Porter, M.A. Graduate Student Clinical Science& Psychopathology Research University of Minnesota

2 1

problem converting .ima files
by Scott Hayes 15 Jul '10

15 Jul '10

Hi, I am trying to convert .ima files, and my command seems to work fine for some series: >mri_convert -it siemens -ot nii 523-2-4.ima ../srs2.nii but not others: >mri_convert -it siemens -ot nii 523-3-132.ima ../srs3.nii These are series collected from the same scan session. The data were reportedly collected at MGH: Siemens Allegra, around the fall of 2001 (if that helps at all). I'm running freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 I don't receive any error messages. The problem seems to be similar to one previously described in the archives, although I was not able to find the final solution: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00890.html Any guidance would be appreciated. Thanks, Scott -- Scott M. Hayes, Ph.D. Memory Disorders Research Center Neuroimaging Research Center VA Boston Healthcare System Assistant Professor Department of Psychiatry Boston University School of Medicine

3 2

Pial edits?
by Kolody, Brianna 15 Jul '10

15 Jul '10

2 1

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Freesurfer July 2010