Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30088 discussions

[New release] - iSurf Brainview 2.1.1
by Pedro Paulo de Magalhães Oliveira Junior 04 May '11

04 May '11

Today it was released a new upgrade of iSurf Brainview. (2.1.1) *New features: * Phone / IPod Touch - IPhone now show webpage with structure description when you tap the name of the structure All iOS - More structures with webpage description - Cache webpages for speedup As usual suggestions are welcome. Upcoming features should include 3D visualization. The link for download is: http://itunes.apple.com/WebObjects/MZStore.woa/wa/viewSoftware?id=381072423… Cheers Pedro Paulo Jr.

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A problem about mri_glmfit result
by soft.join Huang 04 May '11

04 May '11

Hi all, I'm working on a group analysis using mri_glmfit. In analysis directory, I got a X.mat file which containing the matrix X ( size 50x4 ) used to regress analysis, also the beta value from beta.mgh file. Strangely, I loaded the X.mat in Matlab and recalculated the beta using function regress in matlab, but got a different result from that of mri_glmfit. I don't know where the problem is, is there any difference in algorithm between mri_glmfit and matlab function regress( regress(Y,X) )? or I made some mistakes during the procedure. The X.mat file and the dependent variable Y.mat are in the attachment. Thanks in advance Lijie Huang

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resample data to surface that is already in conformed space
by GREGORY R KIRK 03 May '11

03 May '11

I have probabilistic tractography output that is already in freesurfer conformed space, i need to resample it onto the cortical surface, how can I ? i.e. mri_vol2surf does not have an option for the data already being in registration ( requires transform. i know i can load in freesurfer and save but i have hundrends of subjects and many seed regions thank you greg

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Openmi version of freesurfer
by Knut J Bjuland 03 May '11

03 May '11

HI is ther any plans to produce an version of freesurfer for openmpi and/or cuda 4.0? Do Anders Dale produce an version of freesurfer for openmi interface that enable use of freesurfer on supercomputer? Knut J Bjuland

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How to determine gray matter in the aseg.mgz
by Lucas Eggert 03 May '11

03 May '11

Dear Experts, I would like to generate a gray matter mask using the aparc+aseg.mgz file. Now, my question is whether there exists a file in addition to the FreeSurferColorLUT.txt file, which more explicitly, i. e., withouth the abbreviations, explains the labels, because I find it hard to decide whether, e. g., "Left-VentralDC", "Line1", "LeftmOg", or "Left-Interior" belong to gray matter, or not (to name only a few of those labels I cannot clearly classify). Or is there a easier way to create a gray matter mask? Thank you very much in advance! Best regards, Lucas Eggert -- Lucas Eggert, M.Sc. Institute of Cognitive Science University of Osnabrueck Albrechtstrasse 28 D-49076 Osnabrueck Germany Phone: +49-541-969-44-28 Website: http://www.cogsci.uni-osnabrueck.de/~leggert/

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Neuroimaging position
by Centre Recerca Cognitiva 03 May '11

03 May '11

Applications are invited for a position at a Hospital Research Center in Barcelona, Spain. The position is full-time for 15 months (with a probable extension to 18 months). It entails working mainly on neuroimaging data. The postholder will help in analyzing functional, structural, and diffusion tensor data. Essential skills include knowledge of fMRI and/or structural MRI techniques, a proficient management of Freesurfer, SPM and programming skills in MATLAB. The position is available to start 1st of September 2011. Annual salary will be around €26,000 (plus social security, health and unemployment benefits). Please send enquiries or applications (which must include a covering letter detailing professional objectives and interests, CV, all in one pdf file) to cenicogni(a)gmail.com, with the subject line "Neuroimaging position".

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question regarding the comparison of two methods
by Jacobs H (NP) 03 May '11

03 May '11

Dear FreeSurfers, We are comparing two methods to measure the volume of a subcortical structure (our method and FreeSurfer). We want to compare them spatially, by doing a voxel-based analyses. We thought to isolate the structure from the aseg.mgh as well as our own structure. Then we smoothed both data sets. Now we are trying to convert the structure from our method to FreeSurfer space (256 x 256). Then, our plan was to put all the data of the structures of both methods all the subjects together (4D) and to run mri_glmfit (comparing method one with method two). Does this seems logically? But, we were wondering how we should deal with the warping towards the fsaverage (which is ofcourse not similar to the subcortical structure) in the mri_glmfit? Do you have any idea? Thank you very much. Best Heidi Jacobs [cid:149263716@29042011-1A80] Heidi Jacobs, MSc. PhD student Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Alzheimer Center Limburg Division Cognitive Neuropsychiatry and Clinical Neurosciences h.jacobs(a)maastrichtuniversity.nl <mailto:h.jacobs@maastrichtuniversity.nl> www.maastrichtuniversity.nl <http://www.maastrichtuniversity.nl/> Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 126 F +31 43 38 84 092 Note: the email addresses have changed! [cid:149263716@29042011-1A87] Please consider your environmental responsibility before printing this e-mail.

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Compiling stats file for ROI label in QDec
by Krista Kelly 02 May '11

02 May '11

Using QDec, I've created an ROI label (lh.G_cuneus.label) and a .stats file (lh.G_cuneus.stats) that corresponds to this ROI for each participant in my group. Is there a quick way to compile cortical thickness data for this ROI from all participants? The manual suggests using aparcstats2table but I'm not sure how to select the stats for just this one ROI. Any help would be appreciated!

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mri_surfcluster question
by Fernanda Palhano 02 May '11

02 May '11

Hello, I'm running a cortical thickness analysis using Qdec. When I do Find Clusters and Go to Max, I obtain 9 clusters (min threshold 3, max threshold 5): ============================================================ Generating cluster stats using min threshold of 3... Found 9 clusters Contrast: 'lh-Diff-grupo1-grupo2-Intercept-thickness', 10fwhm, DOF: 30 ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation --------- --- ------ --------- ---- ---- ---- ----- ---------- 1 8.8371 89238 5.07 -28.2 12.0 -14.5 16 insula 2 -5.3729 64233 428.45 -35.4 50.5 -8.5 583 parsorbitalis 3 -5.1786 73273 192.98 -8.0 46.4 -13.0 292 medialorbitofrontal 4 -3.8763 121706 38.22 -19.6 61.0 1.5 53 rostralmiddlefrontal 5 -3.8612 93042 93.07 -23.8 40.2 -11.0 153 lateralorbitofrontal 6 -3.5732 14941 41.60 -7.0 41.1 -22.2 79 medialorbitofrontal 7 3.3511 160348 0.34 -30.3 10.7 -14.1 1 insula 8 3.3502 111085 31.96 -33.8 -13.2 -4.6 68 insula 9 -3.2412 99299 19.05 -34.6 47.2 18.4 26 rostralmiddlefrontal ============================================================ Why when using the command line mri_surfcluster with the same thresholds I do not have the same results (same clusters)? # Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.48 2010/04/12 17:36:58 greve Exp $ # $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ # CreationTime 2011/05/02-19:07:52-GMT # cmdline mri_surfcluster --in qdec/lh_g1_g2/lh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh --subject fsaverage --hemi lh --thmin 3 --thmax 5 --sign abs --annot aparc --sum summary_3_5 --olab lh_g1_g2 # cwd /Applications/freesurfer/subjects/dados # sysname Darwin # hostname Fernanda-Palhanos-Mac-Pro.local # machine i386 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input qdec/lh_g1_g2/lh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi lh # surface white # annot aparc # SUBJECTS_DIR /Applications/freesurfer/subjects/dados # Minimum Threshold 3 # Maximum Threshold 5 # Threshold Sign abs # AdjustThreshWhenOneTail 1 # Area Threshold 0 mm^2 # Overall max 8.83713 at vertex 89238 # Overall min -5.37286 at vertex 64233 # NClusters 12 # Total Cortical Surface Area 65416.6 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ NVtxs Annot 1 -4.995 29209 398.78 -33.5 48.6 -10.8 548 rostralmiddlefrontal 2 -4.995 16744 185.39 -8.3 45.3 -12.5 283 medialorbitofrontal 3 4.914 28205 0.34 -28.4 11.8 -11.8 1 insula 4 4.850 22061 2.37 -26.8 9.7 -13.8 8 insula 5 4.512 52766 0.38 -29.8 11.0 -11.4 1 insula 6 -3.876 121706 38.22 -19.4 59.1 -1.6 53 rostralmiddlefrontal 7 -3.861 93042 93.07 -23.5 38.5 -11.2 153 lateralorbitofrontal 8 3.691 89239 0.68 -27.5 11.7 -12.5 2 insula 9 -3.573 14941 41.60 -7.0 38.8 -20.6 79 medialorbitofrontal 10 3.351 160348 0.34 -29.9 9.7 -12.3 1 insula 11 3.350 111085 31.96 -33.5 -12.9 -3.2 68 insula 12 -3.241 99299 19.05 -34.2 46.6 14.7 26 rostralmiddlefrontal In the right hemisphere I have the same problem: ============================================================ Generating cluster stats using min threshold of 3... Found 6 clusters Contrast: 'rh-Diff-grupo1-grupo2-Intercept-thickness', 10fwhm, DOF: 30 ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation --------- --- ------ --------- ---- ---- ---- ----- ---------- 1 16.5175 22102 2.89 33.5 10.7 -13.0 7 insula 2 6.0843 160464 1.08 30.8 13.1 -13.1 3 insula 3 -5.9997 62430 1.08 36.1 3.3 -19.1 3 insula 4 -3.3483 60593 24.75 35.9 55.5 -7.6 36 rostralmiddlefrontal 5 3.2156 23631 10.78 19.8 -65.1 1.5 15 lingual 6 3.1968 120630 0.28 29.1 11.5 -15.8 1 insula ============================================================ cmdline mri_surfcluster --in qdec/rh_g1_g2/rh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh --subject fsaverage --hemi rh --thmin 3 --thmax 5 --sign abs --annot aparc --sum rh_summary_3_5 --olab rh_g1_g2 # cwd /Applications/freesurfer/subjects/dados # sysname Darwin # hostname Fernanda-Palhanos-Mac-Pro.local # machine i386 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input qdec/rh_g1_g2/rh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi rh # surface white # annot aparc # SUBJECTS_DIR /Applications/freesurfer/subjects/dados # Minimum Threshold 3 # Maximum Threshold 5 # Threshold Sign abs # AdjustThreshWhenOneTail 1 # Area Threshold 0 mm^2 # Overall max 16.5175 at vertex 22102 # Overall min -5.99973 at vertex 62430 # NClusters 6 # Total Cortical Surface Area 65020.8 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ NVtxs Annot 1 3.386 130519 0.70 29.7 12.4 -12.0 2 insula 2 -3.348 60593 24.75 35.5 53.5 -9.1 36 rostralmiddlefrontal 3 -3.245 28242 0.36 35.3 2.9 -15.6 1 insula 4 3.216 23631 10.78 19.6 -63.0 4.6 15 lingual 5 3.197 120630 0.28 28.8 10.4 -13.8 1 insula 6 3.067 89363 0.38 34.3 7.1 -12.2 1 insula Am I doing something wrong? I want to use the command line to generate the labels for each cluster found. Thanks in advance, Fernanda

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Customizing FLASH protocol
by Jennifer Addicks 02 May '11

02 May '11

Hello, I need assistance customizing the recommended FLASH acquisition protocol for FreeSurfer for the scanner I'll be using. The document containing the recommended morphometry protocols for use with FreeSurfer provided online mentions that custom multiecho sequences for Siemens scanners are available from the Martinos Center for free. Does anyone know who I can contact to obtain this assistance? Thanks, Jennifer

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