Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

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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switching from v4.5.0-32bits to v5.0.0-64bits
by Daniel Ferreira Padilla 02 May '11

02 May '11

Dear experts, I have been processing my data on FreeSurfer v4.5.0, 32 bits (SUSE). Now we have changed our system to 64bits (UBUNTU) and we are planning to install FreeSurfer v5.0.0, 64 bits. Do I have to process my data again or can I carry on processing my new data on v5.0.0, 64 bits, and then mix all data (v4.5.0 and v5.0.0) for analysis in v5.0.0? Thank you very much in advance Daniel Ferreira

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nii to label on a surface
by Michael Thomas Smith 02 May '11

02 May '11

Hello, I'm trying to get this ROI drawn on a brain surface. http://www.sal.mvm.ed.ac.uk/images/MT_roi.png To do this, I first ran a script (of the form)[1]: mri_cor2label --i ~/roi.nii --l ~/roi.label --id 1 Then opened the new roi.label file in tksurfer: :~$ tksurfer s01 lh orig The ROI seemed very small and in the wrong place: http://www.sal.mvm.ed.ac.uk/images/MT_scatter2.png http://www.sal.mvm.ed.ac.uk/images/MT_scatter3.png (the purple labelled areas are sulci contours) I'm guessing some form of registration went wrong. I tried to first convert it to .nii/.tgh but using the -rl option of mri_convert: :~$ mri_convert -rl ~/fs_subjects/s01/mri/T1.mgz -rt nearest ~/mainpref_mask_1_3.nii ~/test_mask.mgh This still looked ok, when I checked the ROI. I tried mri_cor2label again, but found the region was still in the wrong place. I figured I needed to give it more info about the surface that it's to be drawn on, so I tried: :~$ mri_cor2label --i ~/test_mask.mgh --l ~/test_mask.label --id 1 --surf s01 lh $Id: mri_cor2label.c,v 1.8.2.2 2009/02/20 16:37:50 greve Exp $ Loading mri /home/s0783410/test_mask.mgh Loading /home/s0783410/fs_subjects/s01/surf/lh.white ERROR: dim mismatch between surface (127260) and input (16777216) but that didn't seem to work. To see what might be going on, I tried out the whole thing on V1, which I got segmented by the v1_segment function I asked about in my last email. The output seemed reasonable: http://www.sal.mvm.ed.ac.uk/images/V1before.tiff and I was able to get it to a nice ROI in a nii file (thanks doug!): http://www.sal.mvm.ed.ac.uk/images/V1_nii.png and I got the nii file back to a surface using: :~$ mri_cor2label --i ~/imageA.nii --l ~/imageA.label --id 1 Then viewing it in: :~$ tksurfer s01 lh orig (and loading the imageA.label file). Which is a little odd: http://www.sal.mvm.ed.ac.uk/images/V1mess.tiff (although it seems to be lined up properly, it has a little extra region selected in the Lingual(?) Gyrus). I thought the difference might be because the V1 ROI came from the original T1 image used by freesurfer, while the ROI I'm trying to use is from a functional image. However, to check, I coregistered (resliced) the function ROI to the original anatomical image, but this didn't seem to make any different. Any suggestions or ideas about where I should be looking? This is I guess one of the most common tasks people use freesurfer for, so I guess I just need to look in the right place for help. Thanks for the help! Mike. [1] Actual output: s0783410@spatial2:~$ mri_cor2label --i ~/mainpref_mask_1_3.nii --l ~/mainpref_mask_1_3.label --id 1 $Id: mri_cor2label.c,v 1.8.2.2 2009/02/20 16:37:50 greve Exp $ Loading mri /home/s0783410/mainpref_mask_1_3.nii ------- Vox2RAS of input volume ----------- -1.719 0.000 0.000 110.003; 0.000 0.000 2.400 -30.001; 0.000 -1.719 0.000 110.003; 0.000 0.000 0.000 1.000; Scanning the volume Found 473 label voxels Writing label file /home/s0783410/mainpref_mask_1_3.label LabelWrite: saving to /home/s0783410/mainpref_mask_1_3.label Centroid: -0.91 -6.49 54.15 mri_cor2label completed SUCCESSFULLY -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Minimum n for glmfit maps?
by Adam Nitenson 02 May '11

02 May '11

Hi Freesurfers, Is there a minimum number of subjects that should be used in isxconcat groups and subsequent glmfit analysis? I recently generated activation maps from a group with only 2 subjects, but the resulting image (too large to attach) is very strage. The activation patterns are "whispy", almost looking like someone just doodled red and blue over parts of the brain, sometimes forming hollow circles. Is this just a consequence of only using 2 subjects or is there another problem I'm missing. I find it strange that both of the subjects' individual maps have rather robust (negative) activation)...much more than the group map would suggest. Another group of three subjects is also a bit strange (not nearly as bad as 2) and it doesn't seem until I reach a group of 4 or 5 that the patterns appear "normal". For the record here are the commands I used: isxconcat-sess -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/Apr2011/2_FB_DEP_TT_1T3T5T7T -d /cluster/roffman/users/Stable5_PerRun -analysis SIRP_Stable5 -c Cond1v3 -c Cond1vFix -c Cond3vFix -c Cond1v5 -c Cond1v7 -c Cond5vFix -c Cond7vFix -hemis -o /cluster/roffman/users/Stable5_PerRun/April_2011/2_FB_DEP_TT_1T3T5T7T mri_glmfit --y /cluster/roffman/users/Stable5_PerRun/April_2011/2_FB_DEP_TT_1T3T5T7T/SIRP_Stable5/Cond1v7/lh.ces.nii --fsgd /cluster/roffman/users/fsgd/April_2011/2_FB_DEP_TT_1T3T5T7T.fsgd --osgm --glmdir /cluster/roffman/users/Stable5_PerRun/April_2011/2_FB_DEP_TT_1T3T5T7T/SIRP_Stable5/osgm/LH1v7 --surf fsaverage lh --fwhm 4.6 Thanks! Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital nitenson(a)nmr.mgh.harvard.edu Phone: 617-643-3215

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inflated surface
by Tetiana Dadakova 30 Apr '11

30 Apr '11

Dear FreeSurfer list, When I look at inflated surface of my subjects (healthy males and females), almost all of them have a concavity in the posterior part of the brain (the arrow in attached image). It doesn't look correct to me. What can cause this problem? Thank you, Tanja.

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distortion of flat map
by Yang Liu 30 Apr '11

30 Apr '11

Hi surfers, I am working on generating surface ROIs from the retinotopy surface. We cut the occipital lobe and draw paths on the flattened map to create labels. However, I found that there are distortions on the flat map that cause large errors when drawing these paths. I attached two pictures. The path_example2_dots.jpg are the dots that I selected to draw a path. Basically it is the method we use to demarcate the boundaries of visual areas. And the path_example2_line.jpg are the line that is supposed to connect the dots and to be the correct boundary. Notice the dots and the line do not overlap! so when I draw a line on the flat map, Freesurfer actually doesn't draw the line I want it to be. Has anyone met this problem before? Is there a better solution to create surface ROIs? Drawing the boundary on inflated surface? Yang

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Compiling stats file for ROI label in QDec
by Krista Kelly 29 Apr '11

29 Apr '11

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