Freesurfer

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30096 discussions

rs-fMRI data on pial surface
by René Besseling 15 May '13

15 May '13

Hi Freesurfers, For this analysis I plan to do, I want to map resting-state data in native (T1) space to the pial surface. The command I use for this is: mri_vol2surf --src fMRI_nat.nii --regheader subjID --hemi lh --projfrac-avg 0 1 0.05 --surf pial --o fMRI_2surf.mgh So the intention is to average the resting state data over the cortex and to map this to the pial surface. However, if I'm not mistaken the --projfrac-avg option projects along the outward pointing surface normal. Therefore, when using the pial surface, I expected that the proper call would be --projfrac-avg 0 -1 -0.05. However, this command does not run, whereas the command given above does, and yields (sensible) output. So is the command given above correct after all? And does this imply that for the pial surface, the volumetric data is actually projected along the inward pointing normals? Best regards, René

2 3

mri_glmfit error with design matix
by Sinead Kelly 15 May '13

15 May '13

Dear Members, I am using mri_glmfit for the first time with the .fsgd file below, however, I am receiving the following error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. I have also pasted the design matrix below as I cannot figure out what is wrong with it. I would really appreciate if anyone could help me this issue. Also note that I am running this for just a subset of my total data set as a test before I run it on my full data set. Thank you very much for your help, Sinead GroupDescriptorFile 1 Title MIR137 Class TGFemale Class TGMale Class TTFemale Class TTMale Variables Age Input CON3140/001 TGFemale 37 Input CON3891/001 TTFemale 33 Input CON4664/001 TTFemale 40 Input CON5591/001 TTMale 41 Input CON7009/001 TGMale 21 Input CON7024/001 TTMale 59 Input CON7038/001 TTMale 56 Input CON7050/001 TTMale 30 Input CON7054/001 TTMale 43 Input CON7055/001 TTMale 43 Input CON7072/001 TTFemale 41 Input CON7082/001 TTFemale 29 Input CON7087/001 TTFemale 23 Input CON7090/001 TGFemale 59 Input CON7092/001 TTFemale 21 Input CON9004/001 TGFemale 28 Input CON9009/001 TTMale 42 Input CON9040/001 TTMale 56 Input CON9064/001 TTMale 55 Input CON9069/001 TGFemale 54 Input CON9070/001 TTFemale 55 Input CON9081/001 TTFemale 50 Input CON9091/001 TTMale 27 Input CON9093/001 TTMale 54 DefaultVariable Age Normalized matrix condition is 1e+08 Design matrix ------------------ 1.000 0.000 0.000 0.000 37.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 33.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 40.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 41.000; 0.000 1.000 0.000 0.000 0.000 21.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 59.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 56.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 30.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 43.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 43.000; 0.000 0.000 1.000 0.000 0.000 0.000 41.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 29.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 23.000 0.000; 1.000 0.000 0.000 0.000 59.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 21.000 0.000; 1.000 0.000 0.000 0.000 28.000 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 42.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 56.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 55.000; 1.000 0.000 0.000 0.000 54.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 55.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 50.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 27.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 54.000; -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8

2 1

Recon-all error
by Borzello, Mia 15 May '13

15 May '13

Hi freesurfers, I recently ran a reconstruction, but it's errored. I'm not sure why thought, but I've attached the recon log. Thanks, Mia

3 4

beta v5.3 for fedora 18 and ubuntu 13
by Nick Schmansky 15 May '13

15 May '13

Fedora 18, Ubuntu 13 and Gentoo 64 users, another beta of the upcoming v5.3 is available here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/freesurfer-… this one is just intended for the Fedora 18, Ubuntu 13, Gentoo 64 users who wished to test that the segfault problem in v5.2 and the prior beta v5.3 is fixed. Your help in testing this release is appreciated. Thanks, Nick

4 7

problem with func2roi-sess
by jwaugh＠nmr.mgh.harvard.edu 14 May '13

14 May '13

Hello Freesurfers, I would appreciate any advice or help you can provide. I am using the following command, run under Stable 3 (to keep the current analysis comparable to prior papers): func2roi-sess -roidef MedOrbitofrontal_LH_t6_0_sm5_0thresh -analysis newROIs_tap_lh_long_CD_R01BTX_pat9_sess1_sm5 -maskcontrast newROIs_tap_lh_long_CD_R01BTX_pat9_sess1_sm5_contrast -labelfile /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_R01BTX_pat9_sess1_recon/label/MedOrbitofrontal_LH_CD_R01BTX_pat9_sess1.label -maskthresh 6.0 -masktail pos -maskmap t -s CD_R01BTX_pat9_sess1 -df sessdirfile The error message is as follows (it outputs exactly like this, apparently intermingled with another output): ras2vox src (tkreg) Qsrc ------------- -0.320 -0.000 -0.000 32.000; -0.000 -0.00mri_vol2roi: could not scan # of lines from /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_R01BTX_pat9_sess1_recon/label/MedOrbitofrontal_LH_CD_R01BTX_pat9_sess1.label No such file or directory 0 -0.320 32.000; 0.000 0.200 0.000 15.000; 0.000 0.000 0.000 1.000; I have never seen this error before - any suggestions why I'm getting it? This same command structure ran perfectly on separate ROIs over the last few days. I confirmed that the corresponding .label files are structured identically to those for other ROIs that worked. Just in case it's helpful, this is the command that I used to generate the .label files: mri_cor2label --c /cluster/ablood/1/${experimental_directory}/${recons_directory}/${identifier}_recon/mri/aparc+aseg.mgz --id 1014 --l /cluster/ablood/1/${experimental_directory}/${recons_directory}/${identifier}_recon/label/MedOrbitofrontal_LH_${identifier}.label. Thank you! Jeff

2 2

averaging lh and rh thickness maps on fsaverage_sym surface
by Subhabrata Chaudhury 14 May '13

14 May '13

Hi, I want to create an average thickness map of lh and rh. I have run surfreg steps to map lh to lh sym and rh to rh sym. Can you advise what to do next to mke average thickness maps between two hemispheres ? Will either mris_calc or mri_average work to make the average map ? Thank you Subha

2 1

Problems with hippocampus subfields segmentation
by Lukas.Scheef＠ukb.uni-bonn.de 14 May '13

14 May '13

Hi FreeSurfer Experts! I try to run the hippocampus subfield reconstructions. Because I already run reconall -all on my subjects (without errors, all necessary manual edits were done) I try to reconstruct only the hippo-subfields: recon-all -s my_subjects -hippo-subfields The shell output is given below... Any ideas? Best wishes, Luke Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 INFO: SUBJECTS_DIR is /Users/lscheef/Desktop/subjects Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 lscheef staff 490363 May 14 20:08 /Users/lscheef/Desktop/subjects/p119/scripts/recon-all.log Darwin luke 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 #-------------------------------------------- #@# Hippocampal Subfields processing Tue May 14 20:16:08 CEST 2013 \n mkdir -p /Users/lscheef/Desktop/subjects/p119/tmp/subfieldResults \n kvlSegmentHippocampalSubfields.sh p119 left /Users/lscheef/Desktop/subjects /Users/lscheef/Desktop/subjects/p119/tmp/subfieldResults \n Doing left side meshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gz compressionLookupTableFileName: /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt boundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgz subjectName: p119 side: left inputDirectory: /Users/lscheef/Desktop/subjects outputDirectory: /Users/lscheef/Desktop/subjects/p119/tmp/subfieldResults directory /Users/lscheef/Desktop/subjects/p119/tmp/subfieldResults/p119 already exists directory /Users/lscheef/Desktop/subjects/p119/tmp/subfieldResults/p119/left already exists cd /Users/lscheef/Desktop/subjects/p119/tmp/subfieldResults/p119/left cp -f /Users/lscheef/Desktop/subjects/p119/mri/nu.mgz . cp -f /Users/lscheef/Desktop/subjects/p119/mri/aseg.mgz . cp -f /Users/lscheef/Desktop/subjects/p119/mri/transforms/talairach.xfm . cp /Applications/freesurfer/data/GEMS/imageDump.mgz . kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 dyld: Library not loaded: libITKCommon.3.16.dylib Referenced from: /Applications/freesurfer/bin/kvlApplyTransform Reason: image not found /Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 89411 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 failed to do kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 Darwin luke 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 recon-all -s p119 exited with ERRORS at Tue May 14 20:16:08 CEST 2013

2 1

Rejoindre mon réseau sur LinkedIn
by Soo-Eun Chang 14 May '13

14 May '13

LinkedIn ------------ Soo-Eun Chang souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Soo-Eun Chang http://www.linkedin.com/e/-qq80um-hgp5ye8d-68/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir le profil de Soo-Eun Chang http://www.linkedin.com/e/-qq80um-hgp5ye8d-68/rso/76206546/HgJj/name/664711… ------------------------------------------ Vous recevez des invitations par e-mail. Cet e-mail est destiné à Freesurfer List. Découvrez pourquoi nous avons inclus ceci : http://www.linkedin.com/e/-qq80um-hgp5ye8d-68/plh/http%3A%2F%2Fhelp%2Elinke… (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.

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Re: [Freesurfer] Show curvature and show overlay
by Irina Simanova 14 May '13

14 May '13

Dear freesurfer experts, I am new to freesurfer and I want to project my single-subject MVPA (obtained in Matlab) results on a single-subject brain surface with curvature. I followed the steps from the tutorial: - reconstructed individual subject's brain surface - wrote my MVPA results map as a nifti image - resampled the map onto the surface Now I want to visualize it. The tutorial (http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/NavigateResampledParametri…) suggests to use qsurfer, however I don't seem to have this command. I tried to open the surface with tksurfer and then load the overlay, as described in the tutorial on visualization. However, when I open an inflated surface file, both buttons "show overlay" and "show curvature" are not active (though I have the .sulc file in the /surf). This is probably a very simple question, but I am stuck here. I would appreciate any advise on how to do the visualization: either from the command line or with tksurfer tools. thank you, kind regards, Irina Simanova

2 1

hematoma problem
by LAOUCHEDI MAKHLOUF 14 May '13

14 May '13

hi I am working on severe TBI and most of them suffer from large hematoma and according to litterarture, the apearance on T1 changes accordind to the stage of the trauma, from 3days (early suba acute) to 14 days (late subacute) the T1 signal from hematoma is Hyperintense and after that it becomes hypointense. I want to know how freesurfer, especially the skull stripping or brain extraction step, deals with these two cases (i have both in my database). I want later to extract the cortical ribbon for tractography use. Thanks

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