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30132 discussions

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

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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

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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

2 1

using T2* weighted scans to assist with dura stripping in a GE scanner?
by Katie Surrence 13 May '13

13 May '13

Dear Freesurfer gurus, At the course, André van der Kouwe mentioned in his morphometry methods talk that T2* weighted contrast from MEMPRAGE could be used to further seperate dura from cortex, as also discussed in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/. We have a GE scanner in our lab. The internet suggests that a Multi-echo FSPGR/FGRE exists. Would this be the analog? Would it work the same way? Could you also use these images with the mris_make_surfaces command? Thanks very much for your insight -- and I enjoyed the course! /Katie Surrence -- Research Coordinator Social Cognition Laboratory New York State Psychiatric Institute

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Re: [Freesurfer] Very simple question about Paired Analysis
by Douglas N Greve 13 May '13

13 May '13

Hi Jamie, did you look at the help for mri_glmfit? Run it with --help. doug ps. Please post questions to the list so that others can benefit. thanks! On 05/13/2013 04:12 PM, Jaime Ide wrote: > Dear Douglas, > > Thanks for your helpful page at > https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis > > I am having problems in the last step running mri_glmfit. > It should be a very simple bug to fix... > *"ERROR: you must use '--surface subject hemi' with surface data"* > (the complete message is at the bottom of this email..) > > I wonder to know if you could help me on this. > Thanks very much in advance, > Jaime > > > ***************************************** > cmdline mri_glmfit --glmdir lh.paired-diff --y > lh.paired-diff.thickness.sm05.mgh --fsgd paired-diff.fsgd --C mean.mtx > sysname Linux > hostname unifesp-monkey3 > machine x86_64 > user jaime > FixVertexAreaFlag = 1 > UseMaskWithSmoothing 1 > OneSampleGroupMean 0 > y /home/jaime/ji_freesurfer/ji_scripts/lh.paired-diff.thickness.sm05.mgh > logyflag 0 > usedti 0 > FSGD paired-diff.fsgd > glmdir lh.paired-diff > IllCondOK 0 > ReScaleX 1 > DoFFx 0 > Creating output directory lh.paired-diff > Loading y from > /home/jaime/ji_freesurfer/ji_scripts/lh.paired-diff.thickness.sm05.mgh > *ERROR: you must use '--surface subject hemi' with surface data* > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Resting state analysis
by Efrat Kliper 13 May '13

13 May '13

Dear freeSurfer expert, I am trying to perform whole brain functional connectivity analysis Is there a wiki for resting state analysis? I have only found this wiki page https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastPreProc So far I have run the following commands: preproc-sess -s TB_482 -fsd Rest -stc odd -surface fsaverage lhrh -mni305 -fwhm 5 -per-run What is the next step? Should I use the mkanalysis-sess command? (mkanalysis-sess -TR 3 -fsd Rest -stc odd -surface fsaverage lh -mni305 2 -fwhm 5 -analysis TB_482_lh -notask)? Running this command it seems to create only an output file with a list of information and nothing more, what am i doing wrong? In addition for resting state analysis, band filter of 0.01-0.08Hz needs to be done. How do i do that and to which of the output files? I don’t find any record about that either. Thanks in advance, Efrat

2 1

LGI radius on outer surface ?
by Gregory Kirk 13 May '13

13 May '13

Hello Im preparing an LGI(local gyrification index) manuscript and seems i don't know the default radius that is used for the circular region defined on the outer surface that the boundary of is then projected onto the pial surface to get the corresponding pial region ? hope im clear, not the radius of the closing operator. thank you Greg

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