Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30063 discussions

Creating functional ROI
by a a 09 Nov '17

09 Nov '17

Dear FreeSurfer community, I am new to FreeSurfer and I apologize in advance if my questions are too naiive. I have some nii files for both a localizer and an experiment. I would like to find some ROIs in the localizer, get their coordinates, create a mask, and then find those regions on the experiment data and run MVPA. My main goal is to keep everything in the native space. Also, I am looking for percent signal change in selected ROIs. Here is my approach to analyze the localizer data: First, I ran the recon-all command. Then, I preprocessed the data in native space. The command that I ran was: preproc-sess -s sess01 -fsd bold -stc odd -surface self lhrh -mni305 -fwhm 5 -per-session -force Then, I configured my analyses and contrasts in each hemisphere, as well as the volume. Finally, I ran the analyses for each hemispheres and the volume. I ran this command: selxavg3-sess -s sess01 -analysis ffa.native.rh Lastly, I visualized the results by running these commands: tksurfer-sess -s sess01 -hemi rh -analysis ffa.native.rh -c faces-vs-bodies -self tkmedit-sess -s sess01 -analysis ffa.native.mni -c faces-vs-bodies -self So far, I think I have done everything correctly as am seeing the activation map where I am supposed to. Now, I would like to be able to select some of these ROIs/clusters, take their voxel coordinates/numbers and create a mask. Then, use this mask on the main experiment (non localizer) nii files and get the signal value for only those voxels. Is this possible? I have found this tutorial to create a functional ROI https://surfer.nmr.mgh.harvard.edu/fswiki/CreatingROIs but unfortunately I am not following it. I don't see these options in tksurfer. Also is it possible to create an ROI on the surface? I appreciate any help. Thank you so much Ashley Cole

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preproc-sess with symbolic links
by Tuominen, Lauri Johannes 09 Nov '17

09 Nov '17

Hi all, I’m trying to run preproc-sess using symbolic links in my SUBJECTS_DIR but the program exists with error message: could not find session XXXX. Symbolic links work fine when I run recon-all for instance. Suggestion for a fix would be greatly appreaciated. Cheers! Laurio

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Creating cached versions of Xhemi registrations
by Mehta, Chintan 09 Nov '17

09 Nov '17

Dear FreeSurfer Users, I'm using FreeSurfer version 6.0. I've processing subjects with recon-all and performed surface-based interhemispheric registration (via Xhemi at https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi) I want to run a GLM on the subjects Area and Thickness from the differences (Left minus Right). When stacking subjects asymmetry maps, I wanted to use a "--cache-only". The post at https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg27657.html seems to imply this requires running > recon-all -qcache -measure area -target fsaverage_sym -fwhm 10 -no-isrunning -s subjid -hemi lh for area at FWHM = 10. This would create files with the left hemisphere area registered to fsaverage_sym at smoothing FWHM = 10: $subjid/surf/lh.area.fwhm10.fsaverage_sym.mgh However, how do I do this also for the xhemi registration? I.e. create a file like $subjid/xhemi/surf/lh.area.fwhm10.fsaverage_sym.mgh Then, if I do this, can I stack the subjects using something like: > mris_preproc --target fsaverage_sym --hemi lh --xhemi --paired-diff \ --srcsurfreg fsaverage_sym.sphere.reg \ --cache-in area.fwhm10.fsaverage_sym \ --out lh.lh-rh.area.sm10.mgh \ --s subj1 --s subj2 ... Thank you. Best, Chintan mris_preproc --target fsaverage_sym --hemi lh --xhemi --paired-diff \ --srcsurfreg fsaverage_sym.sphere.reg \ --meas thickness \ --out lh.lh-rh.thickness.sm00.mgh \ --s subj1 --s subj2 ...

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Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0
by Mehta, Chintan 09 Nov '17

09 Nov '17

Dear Doug, Are there reasons why registering to my_subject_average (template defined from, say, average in a cross-sectional sample) can be better than registering to fsaverage? Thank you. Best, Chintan

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Local gyrification index - vertex-wise analysis values
by Buse Merve Ürgen 09 Nov '17

09 Nov '17

Dear Freesurfer developers, I would like to run Local Gyrification Index analysis for a group of healthy controls and a single patient. After running recon-all -s <subj> -localGI command, we get lh.pial_lgi and rh.pial_lgi surf files. In the last stage of this analysis, local gyrification index values are calculated at each pial vertices. In the wiki, it is said that the next process should be done in qdec, but since I have only one patient, GLM analysis would not be suitable. Thus, I would like to get the LGI values of each subject as e.g. text files (like stats files for curvature, thickness, gm volume), and use them for my own analysis (not in qdec). I know that we can get parcel-wise anaysis values using this command: mri_segstats --annot CASE lh aparc \ --i $SUBJECTS_DIR/CASE/surf/lh.pial_lgi \ --sum lh.aparc.pial_lgi.stats But I would like to use vertex-wise analysis values for my won analysis. Is it possible? Can I learn the command I need to use to get these values for each subject? Thank you, Buse -- Buse Urgen

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Repeated amygdala dev7-segmentation volumes do not correspond
by Reetta-Liina Armio 09 Nov '17

09 Nov '17

Hi! I have done twice the analysis of amygdala segmentation (dev 7 version) with exactly same way. The volumes do not correspond each other and there is approximately 2mm3 difference in volumes randomly in either direction. Is this normal or is it something to do with the dev 7 version? Should I be worried? Thank you! Best, Reetta-Liina Armio

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Where is the result of mris_pmake ?
by Hyungjun Kim 09 Nov '17

09 Nov '17

Dear surfers, I am trying to measure the distance between two activated vertices... Now, I run "mris_pmake --optionsFile=options.txt" and here is the options.txt file below ************, But I did not get any result on the window or ./ores.log file... How can I get the result from mris_pmake ? Thanks in advance. Hyungjun Kim (Korea Institute of Oriental Medicine) ******************* # # auto-generated optionsFile # # Input surfaces and curvature functions surfaceFile = /mnt/data1/subjects/csm0928/surf/lh.inflated auxSurfaceFile = /mnt/data1/subjects/csm0928/surf/lh.smoothwm curvatureFile = /mnt/data1/subjects/csm0928/surf/lh.smoothwm.H.crv sulcalHeightFile = /mnt/data1/subjects/csm0928/surf/lh.sulc # Start and End vertices startVertex = 1803 endVertex = 44765 # Control flags and settings controlPort = 1701 timeoutSec = 60 b_transitionPenalties = 0 b_syslogPrepend = 1 b_patchFile_save = 0 b_labelFile_save = 1 b_useAbsCurvs = 0 b_exitOnDone = 1 b_costPathSave = 0 # Output file names and file stems costFile = cost.txt patchFile = dijk labelFile = dijk labelFileAuxSurface = dijkAuxSurface # Messaging channels userMessages = ./user_msg.log sysMessages = ./osys.log resultMessages = ./ores.log # Weights wd = 1.000000 wc = 0.000000 wh = 0.000000 wdc = 0.000000 wdh = 0.000000 wch = 0.000000 wdch = 0.000000 wdir = 0.000000 # Transitional penality weights Dwd = 1.000000 Dwc = 1.000000 Dwh = 1.000000 Dwdc = 1.000000 Dwdh = 1.000000 Dwch = 1.000000 Dwdch = 1.000000 Dwdir = 1.000000 # mpmProg mpmProgID = 2 mpmArgs = startVertex:1803,endVertex:44765 costCurvFile = lh.autodijk.crv # mpmOverlay mpmOverlayID = 3 # Debugging -- change at your own risk! b_mpmProgUse = 1 b_mpmOverlayUse = 0

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Re: [Freesurfer] mris_pmake
by Hyungjun Kim 08 Nov '17

08 Nov '17

Dear Surfer & Rudolph, Hi, I tried to run mris_pmake, but only got this message: I'm sorry, but an error condition has occurred. While I was checking on the options file, I couldn't access the options file. Does it exist? How can I use mris_pmake? I'm working with Vitaly Napadow, and I would like to measure the distance between peak activated voxels on somatotopic stimulation. (I'm running Freesurfer 5.3 stable version on CentOS 6.7 (64 bit machine)) Thanks in advance! Hyungjun Kim Senior Researcher Korea Institute of Oriental Medicine

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Postdoctoral Research Associate in neuroimaging/data science
by Dayan, Eran 08 Nov '17

08 Nov '17

A Postdoctoral Research Associate position is immediately open to work with the Network Neuroscience lab (dayanlab.web.unc.edu<http://neurojobs.sfn.org/jobs/10443717/dayanlab.web.unc.edu>) at the Biomedical Research Imaging Center, University of North Carolina at Chapel Hill. The position is open to accomplished and highly motivated candidates, with an interest in neuroimaging and clinical neuroscience. The lab focuses on fundamental questions relating to brain network organization in health and disease, while aiming to develop methods and tools that could eventually be used in the clinic. The Postdoctoral Research Associate will develop and test a dimensional analysis framework for neurological dysfunction, using rich existing multimodal neuroimaging datasets obtained from patients and age-matched controls. Ample training and career development opportunities will be provided, as well as opportunities to collaborate with other groups at UNC. Ph.D. or an MD/Ph.D. in Neuroscience, Computer Science, Biomedical Engineering, Physics, Psychology or other related fields is required. Excellent quantitative background, relevant programming experience (MATLAB, Python or R), experience analyzing functional and/or structural MRI data and a track record of first-author publications in peer-reviewed journals are required. Experience in machine learning (particularly deep learning) would be advantageous. To apply, please visit https://unc.peopleadmin.com/postings/107413 and click the Apply for this Job link/button. For informal inquiries about the position, please email Dr. Eran Dayan at: eran_dayan(a)med.unc.edu The University of North Carolina at Chapel Hill is an equal opportunity and affirmative action employer. All qualified applicants will receive consideration for employment without regard to age, color, disability, gender, gender expression, gender identity, genetic information, race, national origin

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functional to anatomical registration
by David Beeler 08 Nov '17

08 Nov '17

Hi freesurfer people, I'm trying to understand preprocessing a little better, especially registration of functional data to anatomical space. I am currently running everything in the volume, doing motion correction per-run and then pooling all the runs in the session together for the first level analysis. As far as I can tell, running preproc-sess with -per-run takes the raw functional data (f.nii.gz), pulls out the middle timepoint and calls it template.nii.gz, bbregisters func to anat and creates a register.dof6.lta file in each of the functional run folders, transforms the aparc+aseg from the subject's mri folder and binarizes it into a brainmask (brain.nii.gz), and runs mc-afni using f.nii.gz as the input vol and template.nii.gz as the template vol to create the motion corrected volume (fmcpr.nii.gz). Is this correct? Then when I run selxavg3-sess it somehow mri_converts an intermediary motion corrected volume from the mc-afni command above (eg <run#>/tmp.mc-afni2.20097/outvol.nii.gz) into an fmc.nii.gz file in each run folder. Are these fmc.nii.gz's supposed to be coregistered between runs? (i.e. if the subject moved a bunch between two of the runs, would those two volumes be aligned at all?). How do these files work? At the end I have an analysis directory with my betas, sigmaps, etc. What functional volume is everything registered to? Is the transform between this functional volume and anatomical space the register.dof6.lta file located in the session directory? Thanks for bearing with me! -David

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