Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

smoothwm.H vs curv
by Chris Adamson 26 Oct '18

26 Oct '18

External Email - Use Caution Freesurfer devs, I want to be able to compute mean curvature in a compatible way to ?h.curv with existing tools but not within the recon-all pipeline. I notice that ?h.curv is written in mris_make_surfaces. I want to just use mris_curvature. This is used to write smoothwm.H. So seemingly I can use mris_curvature to write out the same output as ?h.curv. However, why is ?h.smoothwm.H different to ?h.curv? It seems to be produced with exactly the same code, i.e. MRISComputeMetricProperties, MRISComputeSecondFundamentalForm, MRISuseMeanCurvature, MRISaverageCurvatures ... Thanks in advance, Chris Adamson. Disclaimer This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Children’s Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.

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Freesurfer commands not found - unable to install
by Thaker, Ashesh A 25 Oct '18

25 Oct '18

External Email - Use Caution Dear Freesurfer team, Surely there is a simple fix to my problem, but I've been unable to succesfully run Freesurfer commands after many attempts (with my very basic bash knowledge) and searching prior archives. I'm running Freesurfer on a 64-bit machine, Ubuntu 18.04 LTS. No Freesurfer commands work (files not found), except the "freesurfer" command. I've included some pertinent output below. All of the installation files seem to be in the right place and the path seems to be correct, so I'm perplexed. Any help very much appreciated. Kind regards, Ashesh Thaker, MD | Assistant Professor School of Medicine, Department of Radiology University of Colorado Anschutz Medical Campus  720 848 6568 (office) | ashesh.thaker(a)ucdenver.edu ------------------- ashesh@ashesh-gpu:~$ export FREESURFER_HOME=/usr/local/freesurfer ashesh@ashesh-gpu:~$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl ashesh@ashesh-gpu:~$ recon-all bash: /usr/local/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directory ashesh@ashesh-gpu:~$ freeview bash: /usr/local/freesurfer/bin/freeview: /bin/tcsh: bad interpreter: No such file or directory ashesh@ashesh-gpu:~$ freesurfer FreeSurfer is a set of tools for the analysis and visualization of structural and functional brain imaging data. FreeSurfer also refers to the structural imaging stream within the FreeSurfer suite. Users should consult the online documentation available at: http://surfer.nmr.mgh.harvard.edu Alternatively, the 'recon-all' command help-text provides adequate information to begin processing subject data, such as the sample subject 'bert' found in the 'freesurfer/subjects' directory. Type 'recon-all --help' to view this help-text. Direct comments and questions to: freesurfer(a)nmr.mgh.harvard.edu You are running this version of FreeSurfer: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c ashesh@ashesh-gpu:~$ echo $PATH /usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/fsl/bin:/usr/local/freesurfer/mni/bin:/usr/local/fsl/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin

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Thalamic Nuclei Parcellation Label Files Problem
by zhac looch 25 Oct '18

25 Oct '18

External Email - Use Caution Hello Freesurfer team, I just run code 'Recon-all -all' on my analyzed data. Then, I run the code down below; segmentThalamicNuclei.sh bert [SUBJECTS_DIR] That gave me 3 files named; 'ThalamicNuclei.v10.T1.FSvoxelSpace' 'ThalamicNuclei.v10.T1' and 'ThalamicNuclei.v10.T1.volumes' but I need different label files for each parcels. The thing is I don't know how to do it. Can anyone give an idea to do it? Sorry for my ignorance, as step by step guidance through setting up the parcellation would be much appreciated. Thank you...

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Cortical Parcellations in individual space using Yeo et al 2011
by Bailin, Emma 24 Oct '18

24 Oct '18

Hello, I'm preparing to do resting state analyses and I'd like to use the Yeo 2011 network atlas for the cortical parcellations. Looking through the archive, I know that mri_surf2surf with the -sval-annot flag can be used to convert the fsaverage from the Yeo et al 2011 study to an individual subject space, but I noticed a caveat to this when I called mri_surf2surf -help. The caveat is on example 5: "this is not a substitute for running the cortical parcellation! The parcellations that it maps to the new subject may not be appropriate for that subject." Given this information, I've got a few questions: 1) How accurate is the mapping using mri_surf2surf? That is, is it good for preliminary data, but not for the final analysis? 2) How do you run the cortical parcellation using the Yeo 2011 atlas? [I know that mris_ca_train and mris_ca_label exist, but I'm unsure if they are the right commands to run when I'm not building my own atlas] 3) If I do the cortical parcellations using the Yeo 2011 atlas, will the edits/labels I've done using the Desikan atlas remain accurate? This goes back to the second question, as I'm not sure where in the general processing stage I need to go. Thank you! Sincerely, Emma Bailin Emma Bailin Research Coordinator Laboratory for Visual Neuroplasticity Schepens Eye Research Institute Mass. Eye and Ear Infirmary Harvard Medical School Mass. Eye and Ear Confidentiality Notice: This e-mail and any files transmitted with it are confidential and are intended solely for the use of the individual(s) addressed in the message above. This communication may contain sensitive or confidential information. If you are not an intended recipient, dissemination, forwarding, printing, or copying of this e-mail is strictly prohibited. If you believe you have received this e-mail in error and the email contains patient information, please contact the Mass. Eye and Ear Compliance Line at 844-815-4401. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and delete the e-mail.

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Yeo 2011 Functional Cortical Parcellations
by Bronwyn Overs 24 Oct '18

24 Oct '18

Hi Mailing List, I am attempting to apply the Yeo 2011 7-network fucntional parcellations to a set of fs MRIs processed with v5.1.0. Below are listed the first three steps I plan to take and I am seeking advice as to: A) Whether this approach is valid. B) Steps to take next. * Steps 1-3: * *1. Run MNI152 1mm template through recon-all* recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid Yeo2011_MNI152_FS recon-all -all -subjid Yeo2011_MNI152_FS *2. Warp the Yeo_atlas1mm.nii.gz to freesurfer nonlinear volumetric space* mri_vol2vol --mov Yeo2011_7Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii --s Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o Yeo2011_atlas_FSI.nii.gz --nearest *3. warp the Yeo_atlas_freesurfer_internal_space.nii.gz to each subject:* mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ Yeo2011_atlas_FSI.nii.gz --m3z talairach.m3z --o Yeo2011_atlas_subjID.nii.gz --nearest --inv-morph When previously mapping the Choi 2012 straital parcellations, steps 4 and 5 were: 4. *Creating a striatal mask in the native subject's space from freesurfer segmented Caudate (11 & 50), Putamen (12 & 51), and Accumbens (26 & 58)*: mri_binarize --i subjID/mri/aparc+aseg.mgz --match 11 --match 12 --match 26 --match 50 --match 51 --match 58 --o striatum_mask.nii.gz *5. **Using this mask to mask the choi striatal parcellations* fslmaths Choi2012_atlas_subjID.nii.gz -mas striatum_mask_subjID.nii.gz Yeo_atlas_subjID_mask.nii.gz Do I need to do a similar thing for the Yeo cortical parcellations and if so what regions should I include in the cortical mask? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>

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Is the cortical thickness calculated using Hausdorff distance in FreeSurfer?
by Zhiliang Long 24 Oct '18

24 Oct '18

External Email - Use Caution Dear FS experts: I'm doing a project about the changes of cortical thickness after sleep deprivation. I know that cortical thickness is calculated as the closest distance from the gray/white boundary to the gray/CSF boundary at each vertex. Is the thickness calculated using the Hausdorff distance? Best Zhiliang Long

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freeview error
by zhac looch 24 Oct '18

24 Oct '18

External Email - Use Caution Hello freesurfer team, How can ı fix the problem? Ubuntu-brain:~$ freeview Could not set locale No such file or directory This application failed to start because it could not find or load the Qt platform plugin "xcb" in "". Reinstalling the application may fix this problem. Aborted (core dumped) Ubuntu-brain:~$

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5th ventricle in version 6
by Keedy, Sarah [PSY] 24 Oct '18

24 Oct '18

External Email - Use Caution I’m comparing output of Freesurfer5.2 to 6 on the same set of brains. The “5th ventricle” (Cavum septum pellucidum) is not being detected by 6. I had eyeballed the output from 5.2 and convinced myself it was reasonably well detecting this developmentally abnormal finding pretty well. I am wondering what changed in version 6, if anything, that could explain this?

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Surface-based analysis of tfMRI
by Zhi Li 23 Oct '18

23 Oct '18

External Email - Use Caution Hi FreeSurfer Experts, I am trying surface-based analysis of task-fMRI with FS-FAST. However, I would like to apply ICA-based denoising and wavelet-despiking which can be not done with the 'preproc-sess'. I wonder if I can do the preprocessing with other tools before registration with FS anatomical and normalization? If it is available, how can I do it with command line? Another question is if can I use other template for parcellation during using 'recon-all', such as the template of Human Connectome Project? Looking forward to your kind reply. Thank you and best wishes, Zhi

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How to export the image and label
by Min Zhang 23 Oct '18

23 Oct '18

External Email - Use Caution Dear FreeSurfer Team : I used the freeSurfer brainstem structure to segment the brainstem from the MRI successfully. But I have several questions as followed: 1. I want to export this data in dcm file with all the ROI information, what should I do? 2. How to manually adjust the boundaries of existing brainstem segmentation results? 3. How to generate surface of brainstem based on the segmentation. Many Thanks! Best Jackie

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