Freesurfer

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Open positions at The Ohio State University: Post-dococtoral Researcher, Psychometrician, & Study Coordinator
by Teng, James 11 Oct '21

11 Oct '21

External Email - Use Caution The Clinical Neuroscience Lab, in the Department of Psychology, within the College of Arts and Sciences, seeks a Post-Doctoral Researcher (R29059), a Psychometrician (R13824), and a Study Coodinator (29068) to join our team. The Clinical Neuroscience Lab is directed by Dr. Ruchika Prakash, and the laboratory is funded by the National Institute on Aging to conduct a randomized controlled trial of mindfulness meditation for older adults in the Columbus community. The lab recently received additional funding to increase the representation of Black, Indigenous, and/or People of Color in our clinical trial. We are excited to receive this funding, and we hope to find a candidate who is passionate about working with diverse communities and individuals. Apply online at: https://secure-web.cisco.com/11XZ7GSpquo2K34Cy2WyF2fIiLSV2uXiUNvLonCYJRP5v6… under the respective job listings Post-Doctoral Researcher (R29059), Psychometrician (R13824), and Study Coodinator (29068), and submit a CV, a brief statement of your research interests, your expected date of availability, and the names and contact information of three references. If you have questions about the position or the lab, please contact Dr. Ruchika Prakash at prakash.30(a)osu.edu. Lab Website: https://secure-web.cisco.com/1br5PNyboP4J53ZddAEBfrlv5QBGhIfyia8PupfmAqaxSL… To build a diverse workforce, The Ohio State University encourages applications from all individuals. Ohio State is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to age, race, color, religion, sex, sexual orientation, gender identity, national origin, disability status, or protected veteran status.

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error using mri_convert
by Rizzo, Nolan W 11 Oct '21

11 Oct '21

External Email - Use Caution Hello FreeSurfer developers, I am attempting to use mri_convert to convert DICOM files to a NIfTI file. The DICOM images were obtained from a Siemens 3T Prisma scanner with VE11C software version. When mri_convert is run to convert the .dcm files to .nii , an error occurs that displays "bad fd number". I believe the problem occurs when mri_convert is trying to decompress the new JPEG format of the DICOM files. I have listed the FreeSurfer version and OS that I used below. Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 Platform: Ubuntu 16.04 This error did not occur when running mri_convert on the Mac version of FreeSurfer using OS Mojave. The same DICOM files (as above) were used. mri_convert ran without error and produced the .nii file. Thank you.

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Question about fsaverage
by Dongyue Zhou 11 Oct '21

11 Oct '21

External Email - Use Caution Dear FreeSurfer experts: I use the 'qcache' command to get the file '$SUBJECTS_DIR/subjectname/surf/?h.thickness.fwhm10.fsaverage.mgh'. I can get cortical thickness in each vertice by reading this file in matlab. And I know mean CT is computed by dividing sum CT of all ROI vertices by the number of ROI vertices. Is there any way I can get annot for this file in one sub?

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Question about fsaverage
by Dongyue Zhou 10 Oct '21

10 Oct '21

External Email - Use Caution Dear FreeSurfer experts: I want to know cortical thickness in this file 'subjectname/surf/?h.thickness.fwhm10.fsaverage.mgh' is in standard space or in native space. Is not the common coordinate system the same as standard space? And if mean ROI CT measures computed by this file is the same as that computed by file 'subjectname/stats/?h.thickness'. If not,I want to use fsaverage file to compute mean CT measures of each ROI,how should I locate each region?

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Faculty positions at Bilkent University
by Burcu Ayşen Ürgen 10 Oct '21

10 Oct '21

External Email - Use Caution Dear colleagues, Bilkent University has 3 open faculty positions whose details are provided in the links below: *Open-Rank Position at the Department of Psychology, Bilkent University <http://secure-web.cisco.com/1CBqMH2JwP6VpxGPSQ2fHpMHy2LrnuWlgqgU4BIzznq158h…>**Instructor Position at the Department of Psychology, Bilkent University <http://secure-web.cisco.com/1zzq8SzN6sb5MNAZIAqG2QGQ-X7Rcx-WGxTkSG0U8Q5fe7N…>* *Instructor Position in Clinical Psychology at the Department of Psychology, Bilkent University* <http://secure-web.cisco.com/13cr6VZPX_m3HoJr7YJojYmAJf-1o94zUIt3T94wiIPjdLh…> Best, Burcu -- Burcu Ayşen Ürgen, PhD Assistant Professor Department of Psychology Interdisciplinary Neuroscience Program Aysel Sabuncu Brain Research Center National Magnetic Resonance Research Center Bilkent University 06800, Bilkent, Ankara, Turkey Email: burcu.urgen(a)bilkent.edu.tr Website: http://secure-web.cisco.com/1hAG7qa7TBljujr0-X4ey49D3mc8zT6LU6tB2fC6Yo1cVeq… Lab: http://secure-web.cisco.com/1eDYIkzVTvrjlW2_2UoP-GIY_kcwVXVlGGclZJr-iMYDkTh… Tel: +90 312 290 30 91 or +90 312 290 1807

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Freesurfer version help
by Annalisa Lella 09 Oct '21

09 Oct '21

External Email - Use Caution Hi, I was wondering if you could help me or give me more information. I have pre-processed my MRI data using FreeSurfer version 7.0, which has been recalled. I used the same version for the thalamic segmentation. I have elaborated my data one year ago. Do I have to pre-process all my data again? I randomly segmented few subjects with versions 6.0 and 7.2 and I implemented a visual quality check but it seems to me that the images segmented with version 7.0 are good. I runned also t-tests between the extracted cortical volumes of the three versions and there are overall few differences across the versions. Where could I see if my data are not good? Which are the effects of the bug in version 7.0? Thanks a lot for any help you could give to me! Best regards, Annalisa Lella

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individual analysis and visualization
by Zeng, Qi 08 Oct '21

08 Oct '21

External Email - Use Caution Hi Experts, If I want to analyze and visualize baseline and follow-up for an individual subject's change (before-after & after-before). Should I treat it as a cross-sectional analysis for a group analysis? Best, Zeno

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Not seeing effects of manual edits and re-running recon-all
by Kevin Miller 08 Oct '21

08 Oct '21

External Email - Use Caution Hi, I am new to recon-all and Freesurfer and I am having some difficulty tracking down the resulting outputs from when I re-run recon-all or they are not taking hold. So far I have edited two subjects after the initial run by lowering the ws height for the skullstrip in one and by adding white matter voxels by in the other. I followed all the tutorial instructions for both, starting with the edits and including the appropriate recon-all commands, which supposedly finished without error. However, after viewing the new volumes that were overwritten the day they were run, neither seem to have changed. For the wm.mgz, even, the wm voxel edits still exist as though recon-all did not run. If anyone has any tips for finding the proper outputs or what I might be doing incorrectly, I would greatly appreciate any advice. Thanks

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Fmriprep transform matrix
by I. Kelleher-Unger 08 Oct '21

08 Oct '21

External Email - Use Caution Hi there, I have used fmriprep to preprocess my BOLD data. One of the outputs of this pipeline is a T1w-to-MNI transformation matrix in h5 format. I wanted to know if it is possible to apply this transformation with freesurfer tools? Thanks! Isaac

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glmfit sig file all zeros
by Pedersen, Walker Scott 08 Oct '21

08 Oct '21

Hi, I am running glmfit on some functional data (using ces.nii.gz surface files as input) using ROIs and the --mask argument, that I plan to later submit to glmfit-sim for small volume correction. I have some rois that are subcortical and some that are surfaces. For the glmfit run within the surface ROIs the output sig.nii.gz files all voxels have a value of zero. However, this is not the case for the F.nii.gz and z.nii.gz files output by the same glmfit command - they have non-zero voxels. This issue only occurs for the surface ROIs, when I run glmfit in subcortical ROIs the sig.nii.gz files look normal. The surface ROIs were created by using afnis 3dundump to create 10mm spheres from MNI coordinates. I then ran the MNI template through freesurfer, and used the regheader from this to run mri_vol2surf to put the spherical ROIs into fsaverage space. I am able to view the resulting surface ROIs projected onto the fsaverage surface in freeview, and have checked that my ces.nii.gz function files can also be overlayed onto the same fsaverage template in freeview. The output of one of the glmfit commands in question is below. thanks! WARNING: gdfReadV1: no variables on 'Variables' line found Reading source surface /autofs/cluster/neuromod/programs/freesurfer_7.1.1/freesurfer/subjects/fsaverage/surf/lh.white gdfRead(): reading /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/inputFiles/ /fsgd.txt INFO: gd2mtx_method is dods Number of vertices 163842 Number of faces 327680 Total area 65417.000000 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195472 7.1.1 cwd /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast cmdline mri_glmfit --glmdir /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lC S+E_m_lCS-atCS+E/outputFiles/lIFG/ --y /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/concat/postMpre/recal l//recall.sm5.lh/lCS+E_m_lCS-atCS+E/ces.nii.gz --surf fsaverage lh --fsgd /autofs/space/uriline_003/users/projects/OC D_NM/walker_pedersen/data/image/main/recall/inputFiles//fsgd.txt --C /autofs/space/uriline_003/users/projects/OCD_NM/ walker_pedersen/data/image/main/recall/inputFiles//groupDiff.mtx --nii.gz --mask /autofs/cluster/neuromod/NIFTI/OCD_N M/derivatives/fsfast/rois/recall/lIFG_surf_rad10.nii.gz --eres-save sysname Linux hostname r440-28.nmr.mgh.harvard.edu machine x86_64 user wsp6 FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/concat/postMpre/recall/recall.sm5.lh/lCS+E_m_lCS-atCS+E /ces.nii.gz logyflag 0 usedti 0 FSGD /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/inputFiles//fsgd.txt mask /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/rois/recall/lIFG_surf_rad10.nii.gz maskinv 0 glmdir /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lCS+E_m_lCS-atCS+E/outp utFiles/lIFG/ IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lCS+ E_m_lCS-atCS+E/outputFiles/lIFG/ Loading y from /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/concat/postMpre/recall/recall.sm5.lh/lCS+E_m_ lCS-atCS+E/ces.nii.gz ... done reading. INFO: gd2mtx_method is dods Saving design matrix to /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lCS+E_ m_lCS-atCS+E/outputFiles/lIFG//Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1.125 Pruning voxels by thr: 1.175494e-38 Found 512 voxels in mask Saving mask to /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lCS+E_m_lCS-atC S+E/outputFiles/lIFG//mask.nii.gz Reshaping mriglm->mask... search space = 222.026773 DOF = 15 Starting fit and test Fit completed in 0.0002 minutes Computing spatial AR1 on surface Residual: ar1mn=0.987586, ar1std=0.043927, gstd=3.620916, fwhm=8.526606 Writing results groupDiff MRImask(): AllowDiffGeom = 1 INFO: MRImask() using MRImaskDifferentGeometry() maxvox sig=-0 F=4.36504 at index 391 0 0 seed=1632900996 mri_glmfit done

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