Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Creating anatomical ROI's
by Daniel Callow 09 Apr '19

09 Apr '19

External Email - Use Caution Hello, I am trying to create ROI volumes from the hippocampal subfields I get from mri_vol2vol --mov /Volumes/DANIEL/dti_freesurf/dtrecon/${cond}.${subj}/lowb.nii.gz --targ /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/mri/lh.hippoAmygLabels-T1.long.v21.HBT.FSvoxelSpace.mgz --inv --interp nearest --o /Volumes/DANIEL/dti_freesurf/dtrecon/${cond}.${subj}/lhipp2diff.nii.gz --reg /Volumes/DANIEL/dti_freesurf/dtrecon/${cond}.${subj}/register.dat --no-save-reg so that I can merge specific hippocampal subfields I want together into a single ROI (like --id 231 and --id 232). However, when looking through the freesurfer options like mri_vol2vol there isn't an option to index to specific segments of the lh.hippoAmygLabels-T1.long.v21.HBT.FSvoxelSpace.mgz volume I have converted into dti space. My plan is to combine the head and body segments and extract average diffusion information from the combined mask. Anything that can help get me in the right direction would be greatly appreciated! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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Post-doctoral Research Position at the Yale Alzheimer's Disease Research Unit
by Adam Mecca 09 Apr '19

09 Apr '19

External Email - Use Caution The Yale University Alzheimer’s Disease Research Unit and the Yale PET Center has an opening for a highly qualified and motivated individual at the post-doctoral level to work on research involving the development of analysis techniques integrating human imaging data including PET and fMRI for NIH-funded studies and clinical trials in Alzheimer’s disease. Applicants must have obtained a Ph.D. in neuroscience, biomedical engineering, or a related field. Qualifications: Strong experimental, analytical, and programming skills are essential. Experience in fMRI, image analysis, algorithm development, and biological applications is highly desirable. The selected candidate will work under the direction of Drs. Christopher van Dyck and Adam Mecca. The successful candidate should have a Ph.D. or an M.D./Ph.D. with at least three years of experience in fMRI and/or PET imaging. Application Instructions: Interested individuals should email a CV to adam.mecca(a)yale.edu. Adam Mecca, M.D. Ph.D. Yale School of Medicine, Department of Psychiatry Geriatric Psychiatry and the Alzheimer's Disease Research Unit Tel: (203) 764-8100 Fax: (203) 764-8111

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Paired Analysis Questions
by brain health 09 Apr '19

09 Apr '19

External Email - Use Caution Dear Dr. Greve: Thank you so much for your time and help. I am working on the Paired Analysis that you suggested. Very appreciated! I am interested if there are different within-group changes in brain structure for an Intervention (PA) and Control (C) group. Does the paired-diff.fsgd file (peek below) look correct? PAC Groups Class Main Variables Group Input sub107 Main PA Input sub112 Main PA Input sub113 Main C Input sub118 Main PA Input sub131 Main C Input sub132 Main C Input sub136 Main C What would be the contrast of interest to include for my question? Just want to make sure I am running the correct model. I am also reading the guide about how to interpret the results of the mri_glmfit commands (e.g., https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit) Is there another guide to follow regarding the output of the Paired Analysis? I appreciate your guidance!

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Problem with calculating significant clusters' values
by Georgina Angelopoulou 09 Apr '19

09 Apr '19

External Email - Use Caution Hello FreeSurfer Developers, I have compared two groups in area, volume and thickness (using mri_glmfit and mri_glmfit-sim) and I want to extract the total value from each significant cluster so that I can run analysis with behavioural variables in SPSS. I have found some previous posts with the following command: mri_segstats --i <pathway to rh.volume.Study.10.mgh> --seg cache.th13.abs.sig.ocn.mgh --excludeid 0 --sumwf ClusterVolumeValues.dat –accumulate. but also the alternative option in --seg cache.th13.abs.y.ocn.dat. Could you please tell me: 1. Which is the correct option for -- seg and what is their difference? 2. I tried to run both option and I get the exact same error: mri_read(): couldn't determine type of file lh.SexStudy_area.glmdir/MN-FM/cache.th13.abs.y.ocn.dat ERROR: loading lh.SexStudy_area.glmdir/MN-FM/cache.th13.abs.y.ocn.dat Any ideas of how to resolve that? 3. Is that command the right one for volume, area and thickness? Thank you in advance, Best, Georgina

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FSFAST group analysis problem: dimension mismatch between y and X
by Keri Woods 08 Apr '19

08 Apr '19

External Email - Use Caution Hi Freesurfer experts I'm having a problem running an FSFAST group analysis. When I try to run the second level GLM, I get the following error: keri@buddha:~/audio_108_no_stc_tau1,5$ mri_glmfit --y ~/audio/all/audio.lh/tones/ces.nii.gz --wls ~/audio/all/audio.lh/tones/cesvar.nii.gz --fsgd 2groups.fsgd --C groupdiff.mtx --surface fsaverage lh --glmdir all_tones_left_glm.wls --nii.gz gdfRead(): reading 2groups.fsgd INFO: gd2mtx_method is dods Reading source surface /home/keri/recon_all/subjects/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.984375 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /home/keri/audio_108_no_stc_tau1,5 cmdline mri_glmfit.bin --y /home/keri/audio/all/audio.lh/tones/ces.nii.gz --wls /home/keri/audio/all/audio.lh/tones/cesvar.nii.gz --fsgd 2groups.fsgd --C groupdiff.mtx --surface fsaverage lh --glmdir all_tones_left_glm.wls --nii.gz sysname Linux hostname buddha machine x86_64 user keri FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/keri/audio/all/audio.lh/tones/ces.nii.gz logyflag 0 usedti 0 FSGD 2groups.fsgd labelmask /home/keri/recon_all/subjects/fsaverage/label/lh.cortex.label maskinv 0 glmdir all_tones_left_glm.wls IllCondOK 0 ReScaleX 1 DoFFx 0 wFile /home/keri/audio/all/audio.lh/tones/cesvar.nii.gz weightinv 1 weightsqrt 1 Creating output directory all_tones_left_glm.wls Loading y from /home/keri/audio/all/audio.lh/tones/ces.nii.gz ... done reading. INFO: gd2mtx_method is dods Saving design matrix to all_tones_left_glm.wls/Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1.34783 Found 149955 points in label. Pruning voxels by thr: 1.175494e-38 Found 66097 voxels in mask Saving mask to all_tones_left_glm.wls/mask.nii.gz Reshaping mriglm->mask... search space = 31233.070725 ERROR: dimension mismatch between y and X. y has 116 inputs, X has 108 rows. 108 is the number of subjects that I have. I can see that the y file with 116 inputs is /home/keri/audio/all/audio.lh/tones/ces.nii.gz , and checking the dimension of it, it confirms that it is a 4D matrix with the 4th dimension of 116. It seems as if this file is created during isxoconcat-sess, and I have checked and the session ID file being used here has only 108 entries. It appears that 108 subjects are being used in this step, as part of the output is: ninputs = 108 Checking inputs nframestot = 108 Allocing output Done allocing nframes = 108 I think that a source of the error could be the fact that at one time I did have 116 subjects. I've created a new folder, copying in the unpacked files for each subject, and repeating from the preprocessing step, but this doesn't make any difference. Is there are chance that there's a file outside the functional directory that has stored this 116? Any help is greatly appreciated. Best wishes, Keri

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Become an HCP Pipelines pro at HCP Course 2019!
by Jennifer Elam 08 Apr '19

08 Apr '19

External Email - Use Caution *Want to apply tools created by HCP experts to your own neuroimaging data? * *Always wanted to try the HCP Pipelines, but haven't had the time to test them out? * This year's HCP Course July 8 – 12, 2019 in Portland, Oregon is featuring expanded, hands-on sessions to help you discover and use HCP neuroimaging analysis pipelines, which include FreeSurfer. Course attendees will even have the opportunity to try the HCP Pipelines out on their own data! *HCP Pipelines demystified. Hands-on practice. Your data, processed.* We'll cover... - Best practices for high quality image acquisition - Strengths of the HCP's neuroanatomically-driven approach to preprocessing and registration - Unique features of the HCP Pipelines within the growing constellation of open-source neuroimaging analysis tools - Organizing your imaging data to run the pipelines - Diving into the scripts to see what is happening at each step of the processing - Editing the pipeline code and parameters to fit your specific needs - Running the pipelines in a ready to use container and turnkey framework locally or on the cloud to get results - Interfacing pipelines in container turnkey form with the XNAT informatics ecosystem - Tips on how to handle legacy data Plus, understanding HCP processing will put you in a great position to utilize the soon-to-be-released HCP Lifespan Development (ages 5-21) and Aging (ages 35-100+) data and upcoming Connectomes Related to Human Disease projects. For more info visit the <http://store.humanconnectome.org/courses/2019%20%20%20%20%20%20%20%20%20/ex…> HCP Course 2019 website <https://store.humanconnectome.org/courses/2019/exploring-the-human-connecto…>. Register soon, the course is filling up fast! If you have any questions, please contact us at: hcpcourse <hcpcourse(a)humanconnectome.org>@humanconnectome.org <hcpcourse(a)humanconnectome.org> We look forward to seeing you in Portland! Best, 2019 HCP Course Organizers -- Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 elam(a)wustl.edu www.humanconnectome.org

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Specific atlas for medial motor cortex
by Satoko KINA 08 Apr '19

08 Apr '19

External Email - Use Caution Dear Freesurfer experts, I would like to percellate the medial precentral cortex, corresponding to motor cortex of legs, by using Freesurfer. According to the Desikan-Killiany Atlas in current Freesurfer, there is no specific mask for medial precentral cortex. There is a mask for “paracentral cortex” which contains both medial precentral cortex and medial postcentral cortex. But I want to evaluate only medial precentral cortex. Do you have any other way to percellate and quantify only medial precentral cortex? Do you have any command to use other Atlas in Freesurfer? Thank you for help! Satoko

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ERROR: Talairach failed!
by Abby tang 06 Apr '19

06 Apr '19

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to recon_all my subjects which is .nii file. But I usually meet this error. talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0079, pval=0.0000 < threshold=0.0050) Command exited with non-zero status 1 @#@FSTIME 2019:04:04:10:30:25 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P 50% M 6252 F 7 R 243 W 0 c 1 w 8 I 1384 O 0 L 1.11 0.48 0.21 @#@FSLOADPOST 2019:04:04:10:30:25 talairach_afd N 4 1.11 0.48 0.21 Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See:http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach ERROR: Talairach failed! Linux abby-virtual-machine 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 0306A_T1_w4 exited with ERRORS at Thu Apr 4 10:30:25 CST 2019 For more details, see the log file /home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I've searched the list and they advised to check with this website https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview. however,my subject's recon_all folder doesn't have T1.mgz and brainmask.mgz. it just has mri_nu_correct.mni.log orig orig_nu.mgz transforms mri_nu_correct.mni.log.bak orig.mgz rawavg.mgz I run ten files, and almost all of them go wrong, which is very strange.I need your help. please give some advises with program statements in detail. I really appreciate your help 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-dev.tar.gz 2) Platform: ubuntu 18 3) recon-all.log:see attached

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Cortical thickness values more than 5 mm
by Gonzalo Rojas Costa 05 Apr '19

05 Apr '19

External Email - Use Caution Hi: How can I get cortical thickness surface image with values more than 5 mm? Sincerely Gonzalo Rojas Costa

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Post-doctoral Position in Network Neuroscience at the University of Michigan
by Angstadt, Mike 05 Apr '19

05 Apr '19

External Email - Use Caution Post-doctoral Position in Network Neuroscience at the University of Michigan A post-doctoral position is available in network neuroscience at the University of Michigan working with Chandra Sripada in Psychiatry, Liza Levina in Statistics, and Scott Peltier in Biomedical Engineering. The successful candidate will work on funded research projects that: 1) develop new methods for quantifying individual differences and longitudinal change in brain networks (functional and structural imaging modalities); 2) implement these methods in large datasets covering childhood (ABCD) and late adulthood (UKBiobank), with a focus on characterizing changes in neurocognition (executive functions, attention, learning and memory). Required Qualifications: a PhD in cognitive or computational neuroscience coupled with very strong quantitative skills; or a PhD in statistics, biostatistics, computer science, biomedical engineering, or another methodological discipline coupled with ability to work with brain and behavioral data. A strong background in the analysis and interpretation of neuroimaging data is a plus. Strong programming skills are a must; Matlab, R, and/or Python preferred. This is a 2-year position that has a possibility of being extended to a third. Start date is flexible, but September 2019 is preferred. If you are interested in this position, please send a CV and research statement to Chandra Sripada (sripada(a)umich.edu) -- Mike Angstadt Research Area Specialist Lead / PANLab Lab Manager Department of Psychiatry / University of Michigan (734) 936-8229 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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Freesurfer