Freesurfer December 2019

freesurfer@nmr.mgh.harvard.edu

85 participants
117 discussions

Extract single time frame
by Rockers, Elijah D. 16 Oct '22

16 Oct '22

Hello again, I have a large time series in dicom or .nii format. I am interested in extracting a single time frame from it. I did this before, I believe with freesurfer, but I have somehow forgot the name of the command, and I can't seem to find it. I believe it could be used to specify particular regions of the volume, as well as time. I need the entire volume, still, but only one frame. Thanks in advance! Eli Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list 10 years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Job ad: MRI physicist
by Keith Schneider 07 May '21

07 May '21

External Email - Use Caution The Center for Biomedical and Brain Imaging (CBBI) is a core imaging facility at the University of Delaware dedicated to scientific research. It is equipped with a Siemens Prisma 3T MRI scanner, Bruker 9.4T small bore MRI scanner, TMS, and MRI-compatible EEG. It supports a wide range of scientific investigations through imaging of humans, animals and materials. Under general direction of the CBBI Manager, the MRI Physicist is responsible for supporting the operations of the Siemens and Bruker MRI scanners. The MRI Physicist is expected to contribute to both research and training efforts that will include pulse sequence programming, parameter and image quality optimization, protocol design, scanner operation, technical support and user training. The candidate will be expected to maintain a broad knowledge of state-of-the-art MRI technology and equipment. The incumbent must have excellent communication and organizational skills, the ability to positively interact with a diverse group of MRI users, and a strong motivation to learn new MRI techniques. MAJOR RESPONSIBILITIES: • Pulse sequence programming on Bruker 9.4T and Siemens 3T MRI scanners • Assist users on appropriate choice and use of coils • Technical liaison for obtaining sequences or protocols for non-standard imaging (e.g. cardiac, musculoskeletal) from Siemens and other sites • File reports as needed for WIP sequences and Siemens MRA • Ensure data quality from the viewpoint of machine fundamentals • Technical support 9.4T and 3T scanners • Protocol design and testing for 9.4T scanner, including imaging of live animals and awake animals; as-needed for 3T • Routine quality assurance for 9.4T and 3T MRI scanners • Train users, including students, on use of 9.4T and 3T MRI scanners • Help users optimize pulse sequence parameters to maximize SNR and avoid imaging artifacts • Consult on image analysis, as needed • Review journals and abstracts to keep abreast of new developments • Collaborate with ongoing research as needed; may have independent research projects if desired • Consult users about imaging details for manuscript preparation and grant applications, as needed • Perform miscellaneous job-related duties as assigned QUALIFICATIONS: • PhD in MR physics or MS with equivalent experience • expert understanding of MR physics, image acquisition, signal processing, imaging processing and image reconstruction • MR pulse sequence programming • Experience with Bruker and Siemens MRI scanners • MRI scanning experience with both humans and animals—willing to handle animals • Ability to design experiments, optimize MRI protocols, troubleshoot image artifacts, analyze data, and interpret results • Knowledge of functional MRI, DTI, MRS, T1/T2 relaxation and perfusion • Siemens IDEA and ICE certification (or ability to obtain) http://careers.udel.edu/cw/en-us/job/493998/mri-physicist-research-office <http://careers.udel.edu/cw/en-us/job/493998/mri-physicist-research-office> For further information, contact me. keith ----- Keith Schneider Director, Center for Biomedical and Brain Imaging Associate Professor Department of Psychological and Brain Sciences University of Delaware

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Correct for sulcuses & ventricles size
by John Anderson 13 Dec '20

13 Dec '20

External Email - Use Caution Dear Freesurfer experts, I have two groups of subjects (healthy and patients). The patients have different degrees of atrophy. Looking into the individual scans, the subjects are largely different in the space between the sulcuses and the size of ventricles. My questions are: 1. Is there any way to correct for these differences in the surface based analysis? 2. Including eTIV covariate does it help in this case? 3. Does the resampling to "fsaverage" overcome the challenge of these differences between the subjects? I appreciate any advice, John

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Error with "recon-all -make all" following multiple manual editing
by Matthieu VANHOUTTE 03 Jul '20

03 Jul '20

External Email - Use Caution Dear Freesurfer's experts, Havng done multiple types of manual editing in two subjects, I relaunched the recon-all process (Freesurfer 6.0.1) with the flag "-make all". However, during the process, I goth for both subjects the following error message: / / /make: *** [/netapp/vol2_agewell/pro/IMAP/imap_mvh/FS6.0.1/awellv1s097/mri/aseg.presurf.mgz] Error 1/ /recon-all -s /netapp/vol2_agewell/pro/IMAP/imap_mvh/FS6.0.1/awellv3s024 -ccseg ERROR: Flag -ccseg unrecognized./ Following the troubleshooting site (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingDataV6.0) I have over-writed the "recon-all.makefile" file since I use the 6.0.1 version of Freesurfer. Thanks for helping. Best, Matthieu

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group analysis of large data sets
by Wang, Xin 22 Apr '20

22 Apr '20

Hello, FreeSurfer Group, What is the maximal matrix size for glm_fit process? How to use FreeSurfer for group analyses of more than 2000 subjects, 128 variables, and 128 Classes? Thank you. Xin

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eTIV vs. ICV
by Alexopoulos, Dimitrios 20 Apr '20

20 Apr '20

External Email - Use Caution The eTIV from FS 6.0 has been used by many as a normalization measure for regional volumetric analyses. I know it is not a true voxel count but does it conceptually include extra-axial CSF or is it more a total tissue volume? Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Highlighting single atlas structures in freeview
by Francesco Puccettone 05 Feb '20

05 Feb '20

External Email - Use Caution Dear all, I would like to show several structures from the DKT (or the Desikan-Killiany) atlas alone on a "blank" fsaverage brain, rather than have all structures displayed in different colors (as happens by default). For instance, I'd like to just show "medialorbitofrontal" on its own, then "middletemporal" on its own, etc. After I open the parcellation, freeview -v /FS/fsaverage/mri/aparc+aseg.mgz:colormap=lut:opacity=0.4 -f /FS/fsaverage/surf/lh.white:annot=aparc.annot , I expected to be able to turn each label in the list on and off like a layer, but this does not work. [image: 21-01-2019 14.48.54.jpg] I hoped I could use Alt+F to hide/show each atlas label at a time (cf freeview tutorial <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview>), but this instead toggles the entire external surface of the brain on and off. Can anyone help? Thank you! --Francesco

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Cortical segmentation error
by Monica Bondy 02 Feb '20

02 Feb '20

External Email - Use Caution Hello FreeSurfer experts, I am trying to figure out how to fix the segmentation so that the cortex is properly included. I have had this problem with several subjects, especially in the temporal lobe regions. I have tried tkmregister but it unfortunately didn't change anything. I am in the middle of using control points to try to fix this problem but it hasn't been ideal as it is requiring a lot of control points. Do you have any ideas on how to fix this? I have attached an image of what the problem looks like below. Please let me know if you need anything else. Thank you! 1. FreeSurfer version: freesurfer-i386-apple-darwin11.4.2-stable5-20130514 2. Platform: macOS Mojave (version 10.14.6) 3. uname -a: Darwin D20190801 18.7.0 Darwin Kernel Version 18.7.0: Sat Oct 12 00:02:19 PDT 2019; root:xnu-4903.278.12~1/RELEASE_X86_64 x86_64 [image: Screen Shot 2019-12-13 at 9.56.46 AM.png]

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highres fMRI selxavg error
by Nasiriavanaki, Zahra 23 Jan '20

23 Jan '20

Dear Freesurfer experts Happy Holidays! I have a subject with two highres fMRI scan sessions. Attached you can see an image, showing how I organized the sub-folders. I preprocessed the bold1 and bold2 and then copied the preprocessed files to "bold from both sessions" folder. I ran selxavg for bold1 and bold2 seperately and it went well. However, when I ran selxavg for "bold from both sessions" folder, it gives the below error. Could you please let me know what the problem is?Also if you have a better suggestion for how I should organize my subfolders/analysis, I appreciate that. Thanks Mona >> >> >> >> /autofs/cluster/freesurfer/centos7_x86_64/stable6/fsfast/toolbox/fast_selxavg3.m >> /autofs/cluster/freesurfer/centos7_x86_64/stable6/fsfast/toolbox/fast_ldanaflac.m >> /autofs/cluster/freesurfer/centos7_x86_64/stable6/matlab/MRIread.m >> >> >> starting fast_selxavg3b #@# arap_7T_all ############################### /autofs/space/oprah_001/users/zn025/looming_7T/all_subjects/arap_7T_all ------------------------- $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $ ------------------------- outtop = /autofs/space/oprah_001/users/zn025/looming_7T/all_subjects Extension format = nii.gz INFO: key nSliceGroups unrecognized, line 12, skipping 1 app.mat 2 aw.mat 3 caw.mat 4 clo.mat 5 faw.mat 6 fem.mat 7 fm.mat 8 fmaw.mat 9 mal.mat 10 maw.mat 11 oaw.mat 12 oc.mat 13 ocaw.mat 14 ope.mat 15 wit.mat Excluding 6 points nruns = 15 autostimdur = outanadir = /autofs/space/oprah_001/users/zn025/looming_7T/all_subjects/arap_7T_all/loom/loom_native.lh Excluding 6 points Excluding 0 points Excluding 1 points Excluding 5 points Excluding 8 points Excluding 3 points Excluding 8 points Excluding 4 points Excluding 6 points Excluding 10 points Excluding 5 points Excluding 5 points Excluding 5 points Excluding 5 points Excluding 5 points parfiles condition id list: 1 2 3 4 5 6 7 8 Found 41883/148565 (28.2) voxels in mask 1 Creating Design Matrix ... creation time = 0.040 sec DoMCFit = 1 ntptot = 1350, nX = 219, DOF = 1131 Saving X matrix to /autofs/space/oprah_001/users/zn025/looming_7T/all_subjects/arap_7T_all/loom/loom_native.lh/Xtmp.mat XCond = 1873.07 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.456169 (t=1.17104) 2 -0.25 -0.261165 (t=2.14097) 3 0 -0.076309 (t=2.3701) 4 0.25 0.0914527 (t=3.32529) 5 0.5 0.225506 (t=4.09175) AR1 Correction M: 0.138222 1.44983 Computing contrast matrices Computing contrasts Loading previous GLM fit Starting contrasts app J=1 ------------- Error using * Incorrect dimensions for matrix multiplication. Check that the number of columns in the first matrix matches the number of rows in the second matrix. To perform element wise multiplication, use '.*'. Error in fast_fratiow (line 81) ces = C*beta; Error in fast_selxavg3b (line 1153) fast_fratiow(betamat,X,rvarmat,C,acfsegmn,acfseg.vol(:)); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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Cortical inflation and maintenance of surface voxel intensity
by Assis Lopes, Pedro Augusto 21 Jan '20

21 Jan '20

Dear Freesurfer experts, I am a medical student and am currently doing a fellowship at the JPK Stroke Research Center - MGH. My current research project involves measuring the area of a cortical hypointense brain MRI signal (cortical superficial siderosis) , a marker that lays along the subarachnoid space/pial surface, only visible in blood sensitive MRI (SWI in my case). In summary: We are trying to do a parallel to fMRI studies (fMRI x T1w // SWI x T1w), analyzing SWI signal intensity on a registered inflated brain surface; Projecting SWI surface intensity would then allow manual area demarcation of hipointensities in a flat surface. Here is our step-by-step plan (analogous to fMRIxT1w registration/BOLD signal intensity projection to surface): 1. Perform freesurfer recon-all of the subject in question to generate subject-surface models. 2. BET and register the image of interest (SWI) into the freesurfer-subject space (register both SWI and MEMPRAGE sequences) [bbregister] 3. Having SWI in subject space and a surface model (generated in 1); * Split registered SWI into LH and RH * Tkregister2 to get LTA to mri_vol2surf format * Mri_vol2surf each hemisphere to the recon output 4. Display the SWI hemi surface as an overlay 5. Inflate T1 surface and observe its SWI overlay; * Manual demarcation of characteristic SWI hypointense signals 6. Analyze measured signal We did try this approach, but yet with these steps we could only obtain an inflated cortical surface representation that has no correspondence to SWI`s intensity. So, here comes the question: If BOLD signal intensity can be projected onto surface area; is there a way to project SWI intensity onto the cortical surface? Or Can we preserve the info of SWI surface voxel intensity while doing the surface inflation? If not Is it possible to use the positional information of t1w voxel (used in inflation process) as an index to retrieve its correspondent SWI intensity value? Sorry for the long question. In advance I thank you already for being so attentive. Best, Pedro Pedro Augusto Assis Lopes Student Researcher J. Philip Kistler Stroke Research Center Massachusetts General Hospital 175 Cambridge Street, Suite 300 Boston, MA 02114 Phone: (617) 643-3940

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Freesurfer December 2019