Freesurfer January 2019

freesurfer@nmr.mgh.harvard.edu

119 participants
167 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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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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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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Course in Advanced Neuroimaging (Barcelona)
by Erick Canales 20 Sep '19

20 Sep '19

Dear colleagues, I am pleased to announce our upcoming Course in Advanced Neuroimaging held annually in Barcelona. It takes a practical approach and does not require qualifications or previous experience in neuroimaging. It will be taught in Spanish. The multidisciplinary programme provides thorough training in the analysis of brain images from different MRI modalities and data modeling techniques, including voxel-based morphometry, cortical thickness, diffusion tensor imaging, fibre tracking, functional MRI and brain connectivity, as well as the statistical methods behind these techniques including elements of meta-analysis, and more. The course consists of a five-month online theoretical module (starting on November 6th) and a period of practical face-to-face training (split between two days in November and two weeks at the end of April) held in Barcelona. For further information, please visit the website: www.cursoneuroimagen.com Best regards, Erick J. Canales-Rodríguez Joaquim Radua Raymond Salvador Edith Pomarol-Clotet FIDMAG Research Foundation and Sociedad Española de Neuroimagen *www.fidmag.com <http://www.fidmag.com/>*

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T2 seq. for hippocampus ??
by Anik Dar 25 Jun '19

25 Jun '19

External Email - Use Caution Hi All, I have 1x1x3 cubic mm T2 and 1x1x1 cubic mm FLAIR, in addition to 1x1x1 cubic mm MPRAGE. Can you please let me know whether I should use only T1 or should I use one of the additional seq. for hippocampal subfield segmentation ? cheers Nik

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mri_glmfit-sim error correcting for MC for LGI analysis
by C.P.E. Rollins 18 Apr '19

18 Apr '19

External Email - Use Caution Dear Freesurfer Developers, I have a 2-part question: 1) I was advised to use permutation to control for multiple comparisons in an LGI analysis, would you mind elaborating how to do this in command line (in terms of command and parameters)? 2) In running "mri_glmfit-sim --glmdir lh.5.lgi_MAN_new.glmdir --cache 1.3 pos --cwp 0.05 --2spaces --debug", I receive the following error (attached). I was wondering if you might have any advice? The file /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white exists and I can view it in freeview. Many thanks, Colleen

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Errors in white matter surfaces from scan collected on 3T Siemens Skyra scanner at .6 mm resolution
by Lalonde, Francois (NIH/NIMH) [E] 25 Mar '19

25 Mar '19

External Email - Use Caution Hi, We collected an MP-RAGE scan at .6mm isotropic resolution with the TR bumped up to TR=5. Subject motion artifacts were mitigated by using a KinetiCor motion correction system. We followed the recommendations for processing submillimeter scans described in the FreeSurfer Wiki i.e. we added the -cm flag to recon-all and included the mris_inflate -n 100 expert option. The attached PDF of the white matter surfaces shows that they appear to be underestimated. The surface estimates fall short of the actual grey/white matter boundary. Arrows point to the most affected areas and the second image is the same as the first but without the yellow white matter surface line. FTP is disabled on my government computer. Please specify the recipient email if I have to transfer the file using FileDrop. Could you suggest other options either at the time of scanning or in running recon-all that could help better segment the white matter? Thanks, François Lalonde, Ph.D. DNU/HGB/NIMH/NIH 10 Center Drive, Room 4D18 Bethesda, MD. 20892 flalonde(a)nih.gov

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How to extract cortical features of a ROI
by 310913949 06 Mar '19

06 Mar '19

External Email - Use Caution Dear Freesurfer Experts, I want to extract cortical features of a ROI that I drawn manually on the rawavg.mgz in Freesurfer, but i don't know how to do that. I think maybe first the lesion mask should be registered to the standard templates fsaverage, but I don't know what the command line is , could you tell me? And secondly, I should use mri_label2label to map the label to individual subject and extract the cortical features of the ROI, am I right? I am looking forward to your reply!Thanks. Best wishes! Kan Deng

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Freesurfer January 2019