Freesurfer

freesurfer@nmr.mgh.harvard.edu

24 participants
30076 discussions

using freeview7 to set manual paths
by Valeria Centanino 26 May '22

26 May '22

External Email - Use Caution Hello, I need to set manual paths on inflated surfaces, and I would like to use FreeView7, but I couldn't find any option to save the path after creating it. Could you please tell me if this is implemented in FreeView7 and, if yes, how can I do it? Thanks very much, Valeria

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mris_label2annotation issues with individualizing
by Deck,Benjamin 25 May '22

25 May '22

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to create annotation files from label files which have been estimated at the level of the individual. Therefore, some subjects may not have all ROIs. When attempting to take those label files and concatenate them into individual subject-specific annotation files I run into a few issues. The command I have used previously: mris_label2annot --s sub-DAEK --hemi lh \ --ctab /mnt/c/Users/Ben/Documents/GitHub/parcellationPipeline/li2019_to_dti/yeo2011nodesLUT.txt \ --a yeo2011nodes \ --surf orig \ --maxstatwinner \ --ldir-default stdout: subject sub-DAEK hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable /mnt/c/Users/Ben/Documents/GitHub/parcellationPipeline/li2019_to_dti/yeo2011nodesLUT.txt AnnotName yeo2011nodes nlables 0 1. The first issue is that -ldir and -ldir-default don't seem to work as anticipated. After reading many threads on the FS mailing list archives I saw that the LUT should have identical ROI IDs as the file names with the exception of the label file extension. Thus, my LUT looks like the following: * 0 Unknown 0 0 0 0 1 lh.Net_2_ROIs_1_lh 25 5 25 0 2 rh.Net_2_ROIs_1_rh 25 100 40 0 3 lh.Net_2_ROIs_2_lh 70 130 180 0 4 rh.Net_2_ROIs_2_rh 100 100 0 0 5 lh.Net_3_ROIs_1_lh 196 58 250 0 6 rh.Net_3_ROIs_1_rh 100 25 0 0 7 lh.Net_3_ROIs_2_lh 120 70 50 0 8 rh.Net_3_ROIs_2_rh 220 20 10 0 9 lh.Net_3_ROIs_3_lh 220 20 100 0 10 rh.Net_3_ROIs_3_rh 180 40 120 0 11 lh.Net_4_ROIs_1_lh 122 186 220 0 -----------------and so on. * When I list the dir from my subject's label directory the following is presented: i. lh.Net_10_ROIs_1_lh.label lh.Net_2_ROIs_1_lh.label lh.Net_13_ROIs_3_lh.label lh.Net_5_ROIs_1_lh.label rh.Net_2_ROIs_1_rh.label rh.Net_3_ROIs_3_rh.label ------------and so on. * However, when I provide the -l arg with the full path, the file is found and the nlabels arg in stdout is the number of -l args I supply. 1. The next issues is that if I go the route of -l args (there are 116 ROIs so this is not desirable) I receive issues because not all subjects have all the label files that the LUT file expects. Therefore the resulting annotation file has mislabeled ROIs. * Is there a way to force the unfound labels to unknown or a way to bypass this issue? * I recognize the one way to do this may be to create individual specific LUT files but that seems tedious and unnecessary if there is a better way that you all may be wiser to. 1. Another issue I have been running into is that if I even attempt to just remove the -l args where labels do not correspond exactly with the LUT file I have a number of overlapping label file vertices issues. * How do you recommend correcting for this, my best guess is some sort of thresholding scheme. However, these are functional networks so I am unsure what the best route for thresholding would be. Thanks so much for your help in advance! Ben

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ubuntu vm
by Sodoma, Matthew 25 May '22

25 May '22

External Email - Use Caution Hello, I was looking to receive the passcode to unzip the virtual box file below: Freesurfer 7.2.0 release in Ubuntu 18.04.06: FS_7_2_0_Ubuntu_18_04_06.ova.7z<https://secure-web.cisco.com/1QpBVQUbsVdz-ntFx0QiYhbLcmY3KmbxxWUEnqMECp1b6U…> Matt

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Starting a new project
by Raffaele Di Natale 25 May '22

25 May '22

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to develop new functions in the tool for my research activity and I wish to know if there is a guide about to start this kind of activity. 1) freesurfer-linux-ubuntu20_x86_64-7-dev.tar.gz Raffaele Di Natale, PhD Contract Researcher DIEEI, University of Catania +39 095738 2385 (Edificio 13) +39 095738 7903 (OpenLab <http://secure-web.cisco.com/19HCh4dsz8VYs-eTR0dm-vPoxaUmxK1ULuABd3lg8agIWG7…>)

2 1

Deface DICOM
by Victor Montal Blancafort 24 May '22

24 May '22

External Email - Use Caution Dear FS experts, I am using mri_deface to annon our data. Nevertheless, for a recent project, we were requested to share our DICOM original files, instad of .nii or .mgz. Thus, I was wondering if you know a simple way to deface T1 data inputing a DICOM and obtaining a series of DICOM as output? I have tried to 1) deface using mri_deface, 2) convert the .nii to dicom using the nifti2dicom utility and 3) correct DICOM info thats incorrecly parsed at step 2). However, such approach does not work correctly for all our data (it fails for several reasons, such as correctly storing acq direction, or dimensions when sampling from nifti 2 dicom). I have seen that @Doug has been working on a new deface utility (mideface) but it seems to work also only for .nii Any insight? Victor Montal

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Tissue fraction effects correction
by Marina Fernández 24 May '22

24 May '22

External Email - Use Caution Dear FS experts, We are planning to correct for tissue fraction effects on T1w/T2w ratio images using PETsurfer, setting the point spread function estimate to zero. My questions are: 1. Does it make sense to correct for tissue fraction effects on T1w/T2w ratio images even when T1w and T2w images were acquired using the same matrix size with identical voxel resolution (i.e., 1mm3)? 2. If that makes sense, which PVC method would work best for correcting tissue fraction effects (i.e., SGTM, MG, RBV) on structural MRI scans? Many thanks in advance. Best, Marina

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Ubuntu + Freesurfer VM passcode
by Sarah Dziura 24 May '22

24 May '22

External Email - Use Caution Hi, Could I please get the passcode for unzipping the virtual image FS_7_2_0_Ubuntu_18_04_06.ova.7z <https://secure-web.cisco.com/1c1JpTzbKs-wKmYazIR87wrbHFTExyh_O3AcXav_KWBe74…> ? Thank you, Sarah -- Sarah L. Dziura, Ph.D. Postdoctoral Research Associate Developmental Social Cognitive Neuroscience Lab University of Maryland, College Park Pronouns: she/her

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pass code to open ubuntu image for windows
by Juan Ruiz de Miras 23 May '22

23 May '22

External Email - Use Caution Hi, Following the instructions on your web page, with this email I ask you for the pass code to open the freesurfer ubuntu image for windows. Regards, Juan.

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New Postdoc Position in Neuroimaging and Machine Learning in Aging and Neurodegenerative diseases
by Joana Braga Pereira 23 May '22

23 May '22

External Email - Use Caution Dear all, We are looking for a Postdoc to work in an interdisciplinary and internationally competitive environment at Karolinska Institute, one of the top medical universities in the world and the home for the Nobel Prize in Medicine. We combine imaging analyses, statistical tools, machine learning algorithms, biofluid assays and genetics to study brain aging and the earliest signs of Alzheimer’s and Parkinson’s diseases. This project will be carried out under the supervision of Associate Professor Joana B. Pereira and it will involve analyzing cross-sectional and longitudinal imaging data, combining clinical measures and cerebrospinal fluid biomarkers, as well as writing manuscripts and presenting results in international conferences. The Postdoctoral fellow will have the opportunity to work in a friendly and dynamic environment, be involved in many projects, collaborate with group members on different studies, learn new skills, interact with researchers with different backgrounds and from other universities, analyze large datasets from well-characterized cohorts, apply for grants and develop a wide network of international collaborations. The ideal candidate should have the following qualities: - A PhD in medicine, neuroimaging, computational science, physics, neuropsychology, statistics or a related field. - Experience in statistical techniques, programming, and scripting in MATLAB, Python, R or other softwares. - Experience with structural MRI, DTI, fMRI and/or PET imaging analyses. - Experience with different softwares such as SPM, FSL, FreeSurfer, AFNI, etc. - Experience or interest in working with aging and/or neurodegenerative disorders, particularly Alzheimer’s and Parkinson’s diseases. - Good academic record with scientific publications in world-class journals The Postdoctoral studies will be performed for 1 year, with possible extension for an additional year. There are also possibilities for a longer appointment after this 2-year period. To apply please go to: https://secure-web.cisco.com/1Ed62KOtM1rXHyrKg0uzBi4mJwpIswU1t2v-GHYNsF-kVb… (Deadline: 10.Jun.2022) For further information or general inquires, please contact Joana B. Pereira at jbragapereira(a)gmail.com or joana.pereira(a)ki.se. Best wishes, Joana

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The DPABINet Brain Network Open Course is freely available online now!
by YAN Chao-Gan 23 May '22

23 May '22

1 0

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