Freesurfer January 2021

freesurfer@nmr.mgh.harvard.edu

98 participants
132 discussions

Correcting pial surface with Flair sequence
by Georgia Kapizioni 09 Jan '21

09 Jan '21

External Email - Use Caution Hello Freesurfer Developers, I am conducting a group analysis between a patients and a control group. I have accomplished recon-all individual analysis and I want to correct pial surface using 3D Flair. I would like to ask two specific things: 1. Is 3D Flair appropriate or only T2 Flair is recommended for such correction. From what I have read on previous posts, it is usually recommended to use T2 Flair. 2. For my data, for most of my 3D data slice thickness is 1 mm, but for some of them is 1.48 mm. Is that difference going to affect analysis results? Thank you in advance, Georgia

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write .annot files
by Octavian Lie 08 Jan '21

08 Jan '21

External Email - Use Caution Dear All, These are probably rookie questions. 1. I can read an .annot file with read_annotation.m, is there a way to write one? (for example read it to matlab, modify, and save, or create a combined (lh+rh) aparc.annot file etc. 2. On the same line, how one combines all the Brodmann labels into a Brodmann parcellation, if not done already.. Thank you, Octavian

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recon-all issue in vmPFC with high-res T1/T2 data {Disarmed}
by Ben Deen 08 Jan '21

08 Jan '21

External Email - Use Caution Hi all, I'm encountering an issue with surface reconstruction quality in ventromedial prefrontal cortex, using relatively high resolution (.8mm) T1- and T2-weighted input data to recon-all. I'm using the following command, with Freesurfer 7.1.1 running on Mac OS 10.15.7 (freesurfer-darwin-macOS-7.1.1-20200811-8b40551; the options file specifies "mris_inflate -n 30"): recon-all -s ${subject} -i T1w.nii.gz -all -hires -expert ${optsFile} -T2 T2w.nii.gz -T2pial Across four participants I've tested with this approach, there is a consistent reconstruction issue with the gyrus rectus and medial orbital gyrus, in which they are cut off in the white and pial surfaces (see images at https://secure-web.cisco.com/1YjHwYMb6FHlCVkbgjtpceoj_IZMMa8YVArerusSJpfEDY… it's particularly clear against the T2 image). I've tried to correct the issue by manually modifying wm.mgz to include all wm voxels in these gyri. However, when I do so and rerun autorecon2-wm, the orig surface improves to incorporate the edits to wm.mgz, but the white/pial surfaces do not. By debugging individual steps of recon-all, I've found that the -white step seems to be to blame for this: when I rerun this step, the output white.preaparc surface doesn't change to incorporate my edits to wm.mgz. Any thoughts as to what might be causing these issues - both the initial reconstruction problem, and the failure to update with manual edits? There is some signal dropout in the T1 image in this region, which may contribute to the issue, although I would hope the T2 image could compensate for this. Thanks, Ben

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TRACULA
by Weerasekera, Akila 07 Jan '21

07 Jan '21

Hi, I got the following error running tracula: "Error: data and bvals/bvecs do not contain the same number of entries" Could this be because my bvals/bvecs are in the row format and not column? Thank you, Akila Akila Weerasekera, PhD | Postdoctoral Research Fellow Pain and Neuroinflammation Imaging Laboratory | Ratai Lab for Clinical Spectroscopy | Harvard Medical School | A. A. Martinos Center for Biomedical Imaging | Massachusetts General Hospital | 149 Thirteenth Street, Room 1101 | Charlestown, MA 02129 Mobile: (781) 820 4501 aweerasekera(a)mgh.harvard.edu <mailto:aweerasekera@mgh.harvard.edu> www.nmr.mgh.harvard.edu<http://www.nmr.mgh.harvard.edu> https://scholar.harvard.edu/loggia

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Different installers of same FreeSurfer version for preprocessing vs. edits
by lynn.fehlbaum＠jacobscenter.uzh.ch 07 Jan '21

07 Jan '21

External Email - Use Caution Dear FreeSurfer experts, I'd have a quick question on using different installers for the FreeSurfer 7.1.1. release for preprocessing and manual edits: We initially preprocessed our data using the freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b installer, but have accidentally used freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b to edit the pial surface. According to the recommendation of using identical versions of FreeSurfer for all processing steps, we plan on re-creating the final surfaces and compute further analyses using freesurfer-linux-centos7. However, is it okay to use the brainmask files that were edited using freesurfer-linux-centos6 or would we need to edit the files from anew using freesurfer-linux-centos7? Any help is highly appreciated! Kind regards, Lynn

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Recon-all Error
by Dimitri Brigide De Almeida Mantovani 06 Jan '21

06 Jan '21

External Email - Use Caution Hello! I'm experiencing an error while I try to use recon-all in a T1 MRI image, the following error message appears: "[...] using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading mri_src from norm.mgz... error: mghRead(/home/developer/Desktop/BIBE_2020/Simulated_MRI/HC/rf0/t1_icbm_normal_1mm_pn1_rf0/mri/norm.mgz, -1): could not open file error: mri_normalize: could not open source file norm.mgz" Thanks!

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[Freeview] [AnatomiCuts] Usage of embedded colors in tract visualizer + AC runtime error
by Pietro Astolfi 06 Jan '21

06 Jan '21

External Email - Use Caution Hi, In the last days I searched for documentation about the use of embedded colors when visualizing tracts in freeview. I wasn’ t able to find any information online. I also tried to obtain a tract containing the embdedd colors information by using `dmri_AnatomiCuts` (both with fs 7.1.0 on OS X and dev version on Ubuntu ), but despite many trials I always got the same runtime error: terminating with uncaught exception of type std::runtime_error: Gak! Abort trap: 6 If anyone could help me it would be very appreciated, Best, Pietro Pietro Astolfi PhD student ICT school - University of Trento NILab - Bruno Kessler Foundation PAVIS - Italian Institute of Technology -- -- Le informazioni contenute nella presente comunicazione sono di natura privata e come tali sono da considerarsi riservate ed indirizzate esclusivamente ai destinatari indicati e per le finalità strettamente legate al relativo contenuto. Se avete ricevuto questo messaggio per errore, vi preghiamo di eliminarlo e di inviare una comunicazione all’indirizzo e-mail del mittente. -- The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. If you received this in error, please contact the sender and delete the material.

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Postdoc available at FreeSurfer team
by Iglesias Gonzalez, Juan E. 06 Jan '21

06 Jan '21

Dear all, We’re seeking to hire a postdoc at the Martinos to work on a cool new project involving human brains, 3D shape scanning with infrared, registration, and machine learning. Essentially, all the good stuff. More information here: https://scholar.harvard.edu/iglesias/jobs https://scholar.harvard.edu/iglesias/news/new-r01-grant-postdoc-position-av… Kind regards, Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

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creating labels on surfaces with Freeview 7.1.1
by Trisanna Sprung-Much 06 Jan '21

06 Jan '21

External Email - Use Caution Hi there, I am looking for instructions on how to create/edit my own labels directly on surfaces using the latest version of Freesurfer/Freeview but I cannot seem to find this documentation. My understanding is that an annotation file has multiple labels and a look up table. What if I want to just create 1 label? When I go to Annotation --> New and create a label and assign a name and colour, I get the following msg when I try to save: "There are unassigned labels in the annotation. Please assign all the labels first" Any help would be greatly appreciated, Trisanna

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[Brainstem Substructures] Resolution of the image "brainstemSsLabels.v10.mgz"
by ganmian 05 Jan '21

05 Jan '21

External Email - Use Caution Hi, I am using a FreeSurfer v6.0 to analyze volumetric features of brainstem substructures. While reading the document about brainstem module (BrainstemSubstructures - Free Surfer Wiki (harvard.edu) <https://secure-web.cisco.com/1S-b5rCCfiUM_20r5cYkwhXu2P25IPqutTefsWepu1yx8D…>), I was confused by the following sentence: *| brainstemSsLabels.v1x.mgz*: the volume with the segmentation at 0.333 mm resolution because if I load the file "brainstemSsLabels.v10.mgz" using nibabel and check the zoom, it seems to have 0.5 mm resolution. The following is the result of my code: >> img = nib.load('brainstemSsLabels.v10.mgz') >> print(img.affine) [[ -0.5 0. 0. 43. ] [ 0. 0. 0.5 -39. ] [ 0. -0.5 0. 33. ] [ 0. 0. 0. 1. ]] >> print(img.header.get_zooms()) (0.5, 0.5, 0.5) >> print(img.header) <class 'nibabel.freesurfer.mghformat.MGHHeader'> object, endian='>' version : 1 dims : [170 201 138 1] type : 3 dof : 1 goodRASFlag : 1 delta : [0.5 0.5 0.5] Mdc : [[-1. 0. 0.] [ 0. 0. -1.] [ 0. 1. 0.]] Pxyz_c : [ 0.5 -4.5 -17.25] tr : 0.0 flip_angle : 0.0 te : 0.0 ti : 0.0 fov : 0.0 I wonder if the description of the document is not correct. Could you please check if which is correct? My environment is as follows: - FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c - OS: Ubuntu 18.04 Thank you! Best regards Eunpyeong Hong

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Freesurfer January 2021