Freesurfer December 2019

freesurfer@nmr.mgh.harvard.edu

85 participants
117 discussions

Obtaining pre&post values from longitudinal dataset without cross-base-long
by Tudor Popescu 02 Jan '20

02 Jan '20

External Email - Use Caution Dear FS experts, From a pre-&post-intervention data set, is it possible to extract thickness values at those two time points just by using recon-all, that is, without running the full longitudinal processing stream (the Cross, Base and Long steps)? I aim not so much to compute the percentage change measure ( pc1 = (post-pre)/pre ), but simply to use the raw pre&post values for other analyses. Many thanks, and happy holidays to all! Tudor

2 1

FSFAST registration
by Star Xi 02 Jan '20

02 Jan '20

2 1

vol2subfield
by stdp82＠virgilio.it 02 Jan '20

02 Jan '20

External Email - Use Caution Hi list, where/how should I add the file listed below? https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/vol2subf… Thanks

2 1

Problem for mri_glmfit
by Gwang-Won Kim 02 Jan '20

02 Jan '20

2 1

Post-doc position at Harvard Medical School
by Linnman, Clas,Ph.D. 31 Dec '19

31 Dec '19

We are seeking a highly motivated and independent post-doctoral for the Spaulding Neuroimaging Lab. We study brain alterations after spinal cord injury, with a focus on MR metrics, microglia and opioid receptors. The current NIH funded project evaluates the impact of aerobic exercise as a neurorestorative rehabilitation intervention in human SCI. The position encompasses use and development of simultaneous PET-MRI. For more details, apply online at https://partners.taleo.net/careersection/srn/jobdetail.ftl?job=3108990&tz=G… Or send me an email with your CV and scientific goals. Clas ___________________________ Clas Linnman, Ph.D. Assistant Professor Spaulding Neuroimaging Lab Harvard Medical School

1 0

Freeview - command-line label sub-option "opacity" does not work
by Antonin Skoch 30 Dec '19

30 Dec '19

External Email - Use Caution Dear experts, a freeview command-line label sub-option "opacity" does not work for me. Freeview exits with error: Unrecognized sub-option flag 'opacity'. I am using most recent dev version (30 dec 2019). Could you please check that? Regards, Antonin Skoch

2 3

Error in MATLAB while using freesurfer commands
by mahdi mahdavi 30 Dec '19

30 Dec '19

External Email - Use Caution Hi. I'm a medical student and I'm trying to use the QuickNATv2 MATLAB code for structural MRI segmentation for a paper. However, at the last step when I want to execute the Run command for this program, it returns an error related to MRIRead function from freesurfer. I'm, using windows so I Cloned freesurfer library from github and defined its path for MATLAB. The error is: SWITCH expression must be a scalar or a character vector; the MRI data is a .mgz file: Error in load_mgh (line 166) switch type Error in MRIread (line 94) [mri.vol, M, mr_parms, volsz] = load_mgh(fspec,[],[],headeronly); Error in RunFile (line 15) DataVol = MRIread([DataPath,FileName]); I've also tried using linux shell for windows 10 and installed the freesurfer with it but i still get the same error. I didn't find any helpful guides on various forums so I'm mailing you hoping to find a solution cause I really need to run the QuickNAT for a paper. Regards Mahdi

2 4

intensity map
by a Chinese reader 29 Dec '19

29 Dec '19

External Email - Use Caution Dear Freesurfer experts,I have some questions about intensity map: 1. If I would like to calculates the gray matter nulcei to white matter signal intensity ratio (GWR), which command I can use. 2. If I want to calculate half the thickness of the gray matter of the cortex and get the surface file(*.mgh), what should I do? Best regards, Zhang Xia

2 1

Lateral ventricles mask
by Tamir Eisenstein 29 Dec '19

29 Dec '19

External Email - Use Caution Dear FS experts, How can I create a binary mask of the lateral ventricles based on the ASEG output? Thanks! Tamir

2 1

BA_exvivo.thresh.stats
by sarah.kloeppig＠web.de 29 Dec '19

29 Dec '19

2 1

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Freesurfer December 2019