Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30081 discussions

Tracula skip steps
by Jacobs H (NP) 31 May '16

31 May '16

Dear FreeSurfers, The data I have is preprocessed, so I have the all the metrics (FA, MD, L1, L2, L3,..) in nifti format. On this data I would like to start tracula starting from step 1.3. I have organized the data as mentioned on the wiki: For example: <subjID>/<dmri> dtifit_FA.nii.gz I have also filled in the configuration file, canceling out the things I don't need and then I tried to run: Trac-all -intra -c <configuration file> Unfortunately, it does not work, it says: dcmlist: subscript out of range I do not have the original files... is there a way that I can get the script working? Many thanks. Heidi

2 10

mri_cc
by Arash Nazeri 31 May '16

31 May '16

Dear Freesurfer experts, Sorry for resending this post. mri_cc does not seem to be working properly to parcellate corpus callosum. As per one of the previous posts, there is a bug in the current release of mri_cc. However, the link provided in the same thread for an updated version of mri_cc is no longer existent. Our cluster runs on 64bit Ubuntu 14.04 systems. I'd be grateful if someone can post a new link for the corrected mri_cc. Thanks in advance. Cheers, Arash

1 0

Extracting White Matter Structures without using Tracula
by Syeda Wajiha Maryam 31 May '16

31 May '16

Hello Freesurfer experts, I am looking to extract certain white matter pathways (for instance, the superior longitudinal fasciculus, uncinate fasciculus) with freesurfer which I believe are affected by Alzheimer's Disease. But it seems that these can only be obtained by performing tractography using Tracula. I was wondering if there was some other way to obtain the labels for these structures without having to do so? Thanks in advance. Regards, Maryam

2 2

WM & GM Parcellation Edit
by Limachia, Gaurang (NIH/NINDS) [F] 31 May '16

31 May '16

Hi freesurfer community, We are checking to see the accuracy of our subjects’ white and gray matter parcellation. We have found that for some subjects the contour lines for white matter surface and pial surface are somewhat inaccurate, and have been making modifications using the tutorials. Specifically, we made changes to the white matter wm.mgz file; this however did not alter the contour lines. We also used control points, and were able to see changes to the white matter surface contour lines using this approach. How do you recommend that we proceed to obtain the most accurate results? Should we continue making changes to the wm.mgz file as well as adding control points, or is it sufficient just to add control points? I am attaching a screen shot which shows changes to the contour lines after we added control points. Best Regards, Shyam [cid:93CEA6F8-6B62-4483-985C-F540EDDBD2D7] [cid:C981D3FE-7C43-4073-A91F-F26CEDDC4145]

2 5

working with cluster annotations in fs-fast
by Abigail Noyce 31 May '16

31 May '16

Hi folks, I'm trying to split a cluster from mri_glmfit-sim into two separate regions. (Ginormous blob of activation across multiple structures of interest...) I've gotten to the point of generating a new annotation with the separate labels for my separate regions, but am stuck getting a "cluster size" for the new labels. It looks like one can't use mris_anatomical_stats on fsaverage... but something like that must be happening inside of mri_glmfit-sim to get cluster sizes? What's the best way to get these values for my new annotation? (Or is this a terrible idea for some reason I haven't yet considered?) Thanks! Abby Noyce -- Abigail Noyce, Ph.D. Department of Psychological & Brain Sciences Boston University anoyce(a)bu.edu

2 1

recon-all with input T1s at different resolutions
by Satrajit Ghosh 31 May '16

31 May '16

hi folks, does recon-all work if the input T1s for the same participant have different resolutions? (i don't have a dataset to test, but trying to debug some issues another group has been having). cheers, satra

4 7

WM & GM Parcellation Edit
by Limachia, Gaurang (NIH/NINDS) [F] 31 May '16

31 May '16

1 0

WM & Gray Matter Parcellation Edit
by Limachia, Gaurang (NIH/NINDS) [F] 31 May '16

31 May '16

1 0

Algebraic operations with scalars
by Francesco Cardinale 31 May '16

31 May '16

Dear Freesurfer experts, I would like to make some algebraic operations with scalars, such as ?h.thickness or sig.mgh. They are referred to the same surface, of course. How can I export the thickness values to a spreadsheet? (?h.thickness 2 table) How can I export the significance values to a spreadsheet? (sig.mgh 2 table) All my best Cico Francesco Cardinale, MD Neurosurgeon "Claudio Munari" Centre for Epilepsy and Parkinson Surgery - Ospedale Niguarda "Ca' Granda" Piazza dell'Ospedale Maggiore, 3 - 20162 - Milano - Italia <x-apple-data-detectors://0/0> phone 0039 02 64442917 <tel:0039%2002%2064442917> fax 0039 02 64442868 <tel:0039%2002%2064442868> e-mail francesco.cardinale(a)ospedaleniguarda.it <mailto:francesco.cardinale@ospedaleniguarda.it>

2 2

Re: [Freesurfer] Manual segmentation issues
by maryam_koochaki 31 May '16

31 May '16

Hi Antoine,Have you tried control points seeding, I usually place the control points right behind the surface in trouble areas so seeded points would push the surfaces forward.Maryam Sent from my Samsung Galaxy smartphone. -------- Original message --------From: Saturne Fox <saturne.fox(a)gmail.com> Date: 2016-05-31 1:20 AM (GMT-08:00) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Manual segmentation issues Dear freesurfer community, These days I am manually editing some data and this subject is giving me such a hard time. In fact I would like the near-to-cortexartefacts at the top right hand corner to be excluded from the surface but even after changing the intensity of the wanted part to 255 and the one of the excluded parts to 1 (which is nevertheless not visible on these images) the surface is still not what I would like it to become. In adition to editing the wm.mgz file, I also modified the aseg.presurf file to exclude these parts and I re-runned the -normalization2 and -maskbfs flags to generate new brain.mgz and brain.finalsurfs.mgz files. Any idea why these modifications are not affecting the surface ? Best regards, Antoine

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer