Freesurfer July 2017

freesurfer@nmr.mgh.harvard.edu

118 participants
198 discussions

lopsided hemisphere
by Michael Davies 04 Jul '17

04 Jul '17

Hello, I have encountered a lopsided hemisphere when analysing the data. What procedure do i need to employ to fix the problem? Any advice would be greatly appreciated! Kind regards, Michael

2 2

Anterior and posterior insula in fsaverage space
by Juergen Haenggi 04 Jul '17

04 Jul '17

Dear FS experts I am wondering whether there exist labels of the insula other than that provided by aparac and aparc.a2009s. I am searching for labels of the anterior and posterior insula in the fsaverage space. I have drawn such regions (see attachment), but these are rather subjective. Any suggestions are welcome. Thanks in advance Regards Jürgen Hänggi ----------------------------------------------------------------------------------------------------- University of Zurich Dr. Jürgen Hänggi, Ph.D. Department of Psychology Division Neuropsychology Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This email (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this email in error) please notify the sender immediately and destroy this email. Any unauthorised copying, disclosure or distribution of the material in this email is strictly forbidden. -----------------------------------------------------------------------------------------------------

1 0

Re: [Freesurfer] Surface edits: Cortex that extends into the putamen + Missing gray matter
by Vincent Koppelmans 03 Jul '17

03 Jul '17

Hi Bruce, Thank you for your reply. The aseg seems to be okay: https://www.dropbox.com/s/j1ac0ftxw8iiv34/Putamen.png?dl=0 <https://www.dropbox.com/s/j1ac0ftxw8iiv34/Putamen.png?dl=0> Do you have any other suggestions? Here is an extra image of the cortical ribbon. Maybe this helps: https://www.dropbox.com/s/ycav96v91e4ncbg/Cortex.png?dl=0 <https://www.dropbox.com/s/ycav96v91e4ncbg/Cortex.png?dl=0> Thanks! - Vincent On Mon, 03 Jul 2017, Bruce Fischl wrote: Hi Vincent the putamen error probably means that the aseg is wrong, and if so, you can correct the aseg and rerun autorecon2-wm and autorecon3 I believe. For the medial ttemporal lobe issue is that really cortex? I can't really tell from the single coronal slice. I'll cc Jean Augustinack to see if she has an opinion. cheers Bruce On Fri, 30 Jun 2017, Vincent Koppelmans wrote: Hi all, I was wondering how to fix the following issues: 1) The cortical ribbon extends into the gray matter of the putamen (see the top row of the attached image). 2) Cortical gray matter is missing in the medial temporal lobes (see the bottom row of the attached image). I can’t find solutions for these particular issues under https://surfer.nmr.mgh.harvard.edu/fswiki/Edits <https://surfer.nmr.mgh.harvard.edu/fswiki/Edits> <https://surfer.nmr.mgh.harvard.edu/fswiki/Edits <https://surfer.nmr.mgh.harvard.edu/fswiki/Edits>> How should I approach this? Suggestions are very much welcome. Thank you! - Vincent

2 1

Surface edits: Cortex that extends into the putamen + Missing gray matter
by Vincent Koppelmans 03 Jul '17

03 Jul '17

Hi all, I was wondering how to fix the following issues: 1) The cortical ribbon extends into the gray matter of the putamen (see the top row of the attached image). 2) Cortical gray matter is missing in the medial temporal lobes (see the bottom row of the attached image). I can’t find solutions for these particular issues under https://surfer.nmr.mgh.harvard.edu/fswiki/Edits <https://surfer.nmr.mgh.harvard.edu/fswiki/Edits> How should I approach this? Suggestions are very much welcome. Thank you! - Vincent

2 1

Strange Discrepancy Between Activation Location on Surface vs. Volume
by Taylor, Johnmark 03 Jul '17

03 Jul '17

Hello, I am running into an odd issue. In particular, I have run a GLM analysis in *volume* space, and I am visualizing the results both on the surface using tksurfer, and on the volume using tkmedit. In both cases, I am using the register.dof6.dat file to do the registration. Oddly, when I visualize the results on the *surface*, the activation patch falls on the medial surface of the hemisphere, in the *precuneus*, whereas when I visualize the results on the *volume*, the patch is in the *intraparietal sulcus* (which is where we expect to see this particular activation). I have made a label out of the activation in both cases and viewed it in the other space just to make sure that it is in fact the same activation, and it is. Any idea what might be going on? It seems to me that it can't be an issue with the BOLD volume --> structural volume registration, since the activations look normal on tkmedit. It seems to me, then, that it must have to do with the relationship between the anatomical volume and the anatomical surface--could this be where the problem lies? Maybe an imperfect surface reconstruction? Thank you very much, JohnMark

1 0

bad file conversion
by Michael Davies 03 Jul '17

03 Jul '17

Hello, i was wondering if you could possibly help me with a subjects file that has loaded badly. It not only loaded up-side down but looks as though there are additional deficits that need correcting. Any tips or advice would be greatly appreciated! Kind regard, Michael

3 3

Surface edits: Cortex that extends into the putamen + Missing gray matter
by Vincent Koppelmans 01 Jul '17

01 Jul '17

Hi all, I was wondering how to fix the following issues: 1) The cortical ribbon extends into the gray matter of the putamen (see the top row of this image: https://www.dropbox.com/s/x1euf9otl2nv6ff/Fix.png?dl=0) 2) Cortical gray matter is missing in the medial temporal lobes (see the bottom row of this image: https://www.dropbox.com/s/x1euf9otl2nv6ff/Fix.png?dl=0) I can’t find solutions for these particular issues under https://surfer.nmr.mgh.harvard.edu/fswiki/Edits How should I approach this? Suggestions are very much welcome. Thank you! - Vincent

1 0

Using asegstats2table for gtm.stats.dat?
by Elijah Mak 01 Jul '17

01 Jul '17

Hi Unix experts, I am trying to extract the PVC-ed values from gtm.stats.dat for every subject. Is there a fast way to do this using a similar workflow with asegstats2table? Thanks. Best Wishes, Elijah

3 5

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 July 2017