Freesurfer

freesurfer@nmr.mgh.harvard.edu

30088 discussions

Using the new Thalamus tool
by Erik O'Hanlon 12 Sep '18

12 Sep '18

External Email - Use Caution Hi FS Experts I've run my data through the brainstem, hippocampus and amygdala following the usual Recon_all and using the developmental version downloaded and stalled around Jan2018. I'd like to use the new thalamus tool and am wondering if I need to do a full install of the latest DEV version to do so. As I am still working on certain aspects of the analyses I've run so far, I don't want to overwrite my main FS installation mid analysis. Is it possible to download the toolbox and add it to my current dev version or is it best just to do another install with teh complete new Dev version? Is it possible to run the Thalamus analysis as an addtional component without having to rerun the recon_all again? Thanks and regards Erik Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon(a)rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]

3 6

Latest dev version
by stdp82＠virgilio.it 12 Sep '18

12 Sep '18

External Email - Use Caution Please could you send me the link to download the the dev version with thalamus segmentation? Thanks Stefano

1 0

strange eTIV values
by Miguel Ángel Rivas Fernández 11 Sep '18

11 Sep '18

External Email - Use Caution Hello Freesurfer experts, When I exported the Destrieux and Desikian-Killiany volume values from Freesurfer to SPSS I obtained "strange" eTIV values with 16 digits as follows: 101,632,104,008.0000 134,253,072,953.0000 155,967,056,944.0000 142,085,122,028.0000 181,105,664,397.0000 118,051,287,519.0000 896,135,067,103.0000 With how many decimals Freesurfer exports the eTIV values ?, that is, what is the precision of this measure? I do not know how many decimals this measure has. Another doubt, it is necessary to make some kind of numerical transformation on the eTIV values before including it as a covariate in the statistical analysis (for example, a logarithmic transformation). Best, -- *Miguel Ángel Rivas Fernández*

2 3

Segmentation of thalamic nuclei - FreeSurferColorLUT
by stdp82＠virgilio.it 11 Sep '18

11 Sep '18

External Email - Use Caution Hi list, where can I find the list of regions that I obtain by trough the segmentation of thalamic nuclei? Are they in FreeSurferColorLUT? Which are the codes for right and left regions? Thanks Stefano

1 0

Re: [Freesurfer] thalamic segmentation
by Vinny K 10 Sep '18

10 Sep '18

External Email - Use Caution Hi, I ran recon-all to generate the required files for the thalamic segmentation tool (http://freesurfer.net/fswiki/ThalamicNuclei) using the latest development version of Freesurfer (06/09/2018) linux-cent06. The segmented thalamic nuclei were visualized but I could not find a table listing the thalamic nuclei and its associated label to help identify the specific nuclei. Any help would be greatly appreciated. Thanks, Vinny

2 3

Head circumference of fsaverage?
by Gladia Hotan 10 Sep '18

10 Sep '18

External Email - Use Caution Hi, What is the head circumference of the fsaverage subject? Thanks and Best, Gladia

3 2

Seeing the Results in the Original Space
by Maedeh Khalilian 10 Sep '18

10 Sep '18

External Email - Use Caution Dear FreeSurfer Experts, How can i have the results of FreeSurfer in its original space? The results have rotation and also the axial and the coronal images are replaced with each other. Thanks in advance Best regards, Maedeh

2 1

Question on subcortical segmentation
by limiyu 09 Sep '18

09 Sep '18

External Email - Use Caution Dear freesurfer developers Execuse me, I have a problem on subcortical segmentation, about how to output a segmentation which has the same shape with the input MRI image. The input shape of my MRI image is 197*233*189 and I run <recon-all -i mysubject.nii.gz -s bert -all>. Then Freesurfer output files in different foders such as 'label', 'mri', 'scripts' and so on. In the folder called 'mri', there are files about segmentation. and I convert the 'aseg.mgz' file into .nii.gz file by using <mri_convert> After that I load the .nii.gz file into MATLAB, so that I could compare the result with a mannual segmentation with shape of 197*233*189. However the shape of .nii.gz file converted from aseg.mgz is 256*256*256. But what I expect is the shape with 197*233*189 (the same shape with the imput MRI image). Then what should I do? Because I run Freesurfer on a server without GUI, the Graphical User Interface, so the freeview will not work. So could you please give me some help on how to solve the problem using command line? Looking forward to your reply Thank you Mingyuan Liu

2 1

How to display two overlays and its overlap in freeview?
by Fred Sampedro 08 Sep '18

08 Sep '18

External Email - Use Caution Dear FS experts, How could I use freeview to overlay two unrelated significance maps (say sig1.mgh and sig2.mgh) on fsaverage? I would like to display sig1.mgh with a red colorbar, sig2.mgh with a blue one, and its intersection/overlap in purple. Basically, I would like to produce the following figure (attached), also available at: http://pysurfer.github.com/auto_examples/plot_fmri_conjunction.html I am well aware this question has been asked several times in this archive (a recent one being https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41621.html) However, I have struggled to implement and adapt all suggestions in those threads without success. Clearly, being a recent FS user, I am probably missing some very basic concepts regarding LUT tables, annots and common FS commands. Could anyone please provide some exact commands to replicate this figure (same colors, same everything)? (please including LUT files and freeview/tksurfer commands/instructions). Thanks a lot in advance! Fred

1 0

About FreeSurfer source code
by Renew Andrade 08 Sep '18

08 Sep '18

External Email - Use Caution Dear community: I was curious about how the software is made and I decided to write an email to Dr. Bruce Fischl who answered all of the questions I asked, but he gave me the input to ask these questions also in FreeSurfer Community. I first asked the programming language of the software(I didn’t know that it was even open source). He says its mostly C but also some Matlab and C++. I am concerned with the long preprocessing time of raw T1 data so if anyone has some insights about which is the longest part and how faster it can get with nowadays hardware of course share with us. I think perhaps if some of the code of C were translated to C++ may be it could be faster. Although I don’t know how faster in fact but it could be a start. It should be easier if there were someone with clear head picture of time processing in different parts of the program in different hardware specifics. I know there is an entry in FreeSurfer wiki but I’m talking of an exchange of experiences with different machines with the same version of the software. May be I am going too far on my expectations. It would be nice to have a thread where we all shared our knowledge about how to improve performance. May be programming language translation is a bit of a lazy start and a change in some of the algorithms is the what we should encourage. Sincerely, Andrade.

2 1

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