Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Freeview filled in labels along with their outlines
by Pradyumna Bharadwaj 08 Jul '21

08 Jul '21

External Email - Use Caution Hi, In freeview, is it possible to view a collection of labels with different filled in colors, as well as their outlines? So, a combination of the filled in and outline only modes? Best, Prad

2 1

Fwd: Innis Lab postdoc position 2022
by Douglas N. Greve 08 Jul '21

08 Jul '21

-------- Forwarded Message -------- Subject: Innis Lab postdoc position 2022 Date: Thu, 8 Jul 2021 19:45:24 +0000 From: Innis, Robert (NIH/NIMH) [E] <innisr(a)mail.nih.gov> To: Innis, Robert (NIH/NIMH) [E] <innisr(a)mail.nih.gov> A postdoctoral position will be available in my lab starting in the first half of 2022. Please forward the attached advertisement to anyone who may be interested. The two major goals are translational studies of neuroinflammation (i.e., COX-1, COX-2, and TSPO) and indirect markers of cAMP signaling (via PDE4B and PDE4D). The studies extend from transgenic mice to monkeys and to patients, including those with depression or dementia. Stay safe and many thanks, Bob Innis ************************************ Robert B. Innis, MD, PhD Chief, Molecular Imaging Branch National Institute of Mental Health 10 Center Drive, MSC-1026 Bldg. 10, Rm. B1D43 Bethesda, MD 20892-1026 Tel: 301-594-1368 Fax: 301-480-3610 Email: robert.innis(a)nih.gov <mailto:robert.innis@nih.gov> Branch Administrative Manager: Elizabeth Alzona Tel: 301-594-1089 Email: alzonae(a)irp.nimh.nih.gov <mailto:alzonae@irp.nimh.nih.gov> Molecular Imaging Branch website<https://secure-web.cisco.com/1ArBJjYhVhrUft9gNOaLCuNtmSeJ1qPEnHkkGF7qzP9gVj…> ************************************ ____________________________________ LEGAL CONFIDENTIALITY NOTICE: This email message (including all attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure, copying or distribution is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.

1 0

BERT - Example of segmentation
by Rosalia Dacosta Aguayo 08 Jul '21

08 Jul '21

External Email - Use Caution Dear Freesurfer team, It is my first time editing wm segmentation (white matter segmentation errors + topological errors). I wonder if there is a good tutorial on which I could rely. Also, I have read there is an example of segmentation that comes with FreeSurfer that is called Bert. I think it would be great to have it so I can look at it as a good example. Your help on this is very much appreciated Kind regards, Rosie

2 5

Interscanner variability
by AJ 07 Jul '21

07 Jul '21

External Email - Use Caution Hi, I am running Freesurfer on longitudinal datasets all obtained on 3T scanners. Unfortunately, many of the MRIs were done on different scanners, Phillips and GE. Would longitudinal pipeline help reduced scanner variability or should I process crossectionally each time point separately and normalize these time points with eTIV? Many thanks AJ

2 2

Segmentation of hippocampal subfields
by Rosalia Dacosta Aguayo 07 Jul '21

07 Jul '21

External Email - Use Caution Dear Freesurfer team, Following this link: https://secure-web.cisco.com/1JQvIqqm3-q4IvkVi2SEZWuHP3qoo3qga0SfN71vLNIZ9q… It says how to run segmentation of hippocampal subfields before running recon-all but not once you already have recon-all -all run. Any suggestions on how I can get the segmentation of hippocampal subfields under this situation would be appreciated. Kind regards, Rosie

3 13

Question about calculating hausdorff distance
by Hye Min Shin 06 Jul '21

06 Jul '21

External Email - Use Caution Hello experts, I am trying to calculate Hausdorff distance between two mri volumes for cortical and subcortical structures across several subjects. I found a way to calculate hausdorff distance for mri volumes using mri_hausdorff_dist but it only seems to work if I specify one target label at a time. My question is, so to calculate average hausdorff distance between two mri volumes across several subjects should I first calculate hausdoff distance between two mri volumes for each segmentation label for each subject and then calculate the mean hausdorff distance for each segmentation label across subjects? Best, Julia Shin

1 0

retinotopy, visualization
by Akkoyunlu, Beyza 06 Jul '21

06 Jul '21

External Email - Use Caution Dear experts, While visualizing my polar angle results using angle file, I almost don't get any interpretable results. However, if I show results with real+imag file, taken from the following link (http://secure-web.cisco.com/1JbJRUtZSYA97HQvtYOuYEBYhanfcOaUs2V4aEIfByy0FFh…) I have a clearer map. Can you help me? Does it make sense to visualize with real and imag files layered on top of each other? Eccentricity results work fine with both of the visualization approach, what might be wrong it polar angle? I appreciate any cue. Thanks in advance! Beyza

1 0

InfantFS witg segfile exiting with errors
by Fernanda Hansen P. de Moraes 05 Jul '21

05 Jul '21

External Email - Use Caution Dear FreeSurfer experts, I am trying to process some newborn subjects including the segfile. In both situations, including the mask file and using the --forceskullstrip flag I get the following error (log file attached): *lta_convert successful./home/fernanda/Documentos/dHCP/freesurfer1ERROR: Option --noverbose unknown* This is the exact command I am running: *infant_recon_all --s sub-CC00060XX03 --age 0 --segfile sub-CC00060XX03/sub-CC00060XX03_ses-12501_desc-drawem87_space-T2w_dseg.nii.gz --forceskulltrip --force* How can I overcome this? Thank you very much. Fernanda Hansen P. de Moraes fernandahmoraes(a)gmail.com Doutoranda em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino

2 2

Error message when creating a stats table
by Rosalia Dacosta Aguayo 05 Jul '21

05 Jul '21

External Email - Use Caution Dear Freesurfer team, I am having the following error message when I try to run the stats table: rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI/FREESURFER_CAN_RUTI $ asegstats2table --subjects sub-002_ses-BSL sub-003_ses-BSL sub-004_ses-BSL sub-005_ses-BSL sub-006_ses-BSL sub-007_ses-BSL sub-009_ses-BSL --meas volume --tablefile aseg_stats.txt SUBJECTS_DIR : /home/rosalia/Desktop/CAN_RUTI Parsing the .stats files ERROR: Cannot find stats file /home/rosalia/Desktop/CAN_RUTI/sub-002_ses-BSL/stats/aseg.stats Use --skip flag to automatically skip bad or missing stats files rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI/FREESURFER_CAN_RUTI $ The problem is that there is an actual aseg.stats in this directory where it says it cannot find it. Any idea why is this happening? Kind regards, Rosie

1 1

retinotopy in FS with different phases
by Manenti, Giorgio 03 Jul '21

03 Jul '21

External Email - Use Caution Dear Experts, I am running my polar angle and eccentricity following the freesurfer retinotopy analysis. Saddly, i figured out that my eccentricity script has a shorter cycle compared to the polar angle (38sec vs 40sec pro cycle). To bypass this error im splitting the analysis and i run the retinotopy separately on polar angle and eccentricity using two different folders and copying the polar angle as eccentricity ( same for eccentricity as polar angle) just in order to run selxavg3-sess. Is this a legal step for the analysis? Furthermore, im getting negative values for masked angles… is this indicating any specific problem? Many thanks for your help! Giorgio

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