Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

Create an lta or xfm file for mri_vol2vol
by Peled, Noam,PhD 15 Nov '23

15 Nov '23

Dear group, I have 2 images (preop t1 and postop CT), and a 4x4 registration matrix (as a text file). Is there an easy way to create an lta or xfm file to use it with mri_vol2vol? Thanks! Noam

2 1

Does Synthseg include longitudinal processing?
by STACEY M SCHAEFER 15 Nov '23

15 Nov '23

External Email - Use Caution Hello, We are in the midst of longitudinal data collection. Before diving into our first longitudinal structural processing, have a few questions: Does Synthseg include a longitudinal processing stream? If so, how does it compare to the Freesurfer Longitudinal Processing stream? In the past, including both a T1 and T2 has been recommended for optimal segmentations. I don't see any mention of including a T2 in the longitudinal workflow (https://secure-web.cisco.com/1Hs2Tl_vnSro2vTkaUDdxTgiD9pw3XNueD_u5Drjxzqa7l…) Would it be worth including T2 scans if they are available? Thank you for your thoughts and guidance! Stacey M. Schaefer, Ph.D. Leader of the MIDUS Neuroscience Project & Co-Leader of the MIDUS Admin Core Institute on Aging 2245C Medical Sciences Center University of Wisconsin-Madison 1300 University Ave Madison, WI 53706 USA 608-265-3486

1 0

[WARNING: ATTACHMENT UNSCANNED]mri_label2label with Gifti file
by P Pieperhoff 15 Nov '23

15 Nov '23

External Email - Use Caution Hi FreeSurfer developers, I want to transform a label file in Gifti-format from the fsaverage space into the native space of a subject (CON01a). The FreeSurfer reconstruction pipeline was completely executed before for this subject. The label file lh.JulichBrainAtlas_3.0.3.label.gii is in freeview correctly visualized on the surface of fsaverage. But when I call mri_label2label as below, it seems that the Gifti-format is not recognized: mri_label2label --srcsubject fsaverage --srclabel ../atlas/lh.JulichBrainAtlas_3.0.3.label.gii --trgsubject CON01a --trglabel CON01a/label/lh.JulichBrainAtlas_3.0.3.label.gii --hemi lh --trgsurf white --regmethod surface *Output:* srclabel = ../atlas/lh.JulichBrainAtlas_3.0.3.label.gii srcsubject = fsaverage trgsubject = CON01a trglabel = CON01a/label/lh.JulichBrainAtlas_3.0.3.label.gii regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 Loading source label. <!DOCTYPE GIFTI SYSTEM "http://secure-web.cisco.com/10pJypOCaxCr0cVxOqUZEEwUWnA-a8JBJInZZrsmFvbBpZc…"> error: mri_label2label: could not scan # of lines from label file The Gifti-file contains a LabelTable (including a RGB-color for each label), and a DataArray of Labels (for each vertex), but not the vertex coordinates. Please, could you tell me how I can transform this file into the native space of each subject? I have attached the compressed label file to this mail. Best regards, Peter

3 3

Re: [Freesurfer] mri_cvs_register failure
by Antonín Škoch 15 Nov '23

15 Nov '23

External Email - Use Caution Dear Doug, thanks for the response. Talairach registration seems OK. I am not sure, how to check surface-based registration. I have tried to look at subject's ?h.sphere.reg (with ?h.curv loaded) and ?h.sphere of fsaverage overlaid. But I am not sure if it is a correct way to do it: the spheres even do not spatially coincide (screenshot). Regards, Antonin I'm not sure what happened. Have you checked the surface-based registration? Also check the talairach reg. On 10/19/2023 11:35 AM, Anton?n ?koch wrote: > > ????????External Email - Use Caution > > Dear experts, > > I have encountered an failure of > > mri_cvs_register --mov my_subject --mni > > The resulting output file > > final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz > > looks like in the attachment. > > Could you please give me a hint, where could be a problem, or how to > troubleshoot the mri_cvs_register routine? > > Regards, > > Antonin Skoch >

2 1

Aseg fail, pathology affecting anatomy
by Konstantinos Chiotis 15 Nov '23

15 Nov '23

External Email - Use Caution Dear all, I am reaching out regarding a challenging issue I've encountered in the segmentation of an extreme case. This particular case involves a history of a traumatic brain injury in the left lateral frontal lobe, resulting in gliosis in that specific area. My efforts included running recon-all on the case, incorporating T1 + FLAIR imaging. The segmentation of the cortex appears reasonably accurate overall, except for a notable challenge in the segmentation of the medial frontal surface. Notably, in the anterior areas of the brain, the lateral ventricles were not successfully segmented during aseg (aseg value of 0). This omission has notably impacted the parcellation process, particularly concerning the medial surfaces of the medial frontal cortex. Moreover, the aseg also encountered difficulties in parcellating the anterior subcortical areas, specifically the caudate nucleus and portions of the putamen. I am attempting to provide an image for better context. I acknowledge that this case, due to substantial gliosis, presents suboptimal conditions for segmentation. Nevertheless, I am open to any suggestions or insights you might offer to approach and potentially address this challenging issue. Thank you for your time and consideration. Kind regards, Konstantinos [A brain scan with a colorful design Description automatically generated with medium confidence] N?r du skickar e-post till Karolinska Institutet (KI) inneb?r detta att KI kommer att behandla dina personuppgifter. H?r finns information om hur KI behandlar personuppgifter<https://secure-web.cisco.com/1LbGLriTgQNgdXYvDMiuX7zjOnHuhicCi76lawI86XHhG5…>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI's processing of personal data here<https://secure-web.cisco.com/1D7D6_w_SWvPD8r_TkEtei0MyFxzuaSVWLR_BuiIK69eM_…>.

2 1

Doubts about GLM contrasts
by Laura Willers de Souza 15 Nov '23

15 Nov '23

External Email - Use Caution Hello FreeSurfer Developers, Following the FSGD examples on the website, I built the following test: Question: Is there an association between cortisol and cortical thickness regressing out the effect of sex, age, APOE4_carrier (1=1 or 2 alleles, 0=no alleles), abeta, ptau, diagnosis (CU and CI)? Regressors: 2 factors (sex, diagnosis) with 2 levels each, 5 covariates (age, APOE4_carrier (1=1 or 2 alleles, 0=no alleles), abeta, ptau, cortisol) >> 24 regressors Contrast: 0 0 0 0 0.5 -0.5 0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 FSGD: GroupDescriptorFile 1 Title CSF_semgrupos Class MaleCU Class MaleCI Class FemaleCU Class FemaleCI Variables Cortisol Age ABETA ptau APOE4_carrier Input 098_S_4003_I224603 MaleCI 11 81.3 741.5 22.83 1 Does this feel right to you? I am having difficulty understanding how to construct the contrast to answer the following question "Is the interaction between group (CU/CI) and cortisol significant regressing out the effect of sex, age, APOE_carrier, abeta and ptau?" It seems like the contrast would be the same as before.. Can you guys help me with this? Thanks in advance! Laura Willers de Souza PhD Student in Pharmacology and Therapeutics Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

2 1

ANTs denoising
by Alexopoulos, Dimitrios 15 Nov '23

15 Nov '23

External Email - Use Caution To which anatomical volume is ANTs denoising applied to for generating the orig surface? We do ANTS denoising to the input T1 before running recon-all and were wondering if we are denoising our data twice. Thx. Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

2 1

recon_all_clinical and aseg.stat
by Biondo, Francesca 14 Nov '23

14 Nov '23

External Email - Use Caution Hello! I encountered 3 issues with recon_all_clinical: 1. Both version 7.4.0 and version 7.4.1 do not generate aseg.stat file. Is this normal? I would like to extract volume parcellations via asegstats2table given that I need the volume parcellations as typically presented in aseg.stat. Is there a way to extract aseg.stat from aseg.mgz or another solution to extract aseg.stat volumes? 2. Version 7.4.0 throws errors at the end of the script (even with the replacement file). "ERROR: cannot find or read /cluster/project7/brain_age/software/freesurfer-7.4.0/freesurfer/average/colortable_BA_thresh.txt" and "ERROR: cannot find or read /cluster/project7/brain_age/software/freesurfer-7.4.0/freesurfer/average/colortable_BA_thresh.txt." I checked, "colortable_BA.txt" exists but "colortable_BA_thresh.txt" doesn't. If I rename the latter file to "colortable_BA_thresh.txt", then it fixes the errors. Is this the correct way to address the problem? 3. Version 7.4.1 has a similar error as above, but it seems to be due to the incorrect path: ERROR: cannot find or read /usr/local/freesurfer/dev/average/colortable_BA.txt. Any help, particularly with problem 1, would be much appreciated! Thank you, Fran Francesca Biondo, PhD | Senior Research Fellow | Centre for Medical Image Computing | Computer Science | UCL | f.biondo(a)ucl.ac.uk<mailto:f.biondo@ucl.ac.uk>

2 1

Running autorecon2-wm after wm edits
by Fernanda Hansen P. de Moraes 14 Nov '23

14 Nov '23

External Email - Use Caution Dear FreeSurfer experts, I have been trying to manually correct a wm volume to further fix the wm and pial surfaces, but when I ran *recon-all -subjid SUBJxxx -autorecon2-wm -autorecon3* nothing happened to the surfaces. I found an unknown-args.txt file under scripts, and it seems the autorecon2-wm flag is not recognized. How can I create new surfaces and overcome this issue? Thank you very much in advance, Fernanda Hansen P. de Moraes fernandahmoraes(a)gmail.com Pesquisadora no Instituto de Física da UFRJ | metaBIO (IF-UFRJ) Doutora em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino

2 6

TRACULA error: lowb_brain_mask.bbr.nii.gz
by Lauren Stephens 13 Nov '23

13 Nov '23

External Email - Use Caution Hi FreeSurfers, I am attempting to run tracula on longitudinal DTI data however during trac-all -prep the process fails because it does not generate lowb_brain_mask.bbr.nii.gz from mri_concat. #------------------------------------- /Applications/freesurfer/7.3.2/bin/trac-preproc #------------------------------------- #@# Intra-subject registration (base template) Mon Nov 13 14:13:56 PST 2023 mri_concat --i /Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001A.long.R001/dlabel/anatorig/aparc+aseg_mask.nii.gz --min --o /Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001/dlabel/anatorig/aparc+aseg_mask.nii.gz ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Computing min across all frames Writing to /Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001/dlabel/anatorig/aparc+aseg_mask.nii.gz mri_concat --i /Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001A.long.R001/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz --min --o /Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz ninputs = 1 Checking inputs error: niiRead(): error opening file /Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001A.long.R001/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz ERROR: reading /Users/corpuscallosum/Desktop/TRACULA/RRD_Longitudinal/R001A/R001A.long.R001/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz Darwin PSYC-C02DP05D0833.stanford.edu 22.6.0 Darwin Kernel Version 22.6.0: Wed Oct 4 21:25:26 PDT 2023; root:xnu-8796.141.3.701.17~4/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Mon Nov 13 14:13:58 PST 2023 I am using FreeSurfer 7.3.2 on an iMac Pro running Ventura 13.6.1. Any suggestions for how to clear this error would be greatly appreciated! Thank you, Lauren Stephens Lauren Stephens, MS Assistant Clinical Research Coordinator Department of Psychiatry and Behavioral Science Stanford University School of Medicine E: laurenss(a)stanford.edu P: (650)-725-1716

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