Freesurfer January 2021

freesurfer@nmr.mgh.harvard.edu

98 participants
132 discussions

Subfield volume data organization
by Wei Shao 18 Jan '21

18 Jan '21

External Email - Use Caution Hi, dear Freesurfer expert: As I extracted the subfield volume data with the command: quantifyHAsubregions.sh hippoSf from T1 result, the output file looks as follows(Linux system, R, excel), do you know any way that I can use in the Linux system or R to organized the form so each row can fit in each column like normal form? [image: Lin.PNG] [image: Excel.PNG] [image: R.PNG] Best, Wei

2 3

making labels in Freeview/Freesurfer 7.1.1
by Trisanna Sprung-Much 18 Jan '21

18 Jan '21

External Email - Use Caution Hi there As a follow-up to my earlier email, I figured it out. I can create 1 label in an annotation and simply have to assign an "index" value before saving. Could you please confirm that this is the best way to go about create a new label on a surface? Many thanks, Trisanna

3 5

Issue with freeview display in ubuntu/Xming on windows 10: failed to get the current screen resources
by josua.zimmermann＠bli.uzh.ch 18 Jan '21

18 Jan '21

External Email - Use Caution Dear freesurfer experts, I installed freesurfer on ubuntu 18.04 (Windows 10), that uses Xming. Freesurfer seems to work fine. However, I have troubles with freeview. Freeview opens but I cannot display images. I get the following error message when I open freeview: failed to get the current screen resources QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-joszim' QXcbConnection: XCB error: 170 (Unknown), sequence: 174, resource id: 90, major code: 146 (Unknown), minor code: 20 QXcbConnection: XCB error: 170 (Unknown), sequence: 174, resource id: 90, major code: 146 (Unknown), minor code: 20 I have previously also installed FSL on ubuntu, and fsleyes that uses Xming works fine, so I guess Xming installation is not the issue. Any help is appreciated. Best wishes, Josua

1 0

Recon-all error: CTABWriteFileASCII; could not open file for writing
by Loreto, Flavia 18 Jan '21

18 Jan '21

External Email - Use Caution Dear FreeSurfer Experts, Version: FreeSurfer 7.0 Platform: Bash remotely through High Performance Computing (HPC) on a MacOS Mojave We are trying to run recon-all on T1 images but the job stops with the following error: Reading annotation /rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 1000 error: Permission denied error: CTABwriteFileASCII(/tmp/mri_segstats.tmp.APC001.lh.176.ctab): could not open for writing Could you please help us figuring out where is the problem? I am attaching the script we are running and the recon-all log for one of our analysed subjects. Thank you for your help. Kind regards, Flavia

1 0

Holes in my ROIs
by Alberto Del Cerro Leon 18 Jan '21

18 Jan '21

External Email - Use Caution Hello Freesurfers, I created surface image based on AAL with mri_vol2surf. However i see that in some regions there are a lot of holes, i thought that probably is for the presence of subcortical regions in the AAL.ni. There is some workflow to select the regions from my volume to do mri_vol2sur? Can I create another volume from my AAL.nii selecting only the surface regions?

1 0

Changes to lh.pial and rh.pial between FreeSurfer versions 6 and 7
by Mike Schmidt 17 Jan '21

17 Jan '21

External Email - Use Caution I have written a script that reads the binary representations of the vertices and faces from FreeSurfer's surf/{l,r}h.pial files and saves them out unchanged to stl and obj file formats for 3D rendering. I have used it with FreeSurfer 6 and several MRI images, everything working fine. Processing the identical input, a single T1-weighted MPRAGE MRI, FreeSurfer 7 works great and finishes faster than FreeSurfer 6, but we see strange aliasing on the 3D objects. I've spent a lot of time messing with different materials and textures, generating vertex normals at different stages, but I can't find anything that makes any difference except the FreeSurfer version. I have seen several items in the release notes ( https://secure-web.cisco.com/10e4A8ivZBudPVZzB2fSu2TWQAh7jeSCsKiZetlyqyRe4b…) that may be related, but I'm not sure how to go about investigating them. Left cortex images are included, with links if they don't show up in the email, of the same brain processed with FS6 and FS7. FreeSurfer 6.0.0 works well with a smooth surface and working transparency ( https://secure-web.cisco.com/1UQ6aOrt2bryipWe-PkobeSr25YVlze0fFJ35x4ZMQJwBf…) This image is of surf/lh.pial with 149,968 vertices and 299,932 faces. [image: rh_pial_oblique_from_fs6.png] FreeSurfer 7.1.1 results in the same size and shape cortex, but renders strangely with mottled shading of triangles. ( https://secure-web.cisco.com/1VT57uMXFOHM4VZNouJmVogT7JK7OwLFJy5l6ByvUoIQfw…) This image is from the same T1 image as above, but processed with FS7, resulting in 147,292 vertices and 294,580 faces. [image: rh_pial_oblique_from_fs7.png] I'm out of ideas, and the only difference I can find is FreeSurfer version, so thank you to anyone who can point me in the right direction to fix this issue. Mike Schmidt

1 0

3dClustSim
by Meike Hettwer 17 Jan '21

17 Jan '21

External Email - Use Caution Dear Freesurfer experts, I ran a glm analysis a while back and corrected for MC using the glm-fit_sim --cache option / Monte Carlo simulation. I now saw that the AlphaSim algorithm this is based on is not recommended anymore (https://secure-web.cisco.com/1A4g1vq2U_gugbf-mlVAUZcEyLmp9YkEcL2Vw_tFG_wyrN…) Instead, it suggests using 3DClustSim. 1. Does that mean the Monte Carlo simulation as it is implemented in FreeSurfer does not allow for valid analyses / MC corrections anymore? 2. Is 3DClustSim implemented in Freesurfer? And if not, would I need to export the FreeSurfer files as a volume (i.e. 3D) file and analyse it externally? What would you recommend? (My analysis is a regression analysis for one group, so the design matrix is not really suitable for a permutation). Thanks in advance, Meike

1 0

recon-all , fsaverage ?
by Fatemeh Ahmadi 15 Jan '21

15 Jan '21

External Email - Use Caution Hi Dear Dr., I run recon -all and get an ERROR reading /media/sf_shared/fsaverage/label/lh.BA1.label I saw that you answered similar questions as follows: It should be symlinked from you $SUBJECTS_DIR to $FREESUFER_HOME/subjects/fsaverage. How do I do this? Thank you in advance, --------------------- Fatemeh Ahmadi,PhD Student in Computer Science,Department of Mathematics and Computer Science,Amirkabir University of Technology, Tehran, IranEmail: f.ahmadi(a)aut.ac.ir

2 1

almost empty mask.mgh with glmfit
by Julie Ottoy 15 Jan '21

15 Jan '21

External Email - Use Caution Dear Doug, I was wondering why the flag --prune is recommended (petsurfer website) when creating a stacked pet file and during surface-smoothing. If I understood correctly, this would set all vertices that are 0 in at least one subject to 0 ("set vox to 0 unless all frames are non-zero")? In my non-pvc data, it seems as though a lot of the surface-projected values are 0. Hence, when I perform a surface-based regression between PET and a regressor and I use the --prune flag during mri_concat, I don't get any results. Thank you! best regards Julie

3 4

FW: Missing transformation files in longitudinal pipeline
by Nederpelt, D. van (David) 15 Jan '21

15 Jan '21

External Email - Use Caution Hi FS-team, I ran a longitudinal recon-all stream(FS version 7.1.1) and trying to convert the aseg.mgz back to native space. However, in the transform file the <tpid>_to_<tpid>.long.<baseid>.lta is missing. This is the case for every subject I ran, while the recon-all.log showed freesurfer finished without errors. I've attached the .log file. The base dir does have the needed transform files. How can I resolve this and transform ROI to native space? Thank you in advance, Kind regards, David ______________________________________________________ VUmc disclaimer : http://secure-web.cisco.com/17Hm37rdmQA7fExuo50mOppILpRbNMLA_qrH6JxGVW_f9CA… AMC disclaimer : http://secure-web.cisco.com/1ebdk9doSyywTxkQ7Inu7GvhMGGJLlbd6W1lSNC3xIcWP8s…

2 1

← Newer
1
...
5
6
7
8
9
10
11
...
14
Older →

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 January 2021