Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30063 discussions

Talairach of ROI and FindClustersAndGotoMax
by Dongsheng Wu 25 Nov '17

25 Nov '17

Dear Freesurfer Developers, I have two questions about coordinate of ROI when running the QDEC module: (1) After drawing a ROI,the terminal demostrated the results like this: ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs WghtVtx Annot 1 -4.407 13586 966.10 44.2 -39.2 7.1 0.02020 0.01840 0.02200 2402 -4786.73 bankssts Could you tell me what exactly the "TalX TalY TalZ" refers to and whether the coordinate "TalX TalY TalZ" represents the VtxMax of the ROI? When I clicked the button "FindClustersAndGotoMax", the terminal showed the results: ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation --------- --- ------ --------- ---- ---- ---- ----- ---------- 1 -1.6946 7 966.10 45.9 -43.8 7.5 2402 bankssts The size(966.10mm2) and NVtxs(2402) of the two results are the same, but the "Tal X Y Z" is a little different. So are they the same region? (2) I used mris_anatomical_stats to get a set of statistics on each individual label created before, the average thickness,number of vertices, surface area and gray matter volume were saved in the file of stat. Was the average thickness the normalized one? Thank you for your help. Best regards, Dongsheng Wu Huaxi MR Research Center, Westchina Hospital,Sichuan University Chengdu,Sichuan,China

2 1

Create mpm label files
by Luqi Cheng 25 Nov '17

25 Nov '17

Dear freesurfer experts, I have several individual surface label files (eg, lh.MT.label)in the same region, how could I merge them and create a max probability map surface label file? Thank you very much. Best, Luqi

2 1

Re: [Freesurfer] mri_gtmpvc error: failed tissue type check
by Douglas Greve 25 Nov '17

25 Nov '17

sorry, can you send me the details again? On 11/21/17 10:24 AM, Klein, Gregory wrote: > Hello Donatas and Douglas, > > Did you ever find a cause and solution for this problem? I too > occasionally get this error message, and cannot get the results of > mri_gtmpvc for certain subjects. > > Any suggestions are welcome. > Thanks, > Greg > > -- > Gregory Klein, PhD > Principal Scientist, Biomarker Experimental Medicine Leader > F. Hoffmann-La Roche Ltd. > Bldg 01, Floor 16, N445 > Grenazacherstrasse 170, > 4070 Basel, Switzerland > Mobile: +41 79 572 97 89 > Office Phone: +41 61 682 07 59 > email: gregory.klein(a)roche.com <mailto:gregory.klein@roche.com> > > Roche Products Limited, 6 Falcon Way, Shire Park, Welwyn Garden City, > AL7 1TW Registration No:100674 > > Confidentiality note: This message is intended for the use of the > named recipient(s) only and may contain confidential and / or > privileged information. If you are not the intended recipient, please > contact the sender and delete this message. Any unauthorized use of > the information contained in this message is prohibited.

1 0

contrasts mat file
by 박경일 25 Nov '17

25 Nov '17

Dear experts, I am trying to perform mri_glmfit to generate images indicating cortical thickness differences between groups. My data has 6 or 7 covariates such age, sex, smoking, hypertension, diabetes etc. I wonder how to make contrasts.mat files.Those are supposed to be a lot of files. FSTutorial shows only the example of two covariates. Thank you. Sincerely, Kyung

2 1

PET processing seg fault with mri_glmfit --mrtm1
by Conchy PF 25 Nov '17

25 Nov '17

Dear Douglas, I had the same problem as Jonathan described in his post "PET processing seg fault with mri_glmfit --mrtm1" ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-January/043144.… ). In my case, I used this command: mri_glmfit --y gtmpvc/km.hb.tac.nii.gz --mrtm1 gtmpvc/km.ref.tac.dat time.dat --o mrtm1 --no-est-fwhm --nii.gz And I got this message: /Applications/freesurfer/bin/mri_glmfit: line 3: 27756 Segmentation fault: 11 mri_glmfit.bin "$@" Following your advice, I checked if km.hb.tac.nii.gz was all 0 using hb = fast_vol2mat( MRIread('km.hb.tac.nii.gz')); plot(hb) in matlab, but that is not the case [image: Inline image 1] I also checked the table.dat format and it was correct, and I tried using mri_glmfit.bin command insted, but it did not work. Could you give me some advice, so I can keep running the PET surfer pipeline? Thank you in advance and kind regards, CP

3 7

Segmentation Volume to Cortical Labels
by Hengda He 25 Nov '17

25 Nov '17

Hi Freesurfer Developers, I have a manually edited segmentation of the brain cortical regions, and I want to map it to cortical parcellation labels on both white matter surface and pial surface. So I am wondering if there is any way in FreeSurfer that can map the segmentation volume to cortical labels. Something like the inverse of command mri_aparc2aseg. Thanks! All the Best, Hengda

3 2

Error finding glmdir with mri_glmfit-sim
by Nick Corriveau-Lecavalier 25 Nov '17

25 Nov '17

Hi FS team, I ran a mri_glmfit for a 3 groups comparison and now I'm trying to run the cwp correction with mri_glmfit-sim command. When I type in my command, it says: ERROR: cannot find /Applications/freesurfer/subjects/fsgd/lh.thickness.10fhwm/ Which is exactly the emplacement of my group analysis file. The weird thing is, I ran the very same analysis a few months ago with fewer subjects and it ran well. Can you help me with this? Nick Corriveau-Lecavalier Candidat au Ph.D. recherche/intervention, option neuropsychologie clinique Président de l'Association étudiante des cycles supérieurs en psychologie de l'Université de Montréal (AÉCSPUM) Université de Montréal Centre de recherche de l'Institut universitaire de gériatrie de Montréal, bureau M7818

2 1

medial wall label in Freesurfer 6
by Sofia Rodriguez Penuela 23 Nov '17

23 Nov '17

Hello, when using "make_average_subject" in Freesurfer, we have noted that the medial wall label only contains 1 vertex leading, after applying "mri_glmfit, to significant results in regions of the medial wall. This problem didn't appear in Fresurfer 5.3 Is there something different with the command "make_average_subject" in Freesurfer 6 that prevent to correctly mask the cortical surface to avoid significant results on regions of the medial wall? We would like to include only cortical vertices in our analysis. Thank you in advance. Best, Sofia -- Sofía Rodríguez Peñuela, Técnico de Laboratorio. Laboratorio de Neurociencia Funcional Departamento de Fisiología, Anatomía y Biología Celular. Universidad Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - España - Movil: 627273085 Email: srodpen(a)upo.es http://www.upo.es/neuroaging/es/

2 1

contrasts mat file
by 박경일 23 Nov '17

23 Nov '17

1 0

Tilting / orienting brain slices
by Sam Norman-Haignere 23 Nov '17

23 Nov '17

I would like to tilt/rotate a brain image so that I can see multiple activations in a single slice. I don't believe this is possible in Freeview, am I'm curious if there is a brain viewer with this capability (would presumably require some type of activate interpolation)? It seems like a feature that would be quite useful. My best, Sam Norman-Haignere

3 2

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