Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30068 discussions

Left Cerebellum Exterior and Right Cerebellum Exterior mean value generation
by M Janani 20 Jun '17

20 Jun '17

Hi freesurfer team, I apologize, I am new to freesurfer. I'm doing analysis on PiB. I have successfully got my .stats files by running the recon-all command. When I checked for Left Cerebellum Exterior and Right Cerebellum Exterior value in the aseg.stats file, they are not exist. May I know the reason for it? Also is there any command to get the above mentioned segmentations mean value. Any guidance would be much appreciated! Regards, Janani ::DISCLAIMER:: ---------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. ----------------------------------------------------------------------------------------------------------------------------------------------------

2 1

QModeling: a multiplatform, easy-to-use and open-source toolbox for the pharmacokinetic analysis of PET studies
by José Paredes Pacheco 20 Jun '17

20 Jun '17

Dear Freesurfer users, We have created QModeling: a multiplatform, easy-to-use and open-source toolbox for the pharmacokinetic analysis of PET studies. We think this will be useful to many of you if you use SPM. The relevance of this kind of analyses for the study of normal and pathologic brain physiology suggests the need to link kinetic modeling with the established neuroimaging pipelines for preprocessing and statistics. For this reason, QModeling has been developed as a free extension of Statistical Parametric Mapping (SPM). Currently, this new toolbox allows applying SRTM, SRTM2 and Patlak reference models to dynamic PET data. Also, preliminary testing shows reliable results and good computation times. For more details please see: - Post in Spanish: http://uimcimes.es/contenidos/general.action?idsupersection=5&idselectedsec… To download: - Post in English: http://www.uimcimes.es/contenidos/golink?p=1 The toolbox will continue to be developed, so we would be happy to have users feedback. Any question or suggestion can be sent to nroe(a)fguma.es We hope it will be of use to some of you. Best regards, José Neuroimaging technician CIMES Molecular Imaging Unit, Bioengineering department C/ Marques de Beccaria, 3 29010, Málaga Spain Contact email: j.paredes(a)fguma.es Website URL: www.uimcimes.es

2 1

qdec FindClustersAndGotoMax Plot ERROR
by Hossein Rejali 20 Jun '17

20 Jun '17

Hello, I'm fairly new to freesurfer, I've been going through the tutorials to get my hands dirty. Currently on the Surface Group Analysis with Qdec tutorial, when applying the FindClustersAndGotoMax, the command line generates the cluster stats but underneath prints: invalid command name "FsgdfPlot_SetPoint" invalid command name "FsgdfPlot_SetInfo" There is no plot that is generated. I'm running the freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c freesurfer version. Any guidance would be much appreciated! Thank you in advance. Kinds Regards, Hossein Rejali

2 1

Libnetcdf.so.6 error during mris_make_surfaces
by Lisa Kramarenko 20 Jun '17

20 Jun '17

Hi, I am getting the following error when my HCP pipelines come to the mris_make surfaces step: mris_make_surfaces: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory I saw this response: https://www.mail-archive.com/hcp-users@humanconnectome.org/msg02418.html but the files are not available anymore and I cannot find where to download it. I have Ubuntu 14.04 (64-bit). Do you have any idea about what causes this problem and how to solve it? Thanks a lot! Lisa

2 3

Re: [Freesurfer] LME correction in longitudinal analysis
by Livia Liu 19 Jun '17

19 Jun '17

Dear Martin, Thank you so much for all the help that you had given me. Kind regards, Livia

1 0

WM Volume
by Michael Davies 19 Jun '17

19 Jun '17

Hello, i am currently looking at the WM Volume in heat mode and am curious as to if i need to fill in all the small missing voxels located within the boundary as well as the bigger holes? Kind regards, Michael

2 1

Hippocampal sufields
by Erik Lindberg 19 Jun '17

19 Jun '17

Dear Freesurfer experts, I am currently running your new pipeline for hippocampal subfield segmentation. However the resolution on my MRI images is too bad for identifying specific cellular layers such as stratum moleculare. My preferred option would be not to divide the different subfields into different cellular layers and only have one volume for the presubiculum for instance. Is there any way I can know how much volume of the molecular layer that should be included into each separate subfield? So forinstance I can add the volume of subiculum with the volume of the molecular layer in the subicula Best Erik

2 1

PhD-position | clinical MR-physics | Germany
by Theodor Rüber 19 Jun '17

19 Jun '17

Dear colleagues, Please note the following PhD-student job offer: http://www.ukb.uni-bonn.de/42256BC8002B7FC1/vwLookupDownloads/PhD_EPI_Ruebe… This is a highly attractive position between the fields of MR-physcis, clinical research and neuroradiology as part of a research project on imaging of the bbb in the appealing research environment of Bonn University. We are looking forward to receiving your application! Best, Theodor. on behalf of Elke Hattingen, Tony Stöcker, and Christian E. Elger Theodor Rüber, MD .............................................................. Department of Epileptology Bonn University Hospital .............................................................. Sigmund-Freud-Str. 25 53127 Bonn Germany .............................................................. theodor.rueber(a)ukbonn.de www.epileptologie-bonn.de

1 0

e: recon-all exits with error at surf/lh.thickness, mghRead looks for .mgh/.mgz filename extension
by Anup Bidesi 18 Jun '17

18 Jun '17

Thanks Bruce, recon-all finished process without error. Regards, Anup Date: Wed, 14 Jun 2017 10:25:20 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all exits with error at surf/lh.thickness, mghRead looks for .mgh/.mgz filename extension To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.1706141024260.28087(a)door.nmr.mgh.harvard.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed Hi Anup I suspect the problem is choosing a subject with ".mgz" in the ID. I wouldn't include any of ".nii" ".mgz" or ".mgh" in a subject ID. Try rerunning and just using fsMM cheers Bruce On Wed, 14 Jun 2017, Anup Bidesi wrote: > > Hello FreeSurfer Users, > > New to Freesurfer, I'm attempting to recon-all using : > > recon-all -all -i T1.nii -s op.nii.mgz (Attached recon-all log) > > The automated process begins normally and seems to run Autorecon Prrocessing > Stages 1-25, but at step 26 > (I think) and then exits with Error, per log as seen below: > > ------------------------------------------------------------- > > mghRead(/home/brainmind-engineer/freesurfer/subjects/fsMM.nii.mgz/surf/lh.th > ickness, > -1): could not open file. > Filename extension must be .mgh, .mgh.gz > or .mgz > > ------------------------------------------------------------- > > Within the subject .mgz folder in Surf there was a tmp.pctsurfcon.14807 fold > er with > a file named lh.wm.mgh (size 569 kb). > > I ran this process a couple of times and the autorecon process would exit at > same step.I > tried looking up the Archive for any similar previous error messages but did > not find any. > Please advise. > > 1) FreeSurfer version: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > > 2) Platform: Ubuntu 14.04 > > 3) uname -a: Linux brainmindengineer-Precision-Tower-7910 3.13.0-117-generic > #164-Ubuntu > SMP Fri Apr 7 11:05:26 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux > > 4) recon-all.log: see attached > > Thanks for your help, > > Anup

1 0

Re: [Freesurfer] TRACULA: Motion measures only
by Yendiki, Anastasia 16 Jun '17

16 Jun '17

Yep, you can use the dmri_motion command. Run it without any arguments to see usage info. It needs: * Your original, unprocessed DWIs * b-value table * Output from your FSL eddy correction (*.ecclog from eddy_correct or *.eddy_parameters from eddy) Hope this helps, a.y From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Buckless, Colleen" <Buckless(a)kennedykrieger.org<mailto:Buckless@kennedykrieger.org>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Friday, June 16, 2017 at 10:22 AM To: "'freesurfer(a)nmr.mgh.harvard.edu<mailto:'freesurfer(a)nmr.mgh.harvard.edu>'" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] TRACULA: Motion measures only Hi All, I have already preprocessed data in FSL and only want to use TRACULA to get the motion measures to match subjects based on motion. Is there any way I can get out the motion measures without doing all of the other preprocessing steps in TRACULA? Thanks, Colleen Buckless ________________________________ Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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