Freesurfer

freesurfer@nmr.mgh.harvard.edu

1 participants
30089 discussions

V6.1
by Eduard Vilaplana Martinez 20 Feb '18

20 Feb '18

Dear freesurfer experts, Some days ago I unexpectedly found a thread (about including the flair in the pipeline) in which you mentioned the v6.1. In my lab we are thinking about doing the major 5.1 to 6.0 upgrade, but given that we have a huge database of subjects N~2000) we are wondering about the status of the 6.1 version. Is there any estimation about the v6.1 release? And based on that, would you wait for the v6.1? Thanks in advance, Best,, Eduard. Memory Unit, Neurology Dept. Hospital de la Santa Creu i Sant Pau, Sant Antoni Maria Claret 167 Barcelona, Spain

2 1

Re: [Freesurfer] MRI protocol for hippocampal subfield segmentation
by Gabor Perlaki 20 Feb '18

20 Feb '18

Dear Iglesias, We set up our our hippocampal subfield T2 protocol based on the ADNI protocol (with some minor differences). However, we see an artefact similar to the image found in ADNI2 training manual (page 28): http://adni.loni.usc.edu/wp-content/uploads/2012/10/ADNI2MRITrainingManual_… Please see the hyperintense artefact in the anterior part of the sagittal and axial images. Do you also see this artefact in your images? Do you have any idea about the cause of the artefact or do you have any suggestion on how to get rid of it? Thanks, Gabor <petzinger.gabor(a)gmail.com>

1 0

Re: [Freesurfer] Question regarding exporting subcortical segmentation to
by Simon, Joe 20 Feb '18

20 Feb '18

Hi Bruce Thanks, mri_binarize works great! Best, Joe ---------------------------------------------------------------- Dr. Dipl.-Psych. Joe Simon Universitätsklinikum Heidelberg Klinik für Allgemeine Innere Medizin und Psychosomatik Im Neuenheimer Feld 410 69120 Tel.: ++49(0)6221-56-38667 joe.simon(a)med.uni-heidelberg.de ---------------------------------------------------------------- Date: Thu, 15 Feb 2018 12:08:12 -0500 (EST) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Question regarding exporting subcortical segmentation to .nii ROIs for further analysis in SPM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.1802151207140.11691(a)gate.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="iso-8859-1" Hi Joe you can use mri_convert to convert the .mgz volume to nifti if that is what you want: mri_convert aseg.mgz aseg.nii.gz should do the trick. Not sure if that counts as an ROI for SPM. If you want separate volumes for each structure I think you can use mri_binarize with the --match flag cheers Bruce

1 0

Re: [Freesurfer] Read 13, expected 64, could not read .nii.gz as type 24
by Ben Smith 19 Feb '18

19 Feb '18

Thanks for your help on this! It was a corruption problem, just as you said- didn't seem to be a disk space problem, but I deleted the file, re-ran, and things went fine. Cheers Ben _______________________ Ben Smith, MSc. Ph.D. Candidate University of Southern California https://bjsmith.github.io/ w | +1 213-740 7851 m | +1 323-385 9349 skype | ben.smith.nz On Mon, Feb 19, 2018 at 9:11 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Ben > > we find the CC as the region where there is the largest left/right WM > connection. We then orient it to be vertical and find principle directions, > and divvy it up into however many segments you want (I think the default is > 5 but this can be changed). We then grow it out laterally as far as your > specify > > cheers > Bruce > > > On Mon, 19 Feb > 2018, Benjamin Yeske wrote: > > > Hello Freesurfer Experts, > > I was looking through your website to see if I could find any > info/papers that explained what > > landmarks you use for segmenting the corpus callosum, but I couldn't > find anything on the topic. > > Could you please point me to a paper or resource that explains how > freesurfer captures the corpus > > callosum and what landmarks it use to segment it out? We'd like to be > able to hand check this region > > for accuracy in our TBI patients brain scans. > > > > Thank you, > > Ben > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >

1 0

bbregister aparc+aseg to diffusion space
by Michiko H. 16 Feb '18

16 Feb '18

Hi, I understand that bbregister can be used to register diffusion to T1 space but I'm a lot less certain how this can be done in the reverse way, i.e. registering the entire aparc+aseg file to diffusion B0? Do I also do: bbregister --s $subject --mov bo_brain.nii.gz --reg registration2b0.dat --dti --init-fsl To follow up, I'm also unclear whether this method is inferior to registering diffusion to T1 - if so, why may this be so? Thanks a lot in advance, M.

2 3

Difficulties running tracula
by John Davis 16 Feb '18

16 Feb '18

The information you request is in the attachments. Also I sent dmrirc. -- John Davis, PhD Cell: (520) 907-9769 jdavis(a)mrn.org

3 10

Post-Doc position at CAMH, Toronto
by Areti Smaragdi 16 Feb '18

16 Feb '18

Sent on behalf of Dr. Nathan Kolla: The Violence Prevention Neurobiological Research Unit (VPNRU) at the Centre for Addiction and Mental Health (CAMH) in Toronto, Ontario, Canada, which is fully affiliated with the University of Toronto, seeks a motivated and enthusiastic post-doctoral fellow to join our team to help better understand the neural correlates of violence and aggression. The successful candidate will have expertise in MRI data analysis and collection as well as extensive experience working with psychiatric populations in research settings. The VPNRU is a multi-disciplinary group led by Dr. Nathan Kolla, MD, PhD, that uses MRI, positron emission tomography, and genetics to investigate different patient populations at heightened risk for violent behavior. The post-doctoral fellow will lead an innovative project that seeks to understand brain functioning using MRI in young individuals with schizophrenia who have acted aggressively. The ideal candidate for this job will possess: An MD or PhD with an emphasis on psychological theory and/or neuroscience Expertise with MRI (including structural and functional) data collection and analysis Experience in multivariate statistical techniques, programming, and scripting (e.g., R, python, or JAVA) Experience and knowledge of psychological assessments; experience working with clinical populations. Excellent written and verbal skills Publication (or in press) of at least 2 first author papers Interest in working with forensic populations This position is for a duration of up to two years, renewed yearly. Writing manuscripts and applying for independent grants and fellowships will be required. Compensation is competitive and commensurate with experience. The candidate will receive longitudinal mentorship in launching a career as an independent investigator subsequent to the fellowship. A complete application will include a statement of interest, CV, two first-authored publications (published or in press), and the names of 3 referees. Please submit applications to Nathan Kolla at nathan.kolla(a)camh.ca with Postdoctoral Fellowship in the subject line. We thank all applicants but only those selected for an interview will be contacted. The position will remain opened until filled. Start Date: April 3, 2018 Preferred areas of Research: Medical Physics / Imaging, Behavioral Neuroscience, Psychiatry CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. AVIS DE CONFIDENTIALITÉ : Ce message électronique, ainsi que tout fichier qui y est joint, est reserve à l'usage exclusif du destinataire visé et peut contenir des renseignements confidentiels et privilégiés. Toute lecture, utilisation, divulgation ou distribution non autorisée est interdite. Si vous n'êtes pas le destinataire visé, veuillez en aviser l'expéditeur par retour de courriel et détruire toutes les copies du message original.

1 0

How would one run N4 bias corrected T1 and T2 images through FreeSurfer v6.0
by Axelson, Eric D 16 Feb '18

16 Feb '18

We are using N4 to correct some large inhomogeneities in some samples and wanted to insert these images into the v6.0 pipeline and bypass the N3 bias correction done within. What would be the correct sequence of freesurfer commands to achieve this? Thanks Eric ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________

1 0

Re: [Freesurfer] IndexError: list index out of range
by Maksimovskiy, Arkadiy 16 Feb '18

16 Feb '18

Hi Doug, I sent you the tar files, but just wanted to update you that I tried running this with just one subjects and am still getting an error but a different one. The two inputs and output errors in the terminal are pasted below: [arkadiysimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits] amaksimovskiy% asegstats2table --subjects SILVA030 --meas volume --stats aseg.stats --tablefile Subcortical_GM_Volume1.Dec17.txt SUBJECTS_DIR : /Volumes/silverilab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits Parsing the .stats files Traceback (most recent call last): File "/Applications/freesurfer/bin/asegstats2table", line 548, in <module> id_name_map, measurelist = parsed.parse(options.meas) File "/Applications/freesurfer/bin/fsutils.py", line 115, in parse seg = strlst[1] # segmentation id is in the 2nd field IndexError: list index out of range [arkadiysimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits] amaksimovskiy% asegstats2table --subjects SILVA040 --meas volume --stats aseg.stats --tablefile Subcortical_GM_Volume1.Dec17.txt SUBJECTS_DIR : /Volumes/silverilab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits Parsing the .stats files Traceback (most recent call last): File "/Applications/freesurfer/bin/asegstats2table", line 548, in <module> id_name_map, measurelist = parsed.parse(options.meas) File "/Applications/freesurfer/bin/fsutils.py", line 122, in parse self.measurelist.append( float(strlst[self.measure_column_map[measure]] )) ValueError: could not convert string to float: Left-Cerebellum-Cortex Let me know if any further info is needed to troubleshoot. Thank you for helping with this. -arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

3 6

List needed: pathway <==> freesurfer ROI
by Krieger, Donald N. 16 Feb '18

16 Feb '18

Dear List, I need a list of Freesurfer ROIs which are typical endpoints for each standard pathway used in tracula. I think this information is likely included in the default tracula atlas which I have been unable to find although I do not need spatial coordinates but rather just the list of ROI names for each pathway. If this information is contained in publications, I would like to cite them. I hope this is clear and thank you for any help you can provide. Best - Don Don Krieger, Ph.D. Research Scientist Department of Neurological Surgery University of Pittsburgh

2 6

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