Freesurfer March 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
229 discussions

Tracula bedpostx error
by Bharadwaj, Pradyumna - (prad) 07 Mar '16

07 Mar '16

Hello Anastasia, I have been trying to run through the tutorial with one of the subjects from the tutorial(elmo.2008) to familiarize myself with Tracula. The preprocessing step seems to have been completed without any errors (Log file attached).However, when I proceed with the ball and stick model fit step, I get the following error bedpostx_mgh -n 2 /home/biba1/testing_tracula/diffusion/elmo.2008/dmri /apps/freesurfer/bin/bedpostx_mgh: 131: /apps/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected. I'm running the tutorial locally on Ubuntu 12.04 with FSL 5.0.9. In an earlier post where the same error was encountered(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg… you recommended running bedpostx directly. Would this impact the results or run time in any way? and is there something I can do to fix this error if it is likely to take much longer? Thanks! -Prad

2 3

path.pd.trk format
by Peled, Noam 07 Mar '16

07 Mar '16

Hello, I've noticed that in tracula 5.2 there's also a path.pd.trk file in the output directory. How can I read this file? I would like to read the actual splines and not the probabilistic distribution in path.pd.nii.gz. Thanks, Noam Peled

2 8

Hiring: Houston, TX - Data Processing/Analysis
by Rockers, Elijah D. 07 Mar '16

07 Mar '16

Hello, The Nantz National Alzheimer Center, in Houston, TX is looking to fill two positions pertaining to neuroimaging and analysis. Be aware that we cannot accept remote employment, the candidate would have to work day-to-day in the city of Houston. Any interested person is encouraged to review the job postings, which are attached. If you don't see the attachments but you are interested, e-mail me directly and I'll make sure you get them. Thanks, -- Elijah Rockers Research Data Analyst Houston Methodist Neurological Institute O: 713 363 7729 Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties and designated as a Magnet hospital for excellence in nursing. Houston Methodist has also been named to FORTUNE® Magazine's "100 Best Companies to Work For®" list for 10 years in a row. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

1 0

mri_convert Ubuntu 14.04 LTS not working (neither is freeview)
by Veronica.Popescu 07 Mar '16

07 Mar '16

Dear all, I have just installed FreeSurfer 5.3.0. on Ubuntu 14.04 LTS (64-bit). The mri_convert doesn't work with no error message. which mri_convert gives /usr/local/freesurfer/bin/mri_convert. Of course neither does recon-all (which exits with errors with no error message in the log). I made sure all the paths are 777. I did the recommended "sudo ln -s libjpeg.so.8 libjpeg.so.62 sudo ln -s libtiff.so.4 libtiff.so.3" in x86_64-linux-gnu. The same problem with freeview, nothing happens. Thank you in advance! Veronica -- Revalidatie & MS Centrum VZW | Overpelt Boemerangstraat 2 B-3900 Overpelt Tel.: 011 / 809 100 Fax: 011 / 66 28 86 http://www.msreva.be info(a)msreva.be Disclaimer: http://www.msreva.be/default.aspx?main=2

2 2

mysterious fsgd format error (not the end of line problem)
by Joseph Dien 06 Mar '16

06 Mar '16

Hi, I’m having an fsgd error that has totally stumped me. I’m trying to run the following command to compute the second level statistics: mri_glmfit --surf fsaverage lh --y ces.nii.gz --wls cesvar.nii.gz --nii.gz --fsgd RPA-accGT.fsgd --glmdir conVinc_normAcc.wls --C main.mtx --C normAcc.mtx I get the error message: Reading source surface /Volumes/Data2/RP1/freesurfer/fsaverage/surf/lh.white gdfReadHeader: reading RPA-accGT.fsgd FSGDF Format Error: file = RPA-accGT.fsgd, tag=Title I used the utility flip to make sure the file was in UNIX format (with linefeeds). I then double-checked by reading in the binary codes with Matlab’s fread and directly checking the ASCII numbers, which are indeed ASCII 10 (linefeed). Here is the contents of the fsgd file. GroupDescriptorFile 1 Title RP1 Class Main Variables LogoAcc NormAcc OrthAcc PhonAcc Input RPA903 Main 0.75 0.79 0.77 0.62 Input RPA906 Main 0.81 0.81 0.83 0.74 Input RPA907 Main 0.87 1 0.84 0.83 Input RPA908 Main 0.91 0.93 0.95 0.89 Input RPA909 Main 0.74 0.95 0.72 0.72 Input RPA910 Main 0.85 0.96 0.81 0.79 Input RPA912 Main 0.75 0.78 0.73 0.73 Input RPA914 Main 0.7 0.85 0.83 0.81 Input RPA915 Main 0.85 0.89 0.75 0.83 Input RPA916 Main 0.84 0.92 0.87 0.72 Input RPA917 Main 0.83 0.93 0.92 0.83 Input RPA918 Main 0.87 0.91 0.79 0.85 Input RPA919 Main 0.86 0.96 0.91 0.88 Input RPA920 Main 0.84 0.92 0.87 0.84 Input RPA921 Main 0.87 0.92 0.88 0.85 Input RPA922 Main 0.8 0.9 0.9 0.72 What’s really driving me to distraction is that a previous version of this file (with a different set of participants) works fine. I’m attaching both. RPA-accGT.fsgd does not work and RPA-acc.fsgd does work. Using Matlab’s fread, the first 85 characters (first four lines) of both files are identical. I’m running on OS X 10.11.3. I’m using FSFAST 5.20. Matlab 2015b. Any help would be greatly appreciated! Joe -------------------------------------------------------------------------------- Joseph Dien, PhD Senior Research Scientist Maryland Neuroimaging Center University of Maryland, College Park E-mail: jdien07(a)mac.com Cell Phone: 202-297-8117 http://joedien.com

3 4

Re: [Freesurfer] T2pial shrinks pial surface
by Matt Glasser 06 Mar '16

06 Mar '16

What FreeSurfer version are you using? Very small changes to the input images (e.g. a different random see for FreeSurfer) may be able to kick mris_make_surfaces out of that bug, though perhaps Bruce has fixed it. Peace, Matt. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Chris Adamson <chris.adamson(a)mcri.edu.au> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Sunday, March 6, 2016 at 6:14 PM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] T2pial shrinks pial surface The T2pial option mostly works beautifully. I have a few cases where the pial surface just shrinks globally and wraps over the white surface (see attached). I have checked the T2.mgz and the registration with the T1 is fine. This happens sometimes in one hemisphere only. Any ideas? Chris Adamson Senior Research Officer Developmental Imaging Murdoch Childrens Research Institute The Royal Children¹s Hospital Flemington Rd Parkville, Victoria 3052 AUS T: (03) 9936 6780 E: chris.adamson(a)mcri.edu.au www.mcri.edu.au <http://www.mcri.edu.au/> <https://www.facebook.com/MurdochChildrensResearchInstitute> <https://twitter.com/MCRI_for_kids> <http://instagram.com/murdoch_childrens> <http://www.youtube.com/user/MurdochChildrens/videos> <https://donate.mcri.edu.au/> This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. PPlease consider the environment before printing this email ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________ _______________________________________________ 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.

2 1

Deflate surface
by marmaduke woodman 06 Mar '16

06 Mar '16

Hi I would like to resample the cortical surface on the sphere at a lower resolution, and then deflate the surface to its folded form. Is this something which can be done using the inflated surface that FS generates? Thank you, Marmaduke

2 11

Re: [Freesurfer] recon-all -lgi issue with MATLAB Student version - Help!
by Ankita Chatterjee 06 Mar '16

06 Mar '16

Thank you for the pointer Woo-Suk. So to do that, I just do an EXPORT PATH on Matlab? I am not very familiar with linux... Thanks! Ankita

3 5

TRACULA Adding a new tract to the finished analysis
by denizzgursel 05 Mar '16

05 Mar '16

Dear Anastasia and Tracula users, I ran the longitudinal pipeline of Tracula with my subjects and I finished without error. However, I just realized now that I only added cingulum gyrus ending but not the angular bundle. I am interested in tracts that passes through hippocampus so angular bundle should be included. I would like to add this tract to the analysis. My question is, do I have to re-run everything from scratch? Is it possible to run just one tract? Do I have to do the preprocessing again? I really hope there is a way around this as I spent very long time finishing the analysis. Thank you for your help. Best regards, Deniz Gürsel

2 1

Generating Masked Aseg Segmentation Volumes
by Sarah Blankenship 05 Mar '16

05 Mar '16

Hi Freesurfer Team, I'm attempting to calculate the volume of hippocampal subfields (e.g., CA1-3, DG) in the anterior (head), middle (body), and poster (tail) subregions of the hippocampus. I have manually determined the boundaries for head/body/tail using standard anatomical landmarks and included these updated labels in the aseg files. I am attempting to use those (head/body/tail) volumes as masks when generating the hippocampal subfield (CA1-3, DG) volumes. Could you confirm that these are the correct steps to this end? *Note.* Based on the prior literature, the asegs were ac-pc aligned in AFNI to determine unbiased boundaries for head/body/tail. mri_binarize --i aseg_acpc_antpost.mgz --match 91 --o Lhead_mask.nii > #LHead=label 91 > mri_segstats --seg lh.hippoSfLabels-T1-T1T2.v10.1mm_acpc.nii --mask > Lhead_mask.nii --excludeid 0 --pv norm_acpc.nii --sum > ../stats/substats_lhead The outputs appear reasonable (i.e., the volumes generated by mri_segstats with the mask are smaller than without the mask), but I wanted to ensure that this is the appropriate method to generate what I'm looking for. Thank you in advance for your help! Sarah

1 0

← Newer
1
...
16
17
18
19
20
21
22
23
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 March 2016