Freesurfer

freesurfer@nmr.mgh.harvard.edu

1 participants
30089 discussions

Start a nNew thread

(no subject)
by 小萌主大叔 01 Aug '18

01 Aug '18

External Email - Use Caution 1535172522(a)qq.com

1 0

(no subject)
by 小萌主大叔 01 Aug '18

01 Aug '18

External Email - Use Caution confirm 185a0e2daad6a81d7f3f1a9403d86009db538c35

1 0

Mixed Block Event-related Design Optseq Question
by Yu Han 01 Aug '18

01 Aug '18

External Email - Use Caution Hello experts, We would like to use the optseq 2 to optimize a mixed block and event-related design. Is it possible to use optseq for a mixed design? We are specifically not sure how to specify block duration. What commands shall I use in order to do that? Thank you in advance! Best, Yu Emotion Recognition Task. The emotion recognition and perceptual control conditions developed by Greimel et al. have been adapted to include surprise and embarrassment. The task requires participants to either identify the emotions expressed in visually presented faces (emotion recognition) or judge the gender (perceptual control). The emotion recognition task will consist of interspersed expressions of surprise and embarrassment. There will be four blocks, one self-conscious emotion block (e.g., embarrassment and surprise), one typical emotion block to distinguish brain areas of self-conscious emotion to typical emotion (e.g., happy vs. sad), one control block (ask participants to identify gender), one matching shape block. Six images in each block. There are four blocks of 6 images each. 1) Surprise/Embarrassment faces 2) Happy/Sad faces 3) Identify gender of faces 4) Match shapes We planned to have the Match shapes blocks to interleave all other blocks. Yu Han Ph.D. Student, Prelock Lab Neuroscience Graduate Program University of Vermont

2 1

Re: [Freesurfer] Surface editing: recon-all exited with errors
by Rockers, Elijah D. 01 Aug '18

01 Aug '18

External Email - Use Caution Oh, yep, sorry about that. I copy the list on this e-mail, and attach the log. I think the list blocks attachments, but if anyone wants to see full log I can send it. Thanks to all, -Eli ________________________________ From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Sent: Tuesday, July 31, 2018 2:03:05 PM To: Rockers, Elijah D. Subject: Re: Surface editing: recon-all exited with errors can you cc the list on these emails so others can help? On Tue, 31 Jul 2018, Rockers, Elijah D. wrote: > > External Email - Use Caution > > The recon-all -make all command finished relatively quickly, still with errors. It's still showing > the same errors, and I have attached the new recon-all.log. > > ____________________________________________________________________________________________________ > From: Rockers, Elijah D. > Sent: Tuesday, July 31, 2018 12:32:11 PM > To: Bruce Fischl > Subject: Re: Surface editing: recon-all exited with errors > > Odd. I assumed the individual recon-all commands in the log are just what is reported by the general > pipeline, since I definitely did not issue all those commands separately. I just used the recon-all > -make all command after editing. In anycase, I will run it again to see if anything changes, but I > think that would be surprising. > > > Thanks again > > - Eli > > ____________________________________________________________________________________________________ > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Sent: Tuesday, July 31, 2018 11:52:59 AM > To: Rockers, Elijah D. > Subject: Re: Surface editing: recon-all exited with errors > Hi Eli > > it's hard for me to tell since you have so many individual recon-all > commands, but it looks like you didn't recreate all the surfaces after > editing. Errors like thiss one: > > mrisReadTriangleFile(../surf/lh.sphere.reg): surface doesn't match > ../surf/lh.white.preaparc > > typically mean something hasn't been recreated properly. Try running > recon-all -make all > > cheers > Bruce > > > On Tue, > 31 Jul 2018, Rockers, Elijah D. wrote: > > > > > External Email - Use Caution > > > > Hi Bruce, > > > > > > I have attached the recon-all.log, regarding an exit with ERRORS that occured after manually > editing > > the surface. Thanks for taking a look. > > > > > > Also, I double checked - the original recon-all command finished with no errors. So it seems the > > message occurs after surface editing. But the new reconstructed surfaces appear accurate, at least > > with respect to gray and white matter boundaries. Let me know if there's anything else you need. > > > > > > Thanks again, > > > > - Eli > > > > Houston Methodist. Leading Medicine. > > > > Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient > > care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet > hospital > > for excellence in nursing. Visit us at http://houstonmethodist.org. Follow us athttps://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_Methodist… > jkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=ds98HqtzhWqTZ4zNG > seN-axVe5fM_ZPQ9W9OHoSzLLo&s=5CE2NSVpAt16S_bmsgO_Okvmb5bkLvXMIjkxSTQ2C5g&e= > > andhttps://urldefense.proofpoint.com/v2/url?u=http-3A__facebook.com_Houston… > FixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=ds98HqtzhWqTZ > 4zNGseN-axVe5fM_ZPQ9W9OHoSzLLo&s=1x_6X2u7_1TSprfJDQX2_pJs3OEQcXqNYjVB7pVhpzE&e=. > > > > ***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. > > > > > > > > > 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 > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli… > DiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=ds98HqtzhWq > TZ4zNGseN-axVe5fM_ZPQ9W9OHoSzLLo&s=xCXJrzgzXHHAcYBpjDRMUejaZuRv3TRvaTInF4j-rTw&e= . 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. > > Houston Methodist. Leading Medicine. > > Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient > care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital > for excellence in nursing. Visit us at http://houstonmethodist.org. Follow us at https://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_MethodistHo… > and https://urldefense.proofpoint.com/v2/url?u=http-3A__facebook.com_HoustonMet…. > > ***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. > > > 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli… . 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. Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital for excellence in nursing. 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.

3 5

Sag T1 3D post-contrast
by John Absher 01 Aug '18

01 Aug '18

External Email - Use Caution Has anyone else tried to do recon-all with Sagittal 3D T1 post-contrast volumes? We're getting hung in recon-all at the Talairach registration step, and I wonder if the vascular enhancement at the pial surface might be throwing the algorithm off. About half the scans will run smoothly, but the other half --- not so much. Another question is whether a linear registration (e.g., using David MacDonald's register program) would allow us to do the recon-all ... -notal option? Thanks, John John R. Absher, MD, FAAN GHS Neurosciences jabsher(a)ghs.org<mailto:jabsher@ghs.org> 864-350-6655 (mobile)

2 1

Postdoctoral Fellowship for Child Brain Connectome and Genetics
by Anqi Qiu 31 Jul '18

31 Jul '18

External Email - Use Caution Postdoctoral Fellowship for Child Brain Connectome and Genetics Growing Up in Singapore Towards Healthy Outcomes (GUSTO) is the most comprehensive birth cohort longitudinal study over the world. The GUSTO mothers were recruited during pregnancy between 2009 and 2010. We have followed the GUSTO family since then. The GUSTO study collects the unique data on cognitive functions, children behaviors, psychopathology, brain imaging, and epigentic data at multiple points from birth to 7 years of age. We aim to study the development brain structural and functional networks and their relation with cognitive and behavioral development in childhood. Moreover, we aim to investigate genetic roles in brain, cognitive and behavioral development in childhood. We are looking for postdoctoral fellows who have 1. PHD in Cognitive Neuroscience, or Psychology, or Neuroimaging; 2. Experience with MRI-based neuroimage techniques; 3. Knowledge in statistical analysis; 4. Good communication and writing skills in English language. If you are interested in the job listed above, please send your CV to Associate Prof. Anqi QIU, Deans Chair Department of Biomedical Engineering National University of Singapore Email: bieqa(a)nus.edu.sg Phone: +(65) 6516 7002

1 0

Postdoctoral Fellowship for Child Brain Connectome and Genetics
by Anqi Qiu 31 Jul '18

31 Jul '18

1 0

Postdoctoral Fellowship for Child Brain Connectome and Genetics
by Anqi Qiu 31 Jul '18

31 Jul '18

1 0

Re: [Freesurfer] fcseed-config
by shahin＠nmr.mgh.harvard.edu 31 Jul '18

31 Jul '18

Your problem solved?

1 0

Surface editing: recon-all exited with errors
by Rockers, Elijah D. 31 Jul '18

31 Jul '18

External Email - Use Caution Hello. I manually edited the brainmask.mgz file for three subjects. This was done to prevent the pial surface from extending into non-cortical areas, in particular the soft-tissue near the brain stem, and some cerebellar areas. Usually this type of editing (just removing voxels from brianmask.mgz) doesn't give me any trouble, and I use the command recon-all -make all -subjid <subject_id> -sd <subject_dir> to then rebuild the surfaces. However, the tail of the log shows that the pipeline exited with errors, with a few commands near the end related to curvstats and jacobian_white failing. The new surfaces seem to look fine in freeview. The edits to brainmask were registered correctly, but I'm still concerned that the errors might affect an mri_glmfit analysis. This is true for all three subjects I edited, which seems odd, and I'm not sure what would be causing this. Below is a pastebin showing the relevant errors. The rest of the pipeline seems to execute without errors. I could send entire log if necessary. <https://pastebin.com/b4JX04AT>https://pastebin.com/raw/b4JX04AT Thanks, - Eli Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital for excellence in nursing. 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.

2 1

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