Freesurfer

freesurfer@nmr.mgh.harvard.edu

10 participants
30058 discussions

Tracula
by Nicole Mckay 25 Jan '18

25 Jan '18

Hi all, I have previously run full diffusion preprocessing using FSL and would like to now use tracula to construct the paths. Is it possible to input my already processed data into the tracula pipeline for just the path reconstruction and stats steps? I have already run recon-all too. Or perhaps is there a way I can insert my own corrected images into the prep step if it is running extra steps. My main reason for not wanting to start again from scratch is timing (I have 100 participants), but also that my preprocessing steps are slightly different. I use Eddy instead of Eddy_correct, and some of my participants needed individualised values for BET to work correctly. Any advice would be great, Nicole

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Fwd: OHBM Call for Nominations
by Douglas N Greve 25 Jan '18

25 Jan '18

-------- Forwarded Message -------- Subject: OHBM Call for Nominations Date: Thu, 25 Jan 2018 16:15:20 -0600 From: info(a)humanbrainmapping.org Reply-To: info(a)humanbrainmapping.org To: greve(a)nmr.mgh.harvard.edu Organization for Human Brain Mapping *call for nominations* <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…> Dear OHBM Member: Both history and experience teach us that strong leadership is very important to the success of any Society. OHBM is no exception as we continue our strategic growth. The OHBM Nominating Committee is *requesting your participation now in volunteering for or identifying leadership candidates for open seats on the OHBM Council.* Open positions include Chair-Elect, Secretary-Elect, Treasurer-Elect, Program Chair-Elect and Education Chair-Elect. The term of service begins immediately after the Council meeting in June 2018, and each term is for three years. Please nominate yourself or make a nomination by completing the Call for Nominations Form <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…> no later than *Monday, February 19th at 24.00H-US Central.* The Council is committed to supporting a diverse membership and strongly encourages nominations from each geographic region, women, minorities, and members of other underrepresented groups from individuals at various career stages. The OHBM By-Laws <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…>, Article 5 provides the framework and process for the election of new Council members. *OHBM Nominating Committee:* Christian Grefkes, Secretary Shella Keilhotz, Secretary-Elect Tor Wager, Past Secretary Bernard Mazoyer, Chair Vince Calhoun, Chair-Elect Alan Evans, Past Chair Tonya White, Chair, Diversity & Gender Committee Once the final slate is prepared and distributed, members will be able to see a brief bio on each candidate and vote online via the OHBM website. The results of these elections will be announced during the OHBM Annual Meeting in Singpore. All candidates identified on the ballot will be informed of the results prior to the Annual Meeting. Councilors are not eligible for re-election for any Council position for three years after their term ends on Council. Those currently serving on Council are also not eligible. Individuals who are currently ineligible as nominees due to service on Council within the past 3 years are listed below. Current 2017-2018 OHBM Council <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…>. *Not Eligible Until 2021/2022* * Alan Evans, Chair Term Ending 2018 * Michel Thiebaut de Schotten, Treasurer Term Ending 2018 * Tor Wager, Secretary Term Ending 2018 * Michael Greicius, Program Chair Term Ending 2018 * JB Poline, Education Chair Term Ending 2018 *Not Eligible Until 2020/2021* * Karen Berman, Chair Term Ending 2017 * Jeannette Mumford, Treasurer Term Ending 2017 * Doug Greve, Secretary Term Ending 2017 * Jack Van Horn, Program Chair Term Ending 2017 * Niko Kriegeskorte, Education Chair Term Ending 2017 *Not Eligible Until 2019/2020* * Steve Smith, Chair Term Ending 2016 * Jia-Hong Gao, Treasurer Term Ending 2016 * Simon Eickhoff, Secretary Term Ending 2016 * Pedro Valdes Sosa, Program Chair Term Ending 2016 We look forward to your involvement in the identification and election of your Society’s leadership. Please contact the OHBM Executive Office at info(a)humanbrainmapping.org <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…> with any questions. Sincerely, JoAnn Taie Executive Director Organization for Human Brain Mapping (OHBM) <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…> Phone: 1 952-646-2029 · i <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…>nfo(a)humanbrainmapping.org <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…>·humanbrainmapping.org <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…> To opt out of OHBM emails, contact the OHBM Executive Office at info(a)humanbrainmapping.org <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…>. © 2017 Organization for Human Brain Mapping. All Rights Reserved. Click here to Unsubscribe <http://www.humanbrainmapping.org/i4a/etrack/unsub.cfm?campaignID=3545&conta…>

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Re: [Freesurfer] New hippocampal subfields
by Maksimovskiy, Arkadiy 25 Jan '18

25 Jan '18

Hi Eugeno, I am hitting the same error as described in this post, but using a Dev El Capitan version. Here is my error output: [arkadiysnewimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits] arkadiy% segmentHA_T1.sh SILVA053 #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Thu Jan 25 17:26:21 EST 2018 ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer_Dev_El_Capitan/MCRv84//runtime/maci64:/Applications/freesurfer_Dev_El_Capitan/MCRv84//bin/maci64:/Applications/freesurfer_Dev_El_Capitan/MCRv84//sys/os/maci64: Invalid MEX-file '/tmp/MCR_2426959059/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64': dlopen(/tmp/MCR_2426959059/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64, 6): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv Referenced from: /tmp/MCR_2426959059/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64 Expected in: /usr/lib/libstdc++.6.0.9.dylib in /tmp/MCR_2426959059/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64 Error in kvlClear (line 11) Error in segmentSubjectT1_autoEstimateAlveusML (line 115) MATLAB:invalidMEXFile Darwin arkadiysnewimac.mclean.harvard.edu 17.3.0 Darwin Kernel Version 17.3.0: Thu Nov 9 18:09:22 PST 2017; root:xnu-4570.31.3~1/RELEASE_X86_64 x86_64 T1 hippocampal subfields exited with ERRORS at Thu Jan 25 17:26:27 EST 2018 Wondering if you might have resolved this already? Thank you for all of your help, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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Re: [Freesurfer] White Matter Edits: Removing White Matter from the WM Surface
by Maksimovskiy, Arkadiy 25 Jan '18

25 Jan '18

Hi Bruce, My apologies if this email is coming in duplicate- I think the previous one bounced- so resending. Thank you for following up on this. Attached are the unedited (brainmask.auto). the defaced orig.nofix, and edited brainmask (brainmask), as well as the surface files. Let me know if you need any other files. Also attached is a screenshot of the coordinates. Let me know if you need anything additional to diagnose. These was no orig.nofix file inside the transforms, but let me know if these are not enough to diagnose. This is a strange error to me as well. Thank you for all of your help with this! I really appreciate it. Best, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School [cid:image001.png@01D395EA.DA1F0BF0]

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mri_em_register and mri_ca_register
by Ricardo Valle 24 Jan '18

24 Jan '18

Dear Freesurfer community, I would like to get a better sense of how mri_em_register and mri_ca_register work. I understand the former is a linear registration and the latter is nonlinear, and that they are both meant to register an individual to a template space (MNI152?). Would it be possible to update the wiki pages to give more information about the algorithms and cost functions used and other such details? And to provide references to the literature in support of the algorithms if possible? Thank you. Best regards, Ruy

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Does paracentral include precentral area
by Shatil, Anwar Shahadat 24 Jan '18

24 Jan '18

Hi Doug: I am confused about the visualisation of “Paracentral” and “precentral” clusters after running mri_glmfit-sim command. I used two cache values (3 pos and 4 pos) to see if the area changes. Each time the “Paracentral” cluster appears to be the largest significant area, but, the area shrinks during the cache value of 4 pos. It seems that paracentral and precentral areas are not mutually exclusive. I.e. paracentral seems to include precentral. Is that true? If not, then how can I visualize the actual significant area despite seeing a large “Paracentral” or “Precentral” area. Thanks, Anwar This e-mail is intended only for the named recipient(s) and may contain confidential, personal and/or health information (information which may be subject to legal restrictions on use, retention and/or disclosure). No waiver of confidence is intended by virtue of communication via the internet. Any review or distribution by anyone other than the person(s) for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and destroy all copies.

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Hippocampus Subfield analysis error
by Hannah's USC Email 24 Jan '18

24 Jan '18

Hi Freesurfer experts, I tried to do hippocampus subfield analysis but failed. I got this error message: #@# Hippocampal Subfields processing (T1 only) left Fri Jan 19 15:27:36 PST 2018 dirname: Command not found. pwd: Command not found. pwd: Command not found. /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found. #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Fri Jan 19 15:27:36 PST 2018 dirname: Command not found. pwd: Command not found. pwd: Command not found. /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found. Your help would be greatly appreciated. Thanks!

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Which Dev Version is Best?
by Maksimovskiy, Arkadiy 24 Jan '18

24 Jan '18

Dear Experts, I was wondering if the OSX-ElCapitan Dev version of freesurfer is only for ElCapital? It has a later date of modification than the “dev” version, so I wanted to check, in case it has new patches. I am running OSX-Sierra, and would love to hear which one would be best. Thank you, Arkadiy

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White Matter Edits: Removing White Matter from the WM Surface
by Maksimovskiy, Arkadiy 24 Jan '18

24 Jan '18

Dear Experts, I came across white matter that has been included in the WM surface, but should not be there. Screenshots included; this is a little WM surface circle in the anterior prefrontal/parietal brain region. There doesn’t seem to be anything to remove from the WM volume (as screen shots shows). I was wondering if someone might be able to suggest a way to edit this. Thank you for your time, Arkadiy[cid:image001.png@01D3952B.46606090][cid:image002.png@01D3952B.46606090][cid:image003.png@01D3952B.46606090][cid:image004.png@01D3952B.46606090][cid:image005.png@01D3952B.46606090]

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mri_convert trying to find DWI parameters from Philips scans
by Rockers, Elijah D. 24 Jan '18

24 Jan '18

Hello, I am using mri_convert to convert my standard T1-weighted structural images into nifti format. The conversion works, but it might be somewhat delayed due to spamming the console with the following message ERROR: don't know how to get DWI parameters from --Philips Healthcare-- ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 DICOM File: sd_withholder/withholder_MRI/scans/1201_T1W_TFE/DICOM/1.3.46.670589.11.42034.5.0.10936.2017012009011821006-1201-95-sktipi.dcm break DICOMRead.c:5228 As far as I can tell, it spams this message once for each dicom file in the directory, and there being hundreds or even thousands of dicom files for a single subject, this can get old pretty quick. I think this might be new behavior in freesurfer 6, because I don't recall seeing this with 5.3 (although I could be wrong) Is there anyway to disable this? 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.

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