Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30090 discussions

acceptable values for white matter on the T1.mgz volume
by Antonio 31 Aug '17

31 Aug '17

Dear FS community, I have a question regarding T1.mgz normalization values. Is there an established range of acceptable values for white matter around 110? For example, I'm getting values around 100 or so in some areas of low SNR (around the anterior temporal lobe region). Notwithstanding, the wm surfaces seem to look reasonable. I don't know if I should try control points to aid the normalization or if I should try tweaking the intensity correction parameters to somehow force these white matter voxels to be closer to 110. Thanks for your suggestions.

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motion estimates
by James Welsh 31 Aug '17

31 Aug '17

Dear Freesurfer experts, I want to inquire if there are any tools in freesurfer that can help to evaluate T1 quality regarding motion and SNR. Thanks! James

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aparc.stats files from FreeSurfer 6.0
by Mehta, Chintan 31 Aug '17

31 Aug '17

Dear FreeSurfer Users, I have run recon-all on data using both FreeSurfer versions 5.3.0 and 6.0. FS v6.0 generated files named lh.aparc.pial.stats and lh.aparc.stats, whereas FS v5.3.0 created only lh.aparc.stats. I wanted to verify two things: (a) Is it right that surface areas in lh.aparc.pial.stats correspond to pial surface (boundary between gray matter and CSF) of ROIs in the DK atlas, whereas lh.aparc.stats contains surface area at the boundary between gray matter and white matter at those ROIs? (b) There were differences between the values in the lh.aparc.stats from FS 5.3 and FS 6.0, despite my using the same data and same seed (i.e. -norandomness flag) for "recon -all" under both versions. Is it right that there are differences between the algorithms in FS 5.3 and FS 6.0 that could lead to this? Thank you. Best, Chintan

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R: mris_anatomical_stats output
by stdp82＠virgilio.it 31 Aug '17

31 Aug '17

I have more that 50000 clusters (from over 100 subjects, 12 different conditions). Manual extraction is impossible!Any suggestions?ThanksStefano ----Messaggio originale---- Da: stdp82(a)virgilio.it Data: 19-ago-2017 2.38 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: [Freesurfer] mris_anatomical_stats output Hi list,how can I save the outputs of mris_anatomical_stats in xls file?Thanks Stefano

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Software carpentry at the annual meeting of the Society for Neuroscience
by Ariel Rokem 30 Aug '17

30 Aug '17

Software Carpentry <http://software-carpentry.org/> is a non-profit volunteer organization whose members teach researchers computing skills. On November 9th-10th INCF <https://www.incf.org/> will hold a two-day Software Carpentry workshop at the George Washington University Marvin Center in Washington DC, to dovetail with the annual meeting of the Society for Neuroscience. The workshop will focus on software tools to make researchers more effective, allowing them to automate research tasks, track their research over time, and use programming to accelerate their research, and make it more reproducible. For details about the workshop please refer to the following web-page: https://incf.github.io/2017-11-09-sfn/ Participation is *free*, but because space is limited, we ask that participants apply to participate through the following web form: https://goo.gl/forms/09QyOPp3hFzw4ln63 *Application deadline is September 11th* Feel free to distribute this message widely among your colleagues, and to email me (Ariel Rokem: arokem(a)uw.edu) with any questions about the workshop. -- Apologies for cross-posting --

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Call for Nominations - OHBM Student and Postdoc Special Interest Group {Disarmed}
by Michele Veldsman 29 Aug '17

29 Aug '17

*Call for Nominations - OHBM Student and Postdoc Special Interest Group * Dear OHBM Members, The OHBM Student and Postdoc Special Interest Group (SIG) are seeking nominations for our 2017-2018 committee. The SIG provides a community of shared interests for OHBM trainees. The committee aims to provide professional, personal and career development for OHBM trainees as well as social and mentoring opportunities at the annual meeting. Committee members benefit from being an integral part of the SIG, directing its activities, and working with the OHBM Executive and wider community. We are committed to diversity and equality and are seeking representation from trainees across the world. *Eligibility * - Nominees must be current students or postdocs. Students are defined as those working full time towards a graduate degree - M.S., Ph.D. or M.D. degree. Postdocs are individuals who are no more than four years after completing such a degree at the time of next annual meeting. - Nominees must be members of OHBM in good standing at the time of the next annual meeting - Nominees must be planning to attend the next two annual meetings in Seoul 2018 and Rome 2019 (and likely to attend the meeting in 2020). To nominate yourself for a position on the committee please fill out the nomination form and attach your CV: https://goo.gl/forms/iUF7wnMDhbdldGCG2 <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…> Email ohbmtrainees(a)gmail.com <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…> if you have any questions. *Nominations close on the 16th September 2017. * Kind regards, OHBM Student and Postdoc SIG *Organization for Human Brain Mapping (OHBM)* 5841 Cedar Lake Road, Suite 204 Minneapolis, MN 55416 USA Phone: 1 952-646-2029 | Fax: 1 952-545-6073 info(a)humanbrainmapping.org <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…> www.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…> .

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Cortical thickness map
by Esteban, Eva(GE Healthcare) 29 Aug '17

29 Aug '17

Hello everyone, I am trying to overlay a cortical thickness map onto a subject but when I try this command freeview -v good_output/mri/T1.mgz good_output/mri/wm.mgz good_output/mri/brainmask.mgz good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 -f good_output/surf/lh.thickness.fsaverage.mgh:edgecolor=blue or this command: freeview -v good_output/mri/T1.mgz good_output/mri/wm.mgz good_output/mri/brainmask.mgz good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 -f good_output/surf/lh.thickness:edgecolor=blue I get an error saying: nquads=1966084, nvertices=599 ERROR: MRISread: file '/home/eva/Downloads/tutorial_data/buckner_data/tutorial_subjs/good_output/surf/lh.thickness' has many more faces than vertices! Probably trying to use a scalar data file as a surface! Do any of you know how to load it properly? Thank you!

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Cortical Thickness of Hippocampus subfields
by Dev vasu 29 Aug '17

29 Aug '17

Dear Sir, I have performed Subfield segmentation of Hippocampus subfields, I would like to how i can calculate thickness of each subfield post segmentation, are the values in the text files *[lr]h.hippoSfVolumes-<T1>-<analysisID>.v10.txt*: indicate estimated volume of each subfield , Is there any way i can obtain thickness of each subfield w.r.t whole hippocampus ?. Thanks Vasudev

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Centos 7 - hippocampal subfield segmentation in freeview
by Vetterman, Richard 29 Aug '17

29 Aug '17

Dear freesurfer experts, after an update of my computer I finally use Centos 7 now. It seems as if some parts of the lateral hippocampal subfield segmentation are not visualized any more when using freesurfer. When using FSL, everything looks fine, though. Do you have any suggestions, what to do? Thanks, Richard

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PETSURFER - mri_gtmpvc option to use SGTM
by M Janani 28 Aug '17

28 Aug '17

Hi Team, Could you please tell me how to modify this command to perform SGTM mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o gtmpvc.output I have tried with -sgtm and -sgtmx but it's not working. 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. ----------------------------------------------------------------------------------------------------------------------------------------------------

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