Freesurfer August 2018

freesurfer@nmr.mgh.harvard.edu

104 participants
167 discussions

3 positions to post
by Florence M 20 Aug '18

20 Aug '18

External Email - Use Caution Hi, I want to post a positions bellow, thanks to reply where I should go to post it on free surfer please. Best, Florence

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Freesurfer v6.0: Using FLAIR for hippocampal subfields
by Ole Johan Evjenth Sørhaug 20 Aug '18

20 Aug '18

External Email - Use Caution Dear freesurfer experts, I'm interested in doing subfield segmentations of the hippocampus in version 6.0. What I am specifically interested in, is that if I can expect better segmentations if I use a 1mm isotropic FLAIR series in addition to the 1mm isotropic T1 series, rather than using the T1 series alone. Regards Ole Johan Sørhaug

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mri_cvs_register using fsaverage
by Peled, Noam 19 Aug '18

19 Aug '18

I need to transfer one of our patient's electrodes locations (depth electrodes, they aren't located on the cortical surface) to MNI305 space. For that, I'm trying to use mri_cvs_register to register the patient to fsaverage. I'm using to the following command: mri_cvs_register --mov subjid --template fsaverage --outdir output_name --nocleanup And I'm getting the following error: fsaverage : at least one mean and/or Gaussian curvature file is missing (.H, .K) Indeed, fsaverage doesn't have the rh/lh.inflated.K/H files. Any ideas? Thanks, Noam

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Re: [Freesurfer] segmentHA_T1.sh exits with error
by Antonin Skoch 17 Aug '18

17 Aug '18

External Email - Use Caution Dear Eugenio, here it is: asegModBinDilated.mgz asegModBinDilatedResampled.mgz asegModCHA.mgz asegMod.mgz asmr1.mgz asmr2.mgz asmr3.mgz compressionLookupTable.txt discreteLabels_all.mgz discreteLabelsMergedBodyHead.mgz discreteLabels.mgz discreteLabelsWholeBodyHead.mgz error.log hippoAmygBinaryMask_autoCropped.mgz hippoAmygBinaryMask.mgz hippoMaskDilated5mm.mgz hippoMask.mgz hippoMaskResampledDilated.mgz hippoMaskResampled.mgz imageDump.mgz image.mgz T1resampled.mgz trash.lta volumesAmygdala.txt volumesHippo.txt warpedMeshNoAffine.txt.gz warpedMesh.txt.gz warpedOriginalMesh.txt.gz Antonin Dear Antonin, Can you please send me a listing of the files in: /hydra-db/hydra_io/vypocty/freeSurfer/A_analysis_HPC_PFC/A_links_all/ESO_C00577_20160303_1246_1/tmp/hippoSF_T1_v21_right/ Kind regards, /Eugenio-- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-boun...(a)nmr.mgh.harvard.edu> on behalf of Antonin Skoch <a...(a)ikem.cz> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, 17 August 2018 at 18:16 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] segmentHA_T1.sh exits with error External Email - Use Caution Dear experts, I am running segmentHA_T1.sh. In about 3 subjects from 200, the script exits with following error: In an assignment A(:) = B, the number of elements in A and B must be the same. Error in segmentSubjectT1_autoEstimateAlveusML (line 1856) MATLAB:subsassignnumelmismatch Command exited with non-zero status 255 Full log file is attached. I have also uploaded whole subject (named segmentHA_T1_error.tar.gz ), including content of temporary directory hippoSF_T1_v21_right, to your server. I am using dev version, build 2018-07-28. I am using customized recon-all, but it should not relate to this error. Could you please look at this issue? Regards, Antonin Skoch

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Freeview heat map
by James Brown 16 Aug '18

16 Aug '18

External Email - Use Caution Dear Freesurfer developers, I analyzed some data in Freesurfer. At the end, I used "mri_segstats" to measure a parameter of interest for every ROI in DKT atlas. I would like to load the mean values of this parameter to Freeview (every ROI in DKT has one value of the parameter represent the mean signal in the ROI). The objective is to give color code for every ROI in DKT that fit the values of the computed parameter. Is there any way of doing this in Freeview? Thanks john

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DOWNLOAD LINK
by FabLab HGUGM 16 Aug '18

16 Aug '18

External Email - Use Caution Hello, At the FabLab in Hospital Gregorio Marañon in Madrid we have tried to download Free Surfer several times but the download link for mac seems to no longer be working. Is there any other link available? Thanks!

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mri_label2label no registration difference
by Yagmur Ozdemir 19 16 Aug '18

16 Aug '18

External Email - Use Caution Hello FreeSurfer experts, I want to compare the labels produced by two different registration methods in mri_label2label; either using the sphere or TAL space as an intermediate ( --regmethod). However I see that there is no difference between the labels produced with these different registrations. Is this normal or should I look for an error? I looked at the script to match with my outputs and everything seems to have worked allright. Thank you Idil

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Wash U Radiology Department Research Faculty Positions Available
by Moreau, Allison 15 Aug '18

15 Aug '18

External Email - Use Caution FYI Begin forwarded message: From: WUNIC Email List Admin <wunic(a)nrg.wustl.edu<mailto:wunic@nrg.wustl.edu>> Date: August 14, 2018 at 9:26:48 AM CDT To: <amoreau(a)wustl.edu<mailto:amoreau@wustl.edu>> Subject: Radiology Department_Research Faculty Positions Available Reply-To: WUNIC Email List Admin <wunic(a)nrg.wustl.edu<mailto:wunic@nrg.wustl.edu>> View this email in your browser<https://mailchi.mp/c8252eeb516b/radiology-department_research-faculty-posit…> [https://gallery.mailchimp.com/28232c5fb4d47392812342a76/images/1303a9cd-2ee…] Dear all: A new job ad for Radiology research faculty is now out. Neuroimaging is part of this search. https://facultyopportunities.wustl.edu/Posting/Detail/1010318<https://xnat.us10.list-manage.com/track/click?u=28232c5fb4d47392812342a76&i…> Please forward liberally and encourage people to apply. Any questions can be directed to me (tammy(a)wustl.edu<mailto:tammy@wustl.edu>), Joe Culver (culverj(a)wustl.edu<mailto:culverj@wustl.edu>) or Rob Gropler (rgropler(a)wustl.edu<mailto:gropplerr@wustl.edu>). Best Tammy Tamara Hershey, PhD Professor, Psychiatry & Radiology Departments Lab Chief, Neuroimaging Labs (NIL) @ MIR Director, McDonnell Center for Systems Neuroscience Co-Director, Neuroscience PhD Program, DBBS Washington University School of Medicine Campus Box 8225, Room 2204, East Blg 4525 Scott Avenue St. Louis, MO 63110 Phone: 314-362-5593 Email: tammy(a)wustl.edu<mailto:tammy@wustl.edu> Copyright © 2018 WUNIC, All rights reserved. You are receiving this email as a past member of the NIAC mailing list, or as a participant in the WUNIC survey. Our mailing address is: WUNIC 4525 Scott Ave, Campus Box 8225 Saint Louis, MO 63110 Add us to your address book<//xnat.us10.list-manage.com/vcard?u=28232c5fb4d47392812342a76&id=0de7e1e64b> Know someone who would like to receive these emails? You can subscribe to this list here: https://nrg.wustl.edu/contact-us/wunic-email-list-subscription/<https://xnat.us10.list-manage.com/track/click?u=28232c5fb4d47392812342a76&i…> Want to change how you receive these emails? You can update your preferences<https://xnat.us10.list-manage.com/profile?u=28232c5fb4d47392812342a76&id=0d…> or unsubscribe from this list<https://xnat.us10.list-manage.com/unsubscribe?u=28232c5fb4d47392812342a76&i…>.

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Extracting number of vertices in Yeo's 7Networks from significant clusters
by Shatil, Anwar Shahadat 15 Aug '18

15 Aug '18

External Email - Use Caution Hello Doug and other experts: I have done QDEC analysis between two groups (healthy controls vs disease) and obtained different .mgh and .annot files. I got one big cluster covering most part of the brain. I wanted to extract the number of vertices for Yeo's 7 Networks in that big cluster and therefore I ran this: mri_segstats --i cache.th30.pos.sig.masked.mgh --annot fsaverage rh Yeo2011_7Networks_N1000 --excludeid 0 --sum network_param.dat The result was: Col Headers Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 1 22519 14950.0 7Networks_1 1.4816 1.8126 0.0000 3.6990 3.6990 2 2 30207 12514.7 7Networks_2 2.6658 1.6596 0.0000 3.6990 3.6990 3 3 17604 8224.3 7Networks_3 2.6278 1.6778 0.0000 3.6990 3.6990 4 4 19402 8357.2 7Networks_4 3.3453 1.0877 0.0000 3.6990 3.6990 5 5 11614 6205.0 7Networks_5 2.1434 1.7750 0.0000 3.6990 3.6990 6 6 22330 12170.7 7Networks_6 2.6315 1.6761 0.0000 3.6990 3.6990 7 7 26056 13826.2 7Networks_7 3.0249 1.4229 0.0000 3.6990 3.6990 I ran the same code for different --i (input) .mgh files and everytime the NVertices were the same, which means this is not the one I am looking for. Can you please help me in getting the number of vertices of Yeo's each network that fall in that big cluster? Thanks. Anwar -- Anwar S. Shatil Research Assistant Department of Medical Imaging Sunnybrook Health Sciences Centre Room AB204, 2075 Bayview Avenue Toronto, ON M4N 3M5 Tel: 416.480.6100 ext. 89617 Email: anwar.shatil(a)sunnybrook.ca 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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Call for Nominations: OHBM Student and Postdoc Special Interest Group
by Chiara Caldinelli 15 Aug '18

15 Aug '18

External Email - Use Caution Dear All, The *OHBM Student and Postdoc Special Interest Group* (SIG) is seeking nominations for open seats on the 2018-2019 SIG 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 community, directing its activities, and working with the OHBM Executive Office 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.A., 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 Rome 2019 and Montreal 2020 (and likely to attend the meeting in 2021). To nominate yourself for election to the SIG Committee please complete this nomination form: https://goo.gl/forms/DeC5FoQx4nwbel1K3 no later than August 31st, 2018. Email ohbmtrainees(a)gmail.com if you have any questions. Nominations close on the 31st August 2018. Kind Regards, OHBM Student and Postdoc SIG

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Freesurfer August 2018