Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Group level analysis: Specifying contrasts
by Afzal, Afsana 12 Apr '16

12 Apr '16

Hi, I want to perform a linear regression for a task with 3 different risk conditions (low, medium, high) with the following linear trend: low = 1, medium = 2, high = 3. Right now I'm specifying the above weighted under each risk condition in my contrast matrix. Is this the correct approach? I want to make sure I am calculating a regression and not a weighted average. Thank you for your help, Afsana ______________________________ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078

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Bad Segmentation in Left Thalamus
by Grant O'Brien 12 Apr '16

12 Apr '16

Hello, I’m an undergraduate at Duke University working on a study of pediatric structural imaging. We’ve recently come across some segmentation issues with the left thalamus (and very rarely the right thalamus) on many of our scans. Although our study isn’t looking at the thalamus as a region of interest, we’re concerned that it could be indicative of more global segmentation issues. Freesurfer appears to be incorrectly labeling segments of the left thalamus as “left cerebral white matter." We initially thought that perhaps the errors were due to motion artifacts, but we have observed this phenomenon in some scans with striping and some scans without striping (as demonstrated in the two screenshots). My questions are: What could be the possible reasons for this incorrect segmentation? Would scans with this problem need to be excluded? What steps could we take to fix it? Why might it only be occurring in the left thalamus? Thanks so much for your help. Best, Grant O'Brien Duke University Class of 2017 704-467-5449 [cid:BCEC92F0-59BE-4FBC-8E1B-B4DA90099CFB@dhe.duke.edu][cid:5CA3D954-63A9-4C96-B716-817AFCCB25D0@dhe.duke.edu]

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TRACULA
by Jasmin Alves 12 Apr '16

12 Apr '16

Hello Freesurfer Team, I attended the conference last week in Boston and really enjoyed all I learned! But while trying to run through the Tracula tutorial with my own data, I am having an error with my configuration file: ERROR: must specify as many DWI dicoms as subjects. My files are in nifti format, could this possibly be the cause of this error? I have attached my configuration file for reference. FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 14.5.0 x86_64 Thanks so much! Jasmin Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves(a)usc.edu

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Re: [Freesurfer] mri_vol2surf misaligment
by Francesca Strappini 12 Apr '16

12 Apr '16

Hi, I used load_nii and save_nii to read and write out the volume. Thank you! Francesca 2016-04-11 14:33 GMT+02:00 Francesca Strappini <francescastrappini(a)gmail.com >: > Hi, I used load_nii and save_nii to read and write out the volume. > > Thank you! > Francesca > > 2016-04-08 18:31 GMT+02:00 Douglas N Greve <greve(a)nmr.mgh.harvard.edu>: > >> can you show a pic? What were your matlab commands to read in and write >> out the volume? >> >> On 04/04/2016 07:36 AM, Francesca Strappini wrote: >> > Dear Freesurfers, >> > >> > I run the preprocessing step of some functional data with >> > preproc-sess, then the Fourier analysis with matlab. Now, I'm trying >> > to plot this data on the surface: >> > >> > mri_vol2surf --mov Katkov_OT_45.nii.gz --trgsubject MishaK --hemi lh >> > --reg register.dof6.dat --o Katkov_OT_45_LH.nii.gz >> > >> > I used as registration matrix the one produced by the preprocessing >> > step but when I try to visualize the map on the surface it looks like >> > completely misaligned. >> > >> > Thank you >> > Best >> > Francesca >> > >> > >> > >> > -- >> > Francesca Strappini, Ph.D. >> > Neurobiology Department >> > Weizmann Institute of Science >> > 234 Herzl Street, Rehovot 7610001 Israel >> > Tel.: +972 58 444 2584 >> > E-mail: francesca.strappini(a)weizmann.ac.il >> > <mailto:francesca.strappini@weizmann.ac.il> >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> 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. >> >> > > > -- > Francesca Strappini, Ph.D. > Neurobiology Department > Weizmann Institute of Science > 234 Herzl Street, Rehovot 7610001 Israel > Tel.: +972 58 444 2584 > E-mail: francesca.strappini(a)weizmann.ac.il > -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

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Segmentation of supplemental motor area
by Morten Sejer Hansen 12 Apr '16

12 Apr '16

Dear Freesurfer experts, I need to extract the volume of the supplemental motor area (cortical structure) I have used the aparch.stats2table and applied the both the ?h.aparc.stats and the ?h.aparc.a2009s.annot.stats atlas; However, I am having trouble identifying the supplemental motor area. Do you know if it is possible to extract volumes of this area using Freesurfer? Thank you. Kind regards Morten Sejer Hansen Morten Sejer Hansen MD Direct: + 45 26373611 Mail: morten.sejer.hansen(a)regionh.dk / morten.sejer.hansen(a)dadlnet.dk<mailto:morten.sejer.hansen@regionh.dk%20/%20morten.sejer.hansen@dadlnet.dk> Department of anaesthesiology 4231 Centre of head and orthopaedics Copenhagen University Hospital, Rigshospitalet Blegdamsvej 9 2100 Copenhagen Tel: +45 35 45 35 45 Web: www.regionh.dk<http://www.regionh.dk/> This e-mail and any attachment may contain confidential and privileged material intended for the addressee only. If you are not the addressee, you are notified that no part of the e-mail or any attachment may be disclosed, copied or distributed, and that any other action related to this e-mail or attachment is strictly prohibited, and may be unlawful. If you have received this e-mail by error, please notify the sender immediately by return e-mail, and delete this message. ________________________________ Denne e-mail indeholder fortrolig information. Hvis du ikke er den rette modtager af denne e-mail eller hvis du modtager den ved en fejltagelse, beder vi dig venligst informere afsender om fejlen ved at bruge svarfunktionen. Samtidig bedes du slette e-mailen med det samme uden at videresende eller kopiere den.

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3T or nuintensitycor3t
by Kasper Jessen 12 Apr '16

12 Apr '16

Dear freesurfer, To clear up som confusion i would like to ask if there is a difference between adding a -3T or -nuintensitycor3t flag? Best regards, Kasper -- Kasper Jessen, MD, PhD student Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67 2600 Glostrup Tlf.: 24430136 E-mail: kasper_j(a)cnsr.dk eller kasper.jessen(a)regionh.dk

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August FreeSurfer course in Copenhagen, Denmark
by Allison Stevens 11 Apr '16

11 Apr '16

There are still some spots available in the Copenhagen FreeSurfer Course which will be held from August 10th to 12th, 2016. The course will be organized by the Neurobiology Research Unit, Copenhagen University Hospital in cooperation with the Laboratory for Computational Neuroimaging of the Athinoula A. Martinos Center for Biomedical Imaging. The course will be a three-day course for beginners and experienced users of FreeSurfer and the lectures will be held by FreeSurfer developers from the Laboratory for Computational Neuroimaging. For further information and to register for this course, please visit: http://fscph2016.nru.dk/ Please feel free to contact my friends at NRU (cc'd) with any questions. Allison Stevens Lab Manager/Course Organizer Laboratory for Computational Neuroimaging FreeSurfer Development Team

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From Talairach to Vertex Index
by Ilaria Mazzonetto 11 Apr '16

11 Apr '16

Hi FS users, I need to check if a specific point in Talairach coordinates is inside a label that I created from a significative cluster of a previous group analysis (the template is fsaverage). How can I do this quickly? Thanks a lot. Best regards. Ilaria

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$FREESURFER_HOME/sources.csh
by Marco Loggia 11 Apr '16

11 Apr '16

Good morning Doug and all, I am running epidewarp.fsl (using the dev version since I need it to be compatible with the recent versions of FSL; /usr/local/freesurfer/dev/bin/epidewarp.fsl). However, for the first time I see that it complains that it can no longer find /usr/local/freesurfer/stable5_3_0/sources.csh. How can this be fixed?? Thanks! Marco _______________________________________________________ Marco L. Loggia, PhD Assistant Professor of Radiology, Harvard Medical School Associate Director, Center for Integrative Pain NeuroImaging (CiPNI) A. A. Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 Thirteenth Street, Room 2301 Charlestown, MA 02129 Phone: (617) 643-7267 Fax: (617) 726-7422 Email: marco(a)nmr.mgh.harvard.edu Web: http://scholar.harvard.edu/loggia

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Accuracy of D-K atlas for different age ranges
by Kirstie Whitaker 11 Apr '16

11 Apr '16

Hi Freesurfer community, A reviewer has asked how accurate the application of freesurfer regional labels are to different age ranges (specifically our study is between 14 and 24 years old). I'm sure this question has been answered elsewhere so please do forgive me for being lazy and simply asking you to recommend good references rather than searching for them in PubMed! Thank you! Kirstie x -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge *Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB *Phone: *+44 7583 535 307 *Website:* www.kirstiewhitaker.com

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