Freesurfer April 2018

freesurfer@nmr.mgh.harvard.edu

118 participants
177 discussions

Hemodynamic Lag Shift
by Sarah Cole 03 Apr '18

03 Apr '18

Hi Doug, I have a block design experiment. After analyzing the data and plotting the response magnitude across the TRs, we see that there is a systematic lag in the response. For example, in a 16s block (TR=2s), at TR-1 and TR-2 the response goes down and then starts rising from TR-3. This is consistent across the subjects and blocks. We used to shift our raw data by 2 TRs when we were using SPM. How can we do this in FreeSurfer? Thank you, Sarah

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Re: [Freesurfer] Freesurfer Digest, Vol 169, Issue 41
by Darko Komnenić 03 Apr '18

03 Apr '18

Hi Bruce, I attached the recon-all.log! Thanks in advance for taking a look! Darko Message: 3 Date: Sat, 31 Mar 2018 06:47:12 -0400 From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_watershed Error: indices out of bounds To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <23B23889-C042-4A04-9316-4C8ED5468428(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=utf-8 Can you send us the recon-all.log? > On Mar 30, 2018, at 11:32 AM, Darko Komneni? <komnenicd(a)gmail.com> wrote: > > Dear experts, > while running recon-all on FreeSurfer 5.1.0 I encountered the following error: > mri_watershed Error: indices out of bounds > > I searched the email archive and found this thread: > https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subj… > My problem seems identical to the one described by initial poster. > The suggestion was to try the following command: > set mdir=$SUBJECTS_DIR/$subject/mri > mri_add_xform_to_header $mdir/transforms/talairach.xfm $mdir/nu.mgz > $mir/nu.mgz > > When I tried it, the message I got was: > mri_add_xform_to_header: could not open source file /nu.mgz > No such file or directory > And indeed such file does not exist in the mri subfolder of my > current subject's folder. > > Any further suggestions on how to fix this? Like the person asking > originally, this is the only participant where it happened, for > others, recon-all finished without error and all the images were > acquired in the same scanner. > Thanks in advance! > Best, > Darko > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Fwd: Learning Workshop in Bloomington IN (fwd)
by Bruce Fischl 03 Apr '18

03 Apr '18

FYI ---------- Forwarded message ---------- Date: Tue, 3 Apr 2018 11:14:38 -0400 From: Satrajit Ghosh <satra(a)mit.edu> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>, "Jog, Amod" <AJOG(a)mgh.harvard.edu> Subject: Fwd: Learning Workshop in Bloomington IN hi, this may be of interest. please forward. cheers, satra -- satrajit ghosh | satra.cogitatum.org principal research scientist | mibr @ m i t assistant professor of otolaryngology @ harvard medical school faculty member @ speech and hearing bioscience and technology director, data models and integration | repronim: center for reproducible neuroimaging computation ---------- Forwarded message ---------- From: Franco Pestilli <frakkopesto(a)gmail.com> Date: Tue, Apr 3, 2018 at 10:51 AM Subject: Learning Workshop in Bloomington IN To: Satrajit Ghosh <satrajit.ghosh(a)gmail.com> Dear Satra We are organizing a learning workshop in Bloomington Indiana May 14-15: http://www.indiana.edu/~earbmc/LIHAM/ Would you mind spreading the word please? We have travel scholarships for talented trainees. Best regards, Franco Franco Pestilli, PhD Assistant Professor in Psychology, Neuroscience and Cognitive Science Adjunct Professor in Engineering, Computer Science, and Optometry Indiana Network Science Institute 𝞇 Indiana University, Bloomington francopestilli.com | brainlife.io franpest(a)indiana.edu | +1 (812) 856 9967

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Freesurfer for canine
by Khoi Mai 03 Apr '18

03 Apr '18

Hi, I am interested in the automated volumetric analysis for canine. My question is how can we go about adjusting the pipeline to accommodate canine data. Thank you for your reply Best, Khoi

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Brainhack Ireland 2018 - Brainhack Global
by Chiara Caldinelli 03 Apr '18

03 Apr '18

Join us for Brainhack Ireland 2018 <http://www.brainhackireland.org/>, a 2.5-day event at which you can team up with neuroscience researchers, data scientists, hackers, philosophers and anyone else with an interest in working on innovative projects related to neuroscience. There will be prizes for the winning teams, and the results will be shared with more than 30 institutions across the world through Brainhack <http://www.brainhack.org/global2018>Global <http://www.brainhack.org/global2018>. Our goal is to understand more about the brain and mind, while having fun. It will be held from the evening of May 2 until May 4, at the awesome Huckletree D2 <https://www.huckletree.com/locations/dublin-d2> space on Pearse St., Dublin. To see the program and for more information, go to www.brainhackireland.org . There is a small registration fee, which will cover coffee, snacks and lunch. We thank our sponsors, the Cusacklab <http://www.cusacklab.org/> and the Trinity College Institute of Neuroscience <http://www.tcd.ie/neuroscience>, Trinity College Dublin. Twitter: #BrainhackIreland Meetup: https://www.meetup.com/Brainhack-Ireland-2018/events/249221592/ Looking forward to seeing you! Chiara On behalf of The Brainhack Ireland Team

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Download FreeSurfer for Virtualbox
by Karin Westin 03 Apr '18

03 Apr '18

Hi! I've tried downloading the FreeSurfer Virtualbox-file several times, but when I try to unzip, I get a message that the file is broken and that the file cannot be unzipped. What am I doing wrong? I realise that this message doesn't contain a whole lot of information but this is all I know... Best, Karin

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mirroring fsaverage labels between hemispheres
by Abigail Noyce 02 Apr '18

02 Apr '18

Hi, I have pored over (I think) all of the mailing list postings about cross-hemisphere mapping and I can't quite figure out how to do this. I have a bunch of labels on fsaverage, and I want to be able to check/visualize the relationship between lh and rh versions of the labels. I can do mri_label2label to map from fsaverage to fsaverage_sym, but that doesn't do the right thing, and fsaverage doesn't have the same kind of xhemi registration structure that "normal" subjects get with surfreg --xhemi. I guess I could back-project onto a normal subject and then project to fsaverage_sym, but that seems like an unnecessary step. How can I get mirror-projected labels from fsaverage on fsaverage_sym? Thanks! Abby -- Abigail L. Noyce, Ph.D. Psychological & Brain Sciences Boston University anoyce(a)bu.edu 617-440-3640

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Freesurfer April 2018