Freesurfer June 2020

freesurfer@nmr.mgh.harvard.edu

91 participants
130 discussions

samseg with subfields
by Sneha Pandya 08 Jun '20

08 Jun '20

External Email - Use Caution Dear experts, Is it possible to run subfield analysis (hippcampal subfields, amygdalar, thalamic nuclei, and brainstem structures) when we only run samseg on our dataset? Thank you, Sneha

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Fwd: Welcome to the "Freesurfer" mailing list
by Paolo Zanotti Fregonara 08 Jun '20

08 Jun '20

External Email - Use Caution Hi Would it be possible to post this job offer to the mailing list? Thanks Paolo ---------- Forwarded message --------- From: <freesurfer-request(a)nmr.mgh.harvard.edu> Date: Mon, Jun 8, 2020 at 10:30 AM Subject: Welcome to the "Freesurfer" mailing list To: <pzfregonara(a)gmail.com> Welcome to the Freesurfer(a)nmr.mgh.harvard.edu mailing list! To post to this list, send your email to: freesurfer(a)nmr.mgh.harvard.edu General information about the mailing list is at: https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer If you ever want to unsubscribe or change your options (eg, switch to or from digest mode, change your password, etc.), visit your subscription page at: https://mail.nmr.mgh.harvard.edu/mailman/options/freesurfer/pzfregonara%40g… You can also make such adjustments via email by sending a message to: Freesurfer-request(a)nmr.mgh.harvard.edu with the word `help' in the subject or body (don't include the quotes), and you will get back a message with instructions. You must know your password to change your options (including changing the password, itself) or to unsubscribe. It is: Paolofreesurfer73 Normally, Mailman will remind you of your nmr.mgh.harvard.edu mailing list passwords once every month, although you can disable this if you prefer. This reminder will also include instructions on how to unsubscribe or change your account options. There is also a button on your options page that will email your current password to you.

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gtmseg getSignalBehindHead ERROR (no slices behind head)
by Boris Rauchmann 08 Jun '20

08 Jun '20

External Email - Use Caution Dear FS experts, In my dataset I have 4 subjects where the T1 was acquired, planning the FOV very close to the occipital lobe. I guess that triggers the error: getSignalBehindHead ERROR (no slices behind head) WARNING: only 0 < 7 slices behind head! ERROR: xcerebralseg and results in gtmseg exited with errors. How can I fix this? Best regards, Boris

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MRInormFindControlPoints
by Benjamín Garzón 08 Jun '20

08 Jun '20

External Email - Use Caution Dear all, When running the long step for a subject with 7 timepoints with FS version 7.1.0 recon-all -long SUBJECT1.1 SUBJECT1.base -all -hires I get the following error in the mri_normalize step: #------------------------ mri_normalize -g 1 -seed 1234 -mprage -noconform nu.mgz T1.mgz using max gradient = 1.000 setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE not interpolating and embedding volume to be 256^3... reading mri_src from nu.mgz... normalizing image... talairach transform 1.21618 0.04397 -0.03619 2.40797; 0.07241 1.25030 0.38146 -0.66432; 0.05010 -0.63638 1.35133 -5.62093; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 6 Starting OpenSpline(): npoints = 6 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 error: No such file or directory error: MRInormFindControlPoints: could not find enough control points error: No such file or directory error: MRInormFindControlPoints failed Command exited with non-zero status 253 #------------------------ Oddly, it runs without problems for some timepoints but not for others, and there is nothing obviously wrong with the images for the timepoints that fail. Registrations seem fine. The error happens at least in one timepoint of several of our subjects. The image sequence is MP2RAGE and I have skull-stripped the images before running freesurfer, but the cross and base steps run normally and produce the expected results. Do you have any hints on what may be wrong? Best regards, Benjamin -- Benjamín Garzón, PhD Department of Neurobiology, Care Sciences and Society Aging Research Center | 171 65 Stockholm | Tomtebodavägen 18A, floor 10 benjamin.garzon(a)ki.se | www.ki-su-arc.se ______________________________________ Karolinska Institutet – a medical university När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>.

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QDEC correlation analysis
by Jian Ou 08 Jun '20

08 Jun '20

External Email - Use Caution Hello FreeSurfer Developers, I have a few questions about the p value in QDEC. I want to use matlab to calculate the p value in a vertex in the QDEC result. 1. In my design, there is a continuous variable A and two Nuisance factors B and C. How to calculate the p value in the correlation analysis of A and thickness. 2. If there are two groups of subjects F, M. How to calculate the p value.Thank for your help,Jian Ou

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Mixing freesurfer versions
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 08 Jun '20

08 Jun '20

Hi FS developers, I have a dataset that I am working on that has a mix of build stamps, including centos v6.0.0-2beb96c, centos dev-20190118, and dev-20180220 (a mess that was a little bit out of my control). I understand that these are all variations of FS6, and was wondering if its sufficient to leave them as is. Was there any meaningful changes in the recon-all steps that would warrant redoing some of these brains? Thanks, Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

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tkregisterfv -ss
by Boris Rauchmann 08 Jun '20

08 Jun '20

External Email - Use Caution Dear all, is there a way to use freeviews -ss command to obtain snapshots using tkregisterfv? I have a bunch of registrations to check and would prefer to do that using a bash script and snapshots. tkregisterfv --mov template.nii.gz --reg template.reg.lta --surfs -ss Gives back ERROR: Flag -ss unrecognized. Thanks, Boris

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mz3 for freesurfer brain render
by Kate Marvel 08 Jun '20

08 Jun '20

External Email - Use Caution Hi Freesurfer team, I would like to do a brain render using freesurfer ROIs. Is there .mz3 file for freesurfer brain atlas? Thanks, -- kate

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statement on recent events
by Fischl, Bruce R, 08 Jun '20

08 Jun '20

Not everything that is faced can be changed. But nothing can be changed until it is faced" -- James Baldwin. In these troubling times, it is increasingly obvious that silence is tantamount to complicity. If we do not object to objectionable events, we are tacitly condoning them, and as such we have an obligation to use platforms that are available to us. It is the responsibility of those in privilege to speak up. In that light we would like to express our horror and dismay at the recent, and not-so-recent, brutal attacks on George Floyd, Breonna Taylor, Ahmaud Arbery, Sandra Bland, Trayvon Martin, Freddie Gray, Eric Garner, Michael Brown, Tamir Rice, Philando Castile, Amadou Diallo, and so many others, many of whom we will never hear about. While some of us in the ivory tower like to think of ourselves as far-removed from this type of racism, we are of course not, as we all have biases both large and small. As such, it behooves us to consider these events and our own actions, and how we can work to create a more just, equitable and safe society. The global outrage generated by these horrific events is an opportunity to effect change. Racism remains after media coverage ceases, and it is our responsibility to ensure equality and respect are provided to those around us. We are committed to building an equitable and diverse workplace and progressing towards a fairer world. A non-exhaustive set of resources for advancing diversity can be found at: http://wis.martinos.org/black-lives-matter<http://wis.martinos.org/black-lives-matter/> Bruce Fischl Allison Stevens Lilla Zollei Caroline Magnain Chiara Maffei Anastasia Yendiki Brian Edlow Aina Frau-Pascual Matthew Vera Kimberly Nestor Holly Freeman Robert Jones Viviana Siless Andrew Hoopes Eugenio Iglesias Douglas Greve Ruopeng Wang André van der Kouwe Natalya Slepneva David Salat Divya Varadarajan Iman Aganj Hui Wang Robert Frost Matt Larrabee Jean Augustinack Leah Morgan Adrian Dalca Malte Hoffmann Martin Reuter Emily Williams Devani Cordero Paul Wighton Hamid Behjat Danielle Pace

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Freesurfer 7.1.0 - mris_flatten distortions
by Devavrat Vartak 07 Jun '20

07 Jun '20

External Email - Use Caution Hi Freesurfer community, OS: MacOS 10.14.6 I am cutting surfaces to make flat patches in freeview (Freesurfer 7.1.0) on and flatten them. The flat patches appear to have distortions ( https://imgur.com/a/KwG3iTa) This process worked well in FS6. I use mris_flatten -w 10 <input_file.3d> <output_file.flat> to flatten them. Additionally, when I use mri_surf2vol to convert the patch to a 3D nifti volume, I get an error. mri_surf2vol --ribbon <mri/ribbon.mgz> --o /<roi_patch/oc_full_patch.nii.gz> --subject <sub> --so </lh.inflated> </lh.occipital.patch.flat> ERROR: MRISreadCurvAsMRI: <path/to/freesurfer/recon_all/surf/lh.occipital.patch.flat, vals/vertex -12428437 unsupported Any idea why this is happening? Thank you, Dev

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Freesurfer June 2020