Re: [Freesurfer] WM edits, prevent surface from cutting sulcus

External Email - Use Caution Hi Bruce, It was a topological defect. I found it after looking harder. My bad. Hi Chris It sounds like a topological defect, but hard to say without seeing it. Can you post some images? Or follow Doug's instructions about visualizing the defects

[Freesurfer] WM edits, prevent surface from cutting sulcus

om cutting across the sulcus? Thank you. Chris. Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch Childrens Research Institute Murdoch Childrens Research Institute Royal Children's Hospital Flemington Road, Parkville, Victoria 3052, Australia http://secure-web.cisco.

[Freesurfer] FS 7.2 VirtualBox 7z Password

External Email - Use Caution Dear FS experts, I am using the Oracle Virtual Box to install FS 7.2 on Windows. Could you send to me the passcode for the 7z archive? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Request for passcode

External Email - Use Caution Hello , Requesting the passcode to uncompress this archive. FS_7_2_0_Ubuntu_18_04_06.ova.7z Thank you very much! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Use annotation for edgecolor in freeview

in advance, Chris Adamson. Disclaimer This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify

Re: [Freesurfer] [EXTERNAL]Re: mris_transform with flirt transformation wrong result

--src flirtinput.nii --trg flirtoutput.nii) On 10/13/2022 9:40 PM, Chris Adamson wrote: External Email - Use Caution Freesurfer experts, I’m trying to put some subject surfaces into a template space. I have performed the following flirt registration per subject: flirt -in $SUBJECTS_DIR

[Freesurfer] mris_make_average_surface, flirt transformations question

template0.nii.gz but it is offset slightly and not overlaid correctly. Am I doing something wrong? Thanks in advance, Chris. Dr Chris Adamson Senior Research Officer, Developmental Imaging, Clinical Sciences (0.3 EFT) Software Engineer, Cardiovascular Research (0.7 EFT) Murdoch Childrens Research

[Freesurfer] mris_transform with flirt transformation wrong result

the surface is in the wrong orientation and in the wrong position, i.e. not correct. I have tried using lta_convert to make a lta transform and I get the same result. Any thoughts? Thanks, Chris. Dr Chris Adamson Senior Research Officer, Developmental Imaging, Clinical Sciences (0.3 EFT

Re: [Freesurfer] Freeview - hide coordinate labels in scripts for screenshots {Disarmed}

External Email - Use Caution Jocelyn, I need to hide them in a script, not by using the GUI. Chris. From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Mora, Jocelyn S. Sent: Saturday, 14 November 2020 1:37 AM To: Freesurfer support list Subject: Re: [Freesurfer

[Freesurfer] Freeview - hide coordinate labels in scripts for screenshots {Disarmed}

External Email - Use Caution Freesurfer people, Is there an option for freeview scripts to hide the coordinate labels in 2D view? They are appearing in screenshots and I want to get rid of them. Chris. Dr Chris Adamson Senior Research Officer, Developmental Imaging, Clinical

[Freesurfer] brainGraph (graph theory analysis in R) major release v3.0.0

me know if you have any issues, bug reports, feature requests, etc. Chris Watson ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Asymmetry whole thalamus with native vs Iglesias method

that the segmentation method used to create aseg in itself already produces asymmetry + any asymmetry in the data itself, whereas the prior used in ThalamicNuclei.v12 is symmetric and therefore any asymmetry is due to the data only. correct? best wishes, Chris Op wo 9 sep. 2020 om 16:29 schreef Chris

Re: [Freesurfer] Asymmetry whole thalamus with native vs Iglesias method

ile the asymmetry shown by your method is due to the data only and therefore comparing the AI between the two methods is meaningless and definitely not suitable as a quality (or sanity) check? Cheers, Chris Op di 8 sep. 2020 om 09:05 schreef Chris Vriend : > Dear Eugenio, > > Douglas referr

Re: [Freesurfer] Asymmetry whole thalamus with native vs Iglesias method

External Email - Use Caution Dear Eugenio, Douglas referred me to you for this question. Do you have an explanation for the difference in asymmetry between the native (aseg) and ThalamicNuclei.v12 segmentation? kind regards, Chris *I'm not sure about this. The FS segmentation

[Freesurfer] Asymmetry whole thalamus with native vs Iglesias method

we observe this and not just in one dataset or one subject but in multiple. Do you have any words of wisdom or explanation for this phenomenon? Your advice is much appreciated. Kind regards, Chris Vriend Whole_thalamus_lh_Iglesias whole_thalamus_rh_Iglesias AI Fsnative_Left-Thal

Re: [Freesurfer] How to make surface cuts / flatmaps. Alternative for tksurfer in 2020?

External Email - Use Caution Someone messaged me that in the latsest FS7 we can now do this in Freeview. Awesome! I don't think a lot of people know about this. Spread the word! -- Chris Klink (sent from a phone) ___ Freesurfer mailing

Re: [Freesurfer] recon-all for macaque brain

/recoveringyank/precon_all) which I haven't personally used yet, but I've seen results and it looks very promising!  Good luck! Chris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] How to make surface cuts / flatmaps. Alternative for tksurfer in 2020?

ased approach? What are the options in 2020? Best, Chris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Freesurfer 7 long -> cross surfaces

External Email - Use Caution Don’t worry, figured it out with mris_transform. From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Chris Adamson Sent: Monday, 1 June 2020 8:56 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer 7 long -> cross surfa

[Freesurfer] Freesurfer 7 long -> cross surfaces

CROSS/mri/rawavg.mgz for CURHEMI in $HEMIS do for CURSURF in $SURFS do mri_surf2surf --sval-xyz $CURSURF --reg-inv register.native.dat --tval $SUBJECTS_DIR/$OUTDIR/surf/$CURHEMI.$CURSURF --tval-xyz $SUBJECTS_DIR/$CROSS/mri/rawavg.mgz --hemi $CURHEMI --s $LONG

Re: [Freesurfer] mris_register intermediate results display

would just map the ?h.curv from one subject to another and then display them on a single surface and flip back and forth. Would that work for you? On 5/21/2020 9:30 AM, Chris Adamson wrote: External Email - Use Caution Freesurfer devs, Apologies if this has already been asked. I’m looking

[Freesurfer] mris_register intermediate results display

of the curvature maps, how can I take a spherical surface and write out a tif file with the curvature maps of the surface that I'm registering and the target surface. I presume I need to use mrisp_write but it is unclear how I choose the curvature map to write in the image. Thanks in advance, Chris. Dr

[Freesurfer] tktools: Bad CPU type on Mac OSX 10.15. Any workarounds or fixes?

that doesn't require tksurfer and will work on Catalina? (It's not super urgent as I do have a different system available where things do work, but if there's a way this can work I'd like to know about it..) Thanks, -- Chris Klink ___ Freesurfer mailing

Re: [Freesurfer] binary version of brainmask?

of 5 not 0 Cheers Bruce On Aug 26, 2019, at 10:24 PM, Chris Adamson mailto:chris.adam...@mcri.edu.au>> wrote: External Email - Use Caution So all voxels in the brainmask that are non-zero are in the brain mask? In other words zero-valued voxels in the brain are considered to be non

Re: [Freesurfer] binary version of brainmask?

2019 12:18 PM To: Freesurfer support list Subject: Re: [Freesurfer] binary version of brainmask? Hi Chris can't you just use mri_binarize to turn whichever want you want into a binary mask? Or mri_threshold for that matter cheers Bruce On Tue, 27 Aug 2019, Chris Adamson wrote

[Freesurfer] binary version of brainmask?

External Email - Use Caution Freesurfer, Is it possible to get mri_watershed to produce a binary mask version of brainmask.mgz/brainmask.auto.mgz? Thank you, Chris. Dr Chris Adamson Senior Research Officer, Developmental Imaging, Clinical Sciences (0.3 EFT) Software Engineer

Re: [Freesurfer] Freeview update error

External Email - Use Caution Hi Kelly, you can try yum install qt5-qtbase-gui qt5-qtwebkit qt5-qtwebkit-devel And if it still doesn't work, you can try yum install harfbuzz On Mon, Apr 22, 2019 at 9:05 AM Kelly Vaughn wrote: > External Email - Use Caution > > Hello

[Freesurfer] Freeview Scrolling through slices on a Mac

… shift / option / cmd with up / down either zooms or moves up / down. I’m just trying to add control points and definitely need to scroll through slices without clicking on the image. Thanks, -Chris ___ Freesurfer mailing list Freesurfer

[Freesurfer] MRISalloc

External Email - Use Caution I’ve tried processing a healthy brain through v6.0.0 and _dev versions only to get hung at this step in each of the versions. The brain looks normal. I’ve tried adjusting the skull strip and using control points in a location that the brain was

Re: [Freesurfer] smoothwm.H vs curv

External Email - Use Caution Ok ill have a closer look. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Bruce Fischl Sent: Friday, 26 October 2018 3:08 AM To: Freesurfer support list Subject: Re: [Freesurfer] smoothwm.H vs curv Hi Chris I

[Freesurfer] smoothwm.H vs curv

, MRISuseMeanCurvature, MRISaverageCurvatures ... Thanks in advance, Chris Adamson. Disclaimer This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Com

Re: [Freesurfer] mris_register problem

External Email - Use Caution Thanks Bruce. I had to increase the angular search range in the affine part to get it to work. Cheers, Chris. From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Bruce Fischl Sent: Monday, 17 September 2018 11:49 PM To: Freesurfer support

[Freesurfer] mris_register problem

in an incorrect orientation. So it appears as if there is some rotation that is being done internally that isn't shown in freeview. Please advise, Chris. Dr Chris Adamson Senior Research Officer Developmental Imaging, Clinical Sciences Murdoch Childrens Research Institute The Royal Children's

Re: [Freesurfer] 6.0.1 automatic download

External Email - Use Caution Thanks! Best, Chris PS Apologies for brevity and potential typos. This message was composed on a phone. On Wed, Sep 12, 2018, 5:06 PM Hoopes, Andrew wrote: > Hi Chris, that is the same version as before. Sorry, our pubftp disk went > down

[Freesurfer] 6.0.1 automatic download

/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a.tar.gz Is it the same thing or an updated version (if so why not 6.0.2)? Is this the right way to grab the same 6.0.1 version in a programmatic way? Best, Chris ___ Freesurfer mailing list Freesurfer

[Freesurfer] PSIR to refine pial surface?

, Best wishes Chris [cid:image001.png@01D40E30.9B2FFEE0] Dr. C. Vriend | Assistant Professor Anatomy & Neurosciences - section Neuropsychiatry | Psychiatry Location VUmc | O|2 13W09 | De Boelelaan 1118, 1081 HZ Amsterdam T: + 31 (0) 6 25 69 49 12 | E: c.vri...@vumc.nl<mailto:c.vri...@

[Freesurfer] Learning which data derivatives matter most

e does not include very important modalities such as EEG, MEG, iEEG or PET). I hope we will be able to perform followup surveys in the near future to fill in those gaps. Best, Chris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Proposed addition for Freesurfer - automated control points

/freesurfer_cp_tool From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Bruce Fischl Sent: Saturday, 30 June 2018 12:21 AM To: Freesurfer support list Subject: Re: [Freesurfer] Proposed addition for Freesurfer - automated control points Hi Chris can you elaborate a bit? Our intensity normalization

[Freesurfer] Proposed addition for Freesurfer - automated control points

as a tool for people to use if they choose? Thanks in advance, Chris. Dr Chris Adamson Senior Research Officer Developmental Imaging, Clinical Sciences Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adam...@mcri.edu.au

Re: [Freesurfer] Negative areas in mris_sphere, dark in freeview

rface normal calculation and see if your faces are pointing inwards. I think mris_convert -n will write them out cheers Bruce On Mon, 12 Mar 2018, Chris Adamson wrote: > I had already done this, it had no effect. > > -Original Message- > From: freesurfer-boun...@nmr.mgh.ha

Re: [Freesurfer] Negative areas in mris_sphere, dark in freeview

Subject: Re: [Freesurfer] Negative areas in mris_sphere, dark in freeview Hi Chris we have c code for doing this but no binary that calls it in the way you need. This is the code: int MRISevertSurface(MRI_SURFACE *mris) { int v0, fno; FACE *face; for (fno = 0; fno < mris->nfaces;

Re: [Freesurfer] Negative areas in mris_sphere, dark in freeview

Hi Bruce, Thanks for your reply. I had already tried swapping the 2nd and 3rd face indices, no effect. Chris. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Bruce Fischl Sent: Saturday, 10 March 2018 1

[Freesurfer] Negative areas in mris_sphere, dark in freeview

outwards. The darkness in freeview is not fixed by changing the order of the indices of the faces (which should invert the normal). I'm at a loss to explain this. Thanks in advance, Chris. Dr Chris Adamson Senior Research Officer Developmental Imaging, Clinical Sciences Murdoch Childrens Research

Re: [Freesurfer] brainGraph (graph theory analysis in R) major release: v2.0.0

of the User Guide). Chris On Wed, Feb 7, 2018 at 6:00 AM, gabriel robert < gabriel.hadrien.rob...@gmail.com> wrote: > Dear Dr Watson, > > Many thanks for developping your toolbox, > > Is there any project to propose any "courses" or anything related to > course

[Freesurfer] brainGraph (graph theory analysis in R) major release: v2.0.0

- Calculation of network *communicability* and vertex *communicability betweenness centrality* Please let me know if you have any issues, bug reports, feature requests, etc. Chris Watson ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https:

Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

emory of your host machine will be accessible to your docker containers. More details here: https://docs.docker.com/docker-for-mac/#memory Best, Chris On Sun, Feb 4, 2018 at 9:29 AM, Dianne Patterson <d...@email.arizona.edu> wrote: > Dear All, > Pardon my ignorance. I am trying freesurfer for t

Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

This is not expected. You would need to provide more details (recon-all.log) for anyone to be able to help you. It might be also worth googling the specific error message before hand - it could be that someone else run into this before. Best, Chris On Sat, Feb 3, 2018 at 7:55 PM, Dianne

Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

in/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer /bids_dataset /outputs participant --license_file /license.txt Best, Chris On Mon, Jan 22, 2018 at 7:13 PM, Dianne Patterson <d...@email.arizona.edu> wrote: > Dear All, > > After trying the example bids app (which worked fine), I am try

[Freesurfer] Postdoctoral position available in the Poldrack Lab

Apologies for cross-posting. The Poldracklab at Stanford is looking to hire a postdoc with expertise in fMRI data analysis, starting as soon as possible. Our lab is a dynamic and collaborative group that includes basic cognitive neuroscience researchers focused on the study of decision making

[Freesurfer] [job] Program Manager for the Brain Imaging Data Structure project

. The successful candidate will receive relocation support. More details at https://stanford.taleo.net/careersection/2/jobdetail.ftl?job=76713=en#.WeUP-AdO9j4.email. We will start reviewing applications on the 6th of November. Best regards, Chris Gorgolewski PS Apologies for cross posting - please forward

Re: [Freesurfer] Results display tool

: [Freesurfer] Results display tool Thanks Chris, this looks interesting and useful. I just tried |P = cell(1, 2); T = cell(1, 2); for z = 1:2 P{z} = rand(31, 1) * 0.075; T{z} = rand(31, 1) * 5 - 3; end freesurfer_statsurf_p(P, T, 'dkt'); and got the error: Undefined function 'freesurfer_read_annot

[Freesurfer] Results display tool

hope people find it useful. Chris. __ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com

Re: [Freesurfer] Matlab 2016b and localGI

or, in any case. I tried it on my system and it returned the correct location of matlab. I am running CentOS 7.3 and using Freesurfer v5.3 (x86_64-unknown-linux-gnu-stable5-20130513). The version of "getmatlab" is Revision 1.2 Chris On Fri, Aug 11, 2017 at 12:27 PM, Alan Franci

[Freesurfer] FreeSurfer is now available on OpenNeuro.org

Dear all, FreeSurfer BIDS App is now available on the OpenNeuro.org platform. This means that you can run recon-all on your datasets (with longitudinal pipeline and study specific template estimation) in the cloud for free (see example results here

Re: [Freesurfer] mri_normalize problem normalization2

fer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_normalize problem normalization2 sure, send me the input to mri_normalize and I'll fix it On Wed, 28 Jun 2017, Chris Adamson wrote: > > Hello, > >   > > For one subject I’m getting a weird error on mri_normalize in n

[Freesurfer] mri_normalize problem normalization2

_normalize/mri_normalize.c has a block of pixels with HUGE negative values. They are in the background and nowhere near the brain. The data comes from a public dataset so I can send it for debugging if required. Dr Chris Adamson Senior Research Officer Developmental Imaging, Clinical Sciences Murdoch

[Freesurfer] Longitudinal stats: target space

to double-check. In that case, would I then follow the steps on the wiki page for creating a template <https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates#CreatingaregistrationtemplateinitializedwithFreeSurfertemplate.28DG.29> ? Thanks, Chris

Re: [Freesurfer] Setting -openmp flag to more than 8

Thank you - this is very useful! On Tue, May 2, 2017 at 12:05 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Chris > > we have found an almost linear speed improvement up to 4, then it starts > to fall off, with not much at all after 8. > > cheers > Bruce &g

[Freesurfer] Setting -openmp flag to more than 8

parallelization is that there is little benefit of using more than 8-10 cores (even if more are available). Does this also apply to FreeSurfer? Does anyone have done some benchmarking of this? Thanks in advance for your help. Best, Chris ___ Freesurfer

Re: [Freesurfer] R package for graph theory analysis of MRI data {Disarmed}

I apologize but the link to the Github page is: https://github.com/cwatson/brainGraph Chris On Tue, Apr 11, 2017 at 7:37 PM, Chris Watson <cwa...@alum.mit.edu> wrote: > Dear Freesurfer users, (apologies for cross-post) > > I am pleased to announce the first major release

[Freesurfer] R package for graph theory analysis of MRI data {Disarmed}

gelog. This remains a work-in-progress, so I am very happy to receive bug reports, feature requests, general questions asking for help with code, (constructive) criticism, etc. Please join the Google Group that I set up for those purposes: https://groups.google.com/forum/?hl=en#!forum/brainGraph-hel

Re: [Freesurfer] long mri_ca_register error

] On Behalf Of Bruce Fischl Sent: Friday, 7 April 2017 3:37 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] long mri_ca_register error Hi Chris it's possible we never looked at -bigventricle in the long stage. What was your recon-all command line?

Re: [Freesurfer] long mri_ca_register error

It happens when I use -bigventricles. From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Chris Adamson Sent: Thursday, 6 April 2017 12:27 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] long mri_ca_register error Freesurfer devs

[Freesurfer] long mri_ca_register error

Freesurfer devs, In freesurfer 6 stable I'm having a problem at the careg stage of the long. The relevant recon-all log is pasted below. Could you point me to where to debug this problem? Cheers, Chris. mri_ca_register -rusage 136_S_0426_20070604.long.136_S_0426/touch

Re: [Freesurfer] Petsc Error in Freesurfer v6.0

I get these pincher errors as well in VirtualBox. One thing that may fix it is to disable 3D acceleration for the graphics in the VM settings. From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Michael ONeill Sent: Thursday, 23 March 2017

[Freesurfer] "Upgrade" outputs from 5.3 to 6.0

to aseg.presurf.mgz? Thanks in advance? Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch Childrens Research Institute Murdoch Childrens Research Institute Royal Children’s Hospital Flemington Road, Parkville, Victoria 3052, Australia www.mcri.edu.au<http://www.mcri.edu.au/> E chri

[Freesurfer] Freeview 3D brush

Freesurfer devs, I attempted a modification of freeview to insert a 3D brush. I have got it working. If you want to review it to put it in the main version it is there a way to submit the diff with the changes? Cheers, Chris. Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch

Re: [Freesurfer] CUDA in FS6?

I have tested a recon-all -all CPU and GPU with and without the -hires option and everything seems to run fine. So at the moment they seem to be compatible or at least the GPU version doesn't crash. So that is ok. Thanks for your time. Dr Chris Adamson Research Officer, Developmental Imaging

Re: [Freesurfer] CUDA in FS6?

Richard, I understand they are not a priority. But are they compatible with the CPU versions? Should we be using the CUDA versions if they aren't guaranteed to be up-to-date? Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch Childrens Research Institute Murdoch Childrens

[Freesurfer] CUDA in FS6?

Freesurfer devs, Are the CUDA binaries still being developed in FS6? Are they compatible with the CPU only versions? I remember asking questions about this a while ago and apparently the cuda binaries were no longer being developed in favour of openmp. Thanks in advance, Dr Chris Adamson

[Freesurfer] Centre on label double click in freeview

Thanks for putting in the "centre over label" feature in Freeview. Dr Chris Adamson Senior Research Officer Developmental Imaging, Clinical Sciences Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adam...@m

[Freesurfer] More freeview feature requests

points you have to manually change to the tmp directory and save as control.dat. It would be good to have an option that would automatically create this file. Thanks in advance, Chris Adamson. __ This email has been scanned

Re: [Freesurfer] FreeSurfer Version 6

Congratulations! I just updated the FreeSurfer BIDS App <http://bids-apps.neuroimaging.io/> to version 6.0.0: https://github.com/BIDS-Apps/freesurfer It's already on Docker Hub. All you need to do to grab it is to run: docker run -ti --rm bids/freesurfer:v6.0.0-1 Best, Chris On Mon,

[Freesurfer] Feature requests/bug reports in FS 6

It really needs a 3D brush. What would be nice for segmentation images is the ability to double click on a label on the list on the left and have the viewer automatically centre on voxels having that label in the image. Thanks in advance, Chris. Dr Chris Adamson Senior Research Officer

[Freesurfer] 3d brush in freeview

Is there a 3d option for the editing brush in freeview ala tkmedit? Dr Chris Adamson Senior Research Officer Developmental Imaging, Clinical Sciences Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adam...@mcri.edu.au

[Freesurfer] -cw256 and -hires

error about the FOV came up. Any thoughts? Chris. Dr Chris Adamson Senior Research Officer Developmental Imaging, Clinical Sciences Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adam...@mcri.edu.au<mailto:chris.a

Re: [Freesurfer] reusing mri_surf2surf transformation

the process? Best, Chris On Thu, Nov 10, 2016 at 12:37 PM, Chris Filo Gorgolewski < chris.gorgolew...@gmail.com> wrote: > There is only one frame in rh.sig.mgh file (see below). Most time seems to > be spent in calculating forward and reverse loops. Ideas? > > root@36ddc1c5be86:/code#

Re: [Freesurfer] reusing mri_surf2surf transformation

-0. -0. -0. 1. On Thu, Nov 10, 2016 at 12:34 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > 16min is a very long time. How many frames are in rh.sig.mgh? For a > single frame it should only take 10 or 20 sec > > > On 11/10/2016

Re: [Freesurfer] reusing mri_surf2surf transformation

t does not take that much time. > > > On 11/10/2016 02:13 PM, Chris Filo Gorgolewski wrote: > > Thanks for a quick reply. I'm actually in a situation where I do not > > have all of the overlays at the same time so I cannot concatenate them. > > > > To

Re: [Freesurfer] reusing mri_surf2surf transformation

run and most of it is spend on coregistration - which is always the same. If only I could calculate the coregistration once and apply it to every incoming map it would speed things up tremendously. Let me know if you have any ideas. Best, Chris On Thu, Nov 10, 2016 at 10:26 AM, Douglas N Greve

[Freesurfer] reusing mri_surf2surf transformation

of time I was wondering if I could calculate the transformation once and just apply it (which is a common thing in volumetric registration). I perused the website and the command line options, but I could not find anything. Is it possible to save and reuse surface transformations? Best, Chris

[Freesurfer] FTP server error

FYI - there is something wrong with the FTP server: $ wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-HCP/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-HCP.tar.gz --2016-09-15 20:04:51--

Re: [Freesurfer] Support for surface data on NeuroVault.org

hat do you think? > I would probably go the other direction, ie, sample the MNI152 maps into > surface space. > This is exactly what I want to do. The question is what is the most accurate way of sampling MNI152 maps to fs

Re: [Freesurfer] Support for surface data on NeuroVault.org

reeView? What about pysurfer? Generally inflated surfaces are easiest for viewing patterns, but it is > often helpful to include anatomical surfaces as well. > Thanks! Best, Chris > > Peace, > > Matt. > > From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf o

[Freesurfer] Support for surface data on NeuroVault.org

registration of it to fsaverage, and use that to sample statistical maps in MNI space. What do you think? Thank you for any help feedback you can provide! Best, Chris Gorgolewski ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] New way of installing and running Freesurfer - containers

Hi Dan, Users are asked to provide their license key they received from MGH after registration as a command line parameter. I also added links to the registration form. Best, Chris On Tue, Aug 9, 2016 at 12:24 PM, dgw <dgwake...@gmail.com> wrote: > Hi Chris, > > This sounds

[Freesurfer] New way of installing and running Freesurfer - containers

information here: https://github.com/BIDS-Apps/freesurfer Please let me know what do you think! Best, Chris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this

Re: [Freesurfer] Using external software to perform brain extraction, multiple T1s

of the images into the template space created by motioncor? Apologies if this has already been asked. [cid:image001.jpg@01D17AC3.302C3530] Chris Adamson Senior Research Officer Developmental Imaging Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Rd Parkville

Re: [Freesurfer] T2pial shrinks pial surface

1. You should change that line to have -odt short or -odt float so that it doesn't saturate at 255, which is what caused the original problem. On Tue, 8 Mar 2016, Chris Adamson wrote: > I see it now. I will try to perform a bias correction on the image prior to > importing and see if that h

Re: [Freesurfer] T2pial shrinks pial surface

2016 4:23 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] T2pial shrinks pial surface Hi Chris I took a look, and the problem is that there are big changes in contrast between occipital and frontal lobes. If we normalize both posterior and front

Re: [Freesurfer] T2pial shrinks pial surface

Thanks Bruce. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Chris Adamson Sent: Monday, 7 March 2016 1:54 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer]

Re: [Freesurfer] T2pial shrinks pial surface

T2pial shrinks pial surface https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Mon, 7 Mar 2016, Chris Adamson wrote: > How can I upload it to you? > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.ed

Re: [Freesurfer] T2pial shrinks pial surface

surfer] T2pial shrinks pial surface Hi Chris if you upload that dataset I'll try to take a look soon cheers Bruce On Mon, 7 Mar 2016, Chris Adamson wrote: > > The T2pial option mostly works beautifully. I have a few cases where > the pial surface just shrinks globally and wraps

Re: [Freesurfer] T2pial shrinks pial surface

esurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Chris Adamson <chris.adam...@mcri.edu.au<mailto:chris.adam...@mcri.edu.au>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Sunday, March 6, 2016 at 6

Re: [Freesurfer] Shifted surface after gyrification index is calculated

. Perhaps Marie can comment? Or you can try mris_copy_header to see if > that does the trick > > > cheers > Bruce > > > On Thu, 10 Dec 2015, Chris Holdgraf wrote: > > Hey Bruce - thus far I have used pretty default parameters. I first ran >> recon-all on each subjec

Re: [Freesurfer] Shifted surface after gyrification index is calculated

It's a cluster running Linux CentOS 64-bit. If it's as simple as getting the file and adding it to my path I'm happy to give it a try... Chris On Thu, Dec 10, 2015 at 1:47 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > what hardware are you running on? We can send you

[Freesurfer] Shifted surface after gyrification index is calculated

/aestrivex/gselu/issues/7 Anyone have an idea why this is happening? I'm not sure why the pial surface would be correct, while the smoothed surface would be shifted. Chris -- _ PhD Candidate in Neuroscience | UC Berkeley <http://hwni.org/> Editor and Web Di

Re: [Freesurfer] Shifted surface after gyrification index is calculated

or not valid.* --- I highlight that last bit because maybe it's important? Looks like some information goes missing in there... Chris On Thu, Dec 10, 2015 at 10:27 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Chris > > how do you smooth the surface? Are you sure

[Freesurfer] Brainstem Substructures in Freesurfer 6.0 - how to calculate left/right volumes

Hello, I've installed Freesurfer 6.0 beta, and run the -brainstem-structures option to recon-all. The results look ok, but I'd like the left/right volumes for the superior cerebellar peduncle (SCP), rather than the total volume. Is there any easy way to do this? Thanks, Chris

Re: [Freesurfer] FreeSurfer and OpenMP

It is -openmp 8 Delete the less than and greater than characters around the 8 > On 16 Oct 2015, at 3:25 PM, Linda BOUMGHAR wrote: > > I would like to use freesurfer with OpenMP, with 4 processors. I wrote this : > recon-all -all -i >

  1   2   3   >