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

fects and see if there is one in the sulcus you mention below? Cheers Bruce 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 htt

[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.c

[Freesurfer] Use annotation for edgecolor in freeview

w. 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 Communication in error, plea

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

e template 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 Children

[Freesurfer] mris_transform with flirt transformation wrong result

ii.gz 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.

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

s, Jocelyn From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Chris Adamson mailto:chris.adam...@mcri.edu.au>> Sent: Friday, November 13, 2020 6:45 AM To: fr

[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

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

ECTS_DIR/$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 $LO

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

Chris. Dr Chris Adamson Senior Research Officer, Developmental Imaging, Clinical Sciences (0.3 EFT) Software Engineer, Cardiovascular Research (0.7 EFT) Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adam

Re: [Freesurfer] binary version of brainmask?

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

[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] smoothwm.H vs curv

think mris_make_surfaces writes the curvature of the .white surface, not the .smoothwm. And make sure you match the number of smoothing iterations cheers Bruce On Thu, 25 Oct 2018, Chris Adamson wrote: > > External Email - Use Caution > > Freesurfer devs, > >   >

[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

list Subject: Re: [Freesurfer] mris_register problem Hi Chris you need to give us more information. What commands did you run? What was their output? Also, if you can send images of what you think is incorrect that might also be helpful cheers Bruce On Mon, 17 Sep 2018, Chris Adamson wrote

[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

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

on is almost entirely an automated control point finding tool. cheers Bruce On Fri, 29 Jun 2018, Chris Adamson wrote: > > External Email - Use Caution > > Freesurfer devs, > > > > I presented an automated control point adding tool at HBM and a few > freesurfer

[Freesurfer] Proposed addition for Freesurfer - automated control points

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.e

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

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.harvard.edu > On Behalf Of Bruce Fischl > Sent: Tuesday, 13 March 2018 12

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

v0 = face->v[0]; face->v[0] = face->v[1]; face->v[1] = v0; } return (NO_ERROR); } should be easy enough to do in matlab cheers Bruce On Sat, 10 Mar 2018, Chris Adamson wrote: > Hi Bruce, > > Thanks for your reply. I had already tried swapping the 2

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

he surface normal vector field. Sounds like whatever software you used uses the oppposite convention. You could try swapping the order of vertices in the face list cheers Bruce On Fri, 9 Mar 2018, Chris Adamson wrote: > > Freesurfer devs, > >   > > I have a baf

[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 Res

Re: [Freesurfer] Results display tool

supporting software you provide for free! doug | On 09/12/2017 05:31 AM, Chris Adamson wrote: > > Freesurfer users, > > I just wanted to advertise a set of display tools that I wrote for > easy display, in MATLAB, of regional stats like p-values/effect &g

[Freesurfer] Results display tool

Freesurfer users, I just wanted to advertise a set of display tools that I wrote for easy display, in MATLAB, of regional stats like p-values/effect sizes/arbitrary scalars with customisable masks for aparc, dkt, aparc.a2009s. https://chrisadamsonmcri.github.io/freesurfer_statsurf_display I ho

Re: [Freesurfer] mri_normalize problem normalization2

: [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 normalization2. > > When it go

[Freesurfer] mri_normalize problem normalization2

mri_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 Mu

Re: [Freesurfer] long mri_ca_register error

Chris Adamson wrote: > > 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.harva

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

No such file or directory TransformSample: gcam has not been inverted! No such file or directory Dr Chris Adamson Senior Research Officer Developmental Imaging, Clinical Sciences Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Austral

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 11

[Freesurfer] "Upgrade" outputs from 5.3 to 6.0

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 Im

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 Chil

[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

[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 by

[Freesurfer] Feature requests/bug reports in FS 6

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.e

[Freesurfer] -cw256 and -hires

same 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<mail

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 Park

Re: [Freesurfer] T2pial shrinks pial surface

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 helps. Thanks Bruce. > >

Re: [Freesurfer] T2pial shrinks pial surface

mapped to 180 but frontal gray gets >255. This kind of thing can be caused by a transmit "bias" field, or by dielectric effects. I'm not sure why this is a problem with this dataset and not others cheers Bruce On Mon, 7 Mar 2016, Chris Adamson wrote: > Thanks Bruce. >

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 Subject: Re: [Freesurfer] T2pial shrinks pial surface It is

Re: [Freesurfer] T2pial shrinks pial surface

://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.edu] On Behalf Of Bruce > Fischl

Re: [Freesurfer] T2pial shrinks pial surface

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 over the white > surface (see

Re: [Freesurfer] T2pial shrinks pial surface

small changes to the input images (e.g. a different random see for FreeSurfer) may be able to kick mris_make_surfaces out of that bug, though perhaps Bruce has fixed it. Peace, Matt. From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Chris Adamson mailto:chri

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 > /mnt/linuxwin/lboumgha/data/CENTER_TBI/tro/suj1/T1.nii.gz -s

[Freesurfer] Compiling dev version in ubuntu 15.10

+0x28): undefined reference to `vnl_nonlinear_minimizer::is_a[abi:cxx11]() const' ../utils/libutils.a(numerics.o):(.rodata._ZTV9fs_powell[_ZTV9fs_powell]+0x30): undefined reference to `vnl_nonlinear_minimizer::is_class(std::__cxx11::basic_string, std::allocator > const&) const'

Re: [Freesurfer] dev version of mri_ca_label memory leak?

: Freesurfer support list Subject: Re: [Freesurfer] dev version of mri_ca_label memory leak? you can probably just email them to me as they aren't terribly big. Make sure you get every file that is on the mri_ca_label command line cheers Bruce On Thu, 30 Jul 2015, Chris Adamson wrote: > Ok

Re: [Freesurfer] dev version of mri_ca_label memory leak?

“saving > sequentially combined intensity scales to > aseg.auto_noCCseg.label_intensities.txt” the memory consumption continues to > increase. Currently it is at 8.9GB. > >   > > Can I send output to help debug this? > >   > > Chris. > >   > >

[Freesurfer] dev version of mri_ca_label memory leak?

scales to aseg.auto_noCCseg.label_intensities.txt" the memory consumption continues to increase. Currently it is at 8.9GB. Can I send output to help debug this? Chris. Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch Childrens Research Institute Murdoch Childrens Research Institute Royal Chil

Re: [Freesurfer] Segmentation fault in mris_fix_topology when compiling with gcc 4.8 + AVX2

: Freesurfer support list Subject: Re: [Freesurfer] Segmentation fault in mris_fix_topology when compiling with gcc 4.8 + AVX2 Thank you for this information. -Zeke On 06/22/2015 02:22 AM, Chris Adamson wrote: > Everyone, > > I know this is a fairly specific issue but nonetheless. &

[Freesurfer] Segmentation fault in mris_fix_topology when compiling with gcc 4.8 + AVX2

disable AVX2, i.e. use -march=core-avx-i then it does not segfault. Just something to keep in mind. Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch Childrens Research Institute Murdoch Childrens Research Institute Royal Children's Hospital Flemington Road, Parkville, Vic

Re: [Freesurfer] tkmedit SetBrushShape does not enable 3d

enable 3d Hi Chris we stopped developing tkmedit some years ago. Can you use freeview for this instead? cheers Bruce On Wed, 15 Apr 2015, Chris Adamson wrote: > > In tkmedit, if I use a tcl script with > >   > > SetBrushShape 3 0 1 > >   > > The radius and s

[Freesurfer] tkmedit SetBrushShape does not enable 3d

In tkmedit, if I use a tcl script with SetBrushShape 3 0 1 The radius and shape are set to 3 and circular, respectively. However, the brush is not 3d, it only edits in the current slice. This bug is in 5.3.0 and the cvs version. Chris. Dr Chris Adamson Research Officer, Developmental Imaging

[Freesurfer] Readonly CVS access not working

s checkout: failed to obtain dir lock in repository `/usr/fscvsroot/dev' cvs [checkout aborted]: read lock failed - giving up Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch Childrens Research Institute Murdoch Childrens Research Institute Royal Children's Hospital

[Freesurfer] QAtools data-wise html page

option for this? 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 www.mcri.edu.au<http://www.mcri.edu.au/> E

Re: [Freesurfer] Build with CUDA 5.5?

zkauf...@nmr.mgh.harvard.edu] Sent: Wednesday, 2 July 2014 1:41 AM To: Freesurfer support list; Chris Adamson Subject: Re: [Freesurfer] Build with CUDA 5.5? Chris, This is why we no longer actively support CUDA development in freesurfer and instead have focused on openmp to reduce overall runtime. The complexity o

[Freesurfer] Build with CUDA 5.5?

Guys, Would it be possible to get Freesurfer 5.3.0 built with CUDA 5.5? The newest Ubuntu does not have support for 5.0. Thanks in advance, Chris Adamson. Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch Childrens Research Institute Murdoch Childrens Research Institute Royal

Re: [Freesurfer] OpenMP and non-OpenMP output is different at mri_ca_register

ebuilt vtk which you can use to compile against. > > -Zeke > > > > On 03/07/2014 01:13 AM, Chris Adamson wrote: >> I was trying to compile Freesurfer (in a Centos 6.5 VM) with a later gcc >> to see if the performance improved and noticed that the output gcc 4.4 >>

[Freesurfer] tkmedit - display reconstruction toolbar by default

All, Is there any configuration file/source code file that can be edited to display the reconstruction toolbar by default in tkmedit? Thank you. Chris. Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch Childrens Research Institute Murdoch Childrens Research Institute Royal

Re: [Freesurfer] defect_labels to volume

Defect-seg is what I was looking for. Thanks Bruce. -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Saturday, 25 January 2014 12:36 AM To: Chris Adamson Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] defect_labels to volume have you tried

[Freesurfer] defect_labels to volume

Is there a way of making a volume like aparc+aseg with the defect labels so that cortical region where the defects are show up red? Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch Childrens Research Institute Murdoch Childrens Research Institute Royal Children's Hos

Re: [Freesurfer] CUDA problem with FreeSurfer 5.3.0 on CentOS6

Bump, I'm having this problem as well and would really like to use the cuda version of mri_ca_register. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Tran, Kevin (NIH/NIMH) [C] Sent: Saturday, 7 December 2013

[Freesurfer] Bug report: fslregister within reg-feat2anat

During the reg-feat2anat script fslregister produces errors. I tracked it to the argument parsing code 419 case "--fsvol": 420 if ( $#argv < 1) goto arg1err; 421 set fsvol = $argv[1]; shift; 422 set tmp = `fname2stem $fsvol`; 423 if(! $status) set fsvol = $tmp; 424 breaksw The reg-feat2anat scri

Re: [Freesurfer] mri_ca_register_cuda error

d) > > Bruce > On Mon, 22 Oct 2012, Chris Adamson wrote: > >> I downloaded the mri_ca_register_cuda binary from the ftp site >> >> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/mri_ca_register_cuda >> >> I'm not sure w

[Freesurfer] mri_ca_register_cuda error

I downloaded the mri_ca_register_cuda binary from the ftp site ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/mri_ca_register_cuda I'm not sure whether this is an unstable version or not but when I use it the subsequent inversion step does not work: I'm happy to s

[Freesurfer] Can I get verification of some scripts I wrote to parallelize recon-all?

Hey all, Can I send through some shell scripts that I wrote to run all the hemisphere-specific steps so that the lh and rh steps are run together. If I could send them through to make sure I'm doing autorecon2-wm and autorecon3-pial correctly? Thank you. Chris. -- Dr Christopher Adamson, PhD (M

[Freesurfer] CUDA error on mac os x, freesurfer 5.1.0

I get a CUDA error: MRISCcomputeVertexDistances: invalid device function . during mris_sphere_cuda with a Quadro FX 5600, see the log below, any advice?: \n mris_sphere_cuda -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix \n nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 20

[Freesurfer] Unstripped vtk libraries

symbols in the vtk libraries then stripping them should lead to a much smaller download size of the freesurfer distro. Chris Adamson. -- Dr Christopher Adamson, PhD (Melb.), B Software Engineering (Hons., Monash) Research Officer Developmental and Functional Brain Imaging, Critical Care and

[Freesurfer] mri_convert: dicom to mgh

Hello all, I'm wondering how mri_convert computes the centre of the image (shown as ImgPos in the output of mri_convert). I have two questions: 1. I had a non-mosaic SIEMENS format DICOM volume and ImgPos was copied from (0x0020,0x0032) DS Image Position (Patient), but the X and Y values are n