Re: [Freesurfer] freesurfer 6.0 hires fix

You have to rerun from the beginning. (sorry) On 9/9/19 3:12 PM, Aaron Tanenbaum wrote: > > External Email - Use Caution > > I noticed that you guys released a fix to improve the -hires option.  > I have been processing some of our data using the hires flag. if i use > this fix do i

[Freesurfer] freesurfer 6.0 hires fix

External Email - Use Caution I noticed that you guys released a fix to improve the -hires option. I have been processing some of our data using the hires flag. if i use this fix do i need to run recon-all from the beginning or can I run over the old folders?

Re: [Freesurfer] FreeSurfer 6.0 disk image for VirtualBox?

External Email - Use Caution ​Hello Gonzola, I use a CentOS7 VM image (on virtualbox) originally downloaded from osboxes.org. After downloading and bringing up the image, I installed various packages for freesurfer. But apart from my image being CentOS7 (and not CentOS6), I

[Freesurfer] FreeSurfer 6.0 disk image for VirtualBox?

External Email - Use Caution Hi: Where can I find the FreeSurfer 6.0 disk image for VirtualBox? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

recsek mailto:m...@grecsek.com>> Reply-To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Tuesday, September 25, 2018 at 9:57 AM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Freesurfer 6.0 - Trac

Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

--- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Matthew Grecsek < > m...@grecsek.com> > *Sent:* Friday, September 21, 2018 10:27:37 AM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer]

Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault External Email - Use Caution Hi Anastasia, Please see attached screenshots from dwi.nii.gz. The first 4 are rotated 90 degrees around y axis and the last 2 are top and bottom. Thanks, -Matt On Thu, Sep 20, 2018 at 7:19 PM Yendiki

Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

like that? Best, a.y From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Matthew Grecsek Sent: Thursday, September 20, 2018 2:00:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault External

Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

some appear more noisy and pixelated than others. This is a mTBI subject with no other anatomical brain anomalies scanned with a Siemens 3T. Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault Yendiki, Anastasia Wed, 19 Sep 2018 13:20:02

Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault External Email - Use Caution Yes, a part of the brain appears missing. See attached screenshot. I did not use a configuration file, I simply accepted

Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

] Freesurfer 6.0 - Tracula - Segmentation fault Yendiki, Anastasia Wed, 19 Sep 2018 09:02:47 -0700 Hi Matt – It looks like some sort of registration issue. When you display the FA map (dmri/dtifit_FA) and structural segmentation in diffusion space (label/diff/aparc+aseg), do they look fine

Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

urfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault External Email - Use Caution I ran standard recon-all on a single subject and then trac-all -prep. The process ran for approximately 1 hour and exited with errors: Segmenta

Re: [Freesurfer] Freesurfer 6.0 - Hippocampal subfields segmentation (Mode B) - Registration error

ober 2017 at 22:54 To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Freesurfer 6.0 - Hippocampal subfields segmentation (Mode B) - Registration error Hi all, I am using Freesurfer 6.0 for hippocampal subfield segmentation (Mode B: -hip

[Freesurfer] Freesurfer 6.0 - Hippocampal subfields segmentation (Mode B) - Registration error

Hi all, I am using Freesurfer 6.0 for hippocampal subfield segmentation (Mode B: -hippocampal-subfields-T1T2). For each subject, I have a 3T-T1 MRI (whole brain) and a 7T-T2 MRI (partial brain). Segmentation works in most subjects, but in some subjects the co-registration of the 7T-T2 MRI

[Freesurfer] Freesurfer 6.0 and 5.3 differences in eTIV but not in supratentorial volume

Hello all FYI I have found non-negligeable differences in eTIV for 5.3 versus 6.0 in my healthy young sample It is probably due to the cerebellum computation changes (presented in released notes for 6.0) Unsurprisingly the supratentorial volumes 5.3 versus 6.0 are very similar (all was

Re: [Freesurfer] freesurfer 6.0 with some of the analyses

:* freesurfer-boun...@nmr.mgh.harvard.edu [ > freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, > Eugenio [e.igles...@ucl.ac.uk] > > > *Sent:* Thursday, January 26, 2017 11:01 AM > > > *To:* Freesurfer support list > > > *Subject:* Re: [Freesurfer]

Re: [Freesurfer] freesurfer 6.0 with some of the analyses

:* freesurfer-boun...@nmr.mgh.harvard.edu [ > freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, > Eugenio [e.igles...@ucl.ac.uk] > > > *Sent:* Thursday, January 26, 2017 11:01 AM > > > *To:* Freesurfer support list > > > *Subject:* Re: [Freesurfer]

Re: [Freesurfer] freesurfer 6.0 with some of the analyses

: Thursday, January 26, 2017 11:01 AM To: Freesurfer support list Subject: Re: [Freesurfer] freesurfer 6.0 with some of the analyses Dear Batool, Sorry for missing your message. And dear Adam: Thanks for covering me! That’s exactly my standard answer to that question ;-) Juan Eugenio Iglesias ERC

Re: [Freesurfer] freesurfer 6.0 with some of the analyses

Dear Batool, Sorry for missing your message. And dear Adam: Thanks for covering me! That’s exactly my standard answer to that question ;-) Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

Re: [Freesurfer] freesurfer 6.0 with some of the analyses

I believe Dr. Iglesias previous responses on this exact question have been, "yes it's possible, but your results may be harder to reproduce" e.g. If someone wanted to replicate your study they may have a harder time having to download 2 different versions of freesurfer to achieve comparable

Re: [Freesurfer] freesurfer 6.0 with some of the analyses

Hi, Can anyone comment on my question below? I think the FAQ page mentions that the same version should be used to process all cases within a dataset, but my question is whether I can have the same dataset used for two different versions for separate analyses? This is considering that I've

Re: [Freesurfer] Freesurfer 6.0 and MNI template

thanks Doug! -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Wed, Jan 25, 2017 at 6:27 PM, Douglas N Greve wrote: > Still in 305 > > > On 01/25/2017 06:21 PM, Trisanna Sprung-Much wrote: > > Me again, > > > > Are the fsaverage

Re: [Freesurfer] Freesurfer 6.0 and MNI template

Still in 305 On 01/25/2017 06:21 PM, Trisanna Sprung-Much wrote: > Me again, > > Are the fsaverage volumetric coordinates in Freesurfer 6.0 still in > MNI305 space or have they been updated to the MNI152 space? > > many thanks! > > Trisanna > > -- > Ph.D. Candidate > McGill University >

[Freesurfer] Freesurfer 6.0 and MNI template

Me again, Are the fsaverage volumetric coordinates in Freesurfer 6.0 still in MNI305 space or have they been updated to the MNI152 space? many thanks! Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology ___

[Freesurfer] freesurfer 6.0 with some of the analyses

Hi, I'm wondering if it's okay to run some of the analyses within one study on v.5.3 and the other hippocampal analyses on 6.0? Or do you recommend us starting over for the analyses we've already done in 5.3 for that study? Thank you! Batool ___

Re: [Freesurfer] Freesurfer 6.0 link

Thank a lot. Aziz. On Wed, Jan 25, 2017 at 9:38 PM, Z K wrote: > https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall > > On 01/25/2017 05:44 AM, Aziz Nanthaamornphong wrote: > > Hi experts, > > > > How can I download Freesurfer version 6.0? Is there an

Re: [Freesurfer] Freesurfer 6.0 link

https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall On 01/25/2017 05:44 AM, Aziz Nanthaamornphong wrote: > Hi experts, > > How can I download Freesurfer version 6.0? Is there an available URL link? > > Thank you, > Aziz > -- > > Aziz Nanthaamornphong, Ph.D., > Chair of Master of Science

Re: [Freesurfer] Freesurfer 6.0

Please do not forget windows people John On Jan 25, 2017 12:45 PM, "Aziz Nanthaamornphong" wrote: > Hi experts, > > How can I download Freesurfer version 6.0? Is there an available URL link? > > Thank you, > Aziz > -- > > Aziz Nanthaamornphong, Ph.D., > Chair of

[Freesurfer] Freesurfer 6.0 link

Hi experts, How can I download Freesurfer version 6.0? Is there an available URL link? Thank you, Aziz -- Aziz Nanthaamornphong, Ph.D., Chair of Master of Science Program in Information Technology Department of ICT Faculty of Technology and Environment Prince of Songkla University, Phuket

Re: [Freesurfer] Freesurfer 6.0 and ex-vivo T1

thanks for the quick response Bruce! -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Tue, Jan 24, 2017 at 1:18 PM, Bruce Fischl wrote: > Hi Trisanna > > it is better about handling highres data, but the ex vivo recon stream is

Re: [Freesurfer] Freesurfer 6.0 and ex-vivo T1

Hi Trisanna it is better about handling highres data, but the ex vivo recon stream is still a work in progress cheers Bruce On Tue, 24 Jan 2017, Trisanna Sprung-Much wrote: Hi there I am wondering if the Freesurfer 6.0 version is more flexible with the parameters used for ex-vivo scans

[Freesurfer] Freesurfer 6.0 and ex-vivo T1

Hi there I am wondering if the Freesurfer 6.0 version is more flexible with the parameters used for ex-vivo scans other than what 5.3 required, as listed here https://surfer.nmr.mgh.harvard.edu/fswiki/ExVivo. We acquired some ex-vivo scans at 0.4mm iso but not with those above parameters. many

Re: [Freesurfer] FreeSurfer 6.0 (beta) Error in segmentSubjectT1_autoEstimateAlveusML (line 588)

Ciao Daniele, This is weird. Would you mind verifying that file T1resampled.mgz actually exists in the temporary directory of the subject? You can do that by CDing to $SUBJECT_DIR/[SUBJECT_NAME]/tmp and running the command: find . -name “T1resampled.mgz” Cheers, /Eugenio Juan Eugenio Iglesias

[Freesurfer] FreeSurfer 6.0 (beta) Error in segmentSubjectT1_autoEstimateAlveusML (line 588)

Dear experts, I've finished FSv5.3 longitudinal analysis and I'm now running FSv6.0(beta) for hippocampal subfield features extraction (always on Ubuntu 14.01 environment). After several trial I realized that before pipeline ends I've got the following error:

Re: [Freesurfer] Freesurfer 6.0?

Did you receive a reply/ Any news update for 6.0 release? On Mon, Jul 25, 2016 at 1:01 PM, Trisanna Sprung-Much < trisanna.sprung-m...@mail.mcgill.ca> wrote: > > Hi there > > Do we have a potential date for the Freesurfer 6.0 release? I was told I > would want to re-run all my subjects to

Re: [Freesurfer] freesurfer 6.0 release date

Hi Fengji we have frozen the code and are going through various tests now so are hoping sometime in the next few weeks, but of course it's impossible to say as it depends on how well the tests turn out. cheers Bruce On Mon, 1 Aug 2016, Fengji Geng wrote: Hi fs developers,  I am

[Freesurfer] freesurfer 6.0 release date

Hi fs developers, I am wondering if you have any estimation when fs 6.0 will come out. The reason that I ask this is because we are running some analysis using fs 5.1 and planning to switch to a more recent version of fs. If fs 6.0 will come out soon, we will probably hold and wait for it. If

Re: [Freesurfer] FreeSurfer 6.0

<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fis...@nmr.mgh.harvard.edu> Sent: Thursday, July 28, 2016 4:31 PM To: Freesurfer support list Cc: Anastasia Haidar Subject: Re: [Freesurfer] FreeSurfer 6.0 Hi Elisabetta FS 6 is not available yet. We are hoping to have a beta

Re: [Freesurfer] FreeSurfer 6.0

Hi Elisabetta​ FS 6 is not available yet. We are hoping to have a beta in a couple of weeks and are actively working on getting it out cheers Bruce On Thu, 28 Jul 2016, elisabetta_de...@hms.harvard.edu wrote: ​Dear FreeSurfer team, we are trying to find a downloadable version of FS6.0

Re: [Freesurfer] FreeSurfer 6.0

> > ​Dear FreeSurfer team, > we are trying to find a downloadable version of FS6.0 to use on our data. > We can not find it on the web. > Could you help us with that? > Thank you, > best regards, > Elisabetta​ > > -- > *Elisabetta C. del Re, Ph.D.* > > *Instructor,* > *Department of Psychiatry* >

Re: [Freesurfer] Freesurfer 6.0?

thanks, Doug! -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Mon, Jul 25, 2016 at 11:57 PM, Douglas Greve wrote: > We are working pretty hard to get it out but we are still reluctant to set > a hard date. I think we'll have a

Re: [Freesurfer] Freesurfer 6.0?

We are working pretty hard to get it out but we are still reluctant to set a hard date. I think we'll have a beta version in two weeks, but that's just a guess. doug On 7/25/16 4:01 PM, Trisanna Sprung-Much wrote: Hi there Do we have a potential date for the Freesurfer 6.0 release? I was

[Freesurfer] Freesurfer 6.0?

Hi there Do we have a potential date for the Freesurfer 6.0 release? I was told I would want to re-run all my subjects to create better surfaces using Freesurfer 6.0 and I am wondering if it really will improve surface extraction that much. Many thanks! Trisanna -- Ph.D. Candidate McGill

Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

The color still indicates the direction. If you have a signed hypothesis, then you can run it with pos or neg instead of abs, however, in this case it will change the voxel-wise cluster-forming threshold (make it more liberal) because the voxel-wise p-value is computed assuming an unsigned

Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

Hi Doug, Ok this makes more sense now. In my case if I choose abs I would look at the max cdf < 0.05 for the corresponding cluster extent in the TH13 folder. In terms of the |a-b|<0,05 does this mean that if I got results in blue it just means significant but with no directionality as to if

Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

On 05/09/2016 04:11 PM, Ajay Kurani wrote: > Hi Doug, >Thanks for the explanation. In using p=0.05 with my thickness files > (smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ > cdf file. > > In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean > the

Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

Hi Doug, Thanks for the explanation. In using p=0.05 with my thickness files (smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf file. In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean the overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the

Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

Hi Doug, Thanks for the explanation. In using p=0.05 with my thickness files (smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf file. In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean the overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the

Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

It estimates the FWHM from the data (glmdir/fwhm.dat). It does this by computing the pearson correation coefficient of the residual error between adjacent vertices. This is then averaged over all vertices to compute a mean cor coef. A transform is then applied to compute the FWHM. This is

Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

Hi Doug, I wanted to figure out what is the minimum cluster extent for a given monte carlo simulation (ie when you choose p=0.5/T=1.3). I saw the following tutorial : https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo and so I wanted to know if freesurfer estimates the smoothness

Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

Hi Doug, Thanks for the clarification. So in the case of cortical thickness, qcache, mris_fwhm or mri_surf2surf would all do the same thing and so I should be getting similar results if everything is entered in the same fashion. This would be the approriate choice compared to mri_smooth. For

Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

There is not a difference between mris_fwhm and mri_surf2surf. mris_smooth smoothes the xyz coordinates of the vertices of a surface (the others smooth an overlay). On 05/05/2016 03:53 PM, Ajay Kurani wrote: > Hi Doug, >Thanks for the quick reply. > > Is there a difference from

Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

Hi Doug, Thanks for the quick reply. Is there a difference from qcache/mris_fwhm with mris_smooth and mri_surf2surf -fwhm ? If so, which is recommended for cortical thickness analysis? Thanks, Ajay On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani wrote: > Hi

Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

Underneath, they both use the same code, so they should give the same results. Are you saying they are different? I don't know what SurfFWHM is doing so I can't comment on what those results mean. Measuring the FWHM on the surface is quite tricky. doug On 5/4/16 6:41 PM, Ajay Kurani wrote:

Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

Hi Freesurfer Experts, Just as a followup through my reading i've come across posts which use qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing. For my cortical thickness analysis I would like to smooth all of my rh/lh.thickness.fsaverage.mgh files for each subject in order to run

[Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

Hi Freesurfer Experts, I am trying to understand the difference between qcache option and mris_fwhm and which is appropriate for a cortical thickness analysis. I processed my files with qcache and have lh.thickness.fsaverage.fwhm15.gii (converted) files. I used an afni tool SurfFWHM to

Re: [Freesurfer] FreeSurfer 6.0

yes, although the hippocampal stuff hasn't changed I don't think (Eugenio: is that correct)? On Wed, 16 Mar 2016, Alan Francis wrote: Bruce, with Eugenio's guidance, I downloaded 6.0 beta a few months ago and ran the HSF method successfully. Have they retracted that version? best, Alan On

Re: [Freesurfer] FreeSurfer 6.0

Hi Elisabeth we don't have an exact date yet, but have finished our code modifications (hopefully!) and are in the process of freezing a version after which we will run a set of tests and hopefully release it cheers Bruce On Wed, 16 Mar 2016, Elisabeth Paul wrote: > Dear ladies and

Re: [Freesurfer] FreeSurfer 6.0

ge - > From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> > To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > Sent: Wednesday, March 16, 2016 3:49:31 PM > Subject: Re: [Freesurfer] FreeSurfer 6.0 > > yes, although the hippocampal stuff ha

Re: [Freesurfer] FreeSurfer 6.0

ischl" <fis...@nmr.mgh.harvard.edu> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Wednesday, March 16, 2016 3:49:31 PM Subject: Re: [Freesurfer] FreeSurfer 6.0 yes, although the hippocampal stuff hasn't changed I don't think (Eugenio: is that corr

Re: [Freesurfer] FreeSurfer 6.0

Bruce, with Eugenio's guidance, I downloaded 6.0 beta a few months ago and ran the HSF method successfully. Have they retracted that version? best, Alan On Wed, Mar 16, 2016 at 9:57 AM, Bruce Fischl wrote: > actually there is no beta yet, but hopefully within a

Re: [Freesurfer] FreeSurfer 6.0

Hi Elizabeth: I ran the Hippocampal subfields on 6.0 beta. The parcellation looks great. Beta is available for download. Here is the URL: https://surfer.nmr.mgh.harvard.edu/fswiki/Download best, Alan On Wed, Mar 16, 2016 at 6:23 AM, Elisabeth Paul < elisabeth.p...@student.uva.nl> wrote: >

Re: [Freesurfer] FreeSurfer 6.0

gt; www.bcbl.eu >> >> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer >> >> - Original Message - >> From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> >> To: "Freesurfer support list" <freesurfer@nmr.mg

Re: [Freesurfer] FreeSurfer 6.0

actually there is no beta yet, but hopefully within a week or so On Wed, 16 Mar 2016, Alan Francis wrote: Hi Elizabeth: I ran the Hippocampal subfields on 6.0 beta. The parcellation looks great. Beta is available for download. Here is the URL:

Re: [Freesurfer] FreeSurfer 6.0

l-disclaimer > >> > >> - Original Message - > >> From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> > >> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > >> Sent: Wednesday, March 16, 2016 3:

[Freesurfer] FreeSurfer 6.0

Dear ladies and gentlemen, for a research project I need to measure the volume of the different hippocampus subregions. I want to use FreeSurfer 6.0 for that but I can only find FreeSurfer 5.3 online. Is FreeSurfer 6.0 not yet released and if so, when will it be released? If it is already

[Freesurfer] FreeSurfer 6.0 hippocampal subfields error

Dear Eugenio, I am writing because I am getting a mkdir error when I try to run the FreeSurfer 6.0 hippocampal subfields segmentation. I tried moving my installation of freesurfer to a local directory where I have write permission and I also made sure I had write permission in my subject's

Re: [Freesurfer] Freesurfer 6.0 -hires mri_segment potential issue

Hi Ajay it's kind of dicey to use an arbitrary nightly build as we have no idea what was in that that might have been fixed the next day. I would wait for a beta, or at the very least try a new version as I don't think our current version exhibits the behavior you are experiencing. cheers

[Freesurfer] Freesurfer 6.0 -hires mri_segment potential issue

Hello Freesurfer experts, I am using the nightly build of Freesurfer 6.0 (Dec 18, 2015) on Ubuntu 14.04 with a high resolution image (0.5mm isotropic). I set OMP_NUM_THREADS=16 and then passed the -openmp 16 and -itkthreads 16 flags in my autorecon 2 line command. Autorecon1 and the

Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

          An: Falk Lüsebrink             Cc: Freesurfer support list; Bruce Fischl             Betreff: Re: [Freesurfer] Freesurfer 6.0 -             Autorecon2 failure             (mris_euler_number) using high res (0.5mm             i

[Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

? being l or r depending your hemisphere. >> After the fixing stage the >> surfaces got damaged somehow, therefore you have >> to >> recreate it them. I’m >> not entirely sur

Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

      An: Falk Lüsebrink                         Cc: Freesurfer support list; Bruce Fischl                         Betreff: Re: [Freesurfer] Freesurfer 6.0 -                         Autorecon2 failure                         (mris_euler_numbe

Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

ot damaged somehow, therefore you have to >> recreate it them. I’m >> not entirely sure about the qsphere. Probably you >> have to run the -qsphere >> stage again also. >> >> >> >> Best, >&

Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

the -qsphere stage again also. Best, Falk Von: Ajay Kurani [mailto:dr.ajay.kur...@gmail.com] Gesendet: Montag, 30. November 2015 21:50 An: Falk Lüsebrink Cc: Freesurfer support list; Bruce Fischl Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm

Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

Kurani [mailto:dr.ajay.kur...@gmail.com] Gesendet: Montag, 30. November 2015 21:50 An: Falk Lüsebrink Cc: Freesurfer support list; Bruce Fischl Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image   Hi Falk,    I used

Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

it them. I’m >> not entirely sure about the qsphere. Probably you have to run the -qsphere >> stage again also. >> >> >> >> Best, >> >> Falk >> >> >> >> >> >> Von: Ajay Kurani [mailto:dr.ajay.kur...@gmail.com] >> Gesende

Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

reesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image   Hi Falk,    I used the command and got the following error: Command: ris_topo_fixer -mgz -warning -

Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Sonntag, 29. November 2015 22:48 An: Freesurfer support list Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm

Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

29. November 2015 22:48 > An: Freesurfer support list > Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure > (mris_euler_number) using high res (0.5mm isotropic) T1 image > > Hi Ajay > > are you sure you didn't run out of disk space? That error is a sanity > check on

Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

surfer support list Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image Hi Ajay are you sure you didn't run out of disk space? That error is a sanity check on the surfaces that should never

Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

surfer-boun...@nmr.mgh.harvard.edu [mailto: > freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl > Gesendet: Sonntag, 29. November 2015 22:48 > An: Freesurfer support list > Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure > (mris_euler_number) using high res (0

Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

: Sonntag, 29. November 2015 22:48 An: Freesurfer support list Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image Hi Ajay are you sure you didn't run out of disk space? That error is a sanity check on the surfaces that should

[Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

Hello Freesurfer experts, I am trying to run Freesurfer 6.0 beta (downloaded 10/15/15 version) with the -hires flag to process an MNI template image which is 0.5mm isotropic. Stage 1 ran well and on stage 2 there is an error during pocessing: Command run: recon-all -s ICBM -autorecon2 -openmp

Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image

Hi Ajay are you sure you didn't run out of disk space? That error is a sanity check on the surfaces that should never occur cheers Bruce On Sun, 29 Nov 2015, Ajay Kurani wrote: Hello Freesurfer experts,    I am trying to run Freesurfer 6.0 beta (downloaded 10/15/15 version) with the

Re: [Freesurfer] Freesurfer 6.0

Hi Matt this would be a beta - the new version isn't ready to be distributed yet (although we are getting closer) Bruce On Tue, 3 Nov 2015, Hoptman, Matthew wrote: Hi all, I can see a link for Freesurfer 6.0 on the website, but when I click on it to download, it just blinks at me.  I also

Re: [Freesurfer] Freesurfer 6.0

It must be an issue with your browser. Try using either of the following commands (depending on your platform) in a terminal window. Linux: wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-beta/freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015.tar.gz Mac OSX: curl -O

[Freesurfer] Freesurfer 6.0

Hi all, I can see a link for Freesurfer 6.0 on the website, but when I click on it to download, it just blinks at me. I also tried to ftp to your ftp site, and unfortunately, I got the message 421 Proxy is closed (unknown user location). Could you please tell me how I could get the new version

Re: [Freesurfer] FreeSurfer 6.0 dev version Output

13, 2015 10:14:34 PM Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output Hi again I want to use my hippocampal segmentation for masking 2380 brain volumes. Is there a way to find out using Freesurfer if the hippocampal subfields and the 2380 volumes are in the same space? The mean of the 2

Re: [Freesurfer] FreeSurfer 6.0 dev version Output

the segmentation. > >>> >> 2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than > >>> lh.hippoSfLabels-T1.v10.mgz) when you call > >>> >> mri_extract_label. That volume lives in the same voxel > >>> space as T1

Re: [Freesurfer] FreeSurfer 6.0 dev version Output

      - Original Message -       From: Priyanka Mehta priyankamehta0...@gmail.com       To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu       Sent: Wednesday, August 19, 2015 7:50:12 PM       Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output

Re: [Freesurfer] FreeSurfer 6.0 dev version Output

...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, August 19, 2015 7:50:12 PM Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output Hi This is a follow-up question to my

Re: [Freesurfer] FreeSurfer 6.0 dev version Output

- From: Priyanka Mehta priyankamehta0...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, August 19, 2015 7:50:12 PM Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output Hi This is a follow-up question to my

Re: [Freesurfer] FreeSurfer 6.0 dev version Output

...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, August 19, 2015 7:50:12 PM Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output Hi This is a follow-up question to my previous

Re: [Freesurfer] FreeSurfer 6.0 dev version Output

...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, August 19, 2015 7:50:12 PM Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output Hi This is a follow-up question to my previous problem. After I run recon-all -all

Re: [Freesurfer] FreeSurfer 6.0 dev version Output

priyankamehta0...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, August 19, 2015 7:50:12 PM Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output Hi This is a follow-up question to my previous problem. After I run

Re: [Freesurfer] FreeSurfer 6.0 dev version Output

disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Priyanka Mehta priyankamehta0...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, August 19, 2015 7:50:12 PM Subject: Re: [Freesurfer] FreeSurfer 6.0 dev

Re: [Freesurfer] FreeSurfer 6.0 dev version Output

list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, August 19, 2015 7:50:12 PM Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output Hi This is a follow-up question to my previous problem. After I run recon-all -all -i ${subject}.nii -subject ${subject} -hippocampal-subfields-T1, I

Re: [Freesurfer] FreeSurfer 6.0 dev version Output

support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 29, 2015 11:26:04 AM Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output Thanks Eugenio! Thats worked! One more question- how would I convert the lh.CA1.mgz that I get from the previous step to .nii format? Best

Re: [Freesurfer] FreeSurfer 6.0 dev version Output

: www.bcbl.eu/legal-disclaimer - Original Message - From: Priyanka Mehta priyankamehta0...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 29, 2015 11:26:04 AM Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output Thanks Eugenio! Thats

Re: [Freesurfer] FreeSurfer 6.0 dev version Output

- Original Message - From: Priyanka priyankamehta0...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 29, 2015 7:59:37 AM Subject: [Freesurfer] FreeSurfer 6.0 dev version Output Hi, I am new to FreeSurfer and need help with hippocampal segmentation in the 6.0 dev

  1   2   >