Re: [Freesurfer] recon_all error on MacOS 10.12.13 Sierra: during mris_smooth. dyld: lazy symbol binding

Hello Jared, Would it be possible to tar up the subject directory and upload it to our server so I can take a look? https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange -Zeke > On Feb 20, 2017, at 2:47 PM, Jared Saletin wrote: > > Dear Zeke, > > Thanks for

Re: [Freesurfer] mri_cvs_register error : PETSC Error

Hi Lilla, Is there a work around for this because I would at max be able to allocate 8GB for the tool but I dont have the resource for 35GB. *Regards,* *Bhavana*

Re: [Freesurfer] Output from mri_cvs_register

That is the same. You shoudl be fine. Lilla On Mon, 20 Feb 2017, Magnús Ingvi wrote: Hi!I am running mri_cvs_regsiter, on the cvs_avg35 space. In the dt_recon tutorial ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion ), the expected .m3z output file is called

Re: [Freesurfer] apply CVS morph to a list of coordinates

Hi Cristian, The below error message indicates that your morph cannot be read. How much memeory do you have on the machine where you are running this operation? Lilla On Fri, 10 Feb 2017, Donos, Cristian wrote: Hi, I have registered a patient’s MRI over the ColinN27 with mri_cvs_register

Re: [Freesurfer] 答复: Longitudinal proceesing for Pediatric data

Hi Dong, What is the age range that you are working with? Lilla On Mon, 20 Feb 2017, Martin Reuter wrote: No, not that I know of. Also I expect that it also depends on other factors (like image resolution, quality, subject anatomy etc) . Best, Martin Am 15.02.2017 um 08:21 schrieb

Re: [Freesurfer] mri_cvs_register error : PETSC Error

Hi Bhavana, We recommend to assign about 35GB of RAM on our cluster nodes for this operation. I am not sure how that compares to your VB. Lilla On Mon, 20 Feb 2017, Bhavana Ganesh wrote: Hi Lilla, I have allocated 40GB for my VB and 3GB of RAM space. I am not allocating anything specific

Re: [Freesurfer] mri_cvs_register error : PETSC Error

Hi Lilla, I have allocated 40GB for my VB and 3GB of RAM space. I am not allocating anything specific to the function. *Regards,* *Bhavana*

Re: [Freesurfer] issues with -T2pial option in v.5.3

Dear Petr, according to the screenshot, the problem is that there is quite low signal intensity in the cut-out parts of gray matter on T2 images. Apart from HCP pipelines, you can try to increase -nsigma_below parameter of mris_make_surfaces to prevent this cut-out. The default value is 3, try

Re: [Freesurfer] mri_cvs_register error : PETSC Error

Hi Bhavana, How much memory are you allocating to this process? Lilla On Mon, 20 Feb 2017, Bhavana Ganesh wrote: > Hi Developers, > > I'm receiving this error while I try to run mri_cvs_register. The same error > was received when I reran the same even after increasing the memory allocated

Re: [Freesurfer] recon_all error on MacOS 10.12.13 Sierra: during mris_smooth. dyld: lazy symbol binding

Dear Zeke, Thanks for your reply. I can verify that recon-all completes without error on a single thread, but crashes on parallel. I thought it may be hippocampus-subfield specific, but the same pattern remerges regardless of the subfield reconstruction. Is there something in newer OS X that

Re: [Freesurfer] issues with -T2pial option in v.5.3

You could try with the HCP Pipelines and see if that helps: https://github.com/Washington-University/Pipelines Peace, Matt. From: on behalf of Petr Bednarik Reply-To: Freesurfer support list Date:

[Freesurfer] issues with -T2pial option in v.5.3

Hi everyone, I am using Freesurfer version 5.3. I tried to refine the pial surfaces by using -T2pial option: recon-all -subjid $SUBJ -T2/SUBJECT_DIR/$SUBJ/mri/orig/T2raw.mgz -T2pial -autorecon3 This step was helpful - e.g. it removed nicely residuals of venous sinuses, but in some

Re: [Freesurfer] hippocampal subfields in average space

Hi Lauri, it depends on what you mean by template. If you mean an intensity averaged image, then no. But if you mean probabilities in a reference space, then yes. You can visualize the atlas with (warning: the viewer is a big buggy): cd $FREESURFER_HOME/average/HippoSF/atlas

Re: [Freesurfer] Hippocampus eTIV correction (LONGITUDINAL)

Hi Sebastian, the etiv is estimated in the base/subject-template, so it is constant for all time points. And if you want to include it into a longitudinal design depends on what you want. If you look at percent changes , you don't have to, but if you look at yearly rates, it is probably a

Re: [Freesurfer] 答复: Longitudinal proceesing for Pediatric data

No, not that I know of. Also I expect that it also depends on other factors (like image resolution, quality, subject anatomy etc) . Best, Martin Am 15.02.2017 um 08:21 schrieb Dongnandi: Hi Martin Thanks a lot for your reply! Is there any reference that the longitudinal processing

[Freesurfer] hippocampal subfields in average space

Hi everyone, Is there a template of the hippocampal subfields in some average space? Best Lauri Tuominen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in

Re: [Freesurfer] Hipposubfield outputs 6.0

The volumes are already in cubic mm. Cheers, /E Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 20 Feb 2017, at 12:50, std...@virgilio.it wrote: Hi list,

[Freesurfer] Hipposubfield outputs 6.0

Hi list,I wonder whether in the 6.0 the hipposubfield outputs needs for nomalization (by diving for 3 the volumes as well as the 5.3) or they are already corrected?Thanks Stefano___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Trying to download FreeSurfer 6

I was using Chrome, I tried using Firefox and it works. Thanks a lot! Jose 2017-02-17 16:10 GMT+01:00 Z K : > What browser are you using? My first recommendation would be to try > downloading using another browser. If the problem persists than its > probably due

[Freesurfer] Output from mri_cvs_register

Hi! I am running mri_cvs_regsiter, on the cvs_avg35 space. In the dt_recon tutorial ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion ), the expected .m3z output file is called combined_tocvs_avg35_elreg_afteraseg-norm.m3z, but the output I get in the cvs folder is called