Re: [Freesurfer] tkmedit problem with XQuartz-2.3.0

te? tkmedit is known to work on mac > > os 10.5 using the default X setup. > > Nick > > On Wed, 2008-07-23 at 22:43 +0200, Martin Kavec wrote: > > Hi, > > > > On my macbook pro (MAC OS X 10.5) I have recently updated my X to 2.3.0 > > and now I can not

[Freesurfer] Recommended workflow

Greetings to all, I have several pathological subjects, which need substantial editing involving removing of dura reminders, filling WM due to the lesions, and adding control points due to the WM atrophy. I ran "recon-all -all" first to have initial reconstruction, which helps me to focus on co

Re: [Freesurfer] Recommended workflow

Thanks a lot for clarification, Bruce. Best, Martin On Thursday 28 August 2008 22:00:29 Bruce Fischl wrote: > Hi Martin, > > I think "recon-all -autorecon2-cp -autorecon3" should be fine (it's a > superset of the -wm stuff). > > Bruce > > On Thu, 28 Aug 200

Re: [Freesurfer] RE: Freesurfer Digest, Vol 54, Issue 34

Hi Prapti, yesterday I had a similar question and went to search the wiki page to educate myself more, after Bruce responce. The following webpage defines the steps taken during the options you asks: http://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags There you can see that your -autorec

Re: [Freesurfer] (no subject)

Christian, I suspect that in example3-frontal and example2-frontal you have motion artifacts causing increased intensity in the cortex. On the other, example1-horizontal and example1-sagittal seem to have pretty low SNR, specially in GM, but very good GM-WM contrast. I wonder, if they were not

[Freesurfer] SAMSEG mesh format and content

External Email - Use Caution Hi all, previous question from Florent triggered my interest in SAMSEG and I am running now couple of cases to see what it gives. I would like to ask - SAMSEG can also output a mesh. How is the mesh stored in file? - how can it be visualized (Pa

Re: [Freesurfer] Methods for white matter hypointensities measure

Hi guys, I am exactly in the same shoes (T1s and T2 FLAIRs), so could you please also keep me in the club? Many thanks, Martin On Thursday 13 May 2010 02:22:06 Laluz, Victor wrote: > Thank you for the prompt answer, as always Bruce!! > > I would be very interested in the techniques for multis

[Freesurfer] Label two volume conversion

Hi, using tksurfer, I have created labels corresponding to significantly thinner cortex between two groups of my subjects. After that I converted the labels to volumes (mri_label2vol), which I would like to use for further analysis. However, the volumes cover only the interface between gray an

[Freesurfer] mri_aparc2aseg on a custom annotation

Hi, I have a problem using mri_aparc2aseg with a custom annotations containing labels created manually in tksurfer and exported. Basically, I would like to end up with a volume file similar as aparc+aseg.mgz but containing only a strip of a cortex corresponding to a label defined using tksurfe

Re: [Freesurfer] mri_aparc2aseg on a custom annotation

Hi Dough, On Monday 17 May 2010 22:29:28 Douglas N Greve wrote: > So is the problem that cortex is 2000 every where including your label Yes this is the case, but I have already found a way around to get to where I wanted. mri_label2voi --help has the example which helped me. Thanks anyway, Ma

Re: [Freesurfer] cortical parcellations & ProbtrackX

Hi Patrica, recently I asked the question about surface tracking on the FSL mailing list and got an answer that you can track FROM the surface, but not TO surface, in other words you can not use FS label as a waypoint. The way to go is as Dough suggest in his followup. Best, Martin On Thursd

Re: [Freesurfer] cortical parcellations & ProbtrackX

Hi Patricia, when you convert your labels to volume, they will not be actually the cortical masks, but rather a line of voxels on the junction of GM and WM, which should be fine for seeding and targeting the tractography. Best, Martin On Friday 18 June 2010 02:24:52 ox...@yahoo.com wrote: > t

[Freesurfer] Failing mri_cvs_register

Hi, I am trying to run mri_cvs_register between a subject and another set of 10 healthy subjects (all analyzed with FS-5.0.0), but in all cases it fails on: trying to execute elastic registration -> cmd line = surf2vol -fixed_mri . error executing surf2vol at /opt/freesurfer/bin/elastic

[Freesurfer] Potential memory leak in mri_cvs_register

Hi, I am trying to do a mri_cvs_register two subjects analyzed with FS-5.0.0 on a 64-bit Gentoo linux with 4GB memory and another 4GB of swap space. I am running a signle mri_cvs_register and after certain time the PC starts using swap intensively and finally the process terminates. My commandlin

[Freesurfer] CUDA on Mac

Hi all, I wonder if there are any plans to support CUDA on Mac platform. I see there are libraries available for the platform. Thanks a lot for feedback, Martin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu

[Freesurfer] cvs_register: missing surf2vol on MAC

Hi all, I am trying to run mri_cvs_register on MAC distribution o Freesurfer 5.0, but it is failing on surf2vol. Looking into the $FREESURFER_HOME/bin, surf2vol is completely missing. Could you please provide this file? Thanks, Martin ___ Freesurfer ma

[Freesurfer] cvs template missing in 5.1

Hi, I did a fresh download and install of the FS-5.1.0 for CentOS_x86_64 and I am not finding the cvs_avg35 template in $FREESURFER_HOME/subjects. Plus the cvs settings text file is not there either. In contrast Mac distribution has it. Is there any problem with cvs on CentOS_x86_64 platform? Tha

Re: [Freesurfer] error during mri_cvs_register

Hi David, FreeSurfer's binaries for MAC are still 32-bit and apparently cvs tries to allocate more that is possible. The lines of the error code below suggest that. I had the same problem and had to opt for x86_64 linux binaries, where the cvs runs fine. It needs ~ 6 GB of memory and takes ~ 2 day

[Freesurfer] Large number of false negative MS lesions in SAMSEG

External Email - Use Caution Hello, I am testing SAMSEG on my group of MS patients. Unfortunately, even when dropping threshold to 0.005 I have large number of false negative lesions left behind by SAMSEG (80% in about 75 cases I tried), which are clearly visible lesions. I ran/ch

Re: [Freesurfer] Large number of false negative MS lesions in SAMSEG

ve a lesion probability map directly by using the flag > "--save-posteriors Lesions" so you don't need to try different thresholds. > > Thanks, > Stefano > > > Subject: [Freesurfer] Large number of false negative MS lesions in SAMSEG > Date: Sun, 14 Aug 2022 20:54:5

Re: [Freesurfer] FS version 8-beta

External Email - Use Caution Hi, Thanks a lot. I am particularly excited to the Synth* tools. I am trying SynthMorph from docker. I see that it does not use GPU (nvtop). I tried adding —gpus=0 but still see that inference runs on CPU (htop). Are there any experiences in register

Re: [Freesurfer] FS version 8-beta

External Email - Use Caution Hi, I am giving a try to FS 8-beta, but I am not seeing such a speed up as in the release notes: 2 hours and 24 GB of memory. In my case a case runs on average in 4.5 - 5 hours. Also I do not see such a high demands for memory, which could be related t

Re: [Freesurfer] FS version 8-beta

istortion correction. > > Best wishes, > Malte > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Martin Kavec > > Sent: Friday, November 8, 2024 06:12 > To: Freesurfer support list > Subject: Re: [Freesurfer] FS version 8-beta > > Extern

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