[Freesurfer] samseg ground truth's space

External Email - Use Caution Hello dear all, I want to use Freesurfer-Samseg for MS lesion segmentation(cross-sectional). I got the T1 and Flair for this. I registered *flair to t1 *for every patient. My manual lesion masks are on DIR imaging. I am using FSL for registration.

Re: [Freesurfer] Segmentation protocol used by Freesurfer

Yes, that can definitely be the case. Some boundaries are not visible (in e.g. the accumbens) and so the border is defined by geometric means. Other times the definition of what is in or not in a structure can change (e.g. is the fimbria part of the hippocampal label?) From:

Re: [Freesurfer] Thalamic nuclei exited with ERRORS

External Email - Use Caution One error in the logs is from missing symbols in the Matlab java library, and another says to contact the Mathworks for technical support. But Mathworks is not going to support you because MacOS 10.13 does not meet the system requirements for

Re: [Freesurfer] Segmentation protocol used by Freesurfer

External Email - Use Caution Thanks. I am asking Neuromorphometrics to see if they are willing to give the detailed information. In fact, I am comparing Freesurfer with vol2Brain. However, they are using the Neuromorphometrics protocol and thus didn't run this comparison in their

[Freesurfer] Stepwise recon-all to get volumes

External Email - Use Caution Hi all, I am computing volumetry using freesurfer using two different runs. 1. I just use recon-all -all, and then look at the aseg.stats file. 2. I ran recon-all only to the 12th step where gca labeling is done. It doesn't generate the aseg.mgz

Re: [Freesurfer] Segmentation protocol used by Freesurfer

External Email - Use Caution Thanks, Bruce. Actually, I am comparing the volume computations between different segmentation tools. In some software's paper, they mentioned there is a slight difference in protocol from Freesurfer and thus not easy to compare. I am wondering what

Re: [Freesurfer] Stepwise recon-all to get volumes

There is not enough information to understand what you did in #2 On 8/30/2022 3:56 PM, Ruifeng Dong wrote: External Email - Use Caution Hi all, I am computing volumetry using freesurfer using two different runs. 1. I just use recon-all -all, and then look at the aseg.stats file. 2.

Re: [Freesurfer] mri_fwhm and diffusion data

I think it should work for b0 images, but I would avoid using any frames that have a gradient. Note that you will need about 10 images to compute the fwhm using mri_fwhm (also make sure you use a mask) On 8/30/2022 1:33 PM, Igor Nestrašil wrote: External Email - Use Caution Dear

Re: [Freesurfer] Stepwise recon-all to get volumes

External Email - Use Caution Thanks for pointing that out. The step numbers are those from section 5 in

Re: [Freesurfer] Segmentation protocol used by Freesurfer

It really can be anything. Hard to say From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Ruifeng Dong Sent: Tuesday, August 30, 2022 3:01 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation protocol used by Freesurfer External Email - Use Caution Thanks. I

Re: [Freesurfer] samseg dice score is low

Hi Dilek, your bug report is incomplete. Please see https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for how to file an informative bug report. On 8/30/2022 12:51 PM, Dilek Özkan wrote: External Email - Use Caution Hello dear all, I use Freesurfer-Samseg for MS lesion

Re: [Freesurfer] Segmentation protocol used by Freesurfer

Hi Ruifeng I think they are similar, but you would have to ask Neuromorphometrics about the differences. Our protocol was published in the Neuron 2002 paper and the papers it cites, which I think is also where the Neuromorphometrics’ protocol came from Cheers Bruce From:

[Freesurfer] mri_fwhm and diffusion data

External Email - Use Caution Dear FreeSurfer developers, Can "mri_fwhm" be used to estimate FWHM of b0 images (obtained from diffusion-weighted echo-planar sequences) and is it possible to employ for FWHM estimation from aligned diffusion-weighted images of the same b-value

Re: [Freesurfer] Thalamic nuclei exited with ERRORS

External Email - Use Caution Thanks again for your help. I tried with both R2017b and R2019b but no luck. When I soft link either of these versions to MCRv84, I receive the following error: sub-BA_IGP001 Setting ITK threads to 1 # #@#

Re: [Freesurfer] Thalamic nuclei exited with ERRORS

External Email - Use Caution After you install either R2017b or R2019b using the fs_install_mcr script you should end up with either ./freesurfer/MCRv9.3 or ./freesurfer/MCRv9.7 There are no soft links to create manually and there should be no references to MCRv8.4 in

Re: [Freesurfer] Thalamic nuclei exited with ERRORS

External Email - Use Caution This is the error I get when for example, I use MCRv93 sub-BA_IGP001 ERROR: cannot find Matlab 2014b runtime in location: /Applications/freesurfer/7.2.0/MCRv84 It is looking for either: bin/glnxa64/libmwlaunchermain.so(Linux

Re: [Freesurfer] Thalamic nuclei exited with ERRORS

External Email - Use Caution It’s possible something in 7.2.0 still requires MCRv84. If so, it is probably not going to work to use a soft link to fake out the name, and using a different version of Matlab run time could explain the crashes.. Please send along the output

Re: [Freesurfer] Thalamic nuclei exited with ERRORS

External Email - Use CautionThanks for your help!I followed your instructions, but still have these issues.Actually, it seems to happen quite randomly, as I could process some subjects but not other, and also on subjects that I could previously process (I am using a loop for

Re: [Freesurfer] samseg ground truth's space

External Email - Use Caution I decided to register T1 and Flair to DIR at the beginning. with this way, I will get the new mask in already DIR's space which means manually segmented masks' space. In my case, I will give two inputs to the software. The rule that applies to every

Re: [Freesurfer] Vertex-wise analysis using ComBat

I don't think you can. I have not looked at combat in a long time, but I thought they did their own GLM. combat might take a design matrix, in which case you could use mri_glmfit and your FSGD to create the design matrix. On 8/30/2022 9:37 AM, Rene Seiger wrote: External Email - Use

Re: [Freesurfer] samseg ground truth's space

External Email - Use Caution Even if I register 2d T1 to 3D Flair? (form low res to higher res; such as 2D T1: 1*1*5, 3D Flair: 1*1*1) Douglas N. Greve , 30 Ağu 2022 Sal, 17:30 tarihinde şunu yazdı: > If you resample the t1 to another space, it might get blurrier. > > On

Re: [Freesurfer] samseg ground truth's space

If you want to  use FSL, you will have to convert to nifit, eg, mri_convert file.mgz file.nii.gz On 8/30/2022 7:01 AM, Dilek Özkan wrote: External Email - Use Caution Hello dear all, I want to use Freesurfer-Samseg for MS lesion segmentation(cross-sectional). I got the T1 and

[Freesurfer] Vertex-wise analysis using ComBat

External Email - Use Caution Dear FreeSurfer community! We collected structural data from different scanners and we want to conduct a surface-based (vertex-wise) analysis in FreeSurfer using predefined regions of interest. The model is quite simple, as we just want to

Re: [Freesurfer] samseg ground truth's space

If you resample the t1 to another space, it might get blurrier. On 8/30/2022 9:46 AM, Dilek Özkan wrote: External Email - Use Caution I decided to register T1 and Flair to DIR at the beginning. with this way, I will get the new mask in already DIR's space which means manually

Re: [Freesurfer] FSFAST first level covariates

Oh, I think I see now. In realty, each trial is either self or not self and then you have a separate valence measure, so your coding should be 1. Self-offset 2. SelfValence 3. NoSelf-offset 4. NoSelfValence Where 1+2 are used for a self event and 3+4 are used for a noself event. If you want to

[Freesurfer] Segmentation protocol used by Freesurfer

External Email - Use Caution Is Freesurfer using Neuromorphometrics’ General Segmentation Protocol, or something different? What are the differences between different protocols? Thanks! Ruifeng ___ Freesurfer mailing list

Re: [Freesurfer] Thalamic nuclei exited with ERRORS

External Email - Use Caution Interesting… when I leave the folders named MCRv93 or MCRv97 (one at a time, not present together at the same time), then FS tells me I need to install MCRv84! FS7.2.0 seems to only recognise MCRv84, hence why I used for example, sudo ln -s v93

[Freesurfer] samseg dice score is low

External Email - Use Caution Hello dear all, I use Freesurfer-Samseg for MS lesion segmentation(cross-sectional). I use the T1 and Flair for this. (just these are inputs) I registered *flair and t1 to DIR *for every patient. (My manual lesion masks are on DIR imaging.) I

Re: [Freesurfer] segment_subregions failed

If you did not build FreeSurfer from the git repo, could you send the build stamp? It is located in a file called 'build-stamp.txt' in the FREESURFER_HOME directory. Best, Jackson From: Nolan, Jackson Sent: Monday, August 29, 2022 4:25 PM To: Freesurfer support