[Freesurfer] recon-all -hippocampal-subfields-T1 & matlab version

Hi, I'm working with the new version freesurfer 6.0. I found that recon-all with -hippocampal-subfields-T1 could not work well on my system. It reported that matlab 2012b cannot be found (Please see the attached for the error reported. ). I have matlab 2013a and 2016a installed. But it seems that

Re: [Freesurfer] Fw: Analysis of rates or percent changes

Hi Freesurfer team, I am sorry for writing again. Would you please be able to answer my last question? Best Regards, Katarina Trojacanec, M.Sc. Teaching and research assistant Faculty of Computer Science and Engineering Ss. Cyril and Methodius University - Skopje, Republic of Macedonia __

Re: [Freesurfer] recon-all -hippocampal-subfields-T1 & matlab version

Dear Xiangzhen, Have you tried following the instructions in the screen you sent us, to download the 2012b runtime? Did those commands lead to any errors? Cheers, /Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeigle

Re: [Freesurfer] Hippocampal subfield segmentation "error" with T1 image

Hi Gustav, No problem at all (ingen fara!). The idea is that, when our new joint atlas of the hippocampal subfields and amygdala nuclei is ready to be released, we’ll just need to replace the atlas files, without having to touch the code. It was my fault not to wrap that move command inside an I

Re: [Freesurfer] Hippocampal subfield segmentation "error" with T1 image

Hi, Perfect, thank you for the quick response! Best, Gustav On 2017-02-10 14:37, Iglesias Gonzalez, Eugenio wrote: Hi Gustav, No problem at all (ingen fara!). The idea is that, when our new joint atlas of the hippocampal subfields and amygdala nuclei is ready to be released, we’ll just need t

Re: [Freesurfer] recon-all -hippocampal-subfields-T1 & matlab version

Hi Eugenio, Thanks very much for your quick reply. I will try this method and come back soon. As it needs the root permissions, I was just wondering whether there would be other solutions. Thanks. Best, Xiangzhen On Fri, Feb 10, 2017 at 2:28 PM, Iglesias Gonzalez, Eugenio < e.igles...@ucl.ac.uk>

Re: [Freesurfer] chosen between with and without T2

Hi the T2-deformation stuff is still a work in progress, and we have already considerably improved it since 6.0 was released. If you are interested, you might download a dev version and try it out. I also think a FLAIR is better than a straight T2. cheers Bruce On Thu, 9 Feb 2017, 巍 魏 wrot

Re: [Freesurfer] recon-all -hippocampal-subfields-T1 & matlab version

If this is your own machine, you can prepend “sudo” to the curl and tar commands, i.e.: cd /usr/local/apps/freesurfer sudo curl “http://www….. sudo tar xvf runtime2012b.tar.gz (it will require typing your password) Cheers, Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational Im

Re: [Freesurfer] chosen between with and without T2

Hi, Very interesting question. But what you found seems to be opposite to previous findings. For example, the figure from a previous paper (Fig. 14 of this paper ) shows that including T2 data would get thinner (and better) measure

[Freesurfer] Fwd: LGI using Yeo Atlas

Hi everyone, I was wondering if someone could please address the following question regarding FreeSurfer usage. I would really appreciate any help. Thanks. Hi, I used following command to extract LGI values from a set of subjects: recon-all -s -localGI Output stats is saved in lh.aparc_lgi.

Re: [Freesurfer] chosen between with and without T2

yes, the code has some issues that caused the surfaces to expand in places where it wasn't appropriate. That is fixed in dev On Fri, 10 Feb 2017, X K wrote: Hi, Very interesting question. But what you found seems to be opposite to previous findings. For example, the figure from a previous pape

Re: [Freesurfer] orientation in freeview

Can you send your freeview command line and pictures of the mismatch? On 2/9/17 5:58 PM, Zhewei Wang wrote: Hi all, I have a problem maybe relevant to the orientation of images in freeview. I have two images, one is fMRI and one is MRI. They are produced from the same machine at the same ti

[Freesurfer] apply CVS morph to a list of coordinates

Hi, I have registered a patient’s MRI over the ColinN27 with mri_cvs_register and now i need convert an electrode (or voxel) coordinate from the subject’s space to the N27 space. I found an old post in the mailing list, but it did not work for me. The coords.txt file is just one line containing

[Freesurfer] Fwd: FreeSurfer group analysis visualize data

Hi, I am learning GroupAnalysis using FreeSurfer 5.3 on Linux system. I followed the detailed instruction on the tutorial website. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis But I got an error message when running this command to visualize uncorrected significance map

Re: [Freesurfer] orientation in freeview

Dear Zhewei, I think that the problem you report is caused by the fact, that .mat file from FLIRT codes vox2vox transformation, so that cannot be applied to another dataset (in your case fMRI) unless it has the same geometry as the original image the .mat file was generated on. Antonin Can

Re: [Freesurfer] Fwd: FreeSurfer group analysis visualize data

The outline only works on 6.0 On 2/10/17 11:57 AM, Xiuyi Wang wrote: Hi, I am learning GroupAnalysis using FreeSurfer 5.3 on Linux system. I followed the detailed instruction on the tutorial website. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis

[Freesurfer] Intensity Re-scaling Relative to Full Brain Atlas

Hi Experts! Per step 3 of the following tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer I wanted to re-scale the the intensities relative to the full brain atlas. The command: --no-rescale removes scaling relative to the Pons and the command: --rescale rescales the intensit

[Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue

Hello - I'm attempting to run the -trac-all -prep command with FS 5.3. I am running into the same memory allocation issues on my Mac that were present in earlier versions of Freesurfer/Tracula. See below: MRIallocSequence (218, 182, 1):could not allocate 158784 bytes for the 44th slice Cannot a

[Freesurfer] tractstats2table error

Hi there, I generated tractographies using the TRACULA pipeline and I'm not trying to generate the necessary statistics for them using tractstats2table. This is the command I'm using: tractstats2table -- input /usr/local/freesurfer/subjects/control_data/diffusion_tracs/Control200/dpath/lh.slft_PP

[Freesurfer] bbregister

Hi FS experts, I want to register T1 image to its freesurfer space (i.e. wmparc.mgz) using the command  bbregister  --t1 --mov T1.nii --init-fsl --reg t1.reg.dat --s subj   do I need to apply brain extraction tools before this step or bb register can accept non-brain extracted images?   Best,

[Freesurfer] Fwd: LGI using Yeo Atlas

Dear Martin, I think that this thread is relevant for you: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg34508.html You would have to map Yeo atlas to individual brain and then extract the LGI values using command: mri_segstats --annot my_subject_id lh aparc --i $SUBJECTS_DIR/

Re: [Freesurfer] bbregister

Hi John one of the many nice things about bbregister is that it is quite resistant to non-brain tissue, since it's just trying to place the gray/white (and optionally the pial surface) at a reasonable spot in the volume. I guess it might make the initialization less robust, not sure, but I ex

Re: [Freesurfer] tractstats2table error

Hi Adarsh – Is that a space there in between “--“ and “input”? a.y From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Adarsh Nellore mailto:adarsh.nellore...@gmail.com>> Reply-To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Friday, February 10, 2017 a

Re: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue

Hi Abby – When you say you have successfully processed a subject on that machine before, what FS version was that with? What has changed since then? The last I remember memory allocation issues, they were years ago in a very old version of OSX that we don’t even distribute binaries for any more,

Re: [Freesurfer] tractstats2table error

Hi Anastasia, Thanks a lot for your response. I tried tractstats2table with and without the space between "--" and "input" and it still didn't work. Regards, Adarsh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.

Re: [Freesurfer] bbregister

For version 6, it should not matter. On 2/10/17 3:59 PM, John Anderson wrote: Hi FS experts, I want to register T1 image to its freesurfer space (i.e. wmparc.mgz) using the command bbregister --t1 --mov T1.nii --init-fsl --reg t1.reg.dat --s subj do I need to apply brain extraction tools bef

Re: [Freesurfer] tractstats2table error

Hi Adarsh - It should be --inputs. Best, a.y From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Adarsh Nellore mailto:adarsh.nellore...@gmail.com>> Reply-To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Friday, February 10, 2017 at 5:02 PM To: "freesur

Re: [Freesurfer] tractstats2table error

Hi Anastasia, I had tried "inputs" when running the command but had a typo when pasting it in this forum. I tried again just to make sure and it didn't work. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mail

Re: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue

The successfully processed subject was completed using the same FS version (5.3) in December. We have not updated to FS 6. The only thing that was altered was the directory structure in the dmrirc text file, and the subjects. Thanks! Best Abby From: freesurfer-bou

[Freesurfer] Postdoctoral Fellow in Multivariate Analysis and Machine Learning

Job description: Computation functional anatomy laboratory at National University of Singapore focuses on the development of medical image analysis methods, including image segmentation, registration approaches, multivariate statistical analysis, machine learning, and classification algorithms. O

[Freesurfer] Postdoctoral Fellow in Multivariate Analysis and Machine Learning

Job description: Computation functional anatomy laboratory at National University of Singapore focuses on the development of medical image analysis methods, including image segmentation, registration approaches, multivariate statistical analysis, machine learning, and classification algorithms. O