Re: [Freesurfer] mri_segment error

thank you for your attention regards On Fri, Feb 9, 2018 at 1:04 AM, Bruce Fischl wrote: > looks like the acquisition is not what you would need to run FreeSurfer > on. Looking at the log I think your input is a T2-weighted image (we > require a T1) with a slice thickness of 9mm (we require all

[Freesurfer] pre-smoothing coomand line

Hi Freesurfer experts, I found the answer to my previous question on FreeSurfer Wiki regarding pre-smoothing command line for LGI ( I am interested in looking at between-group differences in vertwex-wise LGI values). I am now aware that the following command line must be used: recon-all

Re: [Freesurfer] Wm.mgz editing

Hi Bruce, Thanks for getting back to me. I am trying to upload the data via ftp, but I either get the error " 200 PORT command successful. Consider using PASV. 553 Could not create file." or when I try epsv "?Invalid command." Here is the session history: Name (surfer.nmr.mgh.harvard.edu:admin

[Freesurfer] fmri_readreg

Dear Surfers, Previously we had a matlab function fmri_readreg.m (author: Doug Greve) that could extract the regmat from the register.dof6.dat files. But version 6 does not generate dof6.dat anymore. Rather it generates a dof6.lta that fmri_readreg can not read. I was wondering if there is an

Re: [Freesurfer] fmri_readreg

use read_lta.m doug On 2/9/18 11:15 AM, sha...@nmr.mgh.harvard.edu wrote: > Dear Surfers, > Previously we had a matlab function fmri_readreg.m (author: Doug Greve) > that could extract the regmat from the register.dof6.dat files. But > version 6 does not generate dof6.dat anymore. Rather it

[Freesurfer] FW: Memorandum: Call for CASE Distinguished Postdoctoral Scholar {Disarmed}

Hello, Please see below for a very time-sensitive opportunity for postdoctoral scholars in developmental neuroimaging in the Center for Children and Families (ccf.fiu.edu). Please contact me directly (ad...@fiu.edu) with any interest. Good salary/benefits in a great city (

Re: [Freesurfer] Wm.mgz editing

Hi Emily, Another user had this problem recently, and we weren’t able to resolve it. For now, if your upload is less than 2GiB, I suggest sending your data via the Martinos file drop (directions at the bottom of this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange) Let me know

Re: [Freesurfer] pre-smoothing coomand line

Yes, that is the correct command line On 2/9/18 9:16 AM, Avideh Gharehgazlou wrote: Hi Freesurfer experts, I found the answer to my previous question on FreeSurfer Wiki regarding pre-smoothing command line for LGI ( I am interested in looking at between-group differences in vertwex-wise LGI

Re: [Freesurfer] mri_aparc2aseg labelwm not labelling wm

Hi Sara, can you repost with just the new issue? I'm having problems differentiating them just looking through the email On 2/5/18 6:02 PM, Sims, Sara A wrote: > Doug, > > This is a new problem. I figured out my earlier issue. This makes a > 8V1+aseg.mgz file there are just no 4001 and 3001's i

Re: [Freesurfer] shift to account for hemodynamic response

It is already built into the HRF model. If you need to shift them more or less than what is in the model, that can be accommodated. If you use the -spmhrf option, then you will get the same HRF as is used in spm. On 2/6/18 11:45 PM, Ashley Cole wrote: Dear experts, I just have switched from

Re: [Freesurfer] Removing labels after extending parcellation into white matter

On 2/6/18 5:26 PM, Michiko H. wrote: Hi Doug, That's very helpful, thank you! I have 2 follow-up questions though: 1. Is it possible to merge the cortical label (e.g. label 1001 ctx-lh-bankssts) with its corresponding label that extends into the WM (e.g. label 3001 wm-lh-bankssts)? I'm not

Re: [Freesurfer] Multiple regression FreeSurfer

So you want to have a vertex-specific model that relates CV to X1, Age, and thickness at the vertex? If so, then you will need to use a per-voxel regressor (--pvr option to mri_glmfit). Search through the archives to find examples where I've helped others On 2/6/18 12:36 PM, Martin Juneja wr

Re: [Freesurfer] Gray matter mask

You have to run recon-all through to the end. You can then extract a GM mask from that. You will need to register your PET image to the anatomical (mri_coreg), map the PET into the anatomical space, then use mri_segstats to compute the mean PET in the GM mask. Alternatively, you may want to use

Re: [Freesurfer] Multiple regression FreeSurfer

Thanks a lot Douglas, I will look into that. Thanks a lot for the help. On Fri, Feb 9, 2018 at 10:56 AM, Douglas Greve wrote: > So you want to have a vertex-specific model that relates CV to X1, Age, > and thickness at the vertex? If so, then you will need to use a per-voxel > regressor (--pvr

Re: [Freesurfer] How to analyze fMRI in native volume space

You can run preproc-sess like this (don't include -mni305 or -surf) preproc-sess -per-session -fsd bold -fwhm 5 -s session Then mkanalysis: mkanalysis-sess -a mains -native -fwhm 5 -fsd bold ... This will analyze things in the native fmri space. You can then convert the results to the anatomic

Re: [Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.

If you've already run qcache, then it will be in the subject/surf folder with a name like lh.thickness.fsaverage.fwhm10.mgz On 2/6/18 11:22 PM, 박경일 wrote: Thanks, Bruce. From that, I got thickness data (vertex#, location x/y/z, thickness value). But, amount and location of vertex are differe

Re: [Freesurfer] fmri_readreg

Would you tell me where I can find it. It is not in stable6_0_0>fsfast>toolbox Thanks > use read_lta.m > doug > > > On 2/9/18 11:15 AM, sha...@nmr.mgh.harvard.edu wrote: >> Dear Surfers, >> Previously we had a matlab function fmri_readreg.m (author: Doug >> Greve) >> that could extract the re

Re: [Freesurfer] REPOST: mri_mcsim with mask - How do I map a volume mask to the surface space for mri_mcsim using my own template?

Hi Doug, thank you very much for your help! I am sorry for the naive questions, but I am not very familiar with surface analyses: I ran recon-all on my template ("ANTSaverage") so that I have the surfaces. Is it correct that I have registered my volume mask to my template space before I map it o

Re: [Freesurfer] shift to account for hemodynamic response

Thank you so much. On Fri, Feb 9, 2018 at 11:48 AM, Douglas Greve wrote: > It is already built into the HRF model. If you need to shift them more or > less than what is in the model, that can be accommodated. If you use the > -spmhrf option, then you will get the same HRF as is used in spm. > >

[Freesurfer] V1 functional ROI

Dear Dr. Douge, I am a little bit confused about creating function ROI in V1. Basically, I have some localizers that for some ROIs I need to find activated neurons in a specific contrast in native space and then create that ROI and map it to my experimental scans and extract their voxel data. I

[Freesurfer] no white matter is labelled when using mri_aparc2aseg

Doug, I am sorry that I wasn’t clear before, here is all the info about it all in one place. I am trying to transfer a cortical label to label wm by using the following commands: subjects=/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon; unset SUBJECTS_DIR SUBJECTS_DIR=$subjects export

[Freesurfer] Two versions of FreeSurfer in the same computer

Dear, I will be attending the workshop in April and I started taking the tutorials online to get prepared. My laptop is running an older of freesurfer (5.0.0), because I have data to add to other data analysed by a previous lab member. I am aware that I shouldn't mix versions, but for tutorial

Re: [Freesurfer] Two versions of FreeSurfer in the same computer

Yes, you just need to set the FREESURFER_HOME environment variable correctly. On 2/9/18 5:37 PM, Vania de Aguiar wrote: Dear, I will be attending the workshop in April and I started taking the tutorials online to get prepared. My laptop is running an older of freesurfer (5.0.0), because I

Re: [Freesurfer] Volume to Surface mapping looks great for Vols created in FSL but not SPM

Hi, I just noticed that when I open my volume file in tksurfer using --overlay it gives a better volume to surface mapping than when I do mri_vol2surf. Do you know what .dat file is used implicitly when tksurfer is called with a volume overlay? It also seems to work well when the subject is fsave