[Freesurfer] Thank you

Hi everyone, I would just say you thank you for the help you give to Freesurfer users. I use Freesurfer for my school project and I ended yesterday. I didn't know anything about Linux before and before segmentation software of cortical surface. I don't think I would did an so great job without

[Freesurfer] GIFTI file

Hi, I saw in the documentation that since the version 5.2.0 of Freesurferw ecan open and write .gii file. I have a surface in .gii and I would like open it on FS. The fact is that, I didn't find a way to do that in the documentation. Does anyone know a way? Thanks.

[Freesurfer] Error map

Hi, I am looking for a tool of FreeSurfer. In fact, the tool is supposed to take in input 2 surfaces ( hemispheres) of subjects, registrate the surfaces and display the difference between the 2surfaces ( like 'euclidian distance'). What I want is exactly that output (http://www.sciencedirect.c

[Freesurfer] Extract surface from volume

I have a volume in mnc and nii format. I would like to extract the outer surface from those volumes to be able to use in Freesurfer. I tried 'mri_vol2surf' but I didn't have the registration file. So I try make_register to create a registration file and the system give me an error as it couldn't

[Freesurfer] algorithm mris_anatomical_stats

Hi, Is it possible to get the algorithm of mris_anatomicacl_Stats. Just ot know which files it uses to compute metrics ... Thanks. VP___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mg

Re: [Freesurfer] Brainsuite --> FreeSurfer

it depends on what measures you want Bruce On Wed, 20 Mar 2013, Valtina Pouegue wrote: > Hi Bruces, > It's because i'm doing a comparison between brainsuite and freesrufer. So , I > would like to export results of > segmentation with Brainsuite and make measurements with Fre

Re: [Freesurfer] Brainsuite --> FreeSurfer

and generate them? Bruce On Tue, 19 Mar 2013, Valtina Pouegue wrote: > I could see the created surface in MAtlab ( 'read_surf,) but I could't open > the file in Freesurf

Re: [Freesurfer] Brainsuite --> FreeSurfer

I could see the created surface in MAtlab ( 'read_surf,) but I could't open the file in Freesurfer with tksurfer VP From: pval...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: Brainsuite --> FreeSurfer Date: Tue, 19 Mar 2013 22:34:39 -0400 Hi, I've done a segmentation with B

[Freesurfer] Brainsuite --> FreeSurfer

Hi, I've done a segmentation with Brainsuite ( and FreeSurfer) and I would like to get measurements with FreeSurfer. SO, I convert my rile ( readdfs --> write_surf ) from BRainsuite in Matlab to be usable with Freesurfer. Then, I tried to get measurements with the command .'mris_anatomical_stat

[Freesurfer] Use a dfs file for measurements

Hi Freesurfers, I,ve done a segmentation with Brainsuite and as result I have dfs file for Pial surfaxe L/R hemisphere. I would like to do some measurement with mris_anatomical_stats of Freesurfers. But this fonction of FreeSurfer only accept surface of extension like ( .pial). How can I do

Re: [Freesurfer] mri_convert problem

Thanks a lot! Date: Fri, 15 Mar 2013 13:09:41 -0400 From: fis...@nmr.mgh.harvard.edu To: pval...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert problem just: mri_convert volume.mgz cheers Bruce On Fri, 15 Mar 2013, Valtina Pouegue wrote

Re: [Freesurfer] mri_convert problem

convert direct from MNC to mgz^ Thanks Date: Fri, 15 Mar 2013 10:00:04 -0400 From: fis...@nmr.mgh.harvard.edu To: pval...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert problem can you run ls -l and mri_info on it? On Fri, 15 Mar 2013, Valtina Pouegue wrote

Re: [Freesurfer] mri_convert problem

run ls -l on that file? Or mri_info? > > cheers > Bruce > > On Fri, 15 Mar 2013, Valtina Pouegue wrote: > > > Hi, > > > > I have a problem of conversion. I would like to convert mnc file to mgz. > > But I think I shoul first convert mnc to nii then

[Freesurfer] mri_convert problem

Hi, I have a problem of conversion. I would like to convert mnc file to mgz. But I think I shoul first convert mnc to nii then nii to mgz. , so I try the command mri_convert and I have this error; -[esther@m3012-04 ~]$ mri_convert $SUBJECTS_DIR/Patient1/fichierMnc.mnc Folder1.nii.gz

[Freesurfer] Extract pial surface

Hi Freesurfers, I would like to extract the whole pial surface of a brain volume. I already done the segmentation and i have ( rh.pial and lh.pial surfaces). Does it exist a way to get the whole pial surface without separation? Thanks. VP ___

Re: [Freesurfer] Time

...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu; gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Time what are you trying to do? If run a recon, your first command should have a -all at the end of it cheers Bruce On Fri, 8 Mar 2013, Valtina Pouegue wrote: > I don't t

Re: [Freesurfer] Time

ssion to write to that directory (or the > disk is full) > > On Fri, 8 Mar 2013, Valtina Pouegue wrote: > > > > > VP,I try FreeView,, tit > I dont really know what going on, i try mri-convert with another subject > > aand i get this: > > ---

Re: [Freesurfer] Time

le out.mgz > > tkmedit -f out.mgz > > > > doug > > > > On 03/08/2013 12:54 PM, Valtina Pouegue wrote: > >> If i'm right, the command: > recon-all -s 13A -all execute the whole > >> segmentation ( between 20-40 hours). > >> So , if I j

Re: [Freesurfer] Time

01.mgz > You do not need to run recon-all to get a volume, you can just run > mri_convert, eg > mri_convert /path/to/dicomfile out.mgz > tkmedit -f out.mgz > > doug > > On 03/08/2013 12:54 PM, Valtina Pouegue wrote: > > If i'm right, the command: > recon-all -

Re: [Freesurfer] Time

1.dcm -s > 13A -all > > but now that you have a file there, you can run > > recon-all -s 13A -all > > doug > > > On 03/08/2013 12:31 PM, Valtina Pouegue wrote: > > I convert my set of DICOM of the folder 'Patient13A' > > >

Re: [Freesurfer] Time

00 > From: gr...@nmr.mgh.harvard.edu > To: pval...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu; ni...@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Time > > Does that file exist? What was your command to create the mgz file? > On 03/08/2013 12:12 PM, Valtina Pouegue wrote: > > H

Re: [Freesurfer] Time

of the first .dcm in the series, the software will find the other slices and create the .mgz. On Mar 7, 2013, at 9:02 PM, Valtina Pouegue wrote: Oh yes. It's my mistake. But should I give the adress of the first file of my set for having the result in .mgz. Thanks. > Date: Thu, 7 Ma

Re: [Freesurfer] Time

er] Time > > You cannot give recon-all a folder as input. It must be an image file. > If you have multiple files, you need multiple -i flags. > doug > > > On 03/07/2013 03:48 PM, Valtina Pouegue wrote: > > Hi, > > Here it is > > [esther@IP132-207-67-224

[Freesurfer] Time

Hi, I have 8 folders of 26 slice odf dicom. Yesterday, I launched the conversion to .mgz with the command recon-all -i [-i ] -s . All my folders are created but in the Orig folder I don't fige files .mgz. I think that the processing time is really long but I'm not sure. Do you know somthing

[Freesurfer] Extract cortex surface with Freesurfer

Hi, I'm a new user of Freesurfer. 1) I would like to extract only the cortex cerebrum . So I think I don't need the complete subcortical segmentation ( 20-40 hours). Do you know a way to segment only cortex or only ( cortex+ pial ( left/rigt hemispher)?2) I already try the complete subcorti