Re: [Freesurfer] volume to surface registration

Thanks for the reply! Zhuonan 发件人: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] 代表 Douglas N. Greve [dgr...@mgh.harvard.edu] 发送时间: 2018年5月14日 15:02 收件人: freesurfer@nmr.mgh.harvard.edu 主题: Re: [Freesurfer] volume

Re: [Freesurfer] volume to surface registration

Probably best to run recon-all on the mni152, then sample your 152 data onto the surface, then use the surface-based registration. On 05/10/2018 01:06 PM, Wang, Zhuonan wrote: > Hi Team, > > I have a functional image which located in the FSL volume-based > template(MNI152), and now I wanna to

[Freesurfer] volume to surface registration

Hi Team, I have a functional image which located in the FSL volume-based template(MNI152), and now I wanna to register this image to FS-based surface template (MNI305). How can I do this? Please let me know how to do this! PS: I'm not sure that the MNI152 is same as the FS's MNI152.

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

should be the same as when you use --regheader with tkregister On 02/09/2018 11:24 PM, Rita Elena Loiotile wrote: > 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

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

Re: [Freesurfer] volume vs surface-based and surface smoothing

y, October 12, 2017 at 1:39 PM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] volume vs surface-based and surface smoothing > > Volume-based registration is fine with subject as you have th

Re: [Freesurfer] volume vs surface-based and surface smoothing

Alissa Stafford <alissa.staff...@jhu.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Thursday, October 12, 2017 at 12:42 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] volume vs surface-based and surface smoo

Re: [Freesurfer] volume vs surface-based and surface smoothing

esurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Thursday, October 12, 2017 at 1:39 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] volume vs surface-based and surf

Re: [Freesurfer] volume vs surface-based and surface smoothing

afford <alissa.staff...@jhu.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Thursday, October 12, 2017 at 12:29 PM To: "Freesurfer@nmr.mgh.harvard.edu" <Freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] volume vs surface-based and surf

[Freesurfer] volume vs surface-based and surface smoothing

Hello, I am trying to understand the preprocessing functions to successfully complete surface-based analysis. I am confused about what is happening on the volume level and when exactly the surface is being created. My questions revolve around register-sess and rawfunc2surf-sess. Registration

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

If you have a 3mm MNI152 space, then you should run bbregister to fsaverage to create a new register.dat file. Alternatively, you can register it directly to 32k_fs_LR and cut out the middle man (make sure to use --9 to account for scaling). Please ignore my comment about fsaverage. In that

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

Hi Doug, Thanks for the email. It is in 3mm space, so I guess I should reslice. Can you please clarify the comment about fsaverage? Does the --mni152reg flag not apply to that subject? I'm not sure what you mean about the inclusion indicating ambiguity. Thanks again, Rita On Tue, Apr 4, 2017

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

The --mni152reg flag is only appropriate if the mov file is in the 2mm mni152 space. The inclusion of fsaverage as the source subject indicates some ambiguity about this On 4/3/17 1:56 PM, Rita Elena Loiotile wrote: Hi, I'm trying to compare analyses that I've done entirely on the surface

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

Hi, I'm trying to compare analyses that I've done entirely on the surface to analyses I've done in the volume. I'm comparing the analyses by projecting the volume analyses to the surface (HCP's 32k_fs_LR). The commands I'm using are: mri_vol2surf --mov $niftiFile --mni152reg --hemi ${hemi}

[Freesurfer] Volume or surface?

Dear FS experts, I want to know what is the output (volume or surface) of the following scripts. (The input is file.nii.gz which is a volumetric ) 1. spmregister --s subj --mov file.nii.gz --reg reg.dat --o file_t1.mgh #is the output file (file_t1.mgh) is a volume or a surface    2. 

Re: [Freesurfer] Volume to Surface

...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 1:17 PM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface yes, that's right. You will use mri_vol2surf with the identity matrix with the parcellation, but some

Re: [Freesurfer] Volume to Surface

u] > Sent: Friday, September 30, 2016 4:44 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Volume to Surface > > examine the actual values. They should be constants that correspond to > the values in $FREESURFER_HOME/FreeSurferColorLUT.txt, eg, left superior &g

Re: [Freesurfer] Volume to Surface

[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 4:44 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume to Surface examine the actual values. They should be constants that correspond

Re: [Freesurfer] Volume to Surface

arc+asegS.mgh > Dim: 115984 1 1 > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Friday, September 30, 2016 3:52 PM > To: fre

Re: [Freesurfer] Volume to Surface

[gr...@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 3:52 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume to Surface You should use aparc+aseg.mgz and set the --projfrac 0.5. This should produce something with the same information as the ?h.aparc.annot (though

Re: [Freesurfer] Volume to Surface

h.harvard.edu] > Sent: Friday, September 30, 2016 3:41 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Volume to Surface > > I can't tell from that image if it is right. Why are you mapping the > wmparc to the surface? The wmparc will have segmentation boundarie

Re: [Freesurfer] Volume to Surface

] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 3:41 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume to Surface I can't tell from that image if it is right. Why are you mapping the wmparc to the surface? The wmparc will have segmentation

Re: [Freesurfer] Volume to Surface

, 2016 2:42 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Volume to Surface > > Anna, try removing --out_type paint and instead specify the output file > as wmparcSlh.mgh > > Trisanna, thanks so much for chipping in! > > > > On 09/30/2016 01:14

Re: [Freesurfer] Volume to Surface

arvard.edu >> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >> [freesurfer-boun...@nmr.mgh.harvard.edu >> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of >> Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca >> <mailt

Re: [Freesurfer] Volume to Surface

;mailto:trisanna.sprung-m...@mail.mcgill.ca>] > *Sent:* Friday, September 30, 2016 12:51 PM > > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] Volume to Surface > > My apologies, I meant "--regheader subject" > > -- > P

Re: [Freesurfer] Volume to Surface

f Trisanna Sprung-Much > [trisanna.sprung-m...@mail.mcgill.ca] > Sent: Friday, September 30, 2016 12:51 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Volume to Surface > > My apologies, I meant "--regheader subject" > > -- > Ph.D. Candidate McGill Universit

Re: [Freesurfer] Volume to Surface

___ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much > [trisanna.sprung-m...@mail.mcgill.ca] > Sent: Friday, September 30, 2016 10:48 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] Volu

Re: [Freesurfer] Volume to Surface

arvard.edu] on behalf of Trisanna Sprung-Much > [trisanna.sprung-m...@mail.mcgill.ca] > *Sent:* Friday, September 30, 2016 12:51 PM > > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] Volume to Surface > > My apologies, I meant "--regheader subject" > > -- >

Re: [Freesurfer] Volume to Surface

urfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca] Sent: Friday, September 30, 2016 12:51 PM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface My apologies, I meant "--regheader subject" -- Ph.D. Candida

Re: [Freesurfer] Volume to Surface

-regmethod > > Anna > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ > freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much > [trisanna.sprung-m...@mail.mcgill.ca] > *Sent:* Friday, September 30, 2016 12:41 PM > > *To:* Freesurfer support list &

Re: [Freesurfer] Volume to Surface

To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface hmmm, yup not sure there. Did you try "--regmethod subject" -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna <crawf...@ccf.org

Re: [Freesurfer] Volume to Surface

na Sprung-Much > [trisanna.sprung-m...@mail.mcgill.ca] > *Sent:* Friday, September 30, 2016 12:08 PM > > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] Volume to Surface > > Did you try --regmethod subjid? or --reg sphere.reg ? > > If that doesn't work then I'm

Re: [Freesurfer] Volume to Surface

support list Subject: Re: [Freesurfer] Volume to Surface Did you try --regmethod subjid? or --reg sphere.reg ? If that doesn't work then I'm not sure how to help - Bruce or Doug, any thoughts? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep

Re: [Freesurfer] Volume to Surface

- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ > freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much > [trisanna.sprung-m...@mail.mcgill.ca] > *Sent:* Friday, September 30, 2016 11:04 AM > > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] Vo

Re: [Freesurfer] Volume to Surface

[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca] Sent: Friday, September 30, 2016 11:04 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface Gotcha, so when I was trying to do something similar I used

Re: [Freesurfer] Volume to Surface

er 30, 2016 10:48 AM > > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] Volume to Surface > > Sorry - always helps to read the whole question :D > > So, you are trying to create an inflated white surface? As far as I know > this doesn't exist. Freesurfer cr

Re: [Freesurfer] Volume to Surface

: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca] Sent: Friday, September 30, 2016 10:48 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface Sorry - always helps to read

Re: [Freesurfer] Volume to Surface

16 10:40 AM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] Volume to Surface > > You have to run recon-all to get the surfaces of a volume. > > Trisanna > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology

Re: [Freesurfer] Volume to Surface

. > > Anna > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much > [trisanna.sprung-m...@mail.mcgill.ca] > Sent: Friday, September 30, 2016 10:40 AM > To: Freesurfer support list > Subject: Re: [Freesurf

Re: [Freesurfer] Volume to Surface

] Sent: Friday, September 30, 2016 10:40 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface You have to run recon-all to get the surfaces of a volume. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 9:47 AM

Re: [Freesurfer] Volume to Surface

You have to run recon-all to get the surfaces of a volume. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna wrote: > Hello, > > I am trying to take nay volume that is registered and

[Freesurfer] Volume to Surface

Hello, I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not

[Freesurfer] volume to surface - average across normal

Dear all, I would like to project a volume of statistical values (ang.nii) to the surface. At the moment I do it as in this example: mri_vol2surf --src ang.nii --srcreg register.dat --hemi lh --projfrac 0.5 --out ./ang-lh.w --out_type paint However, what I would like to get is the average

[Freesurfer] volume to surface - average across normal

Hi Bruce, Thanks a lot for your answer! This is exactly what I was looking for. I looked at the https://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2surf website that did not specify these options. Thanks again! Patrik ___ Freesurfer mailing list

Re: [Freesurfer] volume to surface - average across normal

you can try running the commands with --help and see what they tell you (or sometimes -h). That's where this came from cheers Bruce On Wed, 6 May 2015, Andersson, Jonas Patrik wrote: Hi Bruce, Thanks a lot for your answer! This is exactly what I was looking for. I looked at the

Re: [Freesurfer] volume to surface - average across normal

Hi Patrik vol2surf is very flexible about this. If you look at the help you will see: Options for projecting along the surface normal: --projfrac frac : (0-1)fractional projection along normal --projfrac-avg min max del : average along normal --projfrac-max min max del : max along

[Freesurfer] volume to surface registration problem

Hi, When I used preproc-sess processing my data, the registration output is off a great of deal. The functional data was collected using 7T, and the surface was reconstructed successfully from 3T data and was checked visually multiple times. I am using fs5.3 installed on a linux system.

Re: [Freesurfer] volume to surface registration problem

The problem is probabably that the fsl flirt registration failed and that caused bbr to fail. If you have spm and matlab installed, running it with cd /misc/data41/yuex/humanfMRI/human_curvature/subjdata/field090514 bbregister --s field --init-spm --6 --bold --mov bold/template.nii --reg

Re: [Freesurfer] volume to surface registration problem

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] volume to surface registration problem The problem is probabably that the fsl flirt registration failed and that caused bbr to fail. If you have spm and matlab installed, running it with cd /misc/data41/yuex/humanfMRI/human_curvature/subjdata

Re: [Freesurfer] volume to surface registration problem

. Which version should I use? Also, how to change the spm as the inital registration method in the preproc-sess? Xiaomin Date: Thu, 16 Oct 2014 12:00:04 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] volume to surface registration problem

Re: [Freesurfer] volume to surface registration problem

...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] volume to surface registration problem I have not tested it with spm12, so use spm8. There is not currently a way to run the spm init from preproc-sess, so you'll have to run it from register-sess. On 10/16/2014

Re: [Freesurfer] volume to surface registration problem

, is that right? Thanks, Xiaomin Date: Thu, 16 Oct 2014 12:12:23 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] volume to surface registration problem I have not tested it with spm12, so use spm8. There is not currently a way

Re: [Freesurfer] Volume to surface coordinates

See if this page gives you the answer you need http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems On 09/23/2014 10:39 AM, Michael WOODMAN wrote: Hello freesurfers, I would like to identify, in surface/vertex coordinates, certain points in a volume. Is there a straightforward way to

[Freesurfer] Volume to surface coordinates

Hello freesurfers, I would like to identify, in surface/vertex coordinates, certain points in a volume. Is there a straightforward way to obtain relevant transform? Thank you, Marmaduke Woodman ___ Freesurfer mailing list

[Freesurfer] volume to surface

Hi All, I would like to use mri_vol2surf to overlay a volume onto a surface. The synopsis is mri_vol2surf [options] --src inputfile --out outpufile --srcreg registrationfile --hemi hemisphere.But I don't know how to generate the registrationfile. Could someone help me with that? Thanks a lot!

Re: [Freesurfer] volume to surface

Hi Yue you can use bbregister to generate the registration. cheers Bruce On Thu, 19 Dec 2013, 赵越 wrote: Hi All, I would like to use mri_vol2surf to overlay a volume onto a surface. The synopsis is mri_vol2surf [options] --src inputfile --out outpufile --srcreg registrationfile --hemi

Re: [Freesurfer] Volume to surface

Thank you Anderson,It looks like do just what I want to do, but I'm having a problem, I've give the permissions to make the file an executable as follows chmod +x /root/freesurfer/bin/aseg2surf but when I call it  always say that bash: aseg2surf: command not found. My FS v5.1 is working properly

Re: [Freesurfer] Volume to surface

Well now the aseg2srf script is working perfectly, it was a thing of the shell (changed to: #!/bin/sh -f) and the format of the script when I'd downloaded it.Now I'm wanting to use the srf2obj script, and something similar happens, but since it is for gawk I have no idea how to change it or fix it

Re: [Freesurfer] Volume to surface

Hi Gabriel, This sounds like a problem with downloading. Are you copying and pasting the content of the scripts rather than downloading? Are you copying from a Windows computer? Gawk is just a replacement for awk with a more permissive license and more features. It is the default in Linux and

Re: [Freesurfer] Volume to surface

Anderson, I'm downloading using a windows computer (but I always do like that with every single script), which automatically recognizes the scripts as txt files and add the extension, could you send me a link to the downloading page? That way I can try again and see what happens. I did check in my

Re: [Freesurfer] Volume to surface

Hi Gabriel, Please, try downloading from here: http://dl.dropbox.com/u/2785709/aseg2srf http://dl.dropbox.com/u/2785709/srf2obj Right-click and click Save As, to avoid Windows opening it up and messing up with character encoding. I'll write up a page about the aseg2srf and send the link

Re: [Freesurfer] Volume to surface

ok, just posted... please, see here: http://brainder.org On 08/05/12 15:51, Anderson Winkler wrote: Hi Gabriel, Please, try downloading from here: http://dl.dropbox.com/u/2785709/aseg2srf http://dl.dropbox.com/u/2785709/srf2obj Right-click and click Save As, to avoid Windows opening it up

Re: [Freesurfer] Volume to surface

Hi Anderson,Now everything works perfectly, thank you so much!!!Best Regards,Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only

[Freesurfer] Volume to surface

Hello all FS users and experts,I'm wanting to get the sub cortical segmentation as ASCII files, so I'm trying convert the aseg.mgz into a surface file, to finally get an ASCII file,For this I'm using the next commands:First: mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg2raw.niiTo preserve  

[Freesurfer] Volume to surface 2

I did forget to tell you that when I use the last command it always outputs the following error:ERROR: MRISread: cannot read surface data from file lh.aseg2raw.mgh! It gives me the same error when trying to load the surface into tksurfer, Is that I've made something wrong?Regards, Gabriel 

Re: [Freesurfer] Volume to surface

Hi Gabriel, Attached is a script that probably does what you need. Just make it executable and call it without arguments to get usage information. The label indices you can get from the aseg.stats file or from FreeSurferColorLUT.txt. The surfaces will be saved in a subdirectory called ascii

[Freesurfer] Volume to surface dimension mismatch

I have a mask file which I need to overlay on the individual images of a group of subjects to extract thickness values within ht mask. But the mask is of dimension 2X2X2, will this be an issue? Thanks Lena ___ Lena Palaniyappan Clinical

Re: [Freesurfer] Volume to surface dimension mismatch

You'll have to sample that mask onto the surface using mri_vol2surf with the --interp nearest option. You will also have to have a registration matrix, which will depend on where the volume came from. doug Lena Palaniyappan wrote: I have a mask file which I need to overlay on the individual

Re: [Freesurfer] Volume to surface dimension mismatch

Doug, thanks So, is this a correct sequence: Im extracting thickness measures from VBM contrasts generated by FSL VBM analysis (this is 2X2X2): 1. To convert VBM contrast file to a binary mask: mri_binarize --i vbmcontrast.nii.gz --o vbmmask.nii --min 0.95 --max 1 (for fsl vbm generated corrp

Re: [Freesurfer] Volume to surface dimension mismatch

If the source is the FSL standard brain, then use $FREESURFER_HOME/average/mni152.register.dat as the registration. See if that works at stage 4. Lena Palaniyappan wrote: Doug, thanks So, is this a correct sequence: Im extracting thickness measures from VBM contrasts generated by FSL VBM