Re: [Freesurfer] mri_vol2vol anatomical to functional

Have you visually verified that the registration is correct (only work with LTAs) using tkregisterfv ? How are you viewing the combined anatomical/functional in pics? If you just load the functional without a registration file, then that is not right. On 3/29/2022 11:28 AM, Manenti, Giorgio

Re: [Freesurfer] mri_vol2vol anatomical to functional

; 0.0 0.0 0.0 1.0; Resampling Output registration matrix is identity mri_vol2vol done Many thanks again, Best Giorgio Message: 10 Date: Sun, 27 Mar 2022 17:16:25 -0400 From: "Douglas N. Greve" Subject: Re: [Freesurfer] mri_vol2vol anatomical to functional To:

Re: [Freesurfer] mri_vol2vol anatomical to functional

I'm not sure I understand what you are saying or what the problem is. Can you provide the actual command line you are using, all the terminal output, and a picture that shows what the problem is? On 3/23/2022 2:46 PM, Manenti, Giorgio wrote: > External Email - Use Caution > > Dear

[Freesurfer] mri_vol2vol anatomical to functional

External Email - Use Caution Dear Freesurfer experts, I am getting problems to transform my xh.ribbon.mgh from anatomical 256x256x256 to functional 104x104x69 space. When converting the ribbon via “ mri_vol2vol —reg REGfile —mov INPUT —targ funcTEMPLATE —o OUTPUT “ and

Re: [Freesurfer] mri_vol2vol usage

No, that is the output of bbregister On 11/11/2020 1:55 PM, RENXI LI wrote: External Email - Use Caution Wouldn’t --reg still require the registration matrix file in bbregister? Best, Renxi On Nov 11, 2020, at 11:40 AM, Douglas N. Greve mailto:dgr...@mgh.harvard.edu>> wrote:

Re: [Freesurfer] mri_vol2vol usage

External Email - Use Caution Wouldn’t --reg still require the registration matrix file in bbregister? Best, Renxi On Nov 11, 2020, at 11:40 AM, Douglas N. Greve mailto:dgr...@mgh.harvard.edu>> wrote: Yes, use bbregister, run with --help to get docs On 11/11/2020 11:36 AM,

Re: [Freesurfer] mri_vol2vol usage

External Email - Use Caution So I think my functional image processed by SPM12 does not come with any registration matrix file that is required for mri_vol2vol, is there a way to get around with that matrix? Best, Renxi > On Nov 11, 2020, at 10:12 AM, Douglas N. Greve wrote:

Re: [Freesurfer] mri_vol2vol usage

Yes, use bbregister, run with --help to get docs On 11/11/2020 11:36 AM, RENXI LI wrote: > External Email - Use Caution > > So I think my functional image processed by SPM12 does not come with any > registration matrix file that is required for mri_vol2vol, is there a way to > get

Re: [Freesurfer] mri_vol2vol usage

Try --help to get docs and examples On 11/8/2020 5:07 PM, RENXI LI wrote: > External Email - Use Caution > > Hi FreeSurfer Experts: > > I am trying to register the subject’s functional image processed by SPM12 to > the Freesurfer subject anatomical space using mri_vol2vol, what would be

[Freesurfer] mri_vol2vol usage

External Email - Use Caution Hi FreeSurfer Experts: I am trying to register the subject’s functional image processed by SPM12 to the Freesurfer subject anatomical space using mri_vol2vol, what would be the required arguments in this case? Best, Renxi

Re: [Freesurfer] mri_vol2vol with --inv-morph producing unexpected results

Can you try using mri_convert? Like, mri_convert mni152.nii.gz --apply_inverse_transform xform.m3z subject.mgz Let me know if that works On 9/8/2020 8:28 PM, Noriana Jakopin wrote: External Email - Use Caution Hello, I just wanted to follow up on this and see if anyone had any

Re: [Freesurfer] mri_vol2vol with --inv-morph producing unexpected results

External Email - Use Caution Hello, I just wanted to follow up on this and see if anyone had any suggestions, as I still have not resolved the issue. Best, Noriana Jakopin On Tue, Aug 18, 2020 at 12:54 PM Noriana Jakopin wrote: > Hello FreeSurfer Developers, > I am attempting

[Freesurfer] mri_vol2vol with --inv-morph producing unexpected results

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to use the inverse of the final m3z registration file produced by mri_cvs_register to take files in mni152 space back into my subject's space. I used mri_vol2vol with the --inv-morph flag to accomplish this.

Re: [Freesurfer] mri_vol2vol

First, check the overall registration with tkregisterfv --mov lowb.nii.gz --reg register.lta On 8/14/2020 12:30 PM, 侠义江湖，醉笑人生 wrote: External Email - Use Caution Hi, freesurfer experts. I am running dt_recon and mri_vol2vol to obtain FA values of ROI. Everything is OK after running

[Freesurfer] mri_vol2vol

External Email - Use Caution Hi, freesurfer experts. I am running dt_recon and mri_vol2vol to obtain FA values of ROI. Everything is OK after running the dt_recon command. But some subjects in my study show an issue with mri_vol2vol registration. When checking the

Re: [Freesurfer] mri_vol2vol

External Email - Use Caution Thanks, but I want to transform my ROI to the average space from my subjects (as created by make_average_subject). How do i get the xfm file to convert my ROI to this average space? /Ben Am Fr., 27. März 2020 um 16:27 Uhr schrieb Douglas N. Greve <

Re: [Freesurfer] mri_vol2vol

oK, this will not be that pretty, but you can mri_vol2vol --mov yourRoi.mgz --targ orig.mgz --interp nearest --regheader --o yourRoiOrig.mgz mri_convert yourRoiOrig.mgz yourRoiOrigAverageSpace.mgz --apply_transform subject/mri/transforms/talairach.xfm -rt nearest On 3/27/2020 11:03 AM,

Re: [Freesurfer] mri_vol2vol

External Email - Use Caution The space i created from all subjects using make_average_subject. Douglas N. Greve schrieb am Fr. 27. März 2020 um 15:32: > What do you mean by "the average space of the subjects"? > > > On 3/24/2020 2:01 PM, Benjamin Ineichen wrote: > >

Re: [Freesurfer] mri_vol2vol

What do you mean by "the average space of the subjects"? On 3/24/2020 2:01 PM, Benjamin Ineichen wrote: External Email - Use Caution Dear Freesurfer experts, I am aware that these are busy times. Please still allow me to repost my FreeSurfer problem: I created manual masks on the

Re: [Freesurfer] mri_vol2vol

External Email - Use Caution Dear Freesurfer experts, I am aware that these are busy times. Please still allow me to repost my FreeSurfer problem: I created manual masks on the Freesurfer input 001.mgz for several subjects. I would like to to transform all these individual masks

Re: [Freesurfer] mri_vol2vol

External Email - Use Caution the space in which the image was aqcuired. Am Fr., 6. März 2020 um 18:31 Uhr schrieb Douglas N. Greve < dgr...@mgh.harvard.edu>: > what is "native space"? > > On 3/6/2020 12:09 PM, Benjamin Ineichen wrote: > > External Email - Use Caution >

Re: [Freesurfer] mri_vol2vol

what is "native space"? On 3/6/2020 12:09 PM, Benjamin Ineichen wrote: External Email - Use Caution example.mgz is just some example mask created on a template in native space. And I would need to transform it to MNI space. Thus, I ran: mri_vol2vol --talres 1  --interp nearest --mov

Re: [Freesurfer] mri_vol2vol

What is example.mgz? If you want to transfer the orig.mgz, you can do it with mri_vol2vol --tal --talres 1 --interp nearest --mov orig.mgz --s subject --o example.mni305.mgz On 2/20/2020 3:53 PM, Benjamin Ineichen wrote: External Email - Use Caution Dear Freesurfer experts, In

Re: [Freesurfer] mri_vol2vol

yes, that looks right. The one question is about the fill threshold. You may need to play with it a little to get a good looking ROI_2.nii (which should be in registration with the functional -- but you should check it) On 8/24/2019 2:56 PM, Rihana Rayan wrote: External Email - Use

Re: [Freesurfer] mri_vol2vol

External Email - Use Caution Dear Dr. Greve, Thank you so much for your prompt response. I included your advice in the processing steps as bellow: 1- recon all 2- mri_binarize --i aparc.a2009s+aseg.mgz --o ROI.nii --match min max 3- bbregister --s --sub01 --mov

Re: [Freesurfer] mri_vol2vol

You shoul use mri_label2vol with ROI.nii as the --seg input. How do you know that --regheader is right? On 8/15/19 3:13 PM, Rihana Rayan wrote: > > External Email - Use Caution > > Dear FS users, > I have performed recon-all on structural data and created ROIs (using > mri_binarize), I

[Freesurfer] mri_vol2vol

External Email - Use Caution Dear FS users, I have performed recon-all on structural data and created ROIs (using mri_binarize), I want to mask functional data (GLM beta) with ROIs. To match the file sizes, I resampled the ROI.nii by performing the command: mri_vol2vol --mov

Re: [Freesurfer] mri_vol2vol

on behalf of Greve, Douglas N.,Ph.D. Sent: Monday, January 28, 2019 3:17:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2vol that should work On 1/28/19 2:44 PM, Nasiriavanaki, Zahra wrote: Dear Freesurfers Hi I am trying to project a subcortical volume , that I manually

Re: [Freesurfer] mri_vol2vol

that should work On 1/28/19 2:44 PM, Nasiriavanaki, Zahra wrote: Dear Freesurfers Hi I am trying to project a subcortical volume , that I manually made, from fsaverage to individual subject's space. I was wondering if it's ok if I use mri_vol2vol for this purpose. I copied my command

[Freesurfer] mri_vol2vol

Dear Freesurfers Hi I am trying to project a subcortical volume , that I manually made, from fsaverage to individual subject's space. I was wondering if it's ok if I use mri_vol2vol for this purpose. I copied my command below: mri_vol2vol --mov ./${ROI}/ROI4.mgz --targ

Re: [Freesurfer] mri_vol2vol --mni152reg flips volume

You need something like this mri_vol2vol --targ $SUBJECTS_DIR/fsaverage/mri/orig.mgz --mov $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o fsaverage.orig.MNI152.nii.gz --inv --reg $SUBJECTS_DIR/fsaverage/mri/transforms/reg.mni152.2mm.dat On 04/03/2017 10:36 AM, Melanie Ganz wrote: > Hi all, >

[Freesurfer] mri_vol2vol --mni152reg flips volume

Hi all, my colleague Vincent wanted to register a volume in MNI305 to MNI152, unfortunately the final image appears flipped up-down and anterior-posterior when using the --mni152reg flag with mri_vol2vol. For example, trying to resample fsaverage orig.mgz to MNI152 using mri_vol2vol --mov

Re: [Freesurfer] mri_vol2vol question

Sorry for the follow up email, but I realized my mistake. When running the mri_robust_register command even though I used the lta flag for the output register file, I gave the extension .dat to the file. It seems like this is what caused the problem. Panos > Dear FS community, > > I used

[Freesurfer] mri_vol2vol question

Dear FS community, I used mri_robust_register to register a volume to the fsaverage space, and then tried to use the resulting .lta file to register another vol on the same space as the original volume, to fsaverage, using mri_vol2vol. The structure of the command I used is: mri_vol2vol --mov

Re: [Freesurfer] mri_vol2vol binary mask

Add --interp nearest to use nearest neighbor interpolation instead of trilinear On 9/24/15 1:48 AM, Jinsong Tang wrote: Hello, I am try to convert some binary mask (0,1) to native space. I use this command line: mri_vol2vol --mov bin_mask.mgz --targ rawavg.mgz --regheader --o bin_mask

Re: [Freesurfer] mri_vol2vol binary mask

Hi Jinsong do you mean some of the values are not 1? By default I believe vol2vol uses trilinear interpolation. Try including the option --nearest to use nearest neighbor instead cheers Bruce On Wed, 23 Sep 2015, Jinsong Tang wrote: Hello, I am try to convert some binary mask (0,1) to

Re: [Freesurfer] mri_vol2vol binary mask

Hello Bruce, Yes, this works. Thanks, Jinsong On Thu, Sep 24, 2015 at 5:35 AM, Bruce Fischl wrote: > Hi Jinsong > > do you mean some of the values are not 1? By default I believe vol2vol > uses trilinear interpolation. Try including the option --nearest to use >

[Freesurfer] mri_vol2vol binary mask

Hello, I am try to convert some binary mask (0,1) to native space. I use this command line: mri_vol2vol --mov bin_mask.mgz --targ rawavg.mgz --regheader --o bin_mask _rawavg.nii.gz –no-save-reg I found some result of “ bin_mask _rawavg.nii.gz” with intensity of 0.988 instead of 1. Is there

[Freesurfer] mri_vol2vol from subject space to fsaverage space

Hi Freesurfer experts, We are analyzing data for a simultaneous PET-MRI study, and are having trouble registering individual subject BPnd maps to fsaverage space. I attached a photo of a post-registration subject (the left side is cut off). I had previously registered each individual BPnd

[Freesurfer] mri_vol2vol

Hi Freesurfer experts, We are analyzing data for a simultaneous PET-MRI study, and are having trouble registering individual subject BPnd maps to fsaverage space. I attached a photo of a post-registration subject (the left side is cut off). I had previously registered each individual BPnd

Re: [Freesurfer] mri_vol2vol

Anastasia would know better but she is away for a week or two. But looking at it, I would say that your command line is correct. The registration does map the anat to the diffusion space, but mri_vol2vol understands this and simply inverts the matrix. You should just verify it for yourself by

[Freesurfer] mri_vol2vol

Hi Freesurfer experts I am always a little confused with the registration matrices from tracula output. If we need to have the DTI maps like dtifit_MD.nii.gz in the recon space, do we use the matrix anatorig2diff.bbr.dat? mri_vol2vol --mov /recon/dmri/dtifit_MD.nii.gz --targ

Re: [Freesurfer] mri_vol2vol

to 0.25 will generate a huge data. Xiaomin Date: Wed, 15 Apr 2015 09:11:10 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2vol But why do you need to have the same

Re: [Freesurfer] mri_vol2vol

Because resampling from 1.5 to 0.25 will generate a huge data. Xiaomin Date: Wed, 15 Apr 2015 09:11:10 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2vol But why do you need to have the same resolution

Re: [Freesurfer] mri_vol2vol

, Xiaomin Date: Tue, 14 Apr 2015 21:08:15 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2vol So you want it to be in a volume with field of view 256mm in all three

[Freesurfer] mri_vol2vol

Hi Doug, I like to convert a native functional data into the anatomical space using mri_vol2vol with --fstal, so that the resample data has same spatial resolution as the original function data. However, mri_vol2vol give a error: --fstal unknown. I also tried using --fstalres as suggested in

Re: [Freesurfer] mri_vol2vol

: [Freesurfer] mri_vol2vol sorry, I don't understand. fstal would imply that you want talairach space. If you want to map the functional into the anatomical space, then mri_vol2vol --mov res-001.nii --o res-001.t1.space.nii --reg register.dof6.dat --fstarg

Re: [Freesurfer] mri_vol2vol

To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2vol sorry, I don't understand. fstal would imply that you want talairach space. If you want to map the functional into the anatomical space, then mri_vol2vol --mov res-001.nii --o res-001.t1.space.nii --reg register.dof6.dat --fstarg

Re: [Freesurfer] mri_vol2vol

Subject: Re: [Freesurfer] mri_vol2vol So you want it to be in a volume with field of view 256mm in all three dimensions, but the voxel size to be that of the functional data? It is possible to do, but not easy to set up. Can you say why you would want to do

Re: [Freesurfer] mri_vol2vol

sorry, I don't understand. fstal would imply that you want talairach space. If you want to map the functional into the anatomical space, then mri_vol2vol --mov res-001.nii --o res-001.t1.space.nii --reg register.dof6.dat --fstarg On 4/14/15 11:36 AM, Xiaomin Yue wrote: Hi Doug, I like to

[Freesurfer] mri_vol2vol error --o: command not found

Hi all, I'm trying to transform a mean functional image into subject (T1) space using mri_vol2vol. Originally, my code worked successfully, but in attempts to re-run the procedure, both on the same data and on additional data, I've encountered an error in which the log reports an ERROR: Option

Re: [Freesurfer] mri_vol2vol error --o: command not found

please send the command line without variables On 05/28/2014 02:02 PM, Ben Mooneyham wrote: Hi all, I'm trying to transform a mean functional image into subject (T1) space using mri_vol2vol. Originally, my code worked successfully, but in attempts to re-run the procedure, both on the

Re: [Freesurfer] mri_vol2vol memory error

Hi Ben, please post questions to the list and not to us personally. Thanks! I do not have an alternative. I think you are using Thomas Yeo's stream which we are not supporting. He just uses binaries from FS. doug On 05/22/2014 12:16 PM, Ben Mooneyham wrote: Hi Douglas, Thank you for your

Re: [Freesurfer] mri_vol2vol memory error

Hi Ben, There should be a procsurffast flag called -volproj_lowmem which avoids this mri_vol2vol memory issue. -Louis On Wed, 21 May 2014, Douglas N Greve wrote: mri_vol2vol when used in this way does not manage memory very well. It resamples the time series into a 256^3 volume of floats.

[Freesurfer] mri_vol2vol memory error

Hello all, I am doing pre-processing for resting-state fMRI volumes, but I have encountered an error and am unsure of how to correct it: I have previously determined the nonlinear warping transformations from my subjects' anatomical (T1) space to the 2mm MNI template using ANTs. At the end of my

Re: [Freesurfer] mri_vol2vol memory error

mri_vol2vol when used in this way does not manage memory very well. It resamples the time series into a 256^3 volume of floats. Even for a small number of time points, this becomes unmanagebly huge On 05/21/2014 06:06 PM, Ben Mooneyham wrote: Hello all, I am doing pre-processing for

Re: [Freesurfer] mri_vol2vol call problem

Hi Greg, the target (--targ) should be a volume, not the name of a subject (eg, 816/mri/orig.mgz) doug On 02/21/2013 02:23 PM, Gregory Kirk wrote: Greetings lords of freesurfer! I am having a problem getting a combined cvs warp+bbregister to map an FA volume onto a template. mri_vol2vol

Re: [Freesurfer] mri_vol2vol

Thanks Doug! However, now I'm getting the following error: *Resampling Output registration matrix is identity mri_vol2vol done ERROR: canot find norm* I am running: *xhemireg --s fsaverage --reg* Any suggestions? Should I run the following from $SUBJECTS_DIR/fsaverage/mri/?

Re: [Freesurfer] mri_vol2vol

when did you update the xhemi scripts last? Do a search on our wiki for xhemi to get pointers to the most recent ones On 10/02/2012 01:59 PM, Andrew Bock wrote: Thanks Doug! However, now I'm getting the following error: /Resampling Output registration matrix is identity mri_vol2vol done

Re: [Freesurfer] mri_vol2vol

I updated all the xhemi scripts following: http://www.freesurfer.net/fswiki/Xhemi but unfortunately the problem persists for fsaverage, since norm.mgz does not exist for fsaverage. I'm going to try creating norm.mgz for fsaverage to see if xhemireg works. Even if it doesn't, xhemireg does work

Re: [Freesurfer] mri_vol2vol

why are you running xhemireg for fsaverage? On 10/02/2012 06:04 PM, Andrew Bock wrote: I updated all the xhemi scripts following: http://www.freesurfer.net/fswiki/Xhemi but unfortunately the problem persists for fsaverage, since norm.mgz does not exist for fsaverage. I'm going to try

Re: [Freesurfer] mri_vol2vol

I have a custom overlay on the left hemisphere of fsaverage, I wanted to resample that overlay onto the right hemisphere. I thought it would save time to run xhemireg once for fsaverage, and then resample the left and right fsaverage overlays onto the left and right hemispheres for all my

[Freesurfer] mri_vol2vol

Hello, I'm having a problem similar to the one outlined here: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024182.html When I run xhemireg I receive the error ERROR: Option --keep-precision unknown I looked for the newer version of mri_vol2vol described in the previous post,

Re: [Freesurfer] mri_vol2vol

I just put a new version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol doug On 10/1/12 10:56 PM, Andrew Bock wrote: Hello, I'm having a problem similar to the one outlined here: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024182.html

[Freesurfer] mri_vol2vol not downsampling when applying a morph and a rigid registration matrix

Hi Freesurfers, I am struggling to get mri_vol2vol to downsample when I apply an inverse morph and an inverse registration matrix. Specifically, I am bringing a volume in cvs_avg35 space back into an individual subject's functional space. I have already registered the subject's functional to

[Freesurfer] mri_vol2vol

Hellom I coregistered manually a aparc+aseq.nii file to my DWI-space with tkregister2. I saved the .dat file and applied it later to the T1 image in order to apply the same spatial coregistration as to the aparc+aseg. For woth the aparc+aseg and the T1 I used the command mri_vol2vol --mov

Re: [Freesurfer] mri_vol2vol

Hi Constantin, When you used tkregister2 which volume was the target? Acoording to what you write it was the b0 volume. So when you apply the registration to the T1 volume, you should keep it that way. --mov T1 --targ b0image and no -inv is necessary. Let me know if I misunderstood what you

Re: [Freesurfer] mri_vol2vol

Hello Lilla, thanks for the answer. I first used bbregister --s (Freesurfer Directory) --mov b0.nii --reg .dat --dti --init-fsl Afterwards I made some minor spatial changes to the aparc+aseg, bringing it closer to what i believed its position was on the b0space: tkregister2 --mov b0.img --reg

Re: [Freesurfer] mri_vol2vol

Hi Constantin, No, now I understand what you were doing. The T1 / aparc+asge space is your target and the diffusion space is the moving one. Your mri_vol2vol setup should be accurate as you indicated originally. I think the problem might be that the 2nd registration file that you are saving