Re: [Freesurfer] Registration in PETSurfer

bbregister is more sensitive to the smoothing in the PET images. This can create a confound between atrophy and registration. bbregister should only be used on non-smoothed data. On 5/1/2024 5:06 AM, Ruben Dörfel wrote: External Email - Use Caution Hi FreeSurfer Team, I am

[Freesurfer] Registration in PETSurfer

External Email - Use Caution Hi FreeSurfer Team, I am currently using PETSurfer to analyze FDG data. Following the guide

Re: [Freesurfer] Registration of MPF to FLASH 3D image

Of *ERNEST KISSI *Sent:* Thursday, January 11, 2024 3:54 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Registration of MPF to FLASH 3D image *External Email - Use Caution * Dear Freesurfer team, I messaged the team

Re: [Freesurfer] Registration of MPF to FLASH 3D image

A T1-weighted FLASH should work. When you say “it did not work” what do you mean? Can you give us some details? Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of ERNEST KISSI Sent: Thursday, January 11, 2024 3:54 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer

[Freesurfer] Registration of MPF to FLASH 3D image

External Email - Use Caution Dear Freesurfer team, I messaged the team on my MPF map analysis and a suggestion was made that I register the MPF maps on the T1 MPRAGE images. However, I did not acquire MPRAGE but FLASH images. Can I used those instead ? Again, I tried even using

Re: [Freesurfer] registration of a rescaled volume

Do you just need to change the voxel size for that dimension? If so, you can use mri_convert, something like mri_convert -iis newvoxsize input.mgz output.mgz where -iis means the change the voxel size of the first dimension. Use -ijs or -iks for the 2nd and 3rd. You may have to play with it to

[Freesurfer] registration of a rescaled volume

External Email - Use Caution Hi there, I have an animal brain's MRI with 3 volumes, each with a good resolution in one of the planes. (i. 768x768x88, ii. 768x768x150, iii. 768x768x140) As far as I understand freeSurfere doesn't have a 3D ihgh-res reconstruction tool, right?

Re: [Freesurfer] registration error (reCAPTCHA not checked)

. Best! Lizhao Du School of Biomedical Engineering, Shanghai Jiao Tong University lizhao...@sjtu.edu.cn From: fsbuild Date: 2023-09-07 09:04 To: freesurfer Subject: Re: [Freesurfer] registration error (reCAPTCHA not checked) External Email - Use Caution The captcha

Re: [Freesurfer] registration error (reCAPTCHA not checked)

Engineering, Shanghai Jiao Tong University lizhao...@sjtu.edu.cn From: fsbuild Date: 2023-09-07 09:04 To: freesurfer Subject: Re: [Freesurfer] registration error (reCAPTCHA not checked) External Email - Use Caution The captcha authentication will not work if javascript

Re: [Freesurfer] registration error (reCAPTCHA not checked)

External Email - Use Caution The captcha authentication will not work if javascript is blocked from running in your browser. Check that you browser preferences are not set to block/filter javascript in its preferences and/or by using some added browser extension. I’m not aware

[Freesurfer] registration error (reCAPTCHA not checked)

External Email - Use Caution Hi there, I am Oscar. Recently I am using FreeSurfer for fMRI data analysis. A license is required yet I could not get the license.txt from my e-mail. After filling the form from

[Freesurfer] Registration open: FSL Course 2023 - Sept 11th-22nd

External Email - Use Caution Dear all, Registration is now open for FSL Course 2023, which will be held fully online, 11th - 22nd September 2023. You can find details and registration info here:

[Freesurfer] Registration, abstracts, & investigator-led abstracts open for INCF Neuroinformatics Assembly 2023!

External Email - Use Caution Dear FreeSurfers, Apologies for the cross-posting! Join us for Assembly, hosted once again on the Gather platform! We are currently looking for speakers for two investigator-led sessions, poster presenters, and of course Assembly registrants.

[Freesurfer] Registration did not converge in 5 steps

External Email - Use Caution Dear Freesurfer Experts I am trying use segmentHA_T1.sh: During the registration of imageDump.mgz to target hippoAmygBinaryMask_autoCropped.mgz, I get the warning: * WARNING: Registration did not converge in 5 steps! * Problem might be

Re: [Freesurfer] Registration from FreeSurfer to HCP842 Space

You definitely do not want to use mni152.register.dat for this (I'm surprised it even got close). Instead, register the orig.mgz to the HCP842 template space, eg, with mri_coreg --mov orig.mgz --targ HCP842.template.nii.gz --dof 12 --reg reg.HCP842.lta This will print out a tkregisterfv command

[Freesurfer] Registration from FreeSurfer to HCP842 Space

External Email - Use Caution Dear FreeSurfer Team, Hope you are doing well! I've run into an issue I hope you can help me with. After running recon-all on my subjects, I proceeded with the thalamic segmentation step. I'm specifically interested in extracting the mediodorsal (MD)

Re: [Freesurfer] Registration file types confusion

you can use lta_convert with the --outreg option On 3/27/2020 3:20 PM, Xiaojiang Yang wrote: External Email - Use Caution Hi Douglas, The link you gave to me (https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems) has some information about .dat file, but no information about

Re: [Freesurfer] Registration file types confusion

External Email - Use Caution Hi Douglas, The link you gave to me ( https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems) has some information about .dat file, but no information about .lta file at all. I

Re: [Freesurfer] Registration file types confusion

Part of you answer can be found here https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems tkregister2 and the .dat file format are obsolete, use tkregisterfv. This is just a front-end for FreeView; it always uses LTA. I'm not sure if there is documentation for the LTA format. The first

[Freesurfer] Registration file types confusion

External Email - Use Caution Hi everyone, I am confused by the two types of registration files: .lta and .dat. .dat file is simpler and easier to understand. But for the .lta files, there seems to be no detailed explanation regarding it. Can anyone point out to me where can I

Re: [Freesurfer] Registration of DIR (Double Inversion Recovery) series

yes, your command looks correct On 3/3/2020 2:05 PM, Xiaojiang Yang wrote: External Email - Use Caution Hi all, I want to register DIR (Double Inversion Recovery) series to T1 series using Freesurfer. I used the command line similar to that used for FLAIR registration: bbregister

[Freesurfer] Registration of DIR (Double Inversion Recovery) series

External Email - Use Caution Hi all, I want to register DIR (Double Inversion Recovery) series to T1 series using Freesurfer. I used the command line similar to that used for FLAIR registration: bbregister --s subject001 --mov

Re: [Freesurfer] Registration error

Help Date: Monday, February 24, 2020 at 11:16 AM To: FS Help Subject: [Freesurfer] Registration error External Email - Use Caution Hi, I’m trying to learn to use Freesurfer to see if I can use it for some academic work on TBI. I downloaded it to a spare laptop at home, and

[Freesurfer] Registration error

External Email - Use Caution Hi, I'm trying to learn to use Freesurfer to see if I can use it for some academic work on TBI. I downloaded it to a spare laptop at home, and filled out the registration form, and I got a message that stated "Registration Error: Spammer. Go

Re: [Freesurfer] registration of dwi images

, January 18, 2020 6:52:10 PM To: Freesurfer support list Subject: [Freesurfer] registration of dwi images External Email - Use Caution Hello! I have run eddy on all my dwi images and then run bbregister using the first b0 image as the source image. The b0 image is now well aligned

[Freesurfer] registration of dwi images

External Email - Use Caution Hello! I have run eddy on all my dwi images and then run bbregister using the first b0 image as the source image. The b0 image is now well aligned with the anatomical image but how can I apply the same transformation to all other dwi images in my

[Freesurfer] registration

External Email - Use Caution Instead of mri_cvs_register Which type of registration is more accurate or coparative to this. Best Regards Nader ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] registration with bbr and determination of motion regressors with mcdat2mcextreg

That is fine. I don't think that there are any conventions you need to follow (it should just be an Nx6 matrix On 6/13/2019 8:45 PM, Pfannmoeller, Joerg Peter wrote: Hello, I have used bbr to register all EPI volumes in my time series to the brains of my participants. The fMRI time series at

Re: [Freesurfer] Registration of image volumes

External Email - Use Caution Okay, thank you. On Fri, Jun 21, 2019 at 2:24 PM Bruce Fischl wrote: > Hi Shrabani > > I really don't know - I don't have any experience registering skulls. > sorry > Bruce > > On > Fri, 21 Jun 2019, Shrabani Ghosh wrote: > > > > > External

Re: [Freesurfer] Registration of image volumes

Hi Shrabani I really don't know - I don't have any experience registering skulls. sorry Bruce On Fri, 21 Jun 2019, Shrabani Ghosh wrote: External Email - Use Caution I am using elastix. And I think it does something similar like ANTS. Do you think I should get the

Re: [Freesurfer] Registration of image volumes

External Email - Use Caution I am using elastix. And I think it does something similar like ANTS. Do you think I should get the proper output using elastix? On Fri, Jun 21, 2019 at 1:01 PM Shrabani Ghosh wrote: > Okay Thank You for your all the responses. > > On Fri, Jun 21,

Re: [Freesurfer] Registration of image volumes

External Email - Use Caution Okay Thank You for your all the responses. On Fri, Jun 21, 2019 at 12:50 PM Bruce Fischl wrote: > Hi Shrabani > > you can read about FS on our wiki. We generally require a T1-weighted MRI > as input and build models of lots of things from it

Re: [Freesurfer] Registration of image volumes

Hi Shrabani you can read about FS on our wiki. We generally require a T1-weighted MRI as input and build models of lots of things from it (including skull, which will be more accurate if you also have a PD or T2-weighted image). cheers Bruce On Fri, 21 Jun 2019, Shrabani Ghosh wrote:  

Re: [Freesurfer] Registration of image volumes

External Email - Use Caution So in which case, freesurfer is applicable. Because I got a suggestion for CT to CT registration, I can use freesurfer. Thanks On Fri, Jun 21, 2019 at 12:42 PM Bruce Fischl wrote: > Hi Shrabani > > no, that's not really what I'm saying. In any

Re: [Freesurfer] Registration of image volumes

Hi Shrabani no, that's not really what I'm saying. In any case, I'm not sure FreeSurfer is the right tool for you to use for this. cheers Bruce On Fri, 21 Jun 2019, Shrabani Ghosh wrote: External Email - Use Caution So, you mean to say that two volumes need to be exactly

Re: [Freesurfer] Registration of image volumes

External Email - Use Caution So, you mean to say that two volumes need to be exactly same kind and having same information? So I have generated a skull foramina model(which is triangular mesh) from the fixed image volume. Now I want to register the model with a general patient

Re: [Freesurfer] Registration of image volumes

not unless you also have an image of the whole brain. Even then I'm not sure it will do what you want, although I'm still not clear on exactly what you are doing. Registering one image of the skull to a model? Why? On Fri, 21 Jun 2019, Shrabani Ghosh wrote: External Email - Use

Re: [Freesurfer] Registration of image volumes

External Email - Use Caution These are skull images of axial representation. Can't I use freesurfer? Because here interpolation is important. On Fri, Jun 21, 2019 at 11:58 AM Bruce Fischl wrote: > Hi Shrabani > > I'm not even sure what these are images of. If you are looking

Re: [Freesurfer] Registration of image volumes

Hi Shrabani I'm not even sure what these are images of. If you are looking for general-purpose registration tools you can try ANTS or something like that. cheers Bruce On Fri, 21 Jun 2019, Shrabani Ghosh wrote: External Email - Use Caution The fixed volume is my model

Re: [Freesurfer] Registration of image volumes

what kinds of volumes are they and why are you registering them? cheers Bruce On Thu, 20 Jun 2019, Shrabani Ghosh wrote: External Email - Use Caution Hi freesurfer, I want to do registration on two image volumes nifti file. What are the commands I have to use to do the

[Freesurfer] Registration of image volumes

External Email - Use Caution Hi freesurfer, I want to do registration on two image volumes nifti file. What are the commands I have to use to do the registration? Shrabani Ghosh ___ Freesurfer mailing list

[Freesurfer] registration with bbr and determination of motion regressors with mcdat2mcextreg

Hello, I have used bbr to register all EPI volumes in my time series to the brains of my participants. The fMRI time series at each vertex was determined based on this registration. I would like to use motion regressors in the GLM analysis. Is it appropriate to extract the motion parameters

Re: [Freesurfer] registration and resampling in native space

External Email - Use Caution Hi Doug, Sorry to bother, maybe my last message got lost. Do you think you can advice me on this type of registration? Thanks! Best Francesca On Fri, Feb 22, 2019, 11:44 PM Francesca Strappini < francescastrapp...@gmail.com> wrote: > What is the

Re: [Freesurfer] registration and resampling in native space

External Email - Use Caution What is the best procedure? I really have no idea, I've been tried so many things but nothing worked... Il giorno ven 22 feb 2019 alle ore 23:41 Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> ha scritto: > You will need to either get the ROIs into

Re: [Freesurfer] registration and resampling in native space

You will need to either get the ROIs into the anatomical space or compute a new registration to the space of the ROIs from the functional template On 2/22/19 3:43 PM, Francesca Strappini wrote: External Email - Use Caution Thanks! The vox2ras matrices are not same. This is one region:

Re: [Freesurfer] registration and resampling in native space

External Email - Use Caution Thanks! The vox2ras matrices are not same. This is one region: francesca@shalimpc:~/Desktop/sub3/ROIs$ mri_info sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz Volume information for sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz type:

Re: [Freesurfer] registration and resampling in native space

That looks right. Can you verify that the seg (sourcedata...) is in the conformed anatomical space? Use mri_info can compare the output (particularly the vox2ras matrix) against orig.mgz. If they are the same, you can try adding --invertmtx to the mri_label2vol command line. On 2/22/19 2:24

Re: [Freesurfer] registration and resampling in native space

External Email - Use Caution Thanks a lot, Doug! I run the preprocessing: preproc-sess -surface sub3 lhrh -fwhm 0 -s sub3 -fsd bold -per-session And the runs look well registered. Then I run mri_label2vol: mri_label2vol --seg

Re: [Freesurfer] registration and resampling in native space

There should be a registration file called register.dof6.lta. Use that with mri_label2vol passing your segmentation in with --seg. Run with --help to get more info On 2/21/19 11:54 AM, Francesca Strappini wrote: External Email - Use Caution Thanks a lot! Running preproc-sess with the

Re: [Freesurfer] registration and resampling in native space

External Email - Use Caution Thanks a lot! Running preproc-sess with the --per-session flag is exactly was I was looking for! Now that my functional runs are correctly registered to a reference image (so, to each other) I need to register them to a dataset of ROIs that were

Re: [Freesurfer] registration and resampling in native space

Yes,  if you run it with the --targ as orig.mgz for the given subject, then it will sample each run into the anatomical space (this can create enourmous data data files!). Alternatively, you can run preproc-sess with the --per-session flag and it will align all the runs to a single template

Re: [Freesurfer] registration and resampling in native space

External Email - Use Caution I'll try to find some visual way to show what I mean, but it's really something mild and probably negligible. Do you know if is it possible with mri_vol2vol to give to all the runs that belong to the same subject the same system coordinates? So that

Re: [Freesurfer] registration and resampling in native space

Hi Francesca can you send us an image that shows why you think it can be improved? cheers Bruce On Mon, 18 Feb 2019, Francesca Strappini wrote: External Email - Use Caution Thank you!Now the registration is better but still not perfect. Is there a way to improve it? Best

Re: [Freesurfer] registration and resampling in native space

External Email - Use Caution Thank you! Now the registration is better but still not perfect. Is there a way to improve it? Best Il giorno gio 14 feb 2019 alle ore 23:30 Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> ha scritto: > Is func_data.nii.gz an fMRI scan? If so,

Re: [Freesurfer] registration and resampling in native space

Is func_data.nii.gz an fMRI scan? If so, wouldn't be T2 weighted? If so, you should use --t2 instead of --t1 in bbregister On 2/14/19 2:18 PM, Francesca Strappini wrote: > > External Email - Use Caution > > Hi Doug, > > Could you advise me about how to correctly run mri_vol2vol? > The

Re: [Freesurfer] registration and resampling in native space

External Email - Use Caution Hi Doug, Could you advise me about how to correctly run mri_vol2vol? The functional data did not get perfectly registered to the anatomy so I'm afraid I'm not running it correctly. Thanks! Il giorno mar 12 feb 2019 alle ore 17:21 Bruce Fischl <

Re: [Freesurfer] FreeSurfer Registration Error

m: * on behalf of Peng Wang < > pen...@gmail.com> > *Reply-To: *FS Help > *Date: *Wednesday, February 13, 2019 at 12:54 PM > *To: *FS Help > *Subject: *[Freesurfer] FreeSurfer Registration Error > > > > *External Email - Use Caution* > > Whateve

Re: [Freesurfer] FreeSurfer Registration Error

Hi, what are you trying to register for? A wiki account? Andrew From: on behalf of Peng Wang Reply-To: FS Help Date: Wednesday, February 13, 2019 at 12:54 PM To: FS Help Subject: [Freesurfer] FreeSurfer Registration Error External Email - Use Caution Whatever I filled the form I

[Freesurfer] FreeSurfer Registration Error

External Email - Use Caution Whatever I filled the form I got "Spammer. Go away!" message. Please help! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] registration and resampling in native space

Hi Francesca sorry, I defer to Doug on the details of mri_vol2vol. cheers Bruce On Tue, 12 Feb 2019, Francesca Strappini wrote: External Email - Use Caution Thank you for the reply! I run: mri_vol2vol --reg register.dat --mov func_data.nii.gz --targ

Re: [Freesurfer] registration and resampling in native space

External Email - Use Caution Thank you for the reply! I run: mri_vol2vol --reg register.dat --mov func_data.nii.gz --targ /usr/local/freesurfer/subjects/sub3/mri/T1.mgz --o func_data_registered2T1.nii.gz --no-resample Then I checked the registration and it seems that the original

Re: [Freesurfer] registration and resampling in native space

Hi Francesca check out the --no-resample option in mri_vol2vol. It just changes the header, so I think should do what you want. cheers Bruce On Tue, 12 Feb 2019, Francesca Strappini wrote: External Email - Use Caution Dear Freesurfer's experts, I would like to register

[Freesurfer] registration and resampling in native space

External Email - Use Caution Dear Freesurfer's experts, I would like to register some functional data to the T1, that were collected in separate days. I used bbregister: bbregister --s sub3 --mov func_data.nii.gz - --reg register.dat --init-coreg --t1 Now, I would like to

Re: [Freesurfer] Registration

Hi Nazanin 1. The registration is only one step in how we do segmentation, so I wouldn't suggest just using it. If you can convert your registration to .m3z format and put it in the subjects transforms/talairach.m3z you could try running from there forward. 2. Yes, you can edit the aseg in

Re: [Freesurfer] Registration

Hi Bruce as you explain I did the registration somewhere else and now I have the labels_gca in my subject space. 1. is it possible to somehow import this file in freesurfer and run the rest of the analysis ? 2.my question in general is that : can I in anyway do any correction for aseg outputs

Re: [Freesurfer] Registration

Hi Nazanin the nonlinear registration is actually to our segmentation atlas (*.gca). I guess you could try using something else, but you should extract a mean intensity image from the gca as a target, not the MNI305. You can do this with: mri_convert -nth 0 .gca mean_gca.mgz FYI, this:

[Freesurfer] Registration

Dear Experts, In the volume-based stream, if I'm right the FreeSurfer does two registration with MNI305 ,one affine and one nonlinear , is it possible to perform the nonlinear registration somewhere else and then use the result in FreeSurfer and run the rest of the analysis ? thank's alot for

Re: [Freesurfer] Registration of both the brain and the "surf" files to the same template.

you can try mri_coreg with --dof 7 On 4/4/17 2:31 AM, Paolo wrote: For further clarity, we want to evaluate the geometric distortions to test how robust different sequences are to the local magnetic filed/susceptibility variations. So we want to keep the image as untouched as possible, but

Re: [Freesurfer] Registration of both the brain and the "surf" files to the same template.

For further clarity, we want to evaluate the geometric distortions to test how robust different sequences are to the local magnetic filed/susceptibility variations. So we want to keep the image as untouched as possible, but possibly aligned for comparison. Is there an option in FS to register an

Re: [Freesurfer] Registration of both the brain and the "surf" files to the same template.

for volumes you can use either mri_convert -at or mri_vol2vol. For surfaces I think mris_transform should do the trick (and possibly mri_surf2surf, but I defer to Doug on this) Bruce On Fri, 31 Mar 2017, Paolo wrote: Thank you for your answer. I don't want the transformation to

Re: [Freesurfer] Registration of both the brain and the "surf" files to the same template.

Thank you for your answer. I don't want the transformation to distort my image. Is there a command to "apply" the transformation to both the files? Like: $brainmask.mgz brainmask_registered.mgz --apply_transf talairach.lta $lh.white lh_registered.white --apply_transf talairach.lta I

Re: [Freesurfer] Registration of both the brain and the "surf" files to the same template.

Hi Paolo if a linear transform is sufficient for your purposes you could just use the talairach.lta in the subjects/transforms dir. If you want nonlinear you could use talairach.m3z, but it will distort things (of course) cheers Bruce On Fri, 31 Mar 2017, Paolo wrote: > > TO:

[Freesurfer] Registration of both the brain and the "surf" files to the same template.

TO: freesurfer@nmr.mgh.harvard.edu SUBJECT: Registration of both the brain and the "surf" files to the same template. AIM: register e.g. brainmask.mgz and ?h.white for many subjects all to the same template, so that I can then take slices of brainmask.mgz and the superimposed WM surface accross

Re: [Freesurfer] registration for AD, MD and RD images

<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fis...@nmr.mgh.harvard.edu> Sent: Thursday, March 16, 2017 3:57:57 PM To: Freesurfer support list Subject: Re: [Freesurfer] registration for AD, MD and RD images Hi Shiran if you have the FA registered why do you need

Re: [Freesurfer] registration for AD, MD and RD images

Hi Shiran if you have the FA registered why do you need to recompute the transform for the other volumes? They are all derived from the same underlying data so should all be in perfect register with each other and hence should share a registration transform. cheers Bruce On Thu, 16 Mar

Re: [Freesurfer] Registration: Variable Must Begin with a Letter Error

Hi Anderson, Please supply the command input and the error as well as the previous correspondence. Thanks d Sent from my Phone > On Jan 26, 2017, at 16:10, Anderson Napolitano > wrote: > > ​Thank you Dr. Greve and Don. Unfortunately adding '\' after spaces and

Re: [Freesurfer] Registration: Variable Must Begin with a Letter Error

hi, please include previous correspondence so that we know what you are referring to On 01/26/2017 04:10 PM, Anderson Napolitano wrote: > ​Thank you Dr. Greve and Don. Unfortunately adding '\' after spaces > and removing the spaces all together doesn't seem to resolve the said > error. > > >

[Freesurfer] Registration: Variable Must Begin with a Letter Error

?Thank you Dr. Greve and Don. Unfortunately adding '\' after spaces and removing the spaces all together doesn't seem to resolve the said error. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Registration: Variable Must Begin with a Letter Error

> Sent: Wednesday, January 25, 2017 4:53 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Registration: Variable Must Begin with a Letter > Error > > > In the terminal output it says that your movable volume is > > > /Users/djsandoval/Desktop/Se

Re: [Freesurfer] Registration: Variable Must Begin with a Letter Error

In the terminal output it says that your movable volume is /Users/djsandoval/Desktop/Selwyn/M87127996-2016004/Baseline/PETCT/PET/PET BRAIN TOF STATIC 2/2016004A/IM-0001-0001.dcm not template.nii.gz. In principle, that should be fine, except that there are spaces in the path On 01/25/2017

[Freesurfer] Registration: Variable Must Begin with a Letter Error

Hello Experts! I am having trouble checking the registration per step 2 of the pet surfer tutorial: http://freesurfer.net/fswiki/PetSurfer. The line: mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta worked just fine but when checking the registration using the line:

Re: [Freesurfer] Registration Checking Problems

Can you run it with --debug as the first option and send me the terminal output? On 01/19/2017 12:38 PM, Anderson Napolitano wrote: > > Good Morning Experts, > > > I am having trouble checking the registration per step 2 of the pet > surfer tutorial: http://freesurfer.net/fswiki/PetSurfer. The

[Freesurfer] Registration Checking Problems

Good Morning Experts, I am having trouble checking the registration per step 2 of the pet surfer tutorial: http://freesurfer.net/fswiki/PetSurfer. The line: mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta worked just fine but when checking the registration using the line:

Re: [Freesurfer] Registration

Hi Bob, We are moving towards only using m3z files and the only reason you still see tm3d files in your output is that you are using the --nocleanup flag so all intermediate results are kept in your output directory. So this means that you will not need to use the applyMorph tool. The two

[Freesurfer] Registration

My ultimate goal is apply the CVS transforms to ROIs (similar to aseg.mgz) that are defined in MNI space to anatomical space. Unfortunately, I am having trouble doing this. As a start I am trying to transform my T1w image to MNI space. My understanding so far is that I need to do the

Re: [Freesurfer] FreeSurfer registration tool in ASL image

I don't think robust register will work as that assumes that the modalites are the same. You can try using mri_coreg, which you can find here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg On 09/08/2016 03:51 PM, Frank Robert wrote: > Hello FreeSurfer expert > > I

Re: [Freesurfer] Registration of low-resolution EPI time series to CVS MNI (avoiding resampling)

first, you'll need to get two new things: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/cvs152.mri2.mm.tar.gz ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol cd $FREESURFER_HOME/subjects/cvs_avg35_inMNI152 tar xvfz cvs152.mri2.mm.tar.gz # Make a backup

[Freesurfer] Registration of low-resolution EPI time series to CVS MNI (avoiding resampling)

Hi Freesurfer (FS) users, I am a new user in the world of FS and I am trying to normalize rsfMRI EPI series to CVS MNI space. I would like to do it without resampling the EPI images to 1*1*1mm3 resolution. I've registered EPI series to FS T1 space by using following command (after bbregister),

Re: [Freesurfer] registration of intraparietal sulcus

too sad! Thank you anyway - I'll try my luck with matlab. Bastian. On 30 April 2016 at 17:43, Douglas Greve wrote: > I don't have anything to do this. > > On 4/30/16 10:26 AM, Bruce Fischl wrote: >> not that I know of, but Doug might have something. I would do it in

Re: [Freesurfer] registration of intraparietal sulcus

I don't have anything to do this. On 4/30/16 10:26 AM, Bruce Fischl wrote: > not that I know of, but Doug might have something. I would do it in matlab > I guess > > On Sat, 30 Apr 2016, Bastian Cheng wrote: > >> Hi Bruce! >> >> sounds good, thank you! >> >> is there a specific command to do

Re: [Freesurfer] registration of intraparietal sulcus

not that I know of, but Doug might have something. I would do it in matlab I guess On Sat, 30 Apr 2016, Bastian Cheng wrote: > Hi Bruce! > > sounds good, thank you! > > is there a specific command to do that? I would guess that I would > have to mask the sulc image with my label

Re: [Freesurfer] registration of intraparietal sulcus

Hi Bruce! sounds good, thank you! is there a specific command to do that? I would guess that I would have to mask the sulc image with my label (S-intrapariet_and_P_trans) Bastian On 29 April 2016 at 14:46, Bruce Fischl wrote: > Hi Bastien > > maybe it would be

Re: [Freesurfer] registration of intraparietal sulcus

Hi Bastien maybe it would be easier and more accurate to extract the S_inrapriet_and_P_trans then use sulc to remove any vertices that are < 0 (that is, are not sulcal)? cheers Bruce On Fri, 29 Apr 2016, Bastian Cheng wrote: > Dear all, > > I am creating a hand-drawn label of the

[Freesurfer] registration of intraparietal sulcus

Dear all, I am creating a hand-drawn label of the Intraparietal sulcus on fsaverge. When I register it to an individual brain (mri_label2label), the area is incorrectly registered and comprises adjacent brain structures that I am not interested in analyzing (specially the neighboring sulci). I

Re: [Freesurfer] registration errors in longitudinal analysis

Hi Lara, the longitudinal pipeline is designed for adults with the assumption that head size is fixed. We are working on a new pipeline that will allow processing of images from children, but that will take a while. Especially considering that there will be large differences in the brain as

[Freesurfer] registration errors in longitudinal analysis

Dear Freesurfer experts, I am working on a longitudinal analysis of cortical structure and am experiencing some errors with registration. I have 3 timepoints for each participant: time 1: age 2 time 2: age 5 time 3: age 10 Time 1 and 2 are from a 1.5T scanner. Time 3 is from a 3T scanner.

Re: [Freesurfer] registration format conversion

Alright, got it working! Thanks! Any chance I can also get the mri_concatenate_lta mentioned here? http://ftp.nmr.mgh.harvard.edu/pub/docs/wiki/lta_convert.help.xml.html stephen *stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA //

Re: [Freesurfer] registration format conversion

here you go ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/lta_concatenate_lta On 11/10/2015 07:13 PM, S.V.Shepherd [work] wrote: > Alright, got it working! Thanks! > > Any chance I can also get the

Re: [Freesurfer] registration format conversion

try this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_concatenate_lta On 11/10/2015 07:31 PM, S.V.Shepherd [work] wrote: > I think that one got garbled slightly. Can you try again? > > _stephen v. shepherd phd_ > The Rockefeller University / 1230 York Avenue / New

Re: [Freesurfer] registration format conversion

I think that one got garbled slightly. Can you try again? *stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7699 On Tue, Nov 10, 2015 at 7:29 PM, Douglas N Greve wrote: > here you go > >

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