[Freesurfer] mri_convert - returns different image size

Dear all, I want to use N3 on nifti images, and I have different versions installed on two machines. On one machine I have an older version of N3 (1.7.2.2) which uses mri_convert version 4 and everything works fine. On the other machine I have N3 version 1.12 which uses mri_convert version 5;

[Freesurfer] mri-convert

Hi, all,I would like to convert my DTI images from the REC-PAR format to .nii, so I could use in TRACULA and also other tools from freesurfer.Is it possible? What is the right comand line to do so?After the transformation, which image I use to register in the freesurfer domain?Thank you, Carolina

Re: [Freesurfer] Edit Capability of Freeview

Hi Richard, Freeview does not have voxel cloning function between anatomical volumes. It will be added in the future release. The reference option is for boundary finding for flood fill and automatic contour finding when editing labels. Best, Ruopeng On 4/23/12 9:28 PM, Richard Binney

Re: [Freesurfer] mri_convert - returns different image size

Hi Veronica can you send us the command line you are using? N3 by itself doesn't use mri_convert - our wrappers do. cheers Bruce On Tue, 24 Apr 2012, Popescu, V. wrote: Dear all, I want to use N3 on nifti images, and I have different versions installed on two machines. On one machine I

Re: [Freesurfer] mri_convert - returns different image size

Dear Bruce, Sorry about this! I use mri_nu_correct.mni and the versions (1.7.2.2 and 1.12 respectively) are the versions of the wrapper. Thank you! Best wishes, Veronica -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: dinsdag 24 april 2012 15:25 To:

Re: [Freesurfer] mri_convert - returns different image size

thanks. And can you tell us what you are trying to achieve? If it's just running the recons then it shouldn't matter if it's resampled to 256^3 On Tue, 24 Apr 2012, Popescu, V. wrote: Dear Bruce, Sorry about this! I use mri_nu_correct.mni and the versions (1.7.2.2 and 1.12 respectively) are

Re: [Freesurfer] mri_convert - returns different image size

I want to run N3 on it and then use it with FSL, and apply some masks on it (that are the size of the original image). -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: dinsdag 24 april 2012 15:50 To: Popescu, V. Cc: 'freesurfer@nmr.mgh.harvard.edu'

Re: [Freesurfer] mri_convert - returns different image size

I see. Then why use our wrapper at all? Just convert to nifti and run N3 directly. On Tue, 24 Apr 2012, Popescu, V. wrote: I want to run N3 on it and then use it with FSL, and apply some masks on it (that are the size of the original image). -Original Message- From: Bruce Fischl

Re: [Freesurfer] mri_convert - returns different image size

I'll try that. Thank you! -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: dinsdag 24 april 2012 16:24 To: Popescu, V. Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: RE: [Freesurfer] mri_convert - returns different image size I see. Then why use our wrapper

Re: [Freesurfer] bbregister for fmri FEAT data

What images are mismatched? Specifically, which anatomical image are you loading into fslview? If you have not loaded the orig.mgz (converted to nii), then there will be be a mismatch. doug On 04/24/2012 04:29 AM, Erlend Hodneland wrote: Hi again, We are trying to do the same as was done

Re: [Freesurfer] your insight: parameter definition and --tnullmin necessary?

On 04/24/2012 07:34 AM, Betina Ip wrote: Dear Doug, Thank you for your excellent answers, they are very helpful. Please allow me to summarise and ask for additional clarification: 1) The main problem I'd like to solve is, as you spotted, whether the sequence will have required power to

Re: [Freesurfer] How to convert a surface to volume space after using mris_preproc?

How does it look in tkmedit? On 04/23/2012 12:20 PM, Long wrote: Hi Douglas, I tried to do spatial normalization for volume data, all steps are following: 1) bbregister --mov fsubj01_rest_res_co_001.hdr --bold --s subj01 --init-fsl --reg bb_register.dat I checked the result by

[Freesurfer] labels export

Hello FreeSurfers,Does any one of you know if exist a function to export labels as a ROI format?Regards,Gabriel-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de

Re: [Freesurfer] labels export

Hi Gabriel, Have you tried mri_label2vol? If you want the volume in the anatomical space: mri_label2vol --label labelname.label --temp T1_template.nii.gz --identity --o volumename.nii.gz If you want it in some other space, you can specify the registration matrix using --reg and the template

Re: [Freesurfer] labels export

Thanks Priti,I've thought about that before, but actually I'm looking for literally .roi images, do you know if is this format possible from FS?Regards,GabrielEl 24/04/12, Priti Srinivasan rspr...@nmr.mgh.harvard.edu escribió:Hi Gabriel,Have you tried mri_label2vol?If you want the volume in the

Re: [Freesurfer] labels export

I don't think so. What is .roi format? On 04/24/2012 12:21 PM, Gabriel Gonzalez Escamilla wrote: Thanks Priti, I've thought about that before, but actually I'm looking for literally .roi images, do you know if is this format possible from FS? Regards, Gabriel El 24/04/12, *Priti

Re: [Freesurfer] labels export

they are just ascii files so it should be easy enough to do yourself On Tue, 24 Apr 2012, Gabriel Gonzalez Escamilla wrote: Thanks Priti, I've thought about that before, but actually I'm looking for literally .roi images, do you know if is this format possible from FS? Regards, Gabriel

Re: [Freesurfer] mri_convert - returns different image size

Hi Veronica, If you still want to use mri_nu_correct.mni, but retain the original dimensions, you can include '--no-float' to the command line. i.e, mri_nu_correct.mni --i input_vol --o output_vol --no-float That should solve the problem. Regards, Sindhuja I'll try that. Thank you!

[Freesurfer] Running Tracula -bedpostx and -path

Hi Anastasia, I ran bedpost directly: bedpostx dmri It seemed to run fine, not exiting with any errors. the only thing that concerned me was that the last output in the terminal was 50 slices processed [when I have 54] queing post-processing stage then it exited. It seemed to run rather

[Freesurfer] Parcellation Colorscale

Hi- I'm looking to compare two parcellations (one is a stroke patient with her brain as is, the other is the same subject with the lesion fixed run as a separate subject). It would be helpful if the parcellations would color the same area the same color, but currently every single ROI is

Re: [Freesurfer] Parcellation Colorscale

Hi Sarah what parcellation do you mean? Our standard anatomically-based parcellatinos will color the same parcels the same color. cheers Bruce On Tue, 24 Apr 2012, Baum, Sarah H wrote: Hi- I'm looking to compare two parcellations (one is a stroke patient with her brain as is, the other

[Freesurfer] Editing Talairach registration with shear

Hi all, I just ran a recon that produced a Talairach registration error. Viewing the registration in tkregister2, it became clear that it was in fact quite off. I tried to fix the registration manually, but there is a substantial and inaccurate shear component, and I can't seem to adjust

Re: [Freesurfer] Parcellation Colorscale

Hi, Currently it's not doing that. I'm using the aparc.a2009s_rank file that I've aligned to the anatomy with @SUMA_AlignToExperiment. On 4/24/12 2:45 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Sarah what parcellation do you mean? Our standard anatomically-based parcellatinos

Re: [Freesurfer] Parcellation Colorscale

Hi Sarah can you look at the aparc.a2009s.annot in tksurfer and see if it looks right? Bruce On Tue, 24 Apr 2012, Baum, Sarah H wrote: Hi, Currently it's not doing that. I'm using the aparc.a2009s_rank file that I've aligned to the anatomy with @SUMA_AlignToExperiment. On 4/24/12

Re: [Freesurfer] Parcellation Colorscale

It might take me a little longer because our data is organized a little differently, but I will definitely check it out in tksurfer and get back to you on this. On 4/24/12 3:12 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Sarah can you look at the aparc.a2009s.annot in tksurfer and

Re: [Freesurfer] Parcellation Colorscale

Hi Sarah if it is correct, you'll probably need to bug Ziad and the SUMA guys about why the colors are wrong. If you are resampling the parcellation make sure it is done with nearest neighbor and not e.g. trilinear or sinc cheers Bruce On Tue, 24 Apr 2012, Baum, Sarah H wrote: It might take

[Freesurfer] mris_divide_parcellation

Hi Freesurfer users, Does anyone have a method to divide aseg.mgz volumetric regions along a longitudinal axis? Or a simple split after finding a center of mass of an ROI? I found that mris_divide_parcellation only splits up regions from the surface based segmentation as found in the desikan

Re: [Freesurfer] trakula segmentation fault

Hi Viviana - I cannot replicate this on our systems but I think I know what your system may be fussy about and I'll amend it. For now, if you don't get any outputs can you please try running bedpostx directly on /media/vivi/images/freesurfer/00112288Proc/dmri and see if that works?

Re: [Freesurfer] Running Tracula -bedpostx and -path

Hi Richard - I'd check your bedpostx output files, run mri_info on them to make sure they have the right number of slices. The monitoring script that produces the slices processed messages checks only every once in a while, so you won't see a separate message for each slice. The warnings

Re: [Freesurfer] mris_divide_parcellation

Hi Mario, I don't think we've ever written such a thing but it would be pretty straightfoward in matlab. sorry Bruce On Tue, 24 Apr 2012, Mario Ortega wrote: Hi Freesurfer users, Does anyone have a method to divide aseg.mgz volumetric regions along a longitudinal axis? Or a simple split

Re: [Freesurfer] Running Tracula -bedpostx and -path

Thanks - appears as if all is well. On Tue, Apr 24, 2012 at 4:02 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Richard - I'd check your bedpostx output files, run mri_info on them to make sure they have the right number of slices. The monitoring script that produces the