[Freesurfer] possible tkregister2 bugs on OSX 10.6

I couldn't get either of the built-in functions to work to check the registration between two volumes which should have been the same. I also noticed that the tkregister2 wiki pagecontains no info about the command, though it does have a link to

Re: [Freesurfer] Inverse projection query

Hello, I think that the problem may lie with MRIread. I have 1 x 82 Array of phase volumes. I also then have a separate 3 x 82 array of coordinates (that correspond to each of the normalized 0 to 1 phase values above. My question is: if I input the phases in vol, what field do I place the coo

Re: [Freesurfer] freeview and control points

You should be able to pick any location you want to save control point, when the file dialog shows up. As to default filename, there is no option to set it in freeview now. But I believe you only need to manually enter file name the first time you save it. Ruopeng On 2/4/11 6:47 PM, Bruce Fis

Re: [Freesurfer] Inverse projection query

Final question: My values are normalized: from 0 to 1 ... How do I change the overlay colours so that this is scaled correctly? I am assuming I have to make a file of some sort ... Thanks, I think I am almost there ... -jason. On 05/02/2011 01:03, "Bruce Fischl" wrote: try one '-' in '-over

Re: [Freesurfer] Inverse projection query

try one '-' in '-overlay', not two On Sat, 5 Feb 2011, Jason Connolly wrote: > Hi Bruce, > > I used mri_vol2surf, but there appears to be no overlay colours ... Here is > the output ... > > Any ideas would be great ... > > tksurfer bert rh inflated --overlay > /Applications/fesurfer/subjects/ber

Re: [Freesurfer] Inverse projection query

Hi Bruce, I used mri_vol2surf, but there appears to be no overlay colours ... Here is the output ... Any ideas would be great ... tksurfer bert rh inflated --overlay /Applications/fesurfer/subjects/bert/surf/test_LH.mgh WARNING: flag --overlay unrecognized WARNING: flag /Applications/freesurfe

Re: [Freesurfer] Inverse projection query

no, you can use it to sample volume data onto the surface using mri_vol2surf On Sat, 5 Feb 2011, Jason Connolly wrote: > Can I display register.dat in tksurfer? > > Thanks, -j. > > > On 05/02/2011 00:21, "Bruce Fischl" wrote: > > that writes the file named register.dat that has the affine regi

Re: [Freesurfer] Inverse projection query

Can I display register.dat in tksurfer? Thanks, -j. On 05/02/2011 00:21, "Bruce Fischl" wrote: that writes the file named register.dat that has the affine registration matrix (and some other things) On Sat, 5 Feb 2011, Jason Connolly wrote: > Hi Bruce, > > Here it is: > > bbregister --s bert

Re: [Freesurfer] Inverse projection query

that writes the file named register.dat that has the affine registration matrix (and some other things) On Sat, 5 Feb 2011, Jason Connolly wrote: > Hi Bruce, > > Here it is: > > bbregister --s bert --mov /Applications/freesurfer/subjects/bert/mri/f_RH.mgz > --reg register.dat --bold --init-hea

Re: [Freesurfer] Inverse projection query

Hi Bruce, Here it is: bbregister --s bert --mov /Applications/freesurfer/subjects/bert/mri/f_RH.mgz --reg register.dat --bold --init-header -jason. On 05/02/2011 00:18, "Bruce Fischl" wrote: can you send us your command line? On Sat, 5 Feb 2011, Jason Connolly wrote: > Hi Doug, > > I am now

Re: [Freesurfer] Inverse projection query

can you send us your command line? On Sat, 5 Feb 2011, Jason Connolly wrote: > Hi Doug, > > I am now at the bbregister stage ... I ran this but it is not clear to me > where the output is? I don't see an output flag ... > > Can you tell me where to look for my output? > > Almost there! > > Many

Re: [Freesurfer] Inverse projection query

Hi Doug, I am now at the bbregister stage ... I ran this but it is not clear to me where the output is? I don't see an output flag ... Can you tell me where to look for my output? Almost there! Many thanks, Jason. On 04/02/2011 23:49, "Jason Connolly" wrote: Thank you. -jason. On 04/02

Re: [Freesurfer] Inverse projection query

Thank you. -jason. On 04/02/2011 23:48, "Douglas N Greve" wrote: You can load in the functional with MRIread since you are going to be replacing all the pixel data anyway with your single time point. Just use the single argument. The second is if you dont want to read in the pixel data. Jason

Re: [Freesurfer] Inverse projection query

You can load in the functional with MRIread since you are going to be replacing all the pixel data anyway with your single time point. Just use the single argument. The second is if you dont want to read in the pixel data. Jason Connolly wrote: > Thanks. > > So, to clarify, I am trying to just

Re: [Freesurfer] freeview and control points

1. it definitely has to have thatt file name/location for recon-all to find it. I'll leave 2 and 3 for Ruopeng On Fri, 4 Feb 2011, Mehul Sampat wrote: > Hi Folks, > > We used to use tkmedit to add control points and recently started using > freeview. > I have a few basic questions about saving c

Re: [Freesurfer] Inverse projection query

Thanks. So, to clarify, I am trying to just make an overlay. So do I use MRIread with a functional .img as input? Is the second argument in MRIread my scanCoords for my phase-value pixels? Almost there ... On 04/02/2011 23:35, "Douglas N Greve" wrote: It's the vol field. doug Jason Conn

Re: [Freesurfer] Inverse projection query

It's the vol field. doug Jason Connolly wrote: > Hi Doug, > > You state: > > "then replace the pixel data with your > analyzed data" > > I cannot seem to find the field for the pixel data. Can you tell me where to > position these values? > > Thanks! -jason. > > > On 04/02/2011 18:15, "Douglas

Re: [Freesurfer] Inverse projection query

Hi Doug, You state: "then replace the pixel data with your analyzed data" I cannot seem to find the field for the pixel data. Can you tell me where to position these values? Thanks! -jason. On 04/02/2011 18:15, "Douglas N Greve" wrote: You should save it out as nifti (see MRIwrite.m and

[Freesurfer] freeview and control points

Hi Folks, We used to use tkmedit to add control points and recently started using freeview. I have a few basic questions about saving controls points created with freeview. 1. I noticed that in tkmedit edit controls points were saved as "control.dat" in the "subject_dir"/tmp (e.g. bert/tmp). When

Re: [Freesurfer] right hippocampus bad segmentation...

to fix the lack of wm there you mean? Maybe, or you might put a control point or two in the white matter, depending on how dark it is On Fri, 4 Feb 2011, Gonzalo Rojas Costa wrote: Hi Bruce: But, I must edit the wm.mgz file ?... Sincerely, Gonzalo Rojas Costa El 04-02-2011 15:11, Bruce

Re: [Freesurfer] right hippocampus bad segmentation...

Hi Bruce: But, I must edit the wm.mgz file ?... Sincerely, Gonzalo Rojas Costa El 04-02-2011 15:11, Bruce Fischl escribió: > either tkmedit or freeview, then run autorecon2 and 3 to regenerate the > surfaces. ___ Freesurfer mailing list Freesu

Re: [Freesurfer] right hippocampus bad segmentation...

Hi Bruce: But, I must edit the wm.mgz file ?... Sincerely, Gonzalo Rojas Costa El 04-02-2011 15:11, Bruce Fischl escribió: > either tkmedit or freeview, then run autorecon2 and 3 to regenerate the > surfaces. ___ Freesurfer mailing list Freesu

Re: [Freesurfer] Inverse projection query

You should save it out as nifti (see MRIwrite.m and MRIread.m). I would suggest using MRIread.m to read in your file in order to create the proper header information, then replace the pixel data with your analyzed data, then use MRIwrite.m to save it out. Then use bbregister to register this vo

Re: [Freesurfer] right hippocampus bad segmentation...

either tkmedit or freeview, then run autorecon2 and 3 to regenerate the surfaces. On Fri, 4 Feb 2011, Gonzalo Rojas Costa wrote: Hi Bruce: And which freesurfer tool must I use to manually correct it ?... And, how can I generate the aseg.stats file after the manual correction ?... Sincer

Re: [Freesurfer] right hippocampus bad segmentation...

Hi Bruce: And which freesurfer tool must I use to manually correct it ?... And, how can I generate the aseg.stats file after the manual correction ?... Sincerely, Gonzalo Rojas Costa El 04-02-2011 14:59, Bruce Fischl escribió: > you may need to manually correct it. There's not much we

Re: [Freesurfer] right hippocampus bad segmentation...

you may need to manually correct it. There's not much we can do when a big chunk of brain is missing On Fri, 4 Feb 2011, Gonzalo Rojas Costa wrote: Hi: Yes... The patient has a resection of the temporal lobe, and I think that produce the problem in the segmentation, but could I correct the s

Re: [Freesurfer] Inverse projection query

you should be able to use mri_surf2surf to map them all to fsaverage On Fri, 4 Feb 2011, Jason Connolly wrote: > Hi Bruce, > > I guess the problem I have at hand is how to map them to fsaverage. Do I > have to convert the arrays somehow to nifti format first? I tried looking > this up on the

Re: [Freesurfer] problem with spmregister on mac

The spm_flip_analyse_images.m was what I needed! Thanks so much! Katie On Fri, Feb 4, 2011 at 11:53 AM, Y.V. Jiang wrote: > It depends on which version of SPM you're running. It's either the file > called spm_defaults.m, or on my system it's file called > spm_flip_analyze_images.m. There is a

Re: [Freesurfer] problem with spmregister on mac

It depends on which version of SPM you're running. It's either the file called spm_defaults.m, or on my system it's file called spm_flip_analyze_images.m. There is a line that says: flip = 1; (or flip = 0). For my kind of scans I need to set flip = 0, whereas the spm defaults tend to come with fli

Re: [Freesurfer] problem with spmregister on mac

Can you tell me how to check that because I"m having the same problem with spmregister-sess with my linux as well and I've never used SPM at all, and honestly can't even figure out how to open it. Katie On Thu, Feb 3, 2011 at 11:21 PM, Y.V. Jiang wrote: > Hi Maryam, > > You should check your sp

Re: [Freesurfer] right hippocampus bad segmentation...

Hi: Yes... The patient has a resection of the temporal lobe, and I think that produce the problem in the segmentation, but could I correct the segmentation of the hippocampus because I need to get the volume of both hippocampus and the right one will have a big error... Sincerely, Gonz

Re: [Freesurfer] Inverse projection query

Hi Bruce, I guess the problem I have at hand is how to map them to fsaverage. Do I have to convert the arrays somehow to nifti format first? I tried looking this up on the web but couldn't find a solution ... Many thanks, Jason. On 04/02/2011 13:48, "Bruce Fischl" wrote: Hi Jason why no

Re: [Freesurfer] right hippocampus bad segmentation...

Hello, While the segmentation is not so good, the T1 coronal image that you sent suggests that the right medial temporal lobe may not be so normal. I think an underlying abnormality in the temporal lobe is giving rise to the segmentation errors. Perhaps you have other images through the right te

Re: [Freesurfer] Inverse projection query

Hi Jason why not map them all to fsaverage and display them on a common surface? cheers Bruce On Fri, 4 Feb 2011, Jason Connolly wrote: > Dear freesurfer experts: > > I have been using matlab to analyze a retinotopic dataset. > > However, the 3D volumes are not in standardized space (and I wis

[Freesurfer] Inverse projection query

Dear freesurfer experts: I have been using matlab to analyze a retinotopic dataset. However, the 3D volumes are not in standardized space (and I wish to display multiple maps from different subjects on one surface). Although the initial segmentations were done in freesurfer, my question is: Is