Re: [Freesurfer] subcortical structure coordinates

 Hi I tried running the following process. Convert aseg.mgz back to native space using: mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg_nat.mgz --regheader aseg.mgz Then I loaded the aseg_nat (which, to my understanding, should be in native space) to matlab. Now mri.vol (using MRIread) ha

Re: [Freesurfer] subcortical structure coordinates

Thanks! It seems to rotate the data, though. It does convert the data back to the original dimensions (256X256X176), ut the dimensions are switched. When I save the vol as nii and open in brainvoyager, the sagittal appears in coronal, etc. I tried switching the 256 dimensions, but it remains rot

[Freesurfer] Subcortical Labelling correction

Dear FS experts, I 've question concerning the automatic subcortical labelling provided by FS. Is it possible to manually correct the output? That is, if hippocampal segmentation results inaccurate, can I modified the aseg.mgz file ? Thanks for your attention. -

Re: [Freesurfer] Subcortical Labelling correction

You can although we generally advise against it (it's best to try automatic fixes first). What is not correct about the hippocampal segmentation? -- On Thu, 28 Oct 2010, antonio cerasa wrote: > Dear FS experts, > > I 've question concerning the automatic subcortical labelling provided by FS. >

Re: [Freesurfer] Subcortical Labelling correction

sure, you can do this in either tkmedit or freeview On Thu, 28 Oct 2010, antonio cerasa wrote: > Dear FS experts, > > I 've question concerning the automatic subcortical labelling provided by FS. > Is it possible to manually correct the output? That is, if hippocampal > segmentation results inac

Re: [Freesurfer] subcortical structure coordinates

How are you converting to nifti? You can do it with mri_label2vol, just spec nii instead of mgz. doug Aya Ben Yakov wrote: > Hi > I tried running the following process. > Convert aseg.mgz back to native space using: > mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg_nat.mgz > --reghead

Re: [Freesurfer] Retinotopic mapping of only polar data]

Can you send me you mkanalysis-sess command-line and the log file created by selxavg3-sess? It should be using a registration file called register.dof6.dat. You can check the registration with tkregister-sess. tksconcat.nii is a temporary file created by tkmedit-sess and tksurfer-sess; they are

Re: [Freesurfer] Make functional ROI's from clusters

As Allison says, you can use the tools listed below. Alternatively, there is an easier way to do it in tksurfer. 1. Click on cluster you want to convert into a label. 2. Click on the "Custom Fill" button (little paint bucket pouring into a blue blob). This will popup a window 3. Click on the "Up

Re: [Freesurfer] Make functional ROI's from clusters

If the labels and data are surface, you can use the --slabel feature. doug Alice Albrecht wrote: > Thanks Doug, > > I have successfully made the labels, but now I want to use those > labels on other data as ROIs and that is where I am having trouble > using the mri_segstats function. I d

Re: [Freesurfer] Total GM and WM volumes

Ed, can you send the recon-all.log file? The underlying code for mris_volume and the program that creates the stats file is identical. This other program (mri_segstats) prints out the values for the volumes inside the lh.pial, etc, and this will be captured by the recon-all.log file. doug Ed

[Freesurfer] Source matrix with zero determinant

Hello FreeSurfers, I am trying to run autorecon-1 on data (nifti) downloaded from the NIH MRI Study of Normal Brain Development (Pediatric MRI Study) Repository. However, the command exited with errors mentioning that the source matrix has a zero determinant. I've read past e-mail conversations on

Re: [Freesurfer] Source matrix with zero determinant

There is something wrong with the header of that nifti file. Can you send the result of: mri_info *deface_1433_V1_t1w_slice0.nii doug * Lisa F. Akiyama wrote: > Hello FreeSurfers, > > I am trying to run autorecon-1 on data (nifti) downloaded from the NIH > MRI Study of Normal Brain Development

[Freesurfer] [Fwd: scientific programmer position with us]

Anyone interested should send email to Richard Baumgartner at richard_baumgart...@merck.com Original Message Hi Doug, we are urgently looking for a contractor position with us. The person should have good programming skills and some understanding of statistics. He/she will

[Freesurfer] longitudinal base error

Hi, there, %% After running this command with FS v4.5 : recon-all -base 005_S_0221BASE -tp 005_S_0221_45_20070321.105506_1 -tp 005_S_0221v2_45_20061006.104318_1 -all -force %% I get the following error: mri_concatenate_lta -invert1 005_S_0221_45_20070321.105506_1_to_005_S_0221BASE.lta identity

Re: [Freesurfer] longitudinal base error

Haven't seen this before. Can you send the lta file (should be in basid/MRI/transforms) Probably the lta is not correct. Also you can try to delete the base dir and rerun, maybe it was just a hiccup. Does the norm.mgz look good in the base? If not registration did not work. In that case download

[Freesurfer] How to save a new label after cutting an existing label?

Hi freesurfers, I'm trying to generate a new label, from cutting an existed label. The process was shown as attached, First I load a label on fsaverage, lh.inflated, then cut the label along the yellow line and keep the needed part by "cut plane". Now I hope to save the remained label shown in bl

Re: [Freesurfer] How to save a new label after cutting an existing label?

Don't use cutting. Draw boundaries in tksurfer and use the custom fill tool Cheers Bruce On Oct 28, 2010, at 10:04 PM, 李瑾 wrote: > Hi freesurfers, > I'm trying to generate a new label, from cutting an existed label. > The process was shown as attached, First I load a label on fsaverage, > l