Hi Bruce,

It looks like I was using wrong command to view output in tkmedit. I changed it following:

tkmedit bert /home/raghav/Desktop/MRI_DATASETS/SATA/freesurfer/testing-images/8/8/mri/normgz -segmentation /home/raghav/Desktop/MRI_DATASETS/SATA/freesurfer/testing-images/8/8/mri/aseg.mgz

And now both nifti and mgz image output looks similar with minor difference (see attached nifti_mgz.png)

But there is still that question.

How can I convert (256x256x256) to (256x256x268)??

It would be great if you can help me with that.

Once again thanks for your help.

Raghav Mehta

MS by Research (ECE)

Center for Visual Information Technology

International Institute of Information Technology - Hyderabad

​researchweb.iiit.ac.in/~raghav.mehta​

+91 9712990393

On Mon, Oct 10, 2016 at 8:50 AM, Raghav Mehta <raghav.11393@gmail.com> wrote:

Hi Bruce,

I used following command:

recon-all -subject 8 -i /home/raghav/Desktop/MRI_DATASETS/SATA/freesurfer/testing-images/8/8.nii.gz -sd /home/raghav/Desktop/MRI_DATASETS/SATA/freesurfer/testing-images/8 -all -cw256 

I had to use -cw256 option due to the fact that in third dimension my volume has more than 256 slices (256x256x268), so without that option I was getting error.

I got aseg.mgz orig.mgz and norm.mgz files in mri folder.

I checked the segmentation using following command: 

tkmedit bert norm.mgz -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt

(please find the attached screenshot named tkmedit.png)

Now, I wanted to convert this into nifti format so I ran following command:

mri_convert --in_type mgz --out_type nii *.mgz *.niiI

where, * = {aseg,orig,norm}

it converted mgz volumes into nii volumes.

Now I opened the volume and segmentation in ITKSNAP. But I am getting totally different output in ITKSNAP. (see attached ITKSNAP.png) also there are some lables numbered 255, 253 etc when I open segmentation in ITKSNAP, which doesn't make any sense. Also it looks like due to the use of -cw256 option in recon-all command my images are cropped to 256x256x256.

Now, there are two questions:

1) How can I convert this 256x256x256 into original image size 256x256x268

2) Am I using proper syntax for mri_convert ?? as I am getting totally different output in both of them. ( screenshots are for slice 128 in norm.nii)  

Thanks for your help.

Regards,

Raghav Mehta

MS by Research (ECE)

​​​​Center for Visual Information Technology

International Institute of Information Technology - Hyderabad

​researchweb.iiit.ac.in/~raghav.mehta​

+91 9712990393

On Sun, Oct 9, 2016 at 11:54 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Raghav

We don't resample into MNI (or any other space). Was your input already resampled? In general you should send us your full command line and screen output

Cheers
Bruce

> On Oct 9, 2016, at 1:39 PM, Raghav Mehta <raghav.11393@gmail.com> wrote:
>
> Raghav

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