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

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.