Dear Bruce,

Thanks for your patience. Attached you will find the screenshot of my server. In my institute's server, there is an older version of freesurfer, which I then change to a newer version before starting the recon-all.

I look forward to your reply.

Thanks.

Cheers,
Hweeling



On 22 November 2017 at 15:31, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
can you send us the recon-all.log?

On Wed, 22 Nov 2017, Hwee Ling Lee wrote:

Hi Bruce,

I downloaded the latest version of freesurfer, "CentOS 6 x86_64 (64b)".

Cheers,
Hweeling


On 21 November 2017 at 23:57, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
      oh, this may be a version mismatch then. Which version of FS are you using?
      On Tue, 21 Nov 2017, Hwee Ling Lee wrote:

            Dear Bruce,
            Thanks for your reply.
            I checked the folder and did not find the file that was requested.

            What I have in the average folder that has 'RB*.gca' are
            'RB_all_2016-05-10.vc700.gca' and
            'RB_all_withskull_2016-05-10.vc700.gca'.
            The other file in that folder is 'RB_all_2008-03-26.mni152.2mm.lta'.

            Cheers,
            Hweeling

            On Nov 21, 2017 18:05, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote:
                  Hi Hweeling

                  what is FREESURFER_HOME set to in the environment? Does that file
            exist? It is a
                  standard part of our distribution

                  cheers
                  Bruce


                   On Tue, 21 Nov 2017, Hwee Ling Lee wrote:

                        Dear all,

                        I have T1 images collected from the 7T MRI scanner.

                        I downloaded the most recent freesurfer software, and followed
            all
                        instructions to install the software before using it.

                        I would like to segment the T1 data using its high resolution
            image, and
                        also to segment the hippocampal subfields.

                        For command, I use this:

                        recon-all -all -s <subject name> -hires -i <subject dicom T1
            image frame 1
                        location>

                        However, I get an error message:

                        cannot find $FREESURFER_HOME/average/RB_all_2008-03-26.gca

                        I'm not sure what I did wrong.

                        Also, how can I combine high resolution segmentation and
            hippocampal
                        subfields segmentation?

                        Could someone please help?

                        Thanks.

                        Best regards,
                        Hweeling





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