Dear Bruce,

Sorry about the screenshot of text.

You are right that it still uses the older version of recon-all. How do I fix this then?

I can't delete the older version because I don't have access to it at all.

Thanks for your patience.

Cheers,
Hweeling


On 22 November 2017 at 15:52, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Hweeling

please don't send us screenshots of text - either attach the file or include text in the email.

I'm pretty sure you are using an older recon-all script with a newer FREESURFER_HOME. Try typing:

which recon-all

I bet it points to somewhere other than your V6 FREESURFER_HOME/bin dir

cheers
Bruce



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

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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