Re: [Freesurfer] Recon-all -hires

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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