OK, I have it now and am able to verify the problem. It's really strange -- I don't know why it is behaving like this. It may take me a few days to dig into.

On 6/18/2020 11:39 AM, Danielian, Laura (NIH/NINDS) [E] wrote:

        External Email - Use Caution

Sorry I’m not sure why it didn’t upload.  I just tried it again. danielianall.tar.gz  - Should include all parts.  EM2 is the cross-sectional.  EM is the base.  EM2.long.EM is the long. I also tried sending just the base again. danielianbase.tar.gz.

Thanks,

Laura

*From: *"Douglas N. Greve" <dgr...@mgh.harvard.edu>
*Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Date: *Thursday, June 18, 2020 at 9:12 AM
*To: *"freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] Longitudinal Stream Problem

I have not seen that file appear. Can you re-upload it?

On 6/16/2020 10:19 AM, Danielian, Laura (NIH/NINDS) [E] wrote:

    *        External Email - Use Caution *

    Hi Douglas,

    OK I just uploaded the base separately.  danielianbase.tar.gz  I
    thought it was part of the original bundle.  Sorry!

    Laura

    *From: *"Douglas N. Greve" <dgr...@mgh.harvard.edu>
    <mailto:dgr...@mgh.harvard.edu>
    *Reply-To: *Freesurfer support list
    <freesurfer@nmr.mgh.harvard.edu>
    <mailto:freesurfer@nmr.mgh.harvard.edu>
    *Date: *Tuesday, June 16, 2020 at 10:10 AM
    *To: *"freesurfer@nmr.mgh.harvard.edu"
    <mailto:freesurfer@nmr.mgh.harvard.edu>
    <freesurfer@nmr.mgh.harvard.edu>
    <mailto:freesurfer@nmr.mgh.harvard.edu>
    *Subject: *Re: [Freesurfer] Longitudinal Stream Problem

    I have your data, but it does not have the base image. Can you
    upload that as well?

    On 6/15/2020 5:15 PM, Danielian, Laura (NIH/NINDS) [E] wrote:

        *        External Email - Use Caution *

        Hi Douglas,

        I just upload the files as danielian.tar.gz.  I didn’t notice
        any damage or artifact on this particular brain or the others
        that had this same problem.  This subject is a healthy control
        and most of the subjects (3 of 4) that are having this problem
        are healthy.  For each we used 2 T1s for the original
        cross-sectional input.  The cross was reconstructed fine as
        was the base and the 2 other longitudinal timepoints for this
        same subject.  The same is the case with the others I’m having
        trouble with – all of the their other timepoints are fine for
        the cross/base/longitudinal surfaces.  The warped surfaces are
        always lower posterior (cerebellum adjacent) and sometimes
        also temporal.  Upper cortical and frontal regions are unaffected.

        Thanks for your help!

        Laura

        *From: *"Douglas N. Greve" <dgr...@mgh.harvard.edu>
        <mailto:dgr...@mgh.harvard.edu>
        *Reply-To: *Freesurfer support list
        <freesurfer@nmr.mgh.harvard.edu>
        <mailto:freesurfer@nmr.mgh.harvard.edu>
        *Date: *Friday, June 12, 2020 at 10:35 AM
        *To: *"freesurfer@nmr.mgh.harvard.edu"
        <mailto:freesurfer@nmr.mgh.harvard.edu>
        <freesurfer@nmr.mgh.harvard.edu>
        <mailto:freesurfer@nmr.mgh.harvard.edu>
        *Subject: *Re: [Freesurfer] Longitudinal Stream Problem

        Hard to tell from just that view. Was there a lot of brain
        change with that time point? Or was there an MRI artifact? If
        no to both, then you can upload all the cross, the base, and
        that one long. Follow instructions below (you can make one
        tarball for all subjects)

        From the linux command line,
        Create the file you want to upload, eg,
        cd $SUBJECTS_DIR
        tar cvfz subjects.tar.gz ./subject1 ./subject2
        Now log  into our anonymous FTP site:
        ftp surfer.nmr.mgh.harvard.edu
        It will ask you for a user name: use "anonymous" (no quotes)
        It will ask you for a password: use "anonymous" (no quotes)
        cd transfer/incoming
        binary
        put subjects.tar.gz
        Send an email that the file has been and the name of the file.






        On 6/9/2020 6:32 PM, Danielian, Laura (NIH/NINDS) [E] wrote:

            *        External Email - Use Caution *

            Hi, I’ve finished processing a data set that included
            longitudinal data and I’m having a problem with a small
            percentage of the longitudinal timepoints.  To review what
            I’ve done, I edited all of the individual
            (cross-sectional) timepoints until the wm and pial
            surfaces were correct, then created the base and edited
            that until it looked good, and then created the
            longitudinal files for each cross-sectional timepoint. 
            Most of these did not need editing and some needed slight
            edits to either wm or brainmask which corrected the
            longitudinal surfaces.

            However, in a small handful of cases, the wm/pial surfaces
            were so distorted that editing would not fix the problem.
            In these cases, longitudinal surfaces were very different
            from both the original cross-section and base.  I’ve tried
            to attach a file that shows an example – it might only
            affect a small portion of the brain but in these cases I
            don’t think I could edit it to improve the surfaces.  In
            the example I attached, red/blue are from the long file
            and pink/lt blue are from the base.

            Do you have any suggestions for why this might be
            happening and how to fix it?  I’m running v6.0.

            Thanks!

            Laura Danielian





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