Dear Douglas,

1) Does this beta version of FS 6 (freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015.tar.gz) also have problems with the individual data analysis or the volumetric group analysis, e.g. the files in the stats/ folder for each subject?

2) So could I use the results of these surface-based group analyses after running the "-qcache" on the latest "-dev" version (freesurfer-Linux-centos6_x86_64-dev-20160315) available today on the website then? I tried one data for "-qcache" with this latest -dev version, and see the files of ?h.area.fwhm10... and ?h.thickness.fwhm10... are different now (mri_diff), but still the same between ?h.area.fwhm10... and ?h.area.pial.fwhm10... . Is it right?

3) How about the hippocampus and brainstem sub-structure analyses, are there changes on these features within different beta versions too?

Thanks, Kaiming

On 15 March 2016 at 18:00, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

this only has to do with the qcache part of recon-all, so you could use version 5.3 recon-all -qcache and it should be fine. However, it is not a good idea to try to publish using the analysis from the version of FS that you used. That was a beta version of version 6 and things will change.

On 03/15/2016 01:56 PM, Kaiming Yin wrote:

...

Dear Douglas,

Is there anything I can do now to fix this now? I don't want to re-run all the data again.

Thanks, Kaiming

On 15 March 2016 at 16:53, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

OK, this is a bug that I found and fixed in early Nov. Sorry,
that's part of the danger of using a beta version.

On 03/14/2016 12:22 PM, Kaiming Yin wrote:

    Dear Douglas,

    I re-run the "-qcache" on one data and it took 8 mins to
    finish. Still the files are the same, all in 668.6kB size.


    Kaiming

    On 14 March 2016 at 15:56, Douglas Greve
    <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
    <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>> wrote:

        I don't know what happened. I cannot replicate it here.
    Can you
        re-run the recon-all -s -qcache command and verify that
    the files
        are still the same?


        On 3/14/16 11:11 AM, Kaiming Yin wrote:

            Dear Douglas,

            Yes, both of the two pairs of files are the same. i.e.

            mri_diff rh.ad_hv.thick.10.mgh rh.ad_hv.area.10.mgh

            diffcount 0


            mri_diff rh.thickness.fwhm10.fsaverage.mgh
            rh.area.fwhm10.fsaverage.mgh

            diffcount 0


            Does this mean I run the "-qcache" wrongly? I just run
        "recon-all
            -s XX -qcache" on each subject.

            Thanks,
            Kaiming


            On 14 March 2016 at 14:58, Douglas Greve
            <greve@nmr.mgh.harvard.edu
        <mailto:greve@nmr.mgh.harvard.edu>
        <mailto:greve@nmr.mgh.harvard.edu

        <mailto:greve@nmr.mgh.harvard.edu>>> wrote:

                Check whether rh.ad_hv.thick.10.mgh and
        rh.ad_hv.area.10.mgh
                are the same, ie,
                mri_diff  rh.ad_hv.thick.10.mgh rh.ad_hv.area.10.mgh

                If those are the same, then check whether
                thickness.fwhm10.fsaverage and
        area.fwhm10.fsaverage  are the
                same in each subject


                On 3/14/16 10:53 AM, Kaiming Yin wrote:

                    Dear Douglas,

                    My command lines were, e.g. right thickness
            and right white
                    surface (using the same ad_hv.fsgd and
            group_diff.mtx files
                    in the command lines):


                    ad_hv.fsgd

                    GroupDescriptorFile 1
                    Title AD_HV_GroupAnalysis
                    Class AD
                    Class HV
                    InputAD_003AD
                    InputAD_005AD
                    ...
                    InputHV_ABHV
                    InputHV_AEHV


                    group_diff.mtx

                    1 -1


                    right thickness

                    mris_preproc --fsgd ad_hv.fsgd --cache-in
                    thickness.fwhm10.fsaverage --target fsaverage
            --hemi rh
                    --out rh.ad_hv.thick.10.mgh

                    mri_glmfit --y rh.ad_hv.thick.10.mgh --fsgd
            ad_hv.fsgd dods
                    --C group_diff.mtx --surf fsaverage rh
            --cortex --glmdir
                    rh.ad_hv.thick.glmdir

                    mri_glmfit-sim --glmdir rh.ad_hv.thick.glmdir
            --cache 4 neg
                    --cwp 0.05 --2spaces


                    right white surface

                    mris_preproc --fsgd ad_hv.fsgd --cache-in
                    area.fwhm10.fsaverage --target fsaverage
            --hemi rh --out
                    rh.ad_hv.area.10.mgh

                    mri_glmfit --y rh.ad_hv.area.10.mgh --fsgd
            ad_hv.fsgd dods
                    --C group_diff.mtx --surf fsaverage rh
            --cortex --glmdir
                    rh.ad_hv.area.glmdir

                    mri_glmfit-sim --glmdir rh.ad_hv.area.glmdir
            --cache 4 neg
                    --cwp 0.05 --2spaces


                    Their results were all the same.

                    Thanks,
                    Kaiming


                    ---------- Forwarded message ----------
                    From: Douglas N Greve
            <greve@nmr.mgh.harvard.edu
            <mailto:greve@nmr.mgh.harvard.edu>
                    <mailto:greve@nmr.mgh.harvard.edu
            <mailto:greve@nmr.mgh.harvard.edu>>>
                    To: freesurfer@nmr.mgh.harvard.edu
            <mailto:freesurfer@nmr.mgh.harvard.edu>
                    <mailto:freesurfer@nmr.mgh.harvard.edu
            <mailto:freesurfer@nmr.mgh.harvard.edu>>
                    Cc:
                    Date: Mon, 7 Mar 2016 18:47:11 -0500
                    Subject: Re: [Freesurfer] group analysis all
            measures same
                    results
                    what are your command lines?


                    On 5 March 2016 at 02:01, Kaiming Yin
                    <yinkaiming6987@gmail.com
            <mailto:yinkaiming6987@gmail.com>
            <mailto:yinkaiming6987@gmail.com

            <mailto:yinkaiming6987@gmail.com>>>

                    wrote:

                        Dear guys,

                        I was doing group analysis (command-line)
            on two groups
                        (patients and control, no age or other
            information). The
                        data has been "qcached", and after
            following the three
                        steps as "mris_preproc, mri_glmfit and
            mri_glmfit-sim"
                        shown in the tutorial on the Freesurfer
            website, I
                        obtained the difference on thickness in
            both left and
                        right hemispheres, which seems great.
            However, when I
                        repeated the above steps on other
            measures, e.g. area,
                        area.pial, volume (also replaced the parts of
                        "thickness" in the command lines), the
            results seemed to
                        be exactly the same again as those in the
            thickness
                        comparison, even the p-value numbers in
            the file
                        "cache.th40.neg.sig.cluster.summary" were
            the same. I
                        was using Freesurfer v6.0-beta, and I
            performed the
                        individual data analysis on a linux
            cluster and I
                        copied/downloaded the whole "qcached"
            subject directory
                        to my linux laptop to perform the group
            comparison, both
                        using the same version of Freesurfer, does
            it matter? Or
                        do you know why it happened like this?

                        Thanks,
                        Kaiming



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--     Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/