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Thank you
-----Original Message-----
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Subject: [EXTERNAL] Freesurfer Digest, Vol 188, Issue 32
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Today's Topics:
1. Re: FreeSurfer transforms (Bruce Fischl)
2. Re: Learning dti processing tutorial (Yendiki, Anastasia)
3. Re: can?t open an image in Freeview (fsbuild)
4. Re: aseg.stats format FreeSurfer 5 versus 6 (Tim Sch?fer)
5. Re: FSGD file formatting for Xhemi (Jose Graterol)
6. Re: FreeSurfer transforms (Vinny K)
7. tracula FA question - 2 cohorts/2 scanners (Krieger, Donald N.)
8. Incorrect/Negative Hippocampal subfields volumes
(Jayachandra Raghava)
9. subcortical volume-based pet analysis (miracle ozzoude)
10. Re: imperfect segmentation in the occipital lobe in epilepsy
patient (Diamond, Bram Ryder)
----------------------------------------------------------------------
Message: 1
Date: Sun, 20 Oct 2019 15:10:37 -0400 (EDT)
From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FreeSurfer transforms
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.lrh.2.21.1910201509440.26...@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
I see. Yes, a bunch of those are on our to-do list for segmentation but we
don't have anything distributable at the moment. You are probably better off
running some other nonlinear warping like ANTS or VoxelMorph to propagate the
labels.
cheers
Bruce
On Sat, 19 Oct 2019, Vinny K wrote:
>
> ????????External Email - Use Caution????????
>
> Hi Bruce,
> I'm looking at diencephalic and midbrain structures and their various
> subdivisions for application to tractography.? I used the thalamic
> nuclei segmentation feature in the development version of FreeSurfer
> to obtain labeling of individual thalamic nuclei that is run in
> addition to aseg, which has worked out great.? However, for other deep
> brain structures such as the subthalamic or pontine nuclei (e.g.
> pedunculopontine), to my knowledge, aseg does not parcellate these out;
> however, they are available MNI space.?
> FreeSurfer gives an excellent registration?of labeled atlas structures
> in patients with big ventricles, which I've had difficulty with using
> other registration tools.? I was wondering if there was a way that I
> could bring some of these labeled nuclei in MNI space into the
> patient's T1 space using FreeSurfer.
>
> Thanks,
>
> Vinny??
>
> On Sat, Oct 19, 2019 at 12:16 PM Bruce Fischl
> <fis...@nmr.mgh.harvard.edu>
> wrote:
> Hi Vinny
>
> why do you need to brain structures from MNI space? Isn't the
> aseg
> sufficient? Or are there structures that are not in the aseg?
>
> cheers
> Bruce
> On Sat, 19 Oct
> 2019, Vinny K wrote:
>
> >
> > ????????External Email - Use Caution????????
> >
> > Hi,
> > FreeSurfer does a great job in registering atlas structures to
> patients with
> > big ventricles.? I'd like to use the calculated FreeSurfer
> transforms in
> > bringing additional subcortical structures from MNI space
> (either MNI305 or
> > MNI2009b) into native T1 space.? Can you please advise on how
> to do this?
> >
> > Thanks,
> >
> > Vinny??
> >
> >_______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv
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>
>
>
------------------------------
Message: 2
Date: Sun, 20 Oct 2019 19:23:06 +0000
From: "Yendiki, Anastasia" <ayend...@mgh.harvard.edu>
Subject: Re: [Freesurfer] Learning dti processing tutorial
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<bl0pr04mb4833d9194632cc48243f2f488a...@bl0pr04mb4833.namprd04.prod.outlook.com>
Content-Type: text/plain; charset="windows-1252"
Hi, you need to run recon-all on the T1, not on the diffusion scan. This will
produce an anatomical segmentation of each subject based on the T1s, which
TRACULA will then use to extract anatomical priors on white matter tracts, to
aid tractography. When you run trac-all to do the actual tractography, then you
run it on the diffusion scan.
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Renew Andrade
<andradere...@yahoo.com>
Sent: Friday, October 18, 2019 5:02:35 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Learning dti processing tutorial
External Email - Use Caution
I am using a database of NITRC repository
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.nitrc.org_projects_parktdi_&d=DwICAg&c=heEcP2AsrLOv4XP8e7I9NA&r=pVcBZUHksoIOTN75JaLZTZEAPxBaNZr49Od8c24nskU&m=vTpUsyeuuJ15qFWBMe3LprH61_ATtfgG0Pl3TN6dF9M&s=efr4_S0iCMgCGeNCMSDyl8VuSP0gAHStKDbT-sIA0Vk&e=
. This images have a nifti file for 1000s/mm^2 and 2500s/mm^2. I don?t know
if it is MPRAGE or not. Can you help me?
What is the input file that you are supplying? Often this happens when the
input it a multi-echo MPRAGE. If so, you can run mri_concat
multi-echo-mprage.mgz --rms --o mprage.mgz then use mprage.mgz as the input to
recon-all
On 10/12/2019 4:48 PM, Renew Andrade wrote:
> External Email - Use Caution
>
> Dear freesurfer experts:
> I am trying to learn dti processing. For using Tracula it appears
> there is a need for running "recon-all -all -i -s? on every subject
> before starting to run Tracula. But there seems to be a problem. I
> have a Parkinson dwi images database and every subject gives me an
> error of the type ?input(s) cannot have multiple frames!?. I am a
> little bit stuck on this step. Is it a problem of the file as input?
> Am I putting the wrong file? Can it be done a recon-all analysis to a
> dwi image? With trackvis I can obtain the results without any problem.
> My doubt comes from FreeSurfer only and may be my little knowledge about it.
> Thanks for your help!
> Sincerely,
> Andrade.
>
> _______________________________________________
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------------------------------
Message: 3
Date: Mon, 21 Oct 2019 04:28:54 +0200
From: fsbuild <fsbu...@contbay.com>
Subject: Re: [Freesurfer] can?t open an image in Freeview
To: freesurfer@nmr.mgh.harvard.edu
Cc: adam.ryt...@outlook.cz
Message-ID: <1571624934.5dad17e6b4...@trashmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hello Adam,
Please check if you have a ?freeview.bin? program.
$ which freeview.bin
If you get a path back with freeview.bin in it, e.g. something
like/usr/local/freesurfer/bin/freeview.bin
- then try the ldd command on freeview.bin, $ ldd `which freeview.bin` | grep
not
- then see if it lists that something is not found.
- R.
On Oct 19, 2019, at 03:27, Adam Rytina <adam.ryt...@outlook.cz>
wrote: External Email - Use
Caution Hello,I run the command
"$ ldd `which freeview` | grep not" and the result is "not a dynamic
executable". Do you know where the problem is?What I read there could be the
problem regarding 32bit or 64bit system I?m working on. I am running on Windows
10 64bit, 64 bit CPU, 64bit Ubuntu 16.04. I downloaded the 6.0.0. Freesurfer
version from the official
page:https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_DownloadAndInstallPlease&d=DwICAg&c=heEcP2AsrLOv4XP8e7I9NA&r=pVcBZUHksoIOTN75JaLZTZEAPxBaNZr49Od8c24nskU&m=vTpUsyeuuJ15qFWBMe3LprH61_ATtfgG0Pl3TN6dF9M&s=DKa4_mH989K_a8It4a1pI2k9FTBqXKHGul-VPVGBSxI&e=
, could you help me?Thanks a lotAdamOd: fsbuild
<fsbu...@contbay.com>Odesl?no: p?tek 18. ??jna 2019
22:05Komu: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Kopie: adam.ryt...@outlook.cz <adam.ryt...@outlook.cz>P?edm?t: Re:
[Freesurfer] can?t open an image in Freeview Hello Adam,See if you can
run the following command, and if it reports anything is not found (you can cut
and paste the command)- R.$ ldd `which freeview` | grep notAdam
Rytina October 18, 2019 at
14:31 External Email - Use
Caution Hello all,I?m new to
Freesurfer and I?m struggling with loading an image in FreeView. I am running
the Freesurfer 6.0.0. on Ubuntu 16.04. Virtual Machine. While opening FreeView
(typing "freeview" in the shell) just some empty grey windows will pop out
(please see attached the screenshot). Besides this, everything is OK, I
successfully tested Freesurfer installation. I haven?t found any simmilar issue
on the Internet. Thus, please, could you help me to address this issue?Thanks a
lotAdamBez vir?. www.avast.co!
m_______
________________________________________Freesurfer mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer
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iling li
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------------------------------
Message: 4
Date: Mon, 21 Oct 2019 09:09:53 +0200 (CEST)
From: Tim Sch?fer <ts...@rcmd.org>
Subject: Re: [Freesurfer] aseg.stats format FreeSurfer 5 versus 6
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <1646353298.441500.1571641793...@ox.hosteurope.de>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hi Doug,
thanks for the confirmation!
All the best,
Tim
> On October 18, 2019 at 4:01 PM "Greve, Douglas N.,Ph.D."
> <dgr...@mgh.harvard.edu> wrote:
>
>
> They are just different names
>
> On 10/17/19 11:52 AM, Tim Sch?fer wrote:
> > External Email - Use Caution
> >
> > Dear fs experts,
> >
> > I'm parsing aseg.stats files for subjects to extract global brain measures
> > and noticed that at least 2 names changed from FreeSurfer 5.1 versus
> > FreeSurfer 6. It seems that:
> >
> > * "EstimatedTotalIntraCranialVol" is in v6, but "IntraCranialVol" is
> > in v5
> > * "Total cerebral white matter volume" is in v6, but "Total cortical
> > white matter volume" is in v5
> >
> > Have these just been renamed, or do they carry different information? Did I
> > overlook anything else that changed?
> >
> > --
> > Dr. Tim Sch?fer
> > Postdoc Computational Neuroimaging
> > Department of Child and Adolescent Psychiatry, Psychosomatics and
> > Psychotherapy University Hospital Frankfurt, Goethe University
> > Frankfurt am Main, Germany
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.ha
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> > 9NA&r=pVcBZUHksoIOTN75JaLZTZEAPxBaNZr49Od8c24nskU&m=vTpUsyeuuJ15qFWB
> > Me3LprH61_ATtfgG0Pl3TN6dF9M&s=PGkBZSEWRaO864McYbzltpM8SlU0O1AJE6HhOS
> > 5N8bg&e=
>
>
> _______________________________________________
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> Freesurfer@nmr.mgh.harvard.edu
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--
Dr. Tim Sch?fer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
------------------------------
Message: 5
Date: Mon, 21 Oct 2019 10:58:00 +0200
From: Jose Graterol <gpjosealbert...@gmail.com>
Subject: Re: [Freesurfer] FSGD file formatting for Xhemi
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAFMm1s7EqX4vFWi4ZiqZ=Fm8=fv0rcvnguvqod3h_rt_cdk...@mail.gmail.com>
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Thanks for your answer.
I want to correlate TMS values in 17 stroke patients. Following the
instructions provided to Anders in this link
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_search-3Fl-3Dfreesurfer-40nmr.mgh.harvard.edu-26q-3Dsubject-3A-2522-255C-255BFreesurfer-255C-255D-2Bflipping-2Bsurface-2Bdata-2522-26o-3Dnewest-26f-3D1&d=DwICAg&c=heEcP2AsrLOv4XP8e7I9NA&r=pVcBZUHksoIOTN75JaLZTZEAPxBaNZr49Od8c24nskU&m=vTpUsyeuuJ15qFWBMe3LprH61_ATtfgG0Pl3TN6dF9M&s=j3w0fRVwJzUhtaOIQPkf9fb__VbGTwL0cQuETSCiVPg&e=
I created the --y file that joins the affected hemispheres together and the
unaffected hemispheres together. I omitted the --paired-diff flag. When I run
mri_glmfit with --fsgd it asks for 34 inputs. I am guessing those are for the
34 hemispheres of the patients in the order mentioned in my first email. Would
this be the right way to correlate the variables?
In short, I am trying to test if there is a difference in cortical thickness,
while adding covariates, between the affected and unaffected hemispheres in
stroke patients.
Thanks in advance
On Fri, Oct 18, 2019 at 3:57 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> What are you trying to test? Usually you don't have lh and rh in the
> same glm
>
> On 10/17/19 7:09 AM, Jose Graterol wrote:
>
> External Email - Use Caution
> Dear Freesurfer Community,
>
> I have a question regarding the formatting of the FSGD file while
> doing an analysis with Xhemi.
> First the --y file was created as previously explained in another
> discussion (
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_freesurfer-40nmr.mgh.harvard.edu_msg63965.html&d=DwICAg&c=heEcP2AsrLOv4XP8e7I9NA&r=pVcBZUHksoIOTN75JaLZTZEAPxBaNZr49Od8c24nskU&m=vTpUsyeuuJ15qFWBMe3LprH61_ATtfgG0Pl3TN6dF9M&s=FvULHov15P3VfAFiZVDtDzfA_f_tSz4X2e7wwI0aS-A&e=
> ).
> That is, mris_preproc with --xhemi and no --fsgd flag.
>
> If I understood correctly, that would create a mgh file with the
> following
> order: sub01lh, sub01rh, sub02lh, sub02rh...
> Then the FSGD file while running mri_glmfit would be:
> GroupDescriptorFile 1
> Title xxx
> Class sub
> Variables var1
> Input sub01lh sub var1_lh_sub01
> Input sub01rh sub var1_rh_sub01
> Input sub02lh sub var1_lh_sub02
> Input sub02rh sub var1_rh_sub02
>
> Would this be correct? If so, what would be the best case for
> specifying a variable like age? Just repeating the value 2 times?
>
> As always, thanks in advance
>
> Kind Regards
>
> Jos?
>
>
> _______________________________________________
> Freesurfer mailing
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mai
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>
>
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------------------------------
Message: 6
Date: Mon, 21 Oct 2019 06:09:51 -0400
From: Vinny K <vinit.k.srivast...@gmail.com>
Subject: Re: [Freesurfer] FreeSurfer transforms
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<cacugd2zdofhudqqzhjzisms1wf+ux2cw+cks2kdcwwa2reo...@mail.gmail.com>
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Ok thanks for the suggestions.
On Sun, Oct 20, 2019 at 3:11 PM Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
> I see. Yes, a bunch of those are on our to-do list for segmentation
> but we don't have anything distributable at the moment. You are
> probably better off running some other nonlinear warping like ANTS or
> VoxelMorph to propagate the labels.
>
> cheers
> Bruce
> On Sat, 19 Oct 2019, Vinny K wrote:
>
> >
> > External Email - Use Caution
> >
> > Hi Bruce,
> > I'm looking at diencephalic and midbrain structures and their
> > various subdivisions for application to tractography. I used the
> > thalamic nuclei segmentation feature in the development version of
> > FreeSurfer to obtain labeling of individual thalamic nuclei that is
> > run in addition to aseg,
> which
> > has worked out great. However, for other deep brain structures such
> > as
> the
> > subthalamic or pontine nuclei (e.g. pedunculopontine), to my
> > knowledge,
> aseg
> > does not parcellate these out; however, they are available MNI space.
> > FreeSurfer gives an excellent registration of labeled atlas
> > structures in patients with big ventricles, which I've had
> > difficulty with using other registration tools. I was wondering if
> > there was a way that I could
> bring
> > some of these labeled nuclei in MNI space into the patient's T1
> > space
> using
> > FreeSurfer.
> >
> > Thanks,
> >
> > Vinny
> >
> > On Sat, Oct 19, 2019 at 12:16 PM Bruce Fischl <
> fis...@nmr.mgh.harvard.edu>
> > wrote:
> > Hi Vinny
> >
> > why do you need to brain structures from MNI space? Isn't the
> > aseg
> > sufficient? Or are there structures that are not in the aseg?
> >
> > cheers
> > Bruce
> > On Sat, 19 Oct
> > 2019, Vinny K wrote:
> >
> > >
> > > External Email - Use Caution
> > >
> > > Hi,
> > > FreeSurfer does a great job in registering atlas structures to
> > patients with
> > > big ventricles. I'd like to use the calculated FreeSurfer
> > transforms in
> > > bringing additional subcortical structures from MNI space
> > (either MNI305 or
> > > MNI2009b) into native T1 space. Can you please advise on how
> > to do this?
> > >
> > > Thanks,
> > >
> > > Vinny
> > >
> > >_______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.ha
> > rvard.edu_mailman_listinfo_freesurfer&d=DwICAg&c=heEcP2AsrLOv4XP8e7I
> > 9NA&r=pVcBZUHksoIOTN75JaLZTZEAPxBaNZr49Od8c24nskU&m=vTpUsyeuuJ15qFWB
> > Me3LprH61_ATtfgG0Pl3TN6dF9M&s=PGkBZSEWRaO864McYbzltpM8SlU0O1AJE6HhOS
> > 5N8bg&e=
> >
> >
> >_______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv
> ard.edu_mailman_listinfo_freesurfer&d=DwICAg&c=heEcP2AsrLOv4XP8e7I9NA&
> r=pVcBZUHksoIOTN75JaLZTZEAPxBaNZr49Od8c24nskU&m=vTpUsyeuuJ15qFWBMe3Lpr
> H61_ATtfgG0Pl3TN6dF9M&s=PGkBZSEWRaO864McYbzltpM8SlU0O1AJE6HhOS5N8bg&e=
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------------------------------
Message: 7
Date: Mon, 21 Oct 2019 11:37:39 +0000
From: "Krieger, Donald N." <krieg...@upmc.edu>
Subject: [Freesurfer] tracula FA question - 2 cohorts/2 scanners
To: "'freesurfer@nmr.mgh.harvard.edu'"
<freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<sn6pr08mb497485ab370878fbf64bcd3daa...@sn6pr08mb4974.namprd08.prod.outlook.com>
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External Email - Use Caution
I have tracula runs on two cohorts whose imaging was obtained on different
scanners with slightly different beta's and other parameters.
Would the differences in the scanners and scanning parameters be expected to
produce large cohort-wide differences in the FA's?
Can you point to a reference?
Thanks - Don
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------------------------------
Message: 8
Date: Mon, 21 Oct 2019 14:21:18 +0200
From: Jayachandra Raghava <jayachandra9...@gmail.com>
Subject: [Freesurfer] Incorrect/Negative Hippocampal subfields volumes
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<cagpbcyp+xp3cihhamffkksbskarpiofq0w_zu-r8qvat4a0...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
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Hello Freesurfer experts & Eugenio,
I have been trying to extract the volumes of hippocampal subfields using the
longitudinal pipeline (
https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_LongitudinalHippocampalSubfields&d=DwICAg&c=heEcP2AsrLOv4XP8e7I9NA&r=pVcBZUHksoIOTN75JaLZTZEAPxBaNZr49Od8c24nskU&m=vTpUsyeuuJ15qFWBMe3LprH61_ATtfgG0Pl3TN6dF9M&s=MKeQ6VeCbDlm4b7LwhitAD_E2DPexNJfpHLUWmezuNo&e=
) on macOS Mojave using freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c.
For some reason, both the lh.hippoSfVolumes-T1.long.v10.txt and
rh.hippoSfVolumes-T1.long.v10.txt text files show negative volumes as shown
below.
Hippocampal_tail -445.418232
subiculum -339.909193
CA1 -559.134087
hippocampal-fissure -165.590803
presubiculum -263.670386
parasubiculum -55.654556
molecular_layer_HP -541.803219
GC-ML-DG -293.794963
CA3 -222.042205
CA4 -266.645751
fimbria -66.106600
HATA -53.397592
Whole_hippocampus -3107.576783
I have also tried to extract the hippocampal subfield volumes from the
longitudinally processed standard MNI T1 brain template
(MNI152_T1_1mm_brain.nii.gz). And i still encounter the same problem with
negative volumes.
I could not find the suggested solution for this problem in the freesurfer
mailing list. Could you please guide us on this issue?
Thank you for your time and support.
Best wishes
Jay
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------------------------------
Message: 9
Date: Mon, 21 Oct 2019 10:24:00 -0400
From: miracle ozzoude <miracoo...@gmail.com>
Subject: [Freesurfer] subcortical volume-based pet analysis
To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CANfOk0hB=iM=spa_kksqime5myh2paaox3f7tggupjib23f...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hello Experts,
I do have couple questions about using mri_glmfit and mri_glmfit-sim for this
analysis based on the tutorial page.
https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_PetSurfer&d=DwICAg&c=heEcP2AsrLOv4XP8e7I9NA&r=pVcBZUHksoIOTN75JaLZTZEAPxBaNZr49Od8c24nskU&m=vTpUsyeuuJ15qFWBMe3LprH61_ATtfgG0Pl3TN6dF9M&s=e_rhg_M2wD9s9fRo-dNu3X9QNazuxI8aPw5a-E4f7Fk&e=
1) Do i have to add any other flags when using mri_glmfit for this analysis?
mri_glmfit --y ${results_dir}/all.mgx.subctxgm.mni305.sm05.nii.gz --fsgd
$pet_fsgd --C $matrix1 \ --mask
${SUBJECTS_DIR}/fsaverage/mri.2mm/subcort.mask.mgz --glmdir
${results_dir}/sub.pet.B6.glmdir
2) When correcting for multiple comparisons, should i use --2spaces or
--3spaces?
3) I ran a paired ttest analysis using age as regressor of no interest for
amyloid uptake. My contrast is "1 0" based on the tutorial
https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_PairedAnalysis&d=DwICAg&c=heEcP2AsrLOv4XP8e7I9NA&r=pVcBZUHksoIOTN75JaLZTZEAPxBaNZr49Od8c24nskU&m=vTpUsyeuuJ15qFWBMe3LprH61_ATtfgG0Pl3TN6dF9M&s=xTo0S1VdK-8CL2mAHrT58ff5we6wHbc1z3y4c4iJ_Tw&e=
.
How do i interpret the direction of contrast if I get a result from
mri_glmfit-sim (see below)? This is because it doesn't have the Max column for
surface based analysis
# Cluster Size(n) Size(mm^3) MNIX MNIY MNIZ Max
CWP CWPLow CWPHi
1 12709 101672.0 26.00 -69.00 -41.00 5.46844
0.01037 0.00798 0.01316 Right-Cerebellum-White-Matter
Thank you.
best,
Paul
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------------------------------
Message: 10
Date: Mon, 21 Oct 2019 14:29:10 +0000
From: "Diamond, Bram Ryder" <brdiam...@mgh.harvard.edu>
Subject: Re: [Freesurfer] imperfect segmentation in the occipital lobe
in epilepsy patient
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<bn8pr04mb5473f691e87593407c873bace2...@bn8pr04mb5473.namprd04.prod.outlook.com>
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Hi Xiaoquian,
That's correct -- although I did it in a slightly different order because I
wasn't sure what was causing your issue. I first edited the wm.mgz using the
'recon edit' option (changing wm lesion voxels to 255) in FreeView, because I
was hoping that would fix the surfaces. When that didn't work, I instead edited
the brain.finalsurfs.mgz with the 'voxel edit' tool and changed the voxel
values within the wm lesion to 110. As you can see in the attached images, that
seemed to do the trick. The latest run-through applied both the wm and
brain.finalsurfs edits -- but it's likely that the surfaces would have improve
with only the brain.finalsurfs edits. You can test that out for yourself.
Instead of running recon-all between each test, I used the
'mris_make_surfaces<https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_mris-5Fmake-5Fsurfaces&d=DwICAg&c=heEcP2AsrLOv4XP8e7I9NA&r=pVcBZUHksoIOTN75JaLZTZEAPxBaNZr49Od8c24nskU&m=vTpUsyeuuJ15qFWBMe3LprH61_ATtfgG0Pl3TN6dF9M&s=k8ZilpTHLjZSMdHsfTE04zSj46cmriEFuVPqCS6RGHY&e=
>' command exactly how recon-all would call it, but only for the rh (the
hemisphere with the lesion and manual edits). The command can be found in the
ReconAllTableStableV6.0<https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_ReconAllTableStableV6.0&d=DwICAg&c=heEcP2AsrLOv4XP8e7I9NA&r=pVcBZUHksoIOTN75JaLZTZEAPxBaNZr49Od8c24nskU&m=vTpUsyeuuJ15qFWBMe3LprH61_ATtfgG0Pl3TN6dF9M&s=Edp9qo2Nvxv2H9wbO_Y8omiLD9VZoTScHNHlUDHsJ3c&e=
> table: mris_make_surfaces -aseg ../mri/aseg.presurf -whiteonly -noaparc -mgz
-T1 brain.finalsurfs <subjid> ?h . Once I saw that the new edits worked, I ran
recon-all with the remainder of autorecon2 (-white -smooth2 -inflate2 -curvHK
-curvstats) and all of autorecon3 (-autorecon3).
If you are not seeing the same surface improvements, make sure you've replaced
your wm.mgz and brain.finalsurfs.mgz with the edited version I sent you last
week. You can save copies of your original files, but rename them wm_old.mgz
and brain.finalsurfs_old.mgz so that FreeSurfer doesn't accidentally apply them
to your new recon-all.
Going forward, if you have a similar issue, I would first suggest editing the
wm.mgz. If that doesn't work, move to the brain.finalsurfs.mgz.
Let me know if you're still having trouble or would like more detail.
Best,
Bram
___________________
Bram R. Diamond, BSc
Sr. Clinical Research Coordinator
Laboratory for Computational Neuroimaging (LCN)
Laboratory for NeuroImaging of Coma and Consciousness (NICC)
Massachusetts General Hospital
(p): 617-726-6598
LCN:
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.martinos.org_lab_lcn&d=DwICAg&c=heEcP2AsrLOv4XP8e7I9NA&r=pVcBZUHksoIOTN75JaLZTZEAPxBaNZr49Od8c24nskU&m=vTpUsyeuuJ15qFWBMe3LprH61_ATtfgG0Pl3TN6dF9M&s=wrvIWEkXnDU_jYCaAs97WYzFnKp1BjRN9xoBHmevxM4&e=
NICC:
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.massgeneral.org_nicc-3F&d=DwICAg&c=heEcP2AsrLOv4XP8e7I9NA&r=pVcBZUHksoIOTN75JaLZTZEAPxBaNZr49Od8c24nskU&m=vTpUsyeuuJ15qFWBMe3LprH61_ATtfgG0Pl3TN6dF9M&s=FyPn_nwOAT1v4zInFWbTsCV7komEhGiO7o1L7ayNi6w&e=
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Xiaoqian Yan
<yanxq...@gmail.com>
Sent: Friday, October 18, 2019 4:17 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] imperfect segmentation in the occipital lobe in
epilepsy patient
External Email - Use Caution
Dear Bram,
Thanks very much for your help. If I am understanding correctly, you first
filled the lesions in the wm (brain.finalsurfs.mgz) in freeview with 'voxel
edit', brush value = 110. Then you recreated a new wm.mgz, with which commands?
I might run into similar situations in the future, as I am working on a project
with epilepsy patients that will have depth electrodes implanted in their brain
(causing thermal lesions). When that happens again, I want to be able to fix
that by myself.
Thanks again, best wishes
Xiaoqian
On Fri, 18 Oct 2019 at 20:48, Diamond, Bram Ryder
<brdiam...@mgh.harvard.edu<mailto:brdiam...@mgh.harvard.edu>> wrote:
Hi Xiaoqian,
We don't typically recommend this, but it looks like you will need to edit your
brain.finalsurfs.mgz to account for the wm lesion. I tested this out by filling
in the lesion with 110 and recreating the wm surface -- it seems to work quite
well.
Once that is done, you can run the following command to finish your recon-all.
I'm running it now to make sure the output is okay:
recon-all -s <subject_id> -white -smooth2 -inflate2 -curvHK -curvstats
-autorecon3
I also made some edits to the wm.mgz, but I'm not sure they were necessary.
I'll send you copies of the edited files in a private email.
Best,
Bram
___________________
Bram R. Diamond, BSc
Sr. Clinical Research Coordinator
Laboratory for Computational Neuroimaging (LCN)
Laboratory for NeuroImaging of Coma and Consciousness (NICC)
Massachusetts General Hospital
(p): 617-726-6598
LCN:
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.martinos.org_lab_lcn&d=DwICAg&c=heEcP2AsrLOv4XP8e7I9NA&r=pVcBZUHksoIOTN75JaLZTZEAPxBaNZr49Od8c24nskU&m=vTpUsyeuuJ15qFWBMe3LprH61_ATtfgG0Pl3TN6dF9M&s=wrvIWEkXnDU_jYCaAs97WYzFnKp1BjRN9xoBHmevxM4&e=
NICC:
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.massgeneral.org_nicc-3F&d=DwICAg&c=heEcP2AsrLOv4XP8e7I9NA&r=pVcBZUHksoIOTN75JaLZTZEAPxBaNZr49Od8c24nskU&m=vTpUsyeuuJ15qFWBMe3LprH61_ATtfgG0Pl3TN6dF9M&s=FyPn_nwOAT1v4zInFWbTsCV7komEhGiO7o1L7ayNi6w&e=
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Xiaoqian Yan <yanxq...@gmail.com<mailto:yanxq...@gmail.com>>
Sent: Wednesday, October 16, 2019 12:11 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] imperfect segmentation in the occipital lobe in
epilepsy patient
External Email - Use Caution
Dear Bruce,
Thanks for the reply. I have uploaded my data through the Martinos Center
FileDrop, here is the link:
+ Data_Xiaoqian.zip (169.46 MiB)
<https://urldefense.proofpoint.com/v2/url?u=http-3A__gate.nmr.mgh.harvard.edu_filedrop2_-3Fp-3D6wbctqzrzh1&d=DwICAg&c=heEcP2AsrLOv4XP8e7I9NA&r=pVcBZUHksoIOTN75JaLZTZEAPxBaNZr49Od8c24nskU&m=vTpUsyeuuJ15qFWBMe3LprH61_ATtfgG0Pl3TN6dF9M&s=KY59TqXSOYNPlQK0M4Xt2KoZ2TMH4SjKUG5rrNEWfcA&e=
>
I explained my problems in that link, but still copy and past here:
'' I am having troubles doing a good segmentation in the right occipital lobe
in a patient's brain. There is a thermal lesion in that region, a black whole,
that could make the segmentations go wrong. I tried to edit the wm, but the
results were not ideal.
The thermal lesion can be clearly seen from the axial slices 108 - 115, e.g. in
RAS coordinate [40,-50,-4] on the axial slice 112. The bad segmentation (wm and
pial surface) can be seen from the coronal slices 54 - 62, e.g. in coordinate
[42, -52, -10] on the coronal slice 57. The wrong segmentation made it
impossible to overlap the functional activations in the OFA (occipital face
area) region on the surface.
In my uploaded data directory, I already edited the wm and brainmask, and I
only reran 'recon-all -autorecon2-wm -subjid name' to save time. ''
Thanks in advance, and best wishes,
Xiaoqian
On Wed, 16 Oct 2019 at 15:07, Bruce Fischl
<fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>> wrote:
Hi Xiaoqian
it's pretty hard to tell what's going on from these images. If you tar/gzip
your whole subject dir and upload it with an email telling us the specific
voxel coords that you want us to examine
cheers
Bruce
On Wed, 16 Oct 2019, Xiaoqian Yan wrote:
>
> External Email - Use Caution
>
> Dear Douglas,
> Thanks for your reply. I double checked my results. It was true that the
> rh.orig.nofix and rh.orig did not overlap over the region that I was
> interested in. I re-edit the wm, and only ran 'recon-all -autorecon2-wm
> -subjid patientname' to check the results, but the rh.orig.nofix and rh.orig
> were still not overlapped. Do you mind helping me check my wm edits? For me,
> the thermal lesion is a black hole that big enough to confuse the
> segmentation. Maybe there is a way to mark that region or add a label,
> before I run the recon-all?
>
> P.S. in the attached figures, pial is in green, rh.orig.nofix in red, and
> rh.orig in yellow.
>
> Thanks and have a nice day,
>
> Xiaoqian
>
>
>
> On Fri, 11 Oct 2019 at 00:47, Greve, Douglas N.,Ph.D.
> <dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> wrote:
> I think that the wm edits should have worked. Can you load the
> rh.orig.nofix and rh.orig to see if they encompass your edits?
> If not, then maybe your did not re-run it properly.
>
> On 10/8/2019 12:22 PM, Xiaoqian Yan wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer experts,
> I am trying to do the segmentation on a patient's T1 image. I
> did not get error messages running the 'recon-all' (recon-all -i
> T1.nii -subjid PatientName -all), but the segmentation over the
> right occipital lobe was imperfect, which caused failures to map
> the functional activations in this region onto the surface.
>
> I tried to manually edit the wm.mgz several times, but the
> output did not change a lot (please see the attached image). The
> patient had depth EEG electrodes implanted in this region
> before, so there is a thermal lesion which I thought could have
> caused the bad segmentation. Do you have any ideas about what I
> can do next, or it is possible for you to help me editing the
> data?
>
> Thanks in advance, best wishes
>
> Xiaoqian
>
> _______________________________________________
> Freesurfer mailing list
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>
>
>
> _______________________________________________
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>
>
>
>_______________________________________________
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End of Freesurfer Digest, Vol 188, Issue 32
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