> From: freesurfer-request@nmr.mgh.harvard.edu
> Subject: Freesurfer Digest, Vol 119, Issue 6
> To: freesurfer@nmr.mgh.harvard.edu
> Date: Mon, 6 Jan 2014 10:51:33 -0500
>
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> Today's Topics:
>
> 1. erroneuos segmentation labeling of skull outside of brain
> (Yuliya Yoncheva)
> 2. Re: erroneuos segmentation labeling of skull outside of brain
> (Bruce Fischl)
> 3. Re: Motion correction for SPACE FLAIR (Bruce Fischl)
> 4. Re: erroneuos segmentation labeling of skull outside of brain
> (Yuliya Yoncheva)
> 5. Re: erroneuos segmentation labeling of skull outside of brain
> (Bruce Fischl)
> 6. Re: recon-all exited w/errors (Bruce Fischl)
> 7. ROI masks created in FreeSurfer used in FSL?? (Frank Hsieh)
> 8. converting .thickness files of T1 MRI from FreeSurfer into
> AFNI (Muhammad Naveed Iqbal Qureshi)
> 9. brain orientation in qdec (L. Schweren)
> 10. Re: converting .thickness files of T1 MRI from FreeSurfer
> into AFNI (Bruce Fischl)
> 11. recon-all error (Emad Ahmadi)
> 12. Fwd: Anatomical segmentation - question (Rotem Saar)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 5 Jan 2014 15:14:39 -0500
> From: Yuliya Yoncheva <yuliya.yoncheva@gmail.com>
> Subject: [Freesurfer] erroneuos segmentation labeling of skull outside
> of brain
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID:
> <CAGE5uFc2uD9pMefXjRZE0LQP+GcfhHKWeVkHxOGwDzV1=jYrQA@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear FreeSurfer community,
>
> I am visually inspecting the quality of my recon -all output for a large
> dataset and have a rookie question.
>
> In some instances, when skull stripping ended up leaving some of the skull,
> these voxels are associated with a "sgmtn label" (cerebral cortex). In
> other instances, although there are a small number of skull voxels that
> were not removed automatically, these voxels do not have an associated
> "sgmnt label" available in TkMedit Tools.
>
> Is it the case that only the voxels for which there is a segmentation label
> are actually added to the total grey volume estimate?
>
> Thus, voxels, which have not been automatically labelled would not impact
> volume computations?
>
> Thank you kindly for your help.
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> ------------------------------
>
> Message: 2
> Date: Sun, 5 Jan 2014 15:40:24 -0500 (EST)
> From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] erroneuos segmentation labeling of skull
> outside of brain
> To: Yuliya Yoncheva <yuliya.yoncheva@gmail.com>
> Cc: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <alpine.LRH.2.03.1401051539450.16518@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Yuliya
>
> they are included if they are inside of the ?h.pial surface. We don't use
> the cortex aseg label as it is in general less accurate than the surfaces.
>
> cheers
> Bruce
> On Sun, 5 Jan 2014, Yuliya Yoncheva wrote:
>
> > Dear FreeSurfer community,
> > I am visually inspecting the quality of my recon -all output for a large
> > dataset and have a rookie question.
> >
> > In some instances, when skull stripping ended up leaving some of the skull,
> > these voxels are associated with a "sgmtn label" (cerebral cortex). In other
> > instances, although there are a small number of skull voxels that were not
> > removed automatically, these voxels do not have an associated "sgmnt label"
> > available in TkMedit Tools.
> >
> > Is it the case that only the voxels for which there is a segmentation label
> > are actually added to the total grey volume estimate??
> >
> > Thus, voxels, which have not been automatically labelled would not impact
> > volume computations?
> >
> > Thank you kindly for your help.
> >
> >
>
> ------------------------------
>
> Message: 3
> Date: Sun, 5 Jan 2014 15:55:13 -0500 (EST)
> From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] Motion correction for SPACE FLAIR
> To: Octavian Lie <octavian.lie@gmail.com>
> Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <alpine.LRH.2.03.1401051554470.16518@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset="windows-1252"
>
> Hi Octavian
>
> it's not so easy to reduce the bandwidth in the T2-space sequences, but
> certainly you can try. Geometry-matched just means that the FOV and
> matrix sizes are the same.
>
> cheers
> Bruce
> On Fri, 3 Jan 2014, Octavian Lie wrote:
>
> > Dear Bruce,
> >
> > Best wishes for 2014!
> >
> > I will heed your advice and cc to the list. Indeed, the MGH protocol I
> > obtained from Andre has one acquisition (NSA).
> > Related, I cc this post:
> >
> > We have been trying adaptations of the T2spaceFLAIR MGH protocol on
> > our Phillips 3T scanners (sequences called VISTA). Incorporation of
> > the T2 space FLAIR has been mostly successful at editing out the dura
> > from the pial surface. The only concern are minute differences
> > occasionally appearing as small indentations (at most times <1-2mm)
> > between the woFLAIR.pial and the final pial surfaces, including in
> > intrasulcal (duraless) areas; the amount of these small mismatches is
> > variable from patient to patients, with some trials with almost
> > perfect overlap, and others with visible, if small, differences. I
> > wonder if this has been your experience too, and if this is due mostly
> > to bb registration limits or to differences in pixel bandwidth between
> > mprage and space flair sequences (in our case, see below).
> > In FSwiki, the recommendation is that T2 space flair ?should be
> > bandwidth, geometry and readout matched to the mprage?.
> >
> > 1. Speaking about pixel bandwidth, logistics most likely would not
> > allow application of a MEMPR sequence on our Phillips. According to
> > Siemens MPRAGE MGH specs, "exceptions indicate that if a multiple echo
> > sequence is not available, one should choose a bandwidth of 195
> > Hz/pixel for the MPRAGE". In that case/ using the Siemens Trio MPRAGE
> > protocol as if the MEMPR is not available, how one would adjust the
> > bandwidth in T2spaceFLAIR protocol (currently ~650 in the Siemens
> > space flair and MEMPR protocols) to "match" it to the "simple" MPRAGE
> > protocol (decreasing it to 195 ?). Would it be a workaround? (Please
> > comment on the Siemens case, obviously, I do not expect any light on
> > Phillips without further testing).
> > 2. Could you clarify what geometry matched means?
> > Please advise,
> >
> > Thank you,
> >
> > Octavian
> >
> > On Fri, Jan 3, 2014 at 9:12 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
> >> Hi Octavian
> >>
> >> can you cc the list so that others can answer? What is NSA? We don't have a
> >> ton of experience with it, but 1 has seemed ok (not sure if we've ever tried
> >> two)
> >> Bruce
> >>
> >>
> >>
> >> On Thu, 2 Jan 2014, Octavian Lie wrote:
> >>
> >>> Dear Bruce,
> >>>
> >>> Thank you. We used one vs 2 NSA T2 space FLAIR sequences, without a
> >>> consistent difference in results, with the 2-NSA run obviously doubling
> >>> the
> >>> scan time. Is there a preferred number of NSA you recommend, or we should
> >>> be
> >>> fine with one? Both are at resolution 1X1X1 mm.
> >>> Thank you,
> >>>
> >>> Octavian
> >>>
> >>>
> >>>
> >>> On Thu, Jan 2, 2014 at 11:56 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> >>> wrote:
> >>> Hi Octaviaan
> >>> no, not really. You should motion correct and average them using
> >>> something like mri_motion_correct*
> >>>
> >>> We do typically bandwidth/readout match them to the memprages so
> >>> that there is no differential distortion
> >>>
> >>> cheers
> >>> Bruce
> >>>
> >>>
> >>> On Wed, 1 Jan 2014, Octavian Lie wrote:
> >>>
> >>> Dear All,
> >>>
> >>> We recently implemented pial correction using T2
> >>> space FLAIR with freesurfer
> >>> v 5.3, mostly successfully. We use 2-3 MPRAGE
> >>> (sagittal + axial and/or
> >>> coronal) volumes as 001.mgz, 002/003.mgz for the
> >>> motion correction step in
> >>> recon-all pipeline.
> >>> The typical times for acquiring space FLAIR in our
> >>> settings vary from 2.5 to
> >>> 6 min, depending on the resolution/NSA no. I was
> >>> wondering how freesurfer
> >>> deals with motion artifacts in the space FLAIR
> >>> sequence (especially with
> >>> longer acquisition times), and if there is a
> >>> strategy to minimize motion
> >>> distortion with these (such as getting second runs
> >>> for averaging, etc).
> >>> Please advise,
> >>>
> >>> Octavian.
> >>>
> >>>
> >>>
> >>>
> >>> The information in this e-mail is intended only for the person to whom
> >>> it is
> >>> addressed. If you believe this e-mail was sent to you in error and the
> >>> e-mail
> >>> contains patient information, please contact the Partners Compliance
> >>> HelpLine at
> >>> http://www.partners.org/complianceline . If the e-mail was sent to you
> >>> in error
> >>> but does not contain patient information, please contact the sender
> >>> and properly
> >>> dispose of the e-mail.
> >>>
> >>>
> >>>
> >>
> >
> >
> >
>
> ------------------------------
>
> Message: 4
> Date: Sun, 5 Jan 2014 19:25:53 -0500
> From: Yuliya Yoncheva <yuliya.yoncheva@gmail.com>
> Subject: Re: [Freesurfer] erroneuos segmentation labeling of skull
> outside of brain
> To: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> Cc: freesurfer@nmr.mgh.harvard.edu
> Message-ID:
> <CAGE5uFcchoLxBvaf5Lze9z9_QPU4NGa83WFwZ90auZX3-idsFg@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello Bruce,
>
> thank you very much for your fast response and clarifying that potential
> voxels outside the pial surface do not impact cortical measures.
>
> Best,
> Yuliya
>
>
>
> On Sun, Jan 5, 2014 at 3:40 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>wrote:
>
> > Hi Yuliya
> >
> > they are included if they are inside of the ?h.pial surface. We don't use
> > the cortex aseg label as it is in general less accurate than the surfaces.
> >
> > cheers
> > Bruce
> >
> > On Sun, 5 Jan 2014, Yuliya Yoncheva wrote:
> >
> > Dear FreeSurfer community,
> >> I am visually inspecting the quality of my recon -all output for a large
> >> dataset and have a rookie question.
> >>
> >> In some instances, when skull stripping ended up leaving some of the
> >> skull,
> >> these voxels are associated with a "sgmtn label" (cerebral cortex). In
> >> other
> >> instances, although there are a small number of skull voxels that were not
> >> removed automatically, these voxels do not have an associated "sgmnt
> >> label"
> >> available in TkMedit Tools.
> >>
> >> Is it the case that only the voxels for which there is a segmentation
> >> label
> >> are actually added to the total grey volume estimate?
> >>
> >> Thus, voxels, which have not been automatically labelled would not impact
> >> volume computations?
> >>
> >> Thank you kindly for your help.
> >>
> >>
> >>
> >
> > The information in this e-mail is intended only for the person to whom it
> > is
> > addressed. If you believe this e-mail was sent to you in error and the
> > e-mail
> > contains patient information, please contact the Partners Compliance
> > HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to you in
> > error
> > but does not contain patient information, please contact the sender and
> > properly
> > dispose of the e-mail.
> >
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 5
> Date: Sun, 5 Jan 2014 20:29:06 -0500 (EST)
> From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] erroneuos segmentation labeling of skull
> outside of brain
> To: Yuliya Yoncheva <yuliya.yoncheva@gmail.com>
> Cc: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <alpine.LRH.2.03.1401052028520.16518@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset="iso-8859-1"
>
> exactly, or measures derived them them like whole-brain volume
>
> cheers
> Bruce
>
> On Sun, 5 Jan 2014, Yuliya
> Yoncheva wrote:
>
> > Hello Bruce,
> > thank you very much for your fast response and clarifying that potential
> > voxels outside the pial surface do not impact cortical measures.
> >
> > Best,?
> > Yuliya
> >
> >
> >
> > On Sun, Jan 5, 2014 at 3:40 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> > wrote:
> > Hi Yuliya
> >
> > they are included if they are inside of the ?h.pial surface. We
> > don't use the cortex aseg label as it is in general less
> > accurate than the surfaces.
> >
> > cheers
> > Bruce
> > On Sun, 5 Jan 2014, Yuliya Yoncheva wrote:
> >
> > Dear FreeSurfer community,
> > I am visually inspecting the quality of my recon
> > -all output for a large
> > dataset and have a rookie question.
> >
> > In some instances, when skull stripping ended up
> > leaving some of the skull,
> > these voxels are associated with a "sgmtn label"
> > (cerebral cortex). In other
> > instances, although there are a small number of
> > skull voxels that were not
> > removed automatically, these voxels do not have an
> > associated "sgmnt label"
> > available in TkMedit Tools.
> >
> > Is it the case that only the voxels for which there
> > is a segmentation label
> > are actually added to the total grey volume
> > estimate??
> >
> > Thus, voxels, which have not been automatically
> > labelled would not impact
> > volume computations?
> >
> > Thank you kindly for your help.
> >
> >
> >
> >
> > The information in this e-mail is intended only for the person to whom
> > it is
> > addressed. If you believe this e-mail was sent to you in error and the
> > e-mail
> > contains patient information, please contact the Partners Compliance
> > HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to you
> > in error
> > but does not contain patient information, please contact the sender
> > and properly
> > dispose of the e-mail.
> >
> >
> >
> >
>
> ------------------------------
>
> Message: 6
> Date: Sun, 5 Jan 2014 20:50:51 -0500 (EST)
> From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] recon-all exited w/errors
> To: "Boric, Katica A." <KBORIC@mgh.harvard.edu>
> Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <alpine.LRH.2.03.1401052049480.16518@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Katica
>
> what format was the input image to recon-all? Can you verify that tkmedit
> has the directions correct (that is what it labels as anterior is actually
> anatomically anterior, etc...). If so, then the talairach just failed and
> you will need to either try an alternative (like the MNI or SPM talairachs)
> or generate it manually.
>
> cheers
> Bruce
>
>
>
> On Thu, 2 Jan 2014, Boric, Katica A.
> wrote:
>
> > Happy New Year freesuerfers!
> > I run into this error while doing?recon-all :
> >
> > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
> > ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)
> > Manual Talairach alignment may be necessary, or
> > include the -notal-check flag to skip this test,
> > making sure the -notal-check flag follows -all
> > or -autorecon1 in the command string.
> >
> > I would really appreciate if someone could give me some advice on how to fix
> > this error.
> >
> > Thank you very much!
> >
> > Katica Boric,
> >
> >
> > ps:?Here is the error log:
> >
> > #@# Talairach Failure Detection Thu Jan ?2 14:20:32 EST 2014
> > /home/XX/XXX/subjects/XXX_SurferOutput/mri
> >
> > ?talairach_afd -T 0.005 -xfm transforms/talairach.xfm?
> >
> > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
> > ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)
> > INFO: Attempting MINC mritotal to perform Talairach align
> > #--------------------------------------------
> > #@# Talairach Thu Jan ?2 14:20:33 EST 2014
> > /home/XX/XXX/subjects/XXX_SurferOutput/mri
> >
> > ?mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i
> > orig.mgz --o orig_nu.mgz?
> >
> >
> > ?talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm?
> >
> > /home/XX/XXX/subjects/XXX_SurferOutput/mri
> > /usr/local/freesurfer/bin/talairach
> > --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
> > $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $
> > Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42
> > UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
> > Thu Jan ?2 14:21:30 EST 2014
> > tmpdir is transforms/tmp.talairach.34005
> > /home/XX/XXX/subjects/XXX_SurferOutput/mri
> > mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc
> > mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc?
> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> > reading from orig_nu.mgz...
> > TR=8.23, TE=3.22, TI=450.00, flip angle=12.00
> > i_ras = (-1, -9.03383e-08, 0)
> > j_ras = (-1.3411e-07, 2.66591e-08, -1)
> > k_ras = (1.59256e-07, 1, -5.93718e-09)
> > writing to transforms/tmp.talairach.34005/src.mnc...
> > --------------------------------------------
> > mritotal -verbose -debug -clobber -modeldir
> > /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm
> > transforms/tmp.talairach.34005/src.mnc transforms/talairach.auto.xfm
> > Legacy library shellwords.pl will be removed from the Perl core distribution
> > in the next major release. Please install it from the CPAN distribution
> > Perl4::CoreLibs. It is being used at /usr/local/freesurfer/mni/bin/mritotal,
> > line 460.
> > ?
> > ?
> > Thu Jan ?2 14:21:43 EST 2014
> > talairach done
> >
> > ?cp transforms/talairach.auto.xfm transforms/talairach.xfm?
> >
> > #--------------------------------------------
> > #@# Talairach Failure Detection Thu Jan ?2 14:21:44 EST 2014
> > /home/XX/XXX/subjects/XXX_SurferOutput/mri
> >
> > ?talairach_afd -T 0.005 -xfm transforms/talairach.xfm?
> >
> > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
> > ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)
> > Manual Talairach alignment may be necessary, or
> > include the -notal-check flag to skip this test,
> > making sure the -notal-check flag follows -all
> > or -autorecon1 in the command string.
> > See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
> > Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42
> > UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
> >
> > recon-all -s xxx_SurferOutput exited with ERRORS at Thu Jan ?2 14:21:45 EST
> > 2014
> >
> >
> >
> >
> >
> >
>
> ------------------------------
>
> Message: 7
> Date: Sun, 5 Jan 2014 23:35:55 -0800
> From: Frank Hsieh <two.frank@gmail.com>
> Subject: [Freesurfer] ROI masks created in FreeSurfer used in FSL??
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID:
> <CABBeRCEt37ZwE1-jHuZGC3Vw-D_v2+svOAnQUcSP6kW37qT4oQ@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear FreeSurfer Users,
>
> I ran recon -all on my structural image and created ROI masks (using
> mri_label2vol) based on FreeSurfer's cortical parcellation. I'd like to use
> these masks for further analysis with FSL. However, it seems that the ROI
> masks generated with mri_label2vol have different header information than
> that of the original structural image. As a result, I was unable to carry
> out further analysis with FSL (e.g., converting these ROI masks into
> functional space with hires2example_func.mat). I was wondering if there is
> a way to solve this issue.
>
> Many thanks in advance.
> Frank
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> ------------------------------
>
> Message: 8
> Date: Mon, 6 Jan 2014 17:11:54 +0900
> From: Muhammad Naveed Iqbal Qureshi <mniqureshi@hotmail.com>
> Subject: [Freesurfer] converting .thickness files of T1 MRI from
> FreeSurfer into AFNI
> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <BLU174-W27296B6C59F4D34F89293AC4B70@phx.gbl>
> Content-Type: text/plain; charset="ks_c_5601-1987"
>
> Hi,
> I want to know that how can I convert FreeSurfer .thickness files to AFNI readable format
> I tried the following Command but it gives error
>
>
> mri_convert /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (0, 0, -1)
> k_ras = (0, 1, 0)
> writing to /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik...
> AFNI BRIK write unsupported
> ERROR: failure writing /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik
> UN:/media>
>
> Please let me help me to solve this problem
> Thank you :)
>
>
>
> Best Regards,
>
> Muhammad
> Naveed Iqbal Qureshi
>
>
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> ------------------------------
>
> Message: 9
> Date: Mon, 6 Jan 2014 10:45:52 +0100
> From: "L. Schweren" <l.j.s.schweren@umcg.nl>
> Subject: [Freesurfer] brain orientation in qdec
> To: <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <005601cf0ac4$16bda9b0$4438fd10$@umcg.nl>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear experts,
>
>
>
> I ran recon-all with qcache. When loading the right hemisphere of fsaverage
> (or any other surface reconstruction) into tksurfer (for example command:
> tksurfer fsaverage rh white), the left hemisphere surface is displayed, and
> it is upside down. When I import annotations they load in the same
> orientation as the surface. However, the coordinates and the labels,
> displayed in the Tksurfer Tools window, are not. For example, when I move
> the cursor to the temporal lobe, the label says it's postcentral. I do not
> mind manually turning the surfaces in tksurfer, but I do need to be sure I
> am looking at the correct hemispheres, coordinates and labels.
>
> I hope you can help me solve this. Thank you in advance.
>
>
>
> Best wishes,
>
> Lizanne
>
>
>
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> ------------------------------
>
> Message: 10
> Date: Mon, 6 Jan 2014 08:41:58 -0500 (EST)
> From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] converting .thickness files of T1 MRI from
> FreeSurfer into AFNI
> To: Muhammad Naveed Iqbal Qureshi <mniqureshi@hotmail.com>
> Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <alpine.LRH.2.03.1401060840550.16518@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset="iso-8859-15"
>
> Hi Muhammad
>
> try:
>
> set sdir=/home/naveed/freesurfer/subjects/CHR01/surf
> mris_convert -c $sdir/rh.thickness $sdir/rh.orig $sdir/rh.thickness.brik
>
> cheers
> Bruce
>
> On Mon, 6 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
>
> > Hi,
> > I want to know that how can I convert FreeSurfer .thickness files to AFNI
> > readable format
> > I tried the following Command but it gives error
> >
> >
> > mri_convert /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness
> > /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik
> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> > reading from /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness...
> > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> > i_ras = (-1, 0, 0)
> > j_ras = (0, 0, -1)
> > k_ras = (0, 1, 0)
> > writing to /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik...
> > AFNI BRIK write unsupported
> > ERROR: failure writing
> > /media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik
> > UN:/media>
> >
> > Please let me help me to solve this problem
> > Thank you :)?
> >
> > Best Regards,
> > Muhammad Naveed Iqbal Qureshi
> >
> >
>
> ------------------------------
>
> Message: 11
> Date: Mon, 6 Jan 2014 10:40:43 -0500 (EST)
> From: "Emad Ahmadi" <emad@nmr.mgh.harvard.edu>
> Subject: [Freesurfer] recon-all error
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <63234.172.19.2.113.1389022843.squirrel@mail.martinos.org>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello & Happy New Year!
>
> I'm running recon-all for one subject on MGH clusters (ERISone), and it
> exits with error. I would appreciate it if you help me figure out what the
> problem is. The log file is attached.
>
> All the best throughout 2014!
> Emad
>
>
> Emad Ahmadi, MD
> ------------------------------------------------
> Research Fellow
> Department of Radiology
> Massachusetts General Hospital
> Harvard Medical School
>
> 25 New Chardon Street, Suite 400
> Boston, MA 02114
> Tel: 617 726 5237
> Email: emad@nmr.mgh.harvard.edu
>
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> ------------------------------
>
> Message: 12
> Date: Mon, 6 Jan 2014 17:51:18 +0200
> From: Rotem Saar <saar.rotem@gmail.com>
> Subject: [Freesurfer] Fwd: Anatomical segmentation - question
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID:
> <CAMjFEmbcEwbXMOyxw-kuep6NSzdnk=rYHSEvwPGSbiXkBZKxtA@mail.gmail.com>
> Content-Type: text/plain; charset="windows-1252"
>
> Dear freesurfer experts,
>
> I'm performing anatomical segmentation for Philips dicoms (3T scanner). I
> got these two images from the same slice while performing step number 4 in
> the script below ? from some reason, the two images don't fit. Should I use
> "scale brain" ? I know this is not recommended thus want to consult with u
> first ? Can u please comment on why this is happening? Is there any value
> that corresponds to "how good is the segmentation" ? if yes, where can I
> find it ?
>
> My script is written below.
>
> Thanks,
>
> Rotem
>
> Anatomical segmentation:
>
> first step- 23 hours:
>
> *recon-all -autorecon-all -i ~/Desktop/ FOLDER-NAME /I00001.dcm -s
> FOLDER-NAME*
>
> second step:(gyrus=green, sulcus=red)
>
> *tksurfer -curv FOLDER-NAME lh/rh inflated*
>
> third step: (talairch registretion)
>
> *tkmedit FOLDER-NAME brainmask.mgz*
>
> File-> transforms-> load transform AUX-> Browse-> talairch.xfm
>
> forth step: (simetry - allows changing 12df transformation. if we made any
> changes we should click "save reg" and run this command again)
>
> *tkregister2 --mgz --s FOLDER-NAME --fstal --surf orig*
>
> IF WE CHANGE ANYTHING, CLICK "SAVE REG" AND RUN FROM STARTING POING:
> recon-all -all -subjectid FOLDER-NAME
>
> fifth step: (scalp removal: if removed too much, rise up from the value 25:
>
> *recon-all -skullstrip -wsthresh 25 -clean-bm -no-wsgcaatlas -s
> FOLDER-NAME *
>
> to check the result press: *tkmedit FOLDER-NAME brainmask.mgz lh.white -aux
> T1.mgz -aux-surface rh.white *)
>
> for hand correction: *tkmedit FOLDER-NAME brainmask.mgz -aux T1.mgz*
>
> tools-> configure volume brush -> MARK: mode=clone, source=Aux
>
> tools-> configure brush info (for choosing brush size)
>
> click on edit voxels: click in MIDDLE for adding voxels, RIGHT for removing
> voxels : slice by slice.
>
> when finish, click: File-> save main volume
>
> sisxt step: (cp for correcting segmentation)
>
> *tkmedit FOLDER-NAME brainmask.mgz lh.white -aux T1.mgz -aux-surface
> rh.white*
>
> seventh step: (done)
>
> *recon-all -autorecon2-cp -autorecon3 -s FOLDER-NAME*
>
>
>
>
>
> Rotem Saar-Ashkenazy
> Department of Brain and Cognitive Science
> Ben Gurion University of the Negev
> Beer-Sheva 84105
> Israel
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>
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> End of Freesurfer Digest, Vol 119, Issue 6
> ******************************************