Re: [Freesurfer] Surface-based analysis of tfMRI

[Greve, Douglas N.,Ph.D.]

Actually, if you just store the denoised data as f.nii.gz, then run 
preproc-sess it should do ok. It will do motion correction, but it should not 
really do any thing if MC is already done. Just make sure that the image has a 
proper baseline so that the registration will work.

On 10/22/18 11:14 PM, Zhi Li wrote:

External Email - Use Caution

Thank you. But the fmri-denoised.nii.gz will be a volume-based data, how can I 
register and normalize it to the surface-based space, as 'preproc-sess' do that 
will generate the bilateral cortex in surface and subcortical area in volume?

On Mon, 22 Oct 2018 at 17:12, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
If you do all the preprocessing yourself, then store the output in the
run folder with a certain name, fmri-denoised.nii.gz, then when you run
mkanalysis-sess specify -funcstem fmri-denoised and proceed as norm.

On 10/22/2018 04:08 PM, Zhi Li wrote:
>
> External Email - Use Caution
>
> Hi FreeSurfer Experts,
>
> I am trying surface-based analysis of task-fMRI with FS-FAST. However,
> I would like to apply ICA-based denoising and wavelet-despiking which
> can be not done with the 'preproc-sess'. I wonder if I can do the
> preprocessing with other tools before registration with FS anatomical
> and normalization? If it is available, how can I do it with command line?
>
> Another question is if can I use other template for parcellation
> during using 'recon-all', such as the template of Human Connectome
> Project?
>
> Looking forward to your kind reply.
>
> Thank you and best wishes,
>
> Zhi
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] Surface-based analysis of tfMRI

[Zhi Li]

External Email - Use Caution

Thank you. But the fmri-denoised.nii.gz will be a volume-based data, how
can I register and normalize it to the surface-based space, as
'preproc-sess' do that will generate the bilateral cortex in surface and
subcortical area in volume?

On Mon, 22 Oct 2018 at 17:12, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> If you do all the preprocessing yourself, then store the output in the
> run folder with a certain name, fmri-denoised.nii.gz, then when you run
> mkanalysis-sess specify -funcstem fmri-denoised and proceed as norm.
>
> On 10/22/2018 04:08 PM, Zhi Li wrote:
> >
> > External Email - Use Caution
> >
> > Hi FreeSurfer Experts,
> >
> > I am trying surface-based analysis of task-fMRI with FS-FAST. However,
> > I would like to apply ICA-based denoising and wavelet-despiking which
> > can be not done with the 'preproc-sess'. I wonder if I can do the
> > preprocessing with other tools before registration with FS anatomical
> > and normalization? If it is available, how can I do it with command line?
> >
> > Another question is if can I use other template for parcellation
> > during using 'recon-all', such as the template of Human Connectome
> > Project?
> >
> > Looking forward to your kind reply.
> >
> > Thank you and best wishes,
> >
> > Zhi
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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[Freesurfer] Is the cortical thickness calculated using Hausdorff distance in FreeSurfer?

[Zhiliang Long]

External Email - Use Caution

Dear FS experts:
I'm doing a project about the changes of cortical thickness after sleep 
deprivation. I know that cortical thickness is calculated as the closest 
distance from the gray/white boundary to the gray/CSF boundary at each vertex. 
Is the thickness calculated using the Hausdorff distance?


Best


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Re: [Freesurfer] resampling data onto cortical surface

[Greve, Douglas N.,Ph.D.]

I would just do
mri_vol2vol --i vin.nii --regheader --targ orig.mgz --o vout.mgz


On 10/22/2018 05:52 PM, GREGORY R KIRK wrote:
>
> External Email - Use Caution
>
> thanks Doug, one more thing to make sure I get it correct.
>
>
> If I have a volume of quantitative MR volumes in the native space of 
> the T1 and I want them to be in registration with the freesurfer space
>
> of this subject I woiuld
>
>
> mri_convert -it nii -ot mgz vin.nii vout.mgz and then
>
> mri_convert vout.mgz vc.mgz --conform --no_scale --nochange
>
>
> so that it is in the freesurfer space but not scaled and not changed 
> from float to uchar, correct ?
>
>
> thanks
>
>
> greg
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Greve, Douglas 
> N.,Ph.D. 
> *Sent:* Monday, October 22, 2018 11:58:51 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] resampling data onto cortical surface
> Use --s subject instead of --reg (run mri_vol2vol with --help to get
> more info).
> btw, if you have multi echo data, you are probably measuring R2*, not R1.
>
> On 10/22/2018 12:55 PM, GREGORY R KIRK wrote:
> >
> > External Email - Use Caution
> >
> >
> > I have R1 values that I want to resample onto the cortical surface.
> > The R1 values were computed from a multi echo
> >
> > T1 sequence that was also used to create the T1 weighted image that
> > was used in recon-all to produce the cortical surface reconstructions
> >
> > and thus is inherently in registration to the 001.mgz that was used to
> > start recon. There will be a difference in orientation in the volume
> >
> > in that orig.mgz is in coronal and in the .mgz format.
> >
> >
> > I was thinking that if I run the first step of recon-all it should
> > give me an volume named orig.mgz that is in registration to the
> > freesurfer space
> >
> > for the subject ... or else some call to mri_convert reslice_as or
> > whatever is used in the recon-all script to convert 001.mgz to orig.mgz
> >
> >
> >
> >
> > then my problem is to get a file with the resampling of the R1 onto
> > the cortical surface withR1 values at each vertex.
> >
> >
> > when i work with fmri data I run bbregister and get the transformation
> > from the epi volume to the freesurfer space and then use
> >
> > mri_vol2surf --mov sig.nii \to resample the data onto the cortical 
> surface
> >  --reg bb.register.dat \
> >  --projfrac 0.5 --interp nearest \
> >  --hemi lh --o lh.sig.mgh
> >
> > to resample the epi data onto the cortical surface. however in this 
> case the R1 data
> > is already in perfect registration to the T1 other than the 
> reorientation and reslicing
> > done to prepare the orig.mgz volume.
> >
> > so can someone tell me what is the proper way to cook this goose
> >
> > Greg
> >
> >
> >
> > ___
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>
>
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>
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Re: [Freesurfer] resampling data onto cortical surface

[GREGORY R KIRK]

External Email - Use Caution

thanks Doug, one more thing to make sure I get it correct.


If I have a volume of quantitative MR volumes in the native space of the T1 and 
I want them to be in registration with the freesurfer space

of this subject I woiuld


mri_convert -it nii -ot mgz vin.nii vout.mgz and then

mri_convert vout.mgz vc.mgz --conform --no_scale --nochange


so that it is in the freesurfer space but not scaled and not changed from float 
to uchar, correct ?


thanks


greg


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Greve, Douglas N.,Ph.D. 

Sent: Monday, October 22, 2018 11:58:51 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] resampling data onto cortical surface

Use --s subject instead of --reg (run mri_vol2vol with --help to get
more info).
btw, if you have multi echo data, you are probably measuring R2*, not R1.

On 10/22/2018 12:55 PM, GREGORY R KIRK wrote:
>
> External Email - Use Caution
>
>
> I have R1 values that I want to resample onto the cortical surface.
> The R1 values were computed from a multi echo
>
> T1 sequence that was also used to create the T1 weighted image that
> was used in recon-all to produce the cortical surface reconstructions
>
> and thus is inherently in registration to the 001.mgz that was used to
> start recon. There will be a difference in orientation in the volume
>
> in that orig.mgz is in coronal and in the .mgz format.
>
>
> I was thinking that if I run the first step of recon-all it should
> give me an volume named orig.mgz that is in registration to the
> freesurfer space
>
> for the subject ... or else some call to mri_convert reslice_as or
> whatever is used in the recon-all script to convert 001.mgz to orig.mgz
>
>
>
>
> then my problem is to get a file with the resampling of the R1 onto
> the cortical surface withR1 values at each vertex.
>
>
> when i work with fmri data I run bbregister and get the transformation
> from the epi volume to the freesurfer space and then use
>
> mri_vol2surf --mov sig.nii \to resample the data onto the cortical surface
>  --reg bb.register.dat \
>  --projfrac 0.5 --interp nearest \
>  --hemi lh --o lh.sig.mgh
>
> to resample the epi data onto the cortical surface. however in this case the 
> R1 data
> is already in perfect registration to the T1 other than the reorientation and 
> reslicing
> done to prepare the orig.mgz volume.
>
> so can someone tell me what is the proper way to cook this goose
>
> Greg
>
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] Surface-based analysis of tfMRI

[Greve, Douglas N.,Ph.D.]

If you do all the preprocessing yourself, then store the output in the 
run folder with a certain name, fmri-denoised.nii.gz, then when you run 
mkanalysis-sess specify -funcstem fmri-denoised and proceed as norm.

On 10/22/2018 04:08 PM, Zhi Li wrote:
>
> External Email - Use Caution
>
> Hi FreeSurfer Experts,
>
> I am trying surface-based analysis of task-fMRI with FS-FAST. However, 
> I would like to apply ICA-based denoising and wavelet-despiking which 
> can be not done with the 'preproc-sess'. I wonder if I can do the 
> preprocessing with other tools before registration with FS anatomical 
> and normalization? If it is available, how can I do it with command line?
>
> Another question is if can I use other template for parcellation 
> during using 'recon-all', such as the template of Human Connectome 
> Project?
>
> Looking forward to your kind reply.
>
> Thank you and best wishes,
>
> Zhi
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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[Freesurfer] Surface-based analysis of tfMRI

[Zhi Li]

External Email - Use Caution

Hi FreeSurfer Experts,

I am trying surface-based analysis of task-fMRI with FS-FAST. However, I
would like to apply ICA-based denoising and wavelet-despiking which can be
not done with the 'preproc-sess'. I wonder if I can do the preprocessing
with other tools before registration with FS anatomical and normalization?
If it is available, how can I do it with command line?

Another question is if can I use other template for parcellation during
using 'recon-all', such as the template of Human Connectome Project?

Looking forward to your kind reply.

Thank you and best wishes,

Zhi
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Re: [Freesurfer] Myelinated cortical thickness ratio map

[Glasser, Matthew]

External Email - Use Caution

Regression would be better than division.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Damien MARIE mailto:damien.ma...@unige.ch>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, October 22, 2018 at 8:54 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Myelinated cortical thickness ratio map


External Email - Use Caution

Dear experts,

I am working with R1 maps that I project on the surface. The goal is to look at 
intra-cortical myelin.

I detect interesting effects between two groups. Now I would like to compute 
myelinated cortical thickness ratio maps, in order to control for the effect of 
cortical thickness variations occurring with gyrification.

Here is a paper where they describe a way to compute those myelinated cortical 
thickness ratio map with MIPAV and the MPI-CBS toolbox : 
https://www.ncbi.nlm.nih.gov/pubmed/29321232
«  The proportional thickness of the myelinated part of the cortex in relation 
to its overall thickness (myelinated cortical thickness) was computed with a 
fuzzy classification technique combining information about radial and 
tangential fibers.  «

1- Is it possible to do the same in FreeSurfer?

2- What about dividing my individual myelin maps by the individual cortical 
thickness maps? Is it possible to do that in FreeSurfer? SPM ImCalc would do 
the job in the volume but I don’t know how I could do that in FreeSurfer.

Any comments / other suggestions are welcome.

Thank you and best,

Damien




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Re: [Freesurfer] Stuck in "CORRECTING DEFECT"

[Bruce Fischl]

yes, they are surfaces. You need to specify -f on the command line before 
listing the surfaces you want to load
On Mon, 22 Oct 2018, Rosalia Dacosta 
Aguayo wrote:




External Email - Use Caution

I tried. I cannot open them. They are not .mgz files, they are binary files.I 
will try though, and
see what is happening.

Thank you,
Rosalia

El lun., 22 oct. 2018 21:49, Bruce Fischl  escribió:
  with freeview
  On Mon, 22 Oct 2018, Rosalia Dacosta Aguayo wrote:

  >
  > External Email - Use Caution
  >
  > Hi Bruce,
  >
  > I cannot examine those files with gedit. Could you tell me how to open 
them?
  > Thank you,
  > Rosalia
  >
  > On Mon, Oct 22, 2018 at 9:35 PM Bruce Fischl 
 wrote:
  >       Hi Lisa
  >
  >       no, likely you have to identify and correct the source of the 
giant defect,
  >       typically be either fixing the skull stripping, or editing the 
wm.mgz or
  >       adding control points
  >
  >       cheers
  >       Bruce
  >
  >
  >       On Mon, 22 Oct 2018, Lisa Crystal Krishnamurthy wrote:
  >
  >       >        External Email - Use Caution
  >       >
  >       > Hi all,
  >       >
  >       > I have a stroke brain with a large lesion that runs into this 
same problem. Is
  there a
  >       way to push the process along? No white matter segmentations are 
created to try
  and edit
  >       the surface.
  >       >
  >       > Best,
  >       > -Lisa Krishnamurthy
  >       >
  >       > -Original Message-
  >       > From: freesurfer-boun...@nmr.mgh.harvard.edu
  >       [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of 
Bruce Fischl
  >       > Sent: Monday, October 22, 2018 3:30 PM
  >       > To: Freesurfer support list
  >       > Subject: Re: [Freesurfer] Stuck in "CORRECTING DEFECT"
  >       >
  >       > Hi Rosaila
  >       >
  >       > usually when you have a defect that large (>30,000) vertices, 
which is about
  1/4 of
  >       the total surface more or less, something is dramatically wrong 
and it is not
  worth
  >       waiting for it to finish (it might take days or weeks). Examine 
the
  ?h.orig.nofix and
  >       ?h.inflated.nofix surfaces and see if there is some big problem 
like skull or
  cerebellum
  >       attached to the surface.
  >       >
  >       > cheers
  >       > Bruce
  >       >
  >       >
  >       > On Mon, 22 Oct 2018, Rosalia Dacosta Aguayo wrote:
  >       >
  >       >>
  >       >> External Email - Use Caution
  >       >>
  >       >> Dear FreeSurfer team,
  >       >>
  >       >> I Have run -autorecon1 in my sample and the report.log was 
"finished without
  errors"
  >       >> Now, running recon-all -all I have seen that a participant is 
stuck in
  >       >> CORRECTING DEFECT 0 (vertices=31977, convex hull=5359, v0=0) 
for more
  >       >> than an hour. I wonder if this is normal or if I should be 
worried
  >       >> because recon-all takes 4.5 hours approximately for every 
participant but for
  this
  >       one, it seems that is not moving from this step.
  >       >>
  >       >> Anyone could help me with this?
  >       >>
  >       >> Best regards,
  >       >> Rosaila
  >       >>
  >       >>
  >       >>
  >       >>
  >       >
  >       > ___
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  >       >
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  >
  >
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Re: [Freesurfer] Stuck in "CORRECTING DEFECT"

[Rosalia Dacosta Aguayo]

External Email - Use Caution

I tried. I cannot open them. They are not .mgz files, they are binary files.
I will try though, and see what is happening.

Thank you,
Rosalia

El lun., 22 oct. 2018 21:49, Bruce Fischl 
escribió:

> with freeview
> On Mon, 22 Oct 2018, Rosalia Dacosta Aguayo wrote:
>
> >
> > External Email - Use Caution
> >
> > Hi Bruce,
> >
> > I cannot examine those files with gedit. Could you tell me how to open
> them?
> > Thank you,
> > Rosalia
> >
> > On Mon, Oct 22, 2018 at 9:35 PM Bruce Fischl 
> wrote:
> >   Hi Lisa
> >
> >   no, likely you have to identify and correct the source of the
> giant defect,
> >   typically be either fixing the skull stripping, or editing the
> wm.mgz or
> >   adding control points
> >
> >   cheers
> >   Bruce
> >
> >
> >   On Mon, 22 Oct 2018, Lisa Crystal Krishnamurthy wrote:
> >
> >   >External Email - Use Caution
> >   >
> >   > Hi all,
> >   >
> >   > I have a stroke brain with a large lesion that runs into this
> same problem. Is there a
> >   way to push the process along? No white matter segmentations are
> created to try and edit
> >   the surface.
> >   >
> >   > Best,
> >   > -Lisa Krishnamurthy
> >   >
> >   > -Original Message-
> >   > From: freesurfer-boun...@nmr.mgh.harvard.edu
> >   [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of
> Bruce Fischl
> >   > Sent: Monday, October 22, 2018 3:30 PM
> >   > To: Freesurfer support list
> >   > Subject: Re: [Freesurfer] Stuck in "CORRECTING DEFECT"
> >   >
> >   > Hi Rosaila
> >   >
> >   > usually when you have a defect that large (>30,000) vertices,
> which is about 1/4 of
> >   the total surface more or less, something is dramatically wrong
> and it is not worth
> >   waiting for it to finish (it might take days or weeks). Examine
> the ?h.orig.nofix and
> >   ?h.inflated.nofix surfaces and see if there is some big problem
> like skull or cerebellum
> >   attached to the surface.
> >   >
> >   > cheers
> >   > Bruce
> >   >
> >   >
> >   > On Mon, 22 Oct 2018, Rosalia Dacosta Aguayo wrote:
> >   >
> >   >>
> >   >> External Email - Use Caution
> >   >>
> >   >> Dear FreeSurfer team,
> >   >>
> >   >> I Have run -autorecon1 in my sample and the report.log was
> "finished without errors"
> >   >> Now, running recon-all -all I have seen that a participant is
> stuck in
> >   >> CORRECTING DEFECT 0 (vertices=31977, convex hull=5359, v0=0)
> for more
> >   >> than an hour. I wonder if this is normal or if I should be
> worried
> >   >> because recon-all takes 4.5 hours approximately for every
> participant but for this
> >   one, it seems that is not moving from this step.
> >   >>
> >   >> Anyone could help me with this?
> >   >>
> >   >> Best regards,
> >   >> Rosaila
> >   >>
> >   >>
> >   >>
> >   >>
> >   >
> >   > ___
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> >   > Freesurfer@nmr.mgh.harvard.edu
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> >   >
> >   >
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Re: [Freesurfer] Stuck in "CORRECTING DEFECT"

[Bruce Fischl]

with freeview
On Mon, 22 Oct 2018, Rosalia Dacosta Aguayo wrote:



External Email - Use Caution

Hi Bruce,

I cannot examine those files with gedit. Could you tell me how to open them?
Thank you,
Rosalia

On Mon, Oct 22, 2018 at 9:35 PM Bruce Fischl  wrote:
  Hi Lisa

  no, likely you have to identify and correct the source of the giant 
defect,
  typically be either fixing the skull stripping, or editing the wm.mgz or
  adding control points

  cheers
  Bruce


  On Mon, 22 Oct 2018, Lisa Crystal Krishnamurthy wrote:

  >        External Email - Use Caution
  >
  > Hi all,
  >
  > I have a stroke brain with a large lesion that runs into this same 
problem. Is there a
  way to push the process along? No white matter segmentations are created 
to try and edit
  the surface.
  >
  > Best,
  > -Lisa Krishnamurthy
  >
  > -Original Message-
  > From: freesurfer-boun...@nmr.mgh.harvard.edu
  [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
  > Sent: Monday, October 22, 2018 3:30 PM
  > To: Freesurfer support list
  > Subject: Re: [Freesurfer] Stuck in "CORRECTING DEFECT"
  >
  > Hi Rosaila
  >
  > usually when you have a defect that large (>30,000) vertices, which is 
about 1/4 of
  the total surface more or less, something is dramatically wrong and it is 
not worth
  waiting for it to finish (it might take days or weeks). Examine the 
?h.orig.nofix and
  ?h.inflated.nofix surfaces and see if there is some big problem like 
skull or cerebellum
  attached to the surface.
  >
  > cheers
  > Bruce
  >
  >
  > On Mon, 22 Oct 2018, Rosalia Dacosta Aguayo wrote:
  >
  >>
  >> External Email - Use Caution
  >>
  >> Dear FreeSurfer team,
  >>
  >> I Have run -autorecon1 in my sample and the report.log was "finished 
without errors"
  >> Now, running recon-all -all I have seen that a participant is stuck in
  >> CORRECTING DEFECT 0 (vertices=31977, convex hull=5359, v0=0) for more
  >> than an hour. I wonder if this is normal or if I should be worried
  >> because recon-all takes 4.5 hours approximately for every participant 
but for this
  one, it seems that is not moving from this step.
  >>
  >> Anyone could help me with this?
  >>
  >> Best regards,
  >> Rosaila
  >>
  >>
  >>
  >>
  >
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Re: [Freesurfer] Stuck in "CORRECTING DEFECT"

[Rosalia Dacosta Aguayo]

External Email - Use Caution

Hi Bruce,

I cannot examine those files with gedit. Could you tell me how to open them?
Thank you,
Rosalia

On Mon, Oct 22, 2018 at 9:35 PM Bruce Fischl 
wrote:

> Hi Lisa
>
> no, likely you have to identify and correct the source of the giant
> defect,
> typically be either fixing the skull stripping, or editing the wm.mgz or
> adding control points
>
> cheers
> Bruce
>
>
> On Mon, 22 Oct 2018, Lisa Crystal Krishnamurthy wrote:
>
> >External Email - Use Caution
> >
> > Hi all,
> >
> > I have a stroke brain with a large lesion that runs into this same
> problem. Is there a way to push the process along? No white matter
> segmentations are created to try and edit the surface.
> >
> > Best,
> > -Lisa Krishnamurthy
> >
> > -Original Message-
> > From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:
> freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> > Sent: Monday, October 22, 2018 3:30 PM
> > To: Freesurfer support list
> > Subject: Re: [Freesurfer] Stuck in "CORRECTING DEFECT"
> >
> > Hi Rosaila
> >
> > usually when you have a defect that large (>30,000) vertices, which is
> about 1/4 of the total surface more or less, something is dramatically
> wrong and it is not worth waiting for it to finish (it might take days or
> weeks). Examine the ?h.orig.nofix and ?h.inflated.nofix surfaces and see if
> there is some big problem like skull or cerebellum attached to the surface.
> >
> > cheers
> > Bruce
> >
> >
> > On Mon, 22 Oct 2018, Rosalia Dacosta Aguayo wrote:
> >
> >>
> >> External Email - Use Caution
> >>
> >> Dear FreeSurfer team,
> >>
> >> I Have run -autorecon1 in my sample and the report.log was "finished
> without errors"
> >> Now, running recon-all -all I have seen that a participant is stuck in
> >> CORRECTING DEFECT 0 (vertices=31977, convex hull=5359, v0=0) for more
> >> than an hour. I wonder if this is normal or if I should be worried
> >> because recon-all takes 4.5 hours approximately for every participant
> but for this one, it seems that is not moving from this step.
> >>
> >> Anyone could help me with this?
> >>
> >> Best regards,
> >> Rosaila
> >>
> >>
> >>
> >>
> >
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> >
> >
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Re: [Freesurfer] Stuck in "CORRECTING DEFECT"

[Lisa Crystal Krishnamurthy]

External Email - Use Caution

HI Bruce,

Thank you for the quick reply! Are there online tutorials that could show me 
how to implement your suggestions? 

Best,
-Lisa

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Monday, October 22, 2018 3:35 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Stuck in "CORRECTING DEFECT"

Hi Lisa

no, likely you have to identify and correct the source of the giant defect, 
typically be either fixing the skull stripping, or editing the wm.mgz or adding 
control points

cheers
Bruce


On Mon, 22 Oct 2018, Lisa Crystal Krishnamurthy wrote:

>External Email - Use Caution
>
> Hi all,
>
> I have a stroke brain with a large lesion that runs into this same problem. 
> Is there a way to push the process along? No white matter segmentations are 
> created to try and edit the surface.
>
> Best,
> -Lisa Krishnamurthy
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce 
> Fischl
> Sent: Monday, October 22, 2018 3:30 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Stuck in "CORRECTING DEFECT"
>
> Hi Rosaila
>
> usually when you have a defect that large (>30,000) vertices, which is about 
> 1/4 of the total surface more or less, something is dramatically wrong and it 
> is not worth waiting for it to finish (it might take days or weeks). Examine 
> the ?h.orig.nofix and ?h.inflated.nofix surfaces and see if there is some big 
> problem like skull or cerebellum attached to the surface.
>
> cheers
> Bruce
>
>
> On Mon, 22 Oct 2018, Rosalia Dacosta Aguayo wrote:
>
>>
>> External Email - Use Caution
>>
>> Dear FreeSurfer team,
>>
>> I Have run -autorecon1 in my sample and the report.log was "finished without 
>> errors"
>> Now, running recon-all -all I have seen that a participant is stuck 
>> in CORRECTING DEFECT 0 (vertices=31977, convex hull=5359, v0=0) for 
>> more than an hour. I wonder if this is normal or if I should be 
>> worried because recon-all takes 4.5 hours approximately for every 
>> participant but for this one, it seems that is not moving from this step.
>>
>> Anyone could help me with this?
>>
>> Best regards,
>> Rosaila
>>
>>
>>
>>
>
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> %7Clkrishnamurthy%40gsu.edu%7Ca608e1a2f0964f34c96608d638558b63%7C515ad73d8d5e4169895c9789dc742a70%7C0%7C0%7C636758337419537907sdata=NhapXseC%2B1Hn7Yb3%2Fbyq4f1RRzKVmdB2gAfAlUPHnIQ%3Dreserved=0
>
>
>

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Re: [Freesurfer] Stuck in "CORRECTING DEFECT"

[Bruce Fischl]

Hi Lisa

no, likely you have to identify and correct the source of the giant defect, 
typically be either fixing the skull stripping, or editing the wm.mgz or 
adding control points


cheers
Bruce


On Mon, 22 Oct 2018, Lisa Crystal Krishnamurthy wrote:


   External Email - Use Caution

Hi all,

I have a stroke brain with a large lesion that runs into this same problem. Is 
there a way to push the process along? No white matter segmentations are 
created to try and edit the surface.

Best,
-Lisa Krishnamurthy

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Monday, October 22, 2018 3:30 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Stuck in "CORRECTING DEFECT"

Hi Rosaila

usually when you have a defect that large (>30,000) vertices, which is about 
1/4 of the total surface more or less, something is dramatically wrong and it is 
not worth waiting for it to finish (it might take days or weeks). Examine the 
?h.orig.nofix and ?h.inflated.nofix surfaces and see if there is some big problem 
like skull or cerebellum attached to the surface.

cheers
Bruce


On Mon, 22 Oct 2018, Rosalia Dacosta Aguayo wrote:



External Email - Use Caution

Dear FreeSurfer team,

I Have run -autorecon1 in my sample and the report.log was "finished without 
errors"
Now, running recon-all -all I have seen that a participant is stuck in
CORRECTING DEFECT 0 (vertices=31977, convex hull=5359, v0=0) for more
than an hour. I wonder if this is normal or if I should be worried
because recon-all takes 4.5 hours approximately for every participant but for 
this one, it seems that is not moving from this step.

Anyone could help me with this?

Best regards,
Rosaila






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Re: [Freesurfer] Stuck in "CORRECTING DEFECT"

[Lisa Crystal Krishnamurthy]

External Email - Use Caution

Hi all,

I have a stroke brain with a large lesion that runs into this same problem. Is 
there a way to push the process along? No white matter segmentations are 
created to try and edit the surface.

Best,
-Lisa Krishnamurthy

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Monday, October 22, 2018 3:30 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Stuck in "CORRECTING DEFECT"

Hi Rosaila

usually when you have a defect that large (>30,000) vertices, which is about 
1/4 of the total surface more or less, something is dramatically wrong and it 
is not worth waiting for it to finish (it might take days or weeks). Examine 
the ?h.orig.nofix and ?h.inflated.nofix surfaces and see if there is some big 
problem like skull or cerebellum attached to the surface.

cheers
Bruce


On Mon, 22 Oct 2018, Rosalia Dacosta Aguayo wrote:

> 
> External Email - Use Caution
> 
> Dear FreeSurfer team,
> 
> I Have run -autorecon1 in my sample and the report.log was "finished without 
> errors"
> Now, running recon-all -all I have seen that a participant is stuck in 
> CORRECTING DEFECT 0 (vertices=31977, convex hull=5359, v0=0) for more 
> than an hour. I wonder if this is normal or if I should be worried 
> because recon-all takes 4.5 hours approximately for every participant but for 
> this one, it seems that is not moving from this step.
> 
> Anyone could help me with this?
> 
> Best regards,
> Rosaila
> 
> 
> 
>

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Re: [Freesurfer] Stuck in "CORRECTING DEFECT"

[Bruce Fischl]

Hi Rosaila

usually when you have a defect that large (>30,000) vertices, which is 
about 1/4 of the total surface more or less, something is dramatically 
wrong and it is not worth waiting for it to finish (it might take days or 
weeks). Examine the ?h.orig.nofix and ?h.inflated.nofix surfaces and see if 
there is some big problem like skull or cerebellum attached to the surface.


cheers
Bruce


On Mon, 22 Oct 2018, Rosalia Dacosta Aguayo wrote:



External Email - Use Caution

Dear FreeSurfer team,

I Have run -autorecon1 in my sample and the report.log was "finished without 
errors"
Now, running recon-all -all I have seen that a participant is stuck in 
CORRECTING DEFECT 0
(vertices=31977, convex hull=5359, v0=0) for more than an hour. I wonder if 
this is normal or if I
should be worried because recon-all takes 4.5 hours approximately for every 
participant but for this
one, it seems that is not moving from this step.

Anyone could help me with this?

Best regards,
Rosaila



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[Freesurfer] Stuck in "CORRECTING DEFECT"

[Rosalia Dacosta Aguayo]

External Email - Use Caution

Dear FreeSurfer team,

I Have run -autorecon1 in my sample and the report.log was "finished
without errors"
Now, running recon-all -all I have seen that a participant is stuck in
CORRECTING DEFECT 0 (vertices=31977, convex hull=5359, v0=0) for more than
an hour. I wonder if this is normal or if I should be worried because
recon-all takes 4.5 hours approximately for every participant but for this
one, it seems that is not moving from this step.

Anyone could help me with this?

Best regards,
Rosaila
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[Freesurfer] postdoctoral research opportunity

[Bruce Fischl]

FYI

-- Forwarded message --
Date: Mon, 22 Oct 2018 12:16:59 -0700
From: Rahul Desikan 
To: Bruce Fischl 
Subject: one more favor


External Email - Use Caution

One more favor Bruce. If possible could you please post this on the FS/FSL 
lists? Many thanks!

Best,
Rahul

UCSF, Dept. of Radiology & Biomedical Imaging is seeking a Postdoctoral Scholar 
for The Laboratory
for Precision Neuroimaging

We are seeking a postdoctoral candidate with a strong background in genetics 
human imaging and a
desire to use a multi-disciplinary approach to pursue neurodegenerative and 
neurodevelopment
research. The candidate should have a strong statistical/computational 
background with experience
with data analytic tools such as Matlab, R, and PLINK and potentially, MRI 
image analysis tools such
as Freesurfer, FSL, and SPM. Applicants should have a Ph.D. or M.D. degree with 
less than five years
of postdoctoral experience. Highly motivated individuals with a record of 
productive research are
encouraged to apply. The position is available starting immediately.
Salary is commensurate with qualifications and experience.

Job Requirements:
    1.    CV/NIH biosketch (must contain previous research experience)
    2.    Cover Letter - Short statement on why you are interested in this 
position and how this
position will help you achieve your career goals
    3.    Three references

If interested please contact Dr. Leo Sugrue at leo.sug...@ucsf.edu
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Re: [Freesurfer] GE data issue

[Yendiki, Anastasia]

Did you look at the nifti volumes? Are they 2 sets of diffusion-weighted 
images? If so, you can concatenate them into 1 volume with mri_concat. You will 
also have to concatenate the text files that contain the b-values of the 2 
scans, and those that contain the gradient directions of the 2 scans. Make sure 
the 2 are always combined in the same order (for the volumes, b-values, and 
gradient directions). Then you use these combined files as input to TRACULA.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Pan Yunzhi 

Sent: Monday, October 22, 2018 1:11:21 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] GE data issue


External Email - Use Caution

Dear sir/madam,

   I try to use TRACULSR to analysis DTI data of GE machine. But when I 
transfer origin data to nii, I found  2 nii file producted per sample. Can I 
use  these data to run TRACULAR、 If yes, how can I combine 2 nii file?

   I hope someone can help me. Thank you so much



Pan Yunzhi

University of Western Ontario


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[Freesurfer] GE data issue

[Pan Yunzhi]

External Email - Use Caution

Dear sir/madam,
   I try to use TRACULSR to analysis DTI data of GE machine. But when I 
transfer origin data to nii, I found  2 nii file producted per sample. Can I 
use  these data to run TRACULAR、 If yes, how can I combine 2 nii file?
   I hope someone can help me. Thank you so much

Pan Yunzhi
University of Western Ontario

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Re: [Freesurfer] resampling data onto cortical surface

[Greve, Douglas N.,Ph.D.]

Use --s subject instead of --reg (run mri_vol2vol with --help to get 
more info).
btw, if you have multi echo data, you are probably measuring R2*, not R1.

On 10/22/2018 12:55 PM, GREGORY R KIRK wrote:
>
> External Email - Use Caution
>
>
> I have R1 values that I want to resample onto the cortical surface. 
> The R1 values were computed from a multi echo
>
> T1 sequence that was also used to create the T1 weighted image that 
> was used in recon-all to produce the cortical surface reconstructions
>
> and thus is inherently in registration to the 001.mgz that was used to 
> start recon. There will be a difference in orientation in the volume
>
> in that orig.mgz is in coronal and in the .mgz format.
>
>
> I was thinking that if I run the first step of recon-all it should 
> give me an volume named orig.mgz that is in registration to the 
> freesurfer space
>
> for the subject ... or else some call to mri_convert reslice_as or 
> whatever is used in the recon-all script to convert 001.mgz to orig.mgz
>
>
>
>
> then my problem is to get a file with the resampling of the R1 onto 
> the cortical surface withR1 values at each vertex.
>
>
> when i work with fmri data I run bbregister and get the transformation 
> from the epi volume to the freesurfer space and then use
>
> mri_vol2surf --mov sig.nii \to resample the data onto the cortical surface
>  --reg bb.register.dat \
>  --projfrac 0.5 --interp nearest \
>  --hemi lh --o lh.sig.mgh
>
> to resample the epi data onto the cortical surface. however in this case the 
> R1 data
> is already in perfect registration to the T1 other than the reorientation and 
> reslicing
> done to prepare the orig.mgz volume.
>
> so can someone tell me what is the proper way to cook this goose
>
> Greg
>
>
>
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[Freesurfer] resampling data onto cortical surface

[GREGORY R KIRK]

External Email - Use Caution

I have R1 values that I want to resample onto the cortical surface. The R1 
values were computed from a multi echo

T1 sequence that was also used to create the T1 weighted image that was used in 
recon-all to produce the cortical surface reconstructions

and thus is inherently in registration to the 001.mgz that was used to start 
recon. There will be a difference in orientation in the volume

in that orig.mgz is in coronal and in the .mgz format.


I was thinking that if I run the first step of recon-all it should give me an 
volume named orig.mgz that is in registration to the freesurfer space

for the subject ... or else some call to mri_convert reslice_as or whatever is 
used in the recon-all script to convert 001.mgz to orig.mgz




then my problem is to get a file with the resampling of the R1 onto the 
cortical surface withR1 values at each vertex.


when i work with fmri data I run bbregister and get the transformation from the 
epi volume to the freesurfer space and then use

mri_vol2surf --mov sig.nii \to resample the data onto the cortical surface
--reg bb.register.dat \
--projfrac 0.5 --interp nearest \
--hemi lh --o lh.sig.mgh

to resample the epi data onto the cortical surface. however in this case the R1 
data
is already in perfect registration to the T1 other than the reorientation and 
reslicing
done to prepare the orig.mgz volume.

so can someone tell me what is the proper way to cook this goose

Greg

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[Freesurfer] (no subject)

[Pan Yunzhi]

External Email - Use Caution

 
Dear freesurfer,
  I have some question about GE date (have 2 run) to run TRACULAR. How 
can I get some answers?
Sent from Mail for Windows 10

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[Freesurfer] Myelinated cortical thickness ratio map

[Damien MARIE]

External Email - Use Caution

Dear experts,

I am working with R1 maps that I project on the surface. The goal is to look at 
intra-cortical myelin.

I detect interesting effects between two groups. Now I would like to compute 
myelinated cortical thickness ratio maps, in order to control for the effect of 
cortical thickness variations occurring with gyrification.  

Here is a paper where they describe a way to compute those myelinated cortical 
thickness ratio map with MIPAV and the MPI-CBS toolbox : 
https://www.ncbi.nlm.nih.gov/pubmed/29321232 

«  The proportional thickness of the myelinated part of the cortex in relation 
to its overall thickness (myelinated cortical thickness) was computed with a 
fuzzy classification technique combining information about radial and 
tangential fibers.  « 

1- Is it possible to do the same in FreeSurfer?

2- What about dividing my individual myelin maps by the individual cortical 
thickness maps? Is it possible to do that in FreeSurfer? SPM ImCalc would do 
the job in the volume but I don’t know how I could do that in FreeSurfer.

Any comments / other suggestions are welcome.

Thank you and best,

Damien
 
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Re: [Freesurfer] Which command generates the lh.area.pial.fsaverage.mgh file?

[ts+ml]

External Email - Use Caution

Nevermind, I found in the source code of recon-all (line 180) that you have to 
specify the measure as '-measure area.pial' instead of '-measure area' in this 
case.


Sorry for the noise.

Tim


> On October 22, 2018 at 11:23 AM ts...@rcmd.org wrote:
> 
> 
> External Email - Use Caution
> 
> Dear FreeSurfer experts,
> 
> I would like to know how to (re-)generate the files 
> 'lh.area.pial.fsaverage.mgh' and 'rh.area.pial.fsaverage.mgh' for a subject 
> (in the surf/ dir).
> 
> I have tried the following:
> 1.) ensured that the source files, lh.area.pial and rh.area.pial, exist 
> (under surf/).
> 2.) run: 'recon-all -s  -qcache -measure area'
> 
> But this does not generate the expected files (only those for the white 
> surface).
> 
> Any clues?
> 
> Tim


-- 
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Forschung - Klinische Bildgebung
Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und 
Jugendalters
Universitätsklinikum Frankfurt / Haus 93, Raum A 305
Deutschordenstr. 50, 60528 Frankfurt am Main
Email: tim.schae...@kgu.de| Tel.: +49 (0)69 6301 85832

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[Freesurfer] Which command generates the lh.area.pial.fsaverage.mgh file?

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Dear FreeSurfer experts,

I would like to know how to (re-)generate the files 
'lh.area.pial.fsaverage.mgh' and 'rh.area.pial.fsaverage.mgh' for a subject (in 
the surf/ dir).

I have tried the following:
1.) ensured that the source files, lh.area.pial and rh.area.pial, exist (under 
surf/).
2.) run: 'recon-all -s  -qcache -measure area'

But this does not generate the expected files (only those for the white 
surface).

Any clues?

Tim

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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