[Freesurfer] ExploreDTI Workshop in May@Budapest

[Szabolcs David]

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ExploreDTI Workshop -  A course on processing, analyzing, and visualizing
diffusion MRI data
When: 27-29 May, 2019
Where: Budapest, Hungary
Details: http://www.exploredti.com/workshop

Cheers,
Szabolcs

>
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Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

[Matthieu Vanhoutte]

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Hi Douglas,

Any advice ?

Best.

Le jeu. 7 févr. 2019 à 23:12, Matthieu Vanhoutte <
matthieuvanhou...@gmail.com> a écrit :

> Yes that's what I mean. But does this command provide an intensity
> normalized voxel-wise image ?
>
> Could you explain me the realign & reslice steps from the native PET to
> the voxel-wise PVC PET for MGX ans RBV ?
>
> Best,
> Matthieu
>
> Le jeu. 7 févr. 2019 à 23:06, Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> a écrit :
>
>> Do you mean the mean intensity not corrected for PVC? I would just run
>> mri_gtmpvc with --psf 0 --no-tfe to turn off PVC
>>
>> On 2/7/19 4:40 PM, Matthieu Vanhoutte wrote:
>> >
>> > External Email - Use Caution
>> >
>> > Hello experts,
>> >
>> > Anyone would have an advice on my previous questions ?
>> >
>> > Best,
>> > Matthieu
>> >
>> >
>> > Le mer. 30 janv. 2019 à 14:49, Matthieu Vanhoutte
>> > mailto:matthieuvanhou...@gmail.com>> a
>> > écrit :
>> >
>> > Hi Douglas,
>> >
>> > In order to apply intensity normalization to non-PVC PET images
>> > based on mean intensity from reference region in gtmseg.mgz, is it
>> > better to realign & reslice PET image onto gtmseg space or the
>> > reverse way ? How is it done when dealing with PVC images using
>> > gtmpvc command ?
>> >
>> > I would like to avoid too many reslicing operations before volume
>> > to surface projection, how would you deal with it ?
>> >
>> > Best,
>> > Matthieu
>> >
>> >> Le 28 janv. 2019 à 17:41, Greve, Douglas N.,Ph.D.
>> >> mailto:dgr...@mgh.harvard.edu>> a écrit :
>> >>
>> >> If you intend to use one of the aseg structures, then they are
>> >> the same.
>> >>
>> >> On 1/28/19 10:14 AM, Matthieu Vanhoutte wrote:
>> >>>
>> >>> External Email - Use Caution
>> >>>
>> >>> Hi Douglas,
>> >>>
>> >>>
>>  Le 25 janv. 2019 à 18:01, Greve, Douglas N.,Ph.D.
>>  mailto:dgr...@mgh.harvard.edu>> a
>> écrit :
>> 
>> 
>> 
>>  On 1/25/19 7:57 AM, Matthieu Vanhoutte wrote:
>> >
>> > External Email - Use Caution
>> >
>> > Dear Douglas,
>> >
>> > Could you precise me:
>> > 1) Is the intensity rescaling of PET image included in the
>> > mri_gtmpvc command based on reference region in gtmseg.mgz
>> > file rather than aseg.mgz ?
>>  It depends. If you are using pons, then that is not part of the
>>  aseg and is generated as part of the creation of gtmseg. But
>>  most of the rest of gtmseg is derived from the aseg and surfaces.
>> >>>
>> >>> Is it better to use gtmseg.mgz or aseg.mgz to extract reference
>> >>> region’s mean intensity ?
>> >>>
>> >>>
>> > 2) Is this rescaling applied before PVE correction or after
>> > (i.e. based on PVE corrected reference region’s mean intensity)
>> ?
>>  After
>> >
>> > Many thanks in advance for helping.
>> >
>> > Best,
>> > Matthieu
>> >
>> >> Le 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D.
>> >> mailto:dgr...@mgh.harvard.edu>> a
>> >> écrit :
>> >>
>> >>
>> >>
>> >> On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote:
>> >>>
>> >>> External Email - Use Caution
>> >>>
>> >>>
>> >>> I used the following command to obtain only rescaled
>> >>> voxel-wise PET image (with no PVC):
>> >>> /mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta
>> >>> --psf 0 --no-tfe --seg gtmseg.mgz --default-seg-merge
>> >>> --auto-mask PSF .01 --rbv --o  nopvc/
>> >>>
>> >>> If I omitted/--rbv/or/--mgx/option//I didn't get the
>> >>> rescaled voxel-wise PET image (without PVC). Could I obtain
>> >>> the rescaled voxel-wise PET image (without PVC) just by
>> >>> dividing each voxel of the native PET image by the mean of
>> >>> the reference region ?
>> >> Yes
>> >>>
>> >>> Best,
>> >>> Matt
>> >>>
>> >>> Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D.
>> >>> mailto:dgr...@mgh.harvard.edu>> a
>> >>> écrit :
>> >>>
>> >>> I'm not sure what you mean. If you are turning off PVC,
>> >>> why are you computing RBV and MGX? What is your command
>> >>> line? What do you mean that these options don't seem to
>> >>> work?
>> >>>
>> >>> On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:
>> 
>>  External Email - Use Caution
>> 
>>  Hi Douglas,
>> 
>>  Thanks for helping.
>> 
>>  To have an only rescaled voxel-wise PET image, these
>>  options seem to work only when -rbv method is used and
>>  not -mgx.
>> 
>>  Do you know why ?
>> 
>> 

Re: [Freesurfer] Hypointensities in Freesurfer

[Miguel Ángel Rivas Fernández]

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Hi,

Yes, I would like to know the x,y,z MNI coordinates of lesions for each
subject.


BEST,

El vie., 8 feb. 2019 18:34, Greve, Douglas N.,Ph.D. 
escribió:

> not sure what you want. MNI coords for each lesion?
>
> On 2/8/19 7:21 AM, Miguel Ángel Rivas Fernández wrote:
>
> External Email - Use Caution
>
> Hi Freesurfer devs,
>
>
> I saw that Freesurfer export measures of hypointensities. I was wondering
> if it´s possible to know where are located this brain lesions using as
> reference some neuroanatomical atlas.
>
>
> Best,
>
> --
> *Miguel Ángel Rivas Fernández*
>
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Re: [Freesurfer] Hypointensities in Freesurfer

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

not sure what you want. MNI coords for each lesion?

On 2/8/19 7:21 AM, Miguel Ángel Rivas Fernández wrote:

External Email - Use Caution

Hi Freesurfer devs,


I saw that Freesurfer export measures of hypointensities. I was wondering if 
it´s possible to know where are located this brain lesions using as reference 
some neuroanatomical atlas.


Best,

--
Miguel Ángel Rivas Fernández



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Re: [Freesurfer] reporting fsl PALM results

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

Are you using fspalm? If so, there should be a something.y.ocn.dat file 
that has the mean thickness for each subject and cluster

On 2/8/19 6:16 AM, C.P.E. Rollins wrote:
>  External Email - Use Caution
>
> Dear Freesurfer Developers,
> I'm using PALM to run permutation analyses to correct for multiple
> comparisons on Freesurfer cortical thickness and LGI data. fspalm from a
> command like "mri_glmfit-sim --glmdir lh.lgi.glmdir --perm 1000 2 pos
> --cwp .05 --2spaces" produces output files including *.cluster.mgh - map
> of signifcant clusters, *.cluster.summary - text file of of cluster
> table (incl. sizes, cluster annotation, MNI coordinates, and
> significance), and *.y.ocn.dat – text file containing LGI or cortical
> thickness values for each subject from significant clusters. I was
> wondering if PALM produces similar output? From my understanding the
> *clustere_tstat_fwep.mgz file from PALM would be equivalent to the
> *.cluster.mgh from fspalm, but is there any way to get a text file of
> the cluster table or of the LGI/CT values for each subject from
> significant clusters?I would like to report significant clusters (ie.
> coordinates or parcellation, cluster size, pvalue) in a table and also
> to extract the average lgi/thickness from significant clusters for each
> subject.
>
> Thanks very much
> Colleen
>
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Re: [Freesurfer] Mismatch between ?h.BA.thresh.annot and ?h.entorhinal.thresh.label/?h.perirhinal.thresh.label

[Bruce Fischl]

Hi Yi-Leng

can you upload the worst subject to our ftp site (the entire gzipped and 
tarred subject dir please).


cheers
Bruce
On Fri, 8 Feb 2019, Yi Leng Fung wrote:



External Email - Use Caution

[64b4f0f085b91c1f8130601d2cf65e8861fc5b7f.png?u=328927]
Hello Bruce, 

On all four of our studies, the labels and the annot look similar in the sense 
that almost the entire
rh.perirhinal_exvivo.thresh.label was contained within the 
rh.entorhinal_exvivo.thresh.label (screenshot of the
right hemisphere with labels and annot attached for your reference). The 
resulting annot label shows an extremely
under-represented perirhinal on the right hemispheres. The left hemispheres did 
not show such a dramatic overlap.

Cheers,
Yi-Leng


On Fri, Feb 8, 2019 at 3:44 PM Bruce Fischl  wrote:
Do the labels look better than the annot?

On Feb 6, 2019, at 10:15 PM, Yi Leng Fung  wrote:

  External Email - Use Caution

  Hello FreeSurfer team,

Thank you for providing the recon-all patch. We have applied this to four 
studies and have seen a
notable difference between in the representation of entorhinal over perirhinal 
on the right hemisphere
labelling on each analysis ran. The left hemisphere appears to have less 
overlap.

I have attached a screenshot of both hemispheres to demonstrate. Would really 
appreciate any feedback.
Thanks!

Cheers,
Yi-Leng


On Wed, Feb 6, 2019 at 3:11 AM Hoopes, Andrew  wrote:

  Hi Yi Leng, there’s a recon-all patch for 6.0 at
  
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/recon-all. 
You can
  update it with:

   

  cd ${FREESURFER_HOME}/bin

  mv recon-all recon-all.backup

  curl 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/recon-all -o
  recon-all

  chmod +x recon-all

   

  Let us know if that works!

   

  thanks

  Andrew

   

  From:  on behalf of Yi Leng Fung
  
  Reply-To: FS Help 
  Date: Monday, February 4, 2019 at 9:17 PM
  To: FS Help 
  Cc: Jean Augustinack 
  Subject: Re: [Freesurfer] Mismatch between ?h.BA.thresh.annot and
  ?h.entorhinal.thresh.label/?h.perirhinal.thresh.label

 

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Image removed by sender.

Thank you!

 

Cheers,

Yi Leng

 

 

On Tue, Feb 5, 2019 at 1:05 PM Bruce Fischl  wrote:

  thanks. It is almost certainly a bug in recon-all. I'm testing a fix
  tomorrow and hopefully we can have one out to you (and the rest of the
  list) by tomorrow.

  Sorry!
  Bruce
  On Tue, 5 Feb 2019, Yi Leng Fung wrote:

  >
  > External Email - Use Caution
  >
  > [3a1715320c6fbab489126e656ad6e765d6e0a6ee.png?u=328927]
  > Hello Bruce,
  >
  > Yep, the exvivo entorhinal thresh label overlay on the perirhinal 
annotation. I
  have attached a screenshot of it
  > for your reference.
  >
  > Cheers,
  > Yi-Leng
  >
  >
  > On Tue, Feb 5, 2019 at 12:31 PM Bruce Fischl 
 wrote:
  >       Hi Yi-Leng
  >
  >       eek! Can you verify that the lh.entorhinal_exvivo.thresh.label is
  >       correct? Does it overlay on the perirhinal annotation?
  >
  >       thanks
  >       Bruce
  >
  >       On Tue, 5 Feb 2019,
  >       Yi Leng Fung wrote:
  >
  >       >
  >       > External Email - Use Caution
  >       >
  >       > [3f1a37b0d4514e4a90a5d3340afcefe6c789830e.png?u=328927]
  >       > Hello All,
  >       >
  >       > Here it is, both are from bert. 
  >       >
  >       > Thank you for looking into this.
  >       >
  >       > Cheers,
  >       > Yi-Leng
  >       >
  >       > On Tue, Feb 5, 2019 at 7:47 AM Bruce Fischl 

  wrote:
  >       >       Hi Yi-Leng
  >       >
  >       >       can you send us an image of the parcellaton on an 
inflated surface so
  we
  >       >       can see?
  >       >
  >       >       thanks
  >       >       Bruce
  >       >
  >       >
  >       >       On Tue, 5 Feb 2019, Yi Leng Fung wrote:
  >       >
  >       >       >
  >       >       > External Email - Use Caution
  >       >       >
  >       >       > Hello Bruce,
  >       >       > Thank you very much for your quick response. 
  >       >       >
  >       >       > I do have another point of confusion regarding the 
BA.thresh.annot
  file. When visualised in
  >       Freeview
  >       >       (using Bert as
  >       >       > the example), the BA.thresh annotation file labelled 
the medially
  located structure as the
  >       perirhinal
  >       >       cortex and
  >       >       > the laterally located structure as the entorhinal 
cortex. 
  >       >       >
  >       >       > I find that 

[Freesurfer] Hypointensities in Freesurfer

[Miguel Ángel Rivas Fernández]

External Email - Use Caution

Hi Freesurfer devs,


I saw that Freesurfer export measures of hypointensities. I was wondering
if it´s possible to know where are located this brain lesions using as
reference some neuroanatomical atlas.


Best,

-- 
*Miguel Ángel Rivas Fernández*
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[Freesurfer] reporting fsl PALM results

[C.P.E. Rollins]

External Email - Use Caution

Dear Freesurfer Developers,
I'm using PALM to run permutation analyses to correct for multiple 
comparisons on Freesurfer cortical thickness and LGI data. fspalm from a 
command like "mri_glmfit-sim --glmdir lh.lgi.glmdir --perm 1000 2 pos 
--cwp .05 --2spaces" produces output files including *.cluster.mgh - map 
of signifcant clusters, *.cluster.summary - text file of of cluster 
table (incl. sizes, cluster annotation, MNI coordinates, and 
significance), and *.y.ocn.dat – text file containing LGI or cortical 
thickness values for each subject from significant clusters. I was 
wondering if PALM produces similar output? From my understanding the 
*clustere_tstat_fwep.mgz file from PALM would be equivalent to the 
*.cluster.mgh from fspalm, but is there any way to get a text file of 
the cluster table or of the LGI/CT values for each subject from 
significant clusters?I would like to report significant clusters (ie. 
coordinates or parcellation, cluster size, pvalue) in a table and also 
to extract the average lgi/thickness from significant clusters for each 
subject.

Thanks very much
Colleen

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