Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file

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

can you send the cluster summary file?

On 11/24/2019 7:09 PM, Bronwyn Overs wrote:

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Hi Kersten,

Following on from Douglas's reply, you may remember my analysis as I forwarded 
you some files in October (see 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg64148.html). I 
followed your suggestions of removing the '--thmax 5' argument form 
'mri_surfcluster', and now the labels generated by 'mri_label2label' overlap 
perfectly with the significance maps from the LME. However, now my largest 
clusters have a maximum threshold of '-inf' in my cluster summary files. Do you 
have any idea how to get around this problem so that I can use my max threshold 
values to calculate cluster-wise effect sizes?



Kind regards,


Bronwyn Overs

Research Assistant

[cid:part2.69D05ACA.AA1EE7B5@mgh.harvard.edu]


Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1725


neura.edu.au 


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From: "Greve, Douglas N.,Ph.D." 

To: "Freesurfer support list" 
, 
"Kersten Diers, DZNE" 
Sent: Thursday, November 14, 2019 4:23:12 AM
Subject: Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file

I'll have to leave this one for Kersten as it appears that the LME stuff
is generating and inf value

On 11/12/19 7:05 PM, Bronwyn Overs wrote:
>
> External Email - Use Caution
>
> Hi Douglas,
>
> Yes I have looked at it in Freeview and I have attached a screenshot
> for your reference.
>
> The /fsdata/lme/thickness/rh.thickness.B1B7.mgh file was generated
> with a mass-univariate spatiotemporal model using
> 'lme_mass_fit_EMinit' and then FDR correction was applied across both
> hemispheres (lme_mass_FDR). I have provided analysis details and
> syntax below. The B1B7 contrast represents the affect of years in cases.
>
> Sample:
> Our sample includes 112 controls subjects, and 106 cases. All subjects
> are aged between 12 and 30 years. 153 or these subjects have 2
> time-points (77 control, 76 cases), while the remaining 65 individuals
> have only 1 MRI time-point. We also have mixed ethnicites - 165
> Caucasians, 23 Asians, and 30 mixed (Asians-Caucasians).
>
> The QDEC file contains the following 6 variables:
> 1. Y (years between scans)
> 2. A (baseline age)
> 3. G (group, 1=case, 0=control)
> 4. S (sex, 1=female, 0=male)
> 5. E1 (Ethnicity 1, 1=asian, 0=other)
> 6. E2 (Ethnicity 1, 1=mixed-asian-caucasian, 0=other)
>
> Design matrix: [ones(length(M),1) M M(:,1).*M(:,3)]
>i.e. main effects for each of the qdec variables + an
> interaction term for years X group
>
> DVs: Cortical thickness, area and volume
>
> Model: Mass-univariate spatiotemporal model using
> 'lme_mass_fit_EMinit'
> CODE:
>   % Read in surface files
>   [Y,mri] = fs_read_Y(mgh);
>   % Read in qdec file
>   Qdec = fReadQdec(qdec);
>   % Remove fsid from qdec
>   Qdec = rmQdecCol(Qdec,1);
>   % Store col 1 (fsid-base) in sID variable
>   sID = Qdec(2:end,1);
>   % Remove col 1 (fsid-base) from Qdec array
>   Qdec = rmQdecCol(Qdec,1);
>   % Convert Qdec to numeric matrix M
>   M = Qdec2num(Qdec);
>   % Sort data and evaluate design matrix
>   [M,Y,ni] = sortData(M,1,Y,sID);
>   X = eval([ones(length(M),1) M M(:,1).*M(:,3)])
>   % Compute vertex-wise temporal covariance estimates.
>   [Th0, Re] = lme_mass_fit_EMinit(X,[1],Y,ni,cortex,3);
>   %Segmentation and model fitting.
>   [Rgs, RgMeans, stats] = fit(Th0, Re, [1], sphere, cortex, X, Y,
> ni);
>   %Check surfaces.
>   surfcomp(Th0, RgMeans, sphere, fig1, fig2)
>
> Correction for multiple comparisons: FDR across both hemispheres
> CODE:
>   P = [ F_lhstats.pval(lhcortex) F_rhstats.pval(rhcortex) ]; G = [
> F_lhstats.sgn(lhcortex)
>   F_rhstats.sgn(rhcortex) ];
>   [detvtx, sided_pval, pth] = lme_mass_FDR2(P,G,[],0.05,0);
>   altfdr(r,2) = num2cell(abs(log10(lme_mass_FDR(P,0.05;
>   pcor = -log10(pth);
>   [~,~,dflh] = find(F_lhstats.df(2,:));
>   [~,~,dfrh] = find(F_rhstats.df(2,:));
>   dfmodelh(r,2) = {floor(mode(dflh))};
>   dfmoderh(r,2) = {floor(mode(dfrh))};
>   thrlh(r,2) = {pcor};
>   thrrh(r,2) = {pcor};
>   [~,dc] = size(detvtx);
>   dvtx(r,2) = {dc};
>
> Kind regards,
>
>
> Bronwyn Overs
>
> Research Assistant
>
>
> Neuroscience Research Australia
> Margarete Ainsworth Building
> Barker Street Randwick Sydney NSW 2031 Australia
> *M* 0411 308 769 *T* +61 2 9399 1725
>
>
> neura.edu.au 
>
> Twitter 
>  | 
> Facebook
> 

Re: [Freesurfer] PetSurfer questions

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

what ligand are you using? Do you expect it to be higher in GM and in WM? What 
are the values in the gtm.stats file relative to when you run it without PVC? 
How did you choose 5 as the --psf?

On 11/26/2019 2:53 AM, Soo-Jong Kim wrote:

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Dear FreeSurfer experts,

Originally, I want to use RBV method for pvcorrected PET for SUVR analysis.

After generating gtmseg and coregistration to make lta file, I followed this 
code and changed some.

mri_gtmpvc --i PET.nii --reg subj1.reg.lta --psf 5 --seg gtmseg.mgz
--default-seg-merge --auto-mask PSF .01 --no-rescale --no-reduce-fov --rbv --o 
output_pvc

After this, rbv.nii.gz file was generated. and SUVR analysis was performed as 
reference region (cerebellar cortex).  But Compared to original un-pvc PET, 
Cortex SUVR was reduced.

In ideal pv-corrected PET, cortex SUVR was higher than un-pvc PET.

Is is okay if I use the output file as rbv.nii.gz ?

in Thomas et al, 2011,
He used aparc+aseg.mgz file from FreeSurfer. and he merged some regions.
Frontal, Temporal, Occipital and so on. (Only gray matter to correct PET using 
RBV method)

In that case, What are the regions to make rbv.nii.gz method in PetSurfer?  all 
regions in FreeSurfer LUT?

Can I use the rbv.nii.gz as partial volume corrected PET from RBV method?

If not, let me know what is the correct command of mri_gtmpvc.
I need only partial volume corrected PET using RBV method.

Sincerely,

Soo-Jong Kim



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Re: [Freesurfer] [recon-all] [use of -T2] Does only -autorecon3 use -T2?

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

Yes, the T2 is only used to refine the pial surface

On 11/26/2019 5:14 PM, Billah, Tashrif wrote:
Hi all,

Is -T2 used only in -autorecon3 as shown 
here:

recon-all -subject subjectname -T2 /path/to/T2_volume -T2pial -autorecon3

In other words, if I do:

recon-all -subject subjectname -i /path/to/input_volume -T2 /path/to/T2_volume 
-T2pial -all

Will only -autorecon3 make use of the provided -T2 and not -autorecon1 or 
-autorecon2?

I think the answers are yes because -T2 appears under -autorecon3 only in 
ReconAllDevTable.

Best,
Tashrif


-

Tashrif Billah, MS

Research Engineer

Brigham and Women's Hospital

Harvard Medical School

tbil...@bwh.harvard.edu

http://pnl.bwh.harvard.edu/tashrif-billah-m-s/



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Re: [Freesurfer] extract lgi

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

yes, see
https://surfer.nmr.mgh.harvard.edu/fswiki/LGI

On 11/26/2019 2:07 AM, An Lijun wrote:

External Email - Use Caution

Dear Yanyan,
Actually you could refer to the freesurfer tutorial firstly.

Best Regards,
An Lijun


Lin Yanyan mailto:linyan...@outlook.com>> 于2019年11月26日周二 
下午12:49写道：

External Email - Use Caution

Hello, I have a question about lgi computing and extracting. I had run 
recon-all -s  -all, and there are lh.pail/rh.pail under each subject, 
then what should I do?





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[Freesurfer] [recon-all] [use of -T2] Does only -autorecon3 use -T2?

[Billah, Tashrif]

Hi all,

Is -T2 used only in -autorecon3 as shown 
here:

recon-all -subject subjectname -T2 /path/to/T2_volume -T2pial -autorecon3

In other words, if I do:

recon-all -subject subjectname -i /path/to/input_volume -T2 /path/to/T2_volume 
-T2pial -all

Will only -autorecon3 make use of the provided -T2 and not -autorecon1 or 
-autorecon2?

I think the answers are yes because -T2 appears under -autorecon3 only in 
ReconAllDevTable.

Best,
Tashrif


-

Tashrif Billah, MS

Research Engineer

Brigham and Women's Hospital

Harvard Medical School

tbil...@bwh.harvard.edu

http://pnl.bwh.harvard.edu/tashrif-billah-m-s/
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[Freesurfer] Postdoctoral Opportunity at Brigham and Women’s Hospital – Harvard Medical School

[Lois Gomez, Cristina]

Postdoctoral Opportunity at Brigham and Women’s Hospital – Harvard Medical 
School



The Department of Neurology at Brigham and Women’s Hospital (BWH) and Harvard 
Medical School (HMS) in Boston, Massachusetts, has an opening for highly 
qualified individuals at the post-doctoral level to work on NIH-funded research 
investigating the physiological and pathological underpinnings behind age and 
disease related cognitive decline using a multimodal neuroimaging approach. One 
specific research interest is to investigate the neural underpinnings of memory 
self-awareness and the progressive dysfunction of these systems that underlies 
the loss of self-awareness (anosognosia) with Alzheimer’s disease progression. 
Most of the work in this project will be performed at the Athinoula A. Martinos 
Center for Biomedical Imaging.



KEY  RESPONSIBILITIES:

The Post-Doctoral Fellow’s responsibilities will include, but are not limited 
to:

  *   Analyze PET data including amyloid and tau.
  *   Analyze MRI data including functional connectivity, diffusion 
tractography and structural data.
  *   Model complex datasets including imaging, behavioral and clinical data.
  *   Apply and develop MR and PET acquisition methods for longitudinal 
analyses.
  *   Lead and assist in the writing of academic manuscripts
  *   Lead and assist in dissemination of research findings through 
presentations at conferences and for patient and public engagement activities.
  *   Initiate and assist grant applications for further career development.
  *   Assist in mentoring of research assistants.


QUALIFICATIONS:

  *   Ph.D. (or close to anticipated PhD) in Neuroscience, Psychology, 
Engineering or a related field.
  *   Prior experience in brain imaging – PET and/or MRI.
  *   Strong proficiency in various neuroimaging analysis platforms (like 
FreeSurfer, SPM, FSL), multivariate modeling strategies and connectivity 
toolboxes.
  *   Established quantitative and statistical skills, including considerable 
experience in programming in Python and/or Matlab and comfort with diverse 
computing environments.
  *   Prior background in systems/cognitive neuroscience, neuroanatomy and 
psychological/clinical constructs is advantageous but not necessary.
  *   A demonstrated capacity to drive first author publications.
  *   Excellent organizational, oral, and written communication skills.


ADDITIONAL INFORMATION:

This is a 2 to 5 year term position with great opportunities for training in 
human systems neuroscience, translational/clinical applications and diverse 
integrated imaging and brain mapping methodologies. The successful candidate 
will have joint appointments at BWH and HMS and will be closely interacting 
with the Harvard Aging Brain Study team and especially the group of Dr. Jorge 
Sepulcre. If interested, please send your CV, letter describing interests, 
background, qualifications and 3 references (including contact details) to Dr. 
Patrizia Vannini (patri...@bwh.harvard.edu).


BWH & HMS are equal-opportunity, affirmative action employers. Women and 
minority candidates are encouraged to apply.

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Re: [Freesurfer] (no subject)

[Boris Rauchmann]

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Thank you! I have a gca for subcortical  and two gcs (lh/rh) for cortical
structures.
I created an annot (rh/lh) and a mgz using mris_ca_label and mri_ca_label
for parcellation/segmentation stats.

For the PET analysis I have the following problem:

If I use this command: gtmseg --s test --o test.mgz --ctab
/xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz --ctx-annot
BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt'

It gives me the right regions for subcortical structures but it looks like
it uses the standard FS parcellation with my labels for the cortical
parcellations (only 93 cortical regions instead of 210).

If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz --ctx-annot
BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' --no-xcerseg I get all my
210 cortical parcellations but the standard FS subcortical segmentations.

How can I use both in one gtmseg so that I can proceed with it doing my PET
analysis in PETSurfer? It is not totally clear for me what to merge using
xcerebralseg.

Thanks a lot!

On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> It gets the subcortical from apas+head.mgz which gets created along the
> way by xcerebralseg. You can create your own with xcerebralseg by
> specifying your volume as the mergevol. I think this will work, but I'm
> not sure. I'm assuming you've used the GCA to create your own
> subcortical seg for the given subject
>
> On 11/5/19 1:06 PM, Boris Rauchmann wrote:
> >
> > External Email - Use Caution
> >
> > I just realized that the above mentioned command (gtmseg --s XYZ --o
> > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg)
> > gives me only the cortical segmentation. Is there any way to also
> > include the subcortical segmentation based on my individual atlas? I
> > also have an Atlas_subcortex.gca file available.
> >
> > Best,
> > Boris
> >
> > On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > There is no cut off for the minimum size. As it gets smaller, the PVC
> > noise amplification will become bigger (it also depends on the
> > shape as
> > well).
> >
> > I think the --no-xcerseg is the right way to go now
> >
> > On 8/13/19 11:00 AM, Boris Rauchmann wrote:
> > >
> > > External Email - Use Caution
> > >
> > > Thank you for your prompt answer - the command worked. This is the
> > > atlas mentioned: http://atlas.brainnetome.org/brainnetome.html
> > > What is approximately the smallest possible segment when using PVC?
> > > Also, does the exclusion of extracerebral structures harm? I
> > used that
> > > flag because it complained:
> > >
> > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
> > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt'
> > > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok
> > > but you must indicate whether to use what is there (--no-xcerseg)
> > > or create a new one and overwrite what is there (--xcerseg)
> > > or specify your own headseg (--head)
> > >
> > > and did not want to override my apas+head.mgz
> > >
> > > Thanks,
> > > Boris
> > >
> > > On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D.
> > > mailto:dgr...@mgh.harvard.edu>
> > >>
> > wrote:
> > >
> > > I don't know what the Brainnetome is, but it looks like you
> have
> > > it in
> > > annotation form. I think that command should work. Why are
> > you using
> > > --no-xcerseg? This will cause it to not include extracerebral
> > > structures. Also note that you cannot use arbitrarily small
> > segments
> > > when doing PVC.
> > >
> > > On 8/13/19 10:26 AM, Boris Rauchmann wrote:
> > > >
> > > > External Email - Use Caution
> > > >
> > > > Dear all,
> > > >
> > > > my intention is to use the Brainnetome Atlas
> > > parcellation/segmentation
> > > > in PETSurfer to obtain PVC corrected SUVRs for the atlas
> > ROIs. I
> > > used:
> > > >
> > > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot
> > BN_Atlas.annot --ctab
> > > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt'
> > --no-xcerseg
> > > >
> > > > Is this the right approach to obtain a high resolution
> > > segmentation to
> > > > run PVC methods?
> > > >
> > > > Thanks,
> > > > Boris
> > > >
> > > > ___
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > 

[Freesurfer] Freesurfer dev version: Hyppocampus, amygdala and thalamus segementation

[Steve Petersen]

External Email - Use Caution

 Dear Freesurfer devs,

We are considering segmenting with the Freesurfer 6 dev version the
hippocampus, the amygdala and the thalamus of several subjects who have
already done the recon-all. Since we have a T1 image and T2 image with
smaller voxel size, we have thought about using the *mode B: segmetation
with an additional scan* as explained in the freesurfer webpage. In
addition to voxel size, both images have slight differences in acquisition
parameters. Taking into account this situation we have these questions:

- Since there are other slightly different parameters between image T1 and
T2 in addition to voxel size (e.g. matrix size), it is correct to use B
mode with additional scan or we should use multispectral segmentation?

- Is it necessary to make some previous modification on some image before
running the script segment_HA.sh (e.g. coregister both images)?

- Is there a quality control that you can recommend after segmenting these
structures?


Thanks for your help!


Best regards,
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Re: [Freesurfer] How do I fix this white matter boundary issue? {Disarmed}

[Taylor, Lisa Marie]

External Email - Use Caution

This addressed my concern! Thank you for the insight.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Greve, Douglas N.,Ph.D. 
[dgr...@mgh.harvard.edu]
Sent: Friday, November 22, 2019 2:32 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] How do I fix this white matter boundary issue?

Is the ventricle properly segmented in the aseg.presurf.mgz? If not, try 
running recon-all with -bigventricles

On 11/22/2019 2:21 PM, Taylor, Lisa Marie wrote:

External Email - Use Caution

Hi there,

I am working on a participant that has abnormally large ventricles. This has 
previously posed an issue with freesurfer by failing with errors but I have 
been successful this cycle without the job failing. However, after my first 
round of edits and running recon-all there is a major issue with the WM and 
Pial boundary area. I am unaware of how to address it. I have attached images 
to highlight where my concern is. Any insight?

Thank you so much!

Lisa



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the intended recipient(s). If you are not the intended recipient, do not use, 
distribute, or copy this e-mail. Please notify the UC Irvine Health – 
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could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or 
contain viruses. The sender therefore does not accept liability for any errors 
or omissions in the contents of this message, which arise as a result of e-mail 
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Re: [Freesurfer] V1 length

[Ruopeng Wang]

Hi Melissa,


You can now measure the length of a path on surfaces in the development 
version of freeview. You can download the dev build here:


https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview


On the surface panel, click on "Path/Custom Fill" icon and draw the 
path. Then hold the shift and move your mouse cursor over on the path, 
you should see the length of the path on the Info panel at the bottom.



Best,

Ruopeng


On 11/25/19 5:36 AM, Melissa Wright wrote:


External Email - Use Caution

Hi everyone,

I'm currently using mris_divide_parcellation to create segmentations 
of V1 by dividing along its long axis. However, I would like to 
extract the length of this long axis (in mm), in order to compare it 
with CMF. Would anyone know how best to go about this?


Sorry if there's an obvious answer! I have tried looking online and at 
the function scripts, but no luck.


Thank you and best wishes,

Melissa E Wright

*Melissa E Wright, MSc*

*PhD student*

School of Optometry and Vision Sciences

& Cardiff University Brain Research Imaging Centre (CUBRIC), School of 
Psychology


Cardiff University

Maindy Road

Cardiff   CF24 4HQ

UK

/*Tel*/: +44 (0)29 208 20275

/*Email*/: wrigh...@cardiff.ac.uk 

/*Web*/: Cardiff University webpage 



*Twitter: *@MEW_Neuro



*Melissa E Wright, MSc*

*Myfyrwraig PhD*

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr 
Ysgol Seicoleg


Prifysgol Caerdydd

Heol Maindy

Caerdydd CF24 4HQ

DU

/*Ffôn*/: +44 (0)29 208 20275

/*E-bost*/: wrigh...@caerdydd.ac.uk 


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[Freesurfer] freeview parallelized binary

[Clark, Dustin Christopher]

External Email - Use Caution

Hello,

We recently noticed freeview on the MGH cluster was using multiple cores when 
loading niftis, however, our local installation only uses one core when loading 
the same nifiti. Is it possible to get access to this freeview binary or the 
source code to build it for parallelization on our system? Thank you,

Dustin Clark
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Re: [Freesurfer] Using pre-segmented results

[Bruce Fischl]

Hi Jordi

yes, this should be possible. You might need to run recon-all in stages 
though. Although if you set the wm.mgz values from SPM to 255 and 1 (not 0) 
recon-all should detect them as "edits" and retain them


cheers
Bruce


On Tue, 26 Nov 2019, Jordi Huguet wrote:



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Hi there,
I wonder if its somehow possible to feed FreeSurfer's recon-all with 
pre-existing segmented maps
(based on prior segmentation procedure e.g. SPM or ANTs) to "improve" 
FreeSurfer results. 

For some images I am working with the FreeSurfer's WM segmentation output is 
not optimal so I am
looking for alternatives to improve the final results on such specific cases 
without requiring any
manual intervention. 

Any comments, examples or shared reflections on this regard are kindly welcome. 

Thanks in advance,
Jordi Huguet

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[Freesurfer] Using pre-segmented results

[Jordi Huguet]

External Email - Use Caution

Hi there,

I wonder if its somehow possible to feed FreeSurfer's recon-all with
pre-existing segmented maps (based on prior segmentation procedure e.g. SPM
or ANTs) to "improve" FreeSurfer results.

For some images I am working with the FreeSurfer's WM segmentation output
is not optimal so I am looking for alternatives to improve the final
results on such specific cases without requiring any manual intervention.

Any comments, examples or shared reflections on this regard are kindly
welcome.

Thanks in advance,
Jordi Huguet
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