[Freesurfer] Group analysis Cortical Thickness

[Dev vasu]

Dear Freesurfer Group,

I would like to perform group analysis for 50 Subjects (25 healthy controls
and 25 Subjects with BLVP  ) and examine the changes in cortical thickness
between 2 groups, could you please kindly inform me some methods that i
should adapt to perform the analysis.


Thanks
Vasudev
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Re: [Freesurfer] White matter surface don't change after editing

[Bruce Fischl]

Hi Cong

looking at your original data there is simply no contrast in the gray 
matter in those regions. I'm not sure why this would be the case, but it 
isn't recoverable as the images don't contain any information that we can 
use - the gray matter there is uniformly brighter than the white matter. It 
looks like some kind of coil issue as it is spatially localized, although 
it is true in the right hemi as well. If you give us the details of your 
acquisition we might be able to help in the future, but with these images 
you won't be able to get any reliable thickness/volume info in those spots. 
That said, the recon did a surprisingly good job at building accurate 
surfaces despite these artifacts, so they should still provide usable 
information elsewhere


cheers
Bruce


On Wed, 26 Oct 2016, Cong wrote:


Hi Dear Bruce
   My problem is bilateral high signal grey matter in T1 image. For example, in 
uploaded subject at coordinate of TkReg RAS -59.00 3.00 5.00, white matter 
surface is too far out even though I have erased extra white matter voxel in 
wm.mgz and rerun. Another  problem is grey matter surface bend inward, for 
example  at coordinate of TkReg RAS -61.00 3.00 -14.00.  I tried to use expert 
options to improve min_border_white and max_gray but couldn’t get satisfied 
surface. So I want to know whether freesurfer can fix these two problems and 
how. I’m sorry to occupy you so much time. Thanks very much.

Best Wishes
Cong Chen


Date: Mon, 24 Oct 2016 23:22:58 -0400
From: Bruce Fischl 


Can you send us specific coordinates of things to look at?


On Oct 24, 2016, at 10:44 PM, Cong <3110103...@zju.edu.cn> wrote:

Hi Dear Bruce
   I have uploaded a subject named Cong2Bruce.zip through ftp.  I can?t fix it 
by myself. Could you help me how to use expert options to get correct white 
matter and gray matter surface. Thank you very much.

Best Wished
Cong Chen


Date: Tue, 20 Sep 2016 10:45:30 -0400 (EDT)
From: Bruce Fischl 
Subject: Re: [Freesurfer] White matter surface don't change after
  editing

Hi Cong

we are experiencing serious disk problems at Martinos, so the ftp site is
down.

Try changing the values for mri_segment also. Note that what you are
seeing are NOT topological defects as mris_make_surfaces preserves the
input topology whatever its settings. Make sure to look in 3D and scoll
through your slices. You can also try changing the gm thresholds

cheers
Bruce


On Tue, 20 Sep 2016, Cong wrote:

   Hi Dear Bruce
? ? ?Thanks very much for your reply, I ?improved min_border_white to
100, the lh.white line shrinks but still is far out in some area, ?and
I notice many topological defect appears as a result.
? ? ?I failed to upload subject through ftp, it's always appear an
error called "550 Failed to change directory", so I send a subject to
you through FileDrop. Can you receive a file named Cong2Bruce.zip??

   ? ? ?Thanks again for your help.

Best Wishes
Cong Chen

 Date: Thu, 8 Sep 2016 10:12:29 -0400 (EDT)
From: Bruce Fischl 
Hi Cong

you could try using expert options to modify the
mris_make_surfaces?
parameters. It looks like you white surface is too far out. Try?
increasing min_border_white and/or increasing max_gray. If you
can't get it?
working feel free to upload the entire subject dir and we will
take a look

cheers
Bruce


On Thu, 8 Sep 2016, Cong wrote:

Hi dear all
? ? I attach a new picture to illustrate this problem. ?I erased
some voxels in wm.mgz and rerun. The lh.orig(blue line) looks
well, but lh.white(yellow line) don?t along the white surface in
some area. Could anyone give me some advice? Thanks very much.

Best wishes
Cong Chen


Date: Sun, 4 Sep 2016 15:15:42 +0800
From: Cong <3110103...@zju.edu.cn>
Subject: [Freesurfer] White matter surface don't change after
editing

Dear freesurfer team?
?I have some MRI images from a GE scanner, ?it seems that
images? quality is poor because grey matter is bright in so much
area and these grey matter is included in wm.mgz. So I deleted
wrong voxels in wm.mgz by freeview and rerun through command ?
recon-all -autorecon2-wm -autorecon3 -subjid subjname?. But
?h.white (yellow line) don?t change after rerunning as you can
see in the attached picture. ?Is this problem caused by deleting
too many voxels and how to fix it? ?Thanks very much.

Regards
Cong Chen







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Re: [Freesurfer] Obtain images extracted from aseg.mgz that have been corrected for partial volume effects

[Bruce Fischl]

Hi Andrea

sorry, I don't think we do, although could add such a thing I guess, 
although the format isn't clear to me. I guess you would have to save 
multiple labels at each voxel with the mixing coefficient of each one.


cheers
Bruce



On Tue, 25 Oct 2016, Andrea Shafer wrote:


Hello FreeSurfer Developers,

I'm attempting to create partial volume (pve) corrected images for some of
the subcortical segmentations. I have searched the list and found
discussions regarding how the volumes for pve corrected data can be obtained
by default with the asegstats2table command, or when using the mri_segstats
command with the --pv flag. However, I am wondering if it is possible to
save the mixed coefficient map of the pve correction process or save a
aseg.mgz file that has been pve corrected?      

Sincerely,
Andrea

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Re: [Freesurfer] ROI NumVert

[Daya P]

Thank you for your help!

I created a registration template and atlas from scratch could I input that
in the interhemispheric registration analysis?

The ROIs for the diffrerent regions per hemisphere are 50-100 vertices
On Oct 24, 2016 5:03 PM, "Douglas N Greve" 
wrote:

> It would depend on how big the ROI is to begin with. Do you know that we
> have our own interhemispheric analysis that might be better for this?
> Check out
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
>
>
> On 10/24/2016 12:33 PM, Daya P wrote:
> > Hi Bruce,
> >
> > I drew ROIs on an initial subject and then after registering all other
> > subjects to the initial one, used mri_label2label to map the ROIs from
> > the initial subject to subsequent ones.
> > I am interested in looking at asymmetry between left and right regions.
> >
> > I had two concerns, one that the ROIs have different # vertices on
> > different subjects, but as you mentioned the nonlinear process makes
> > sense, since each subject does not have the exact same brain size and
> > curvature.
> >
> > Another concern was that the ROIs on the left and right hemisphere in
> > a subject do not have the exact same number of vertices. Would a
> > difference of 10 vertices max bias results?
> >
> > Thank you for your help,
> >
> > Daiana R. Pur
> > Research Assistant
> > Canadian Surgical Technologies & Advanced Robotics
> > Brain and Mind Institute
> > Western University
> > London, ON, N6A 5B7
> > Canada
> >
> > On Mon, Oct 24, 2016 at 12:09 PM, Bruce Fischl
> > mailto:fis...@nmr.mgh.harvard.edu>> wrote:
> >
> > Hi Daiana
> >
> > yes, that is to be expected given the nonlinear nature of the
> > cross-subject registration. It shouldn't bias things, although
> > you'll need to give us more details if you want a more definitive
> > answer.
> >
> > cheers
> > Bruce
> >
> >
> >
> > On Mon, 24 Oct 2016, Daya P wrote:
> >
> > Hi All,
> >
> > My question is about using mri_label2label. When mapping the
> > labels from one
> > subject to another the number of vertices of each ROI is
> > different. Is that
> > something to be expected?
> >
> > How much of a difference does a number of vertices of 50
> > compare to 40 have
> > on measures like thickness, grey matter and surface area?
> >
> > I would really appreciate some help
> >
> > Thank you,
> >
> > Daiana R. Pur
> > Research Assistant
> > Canadian Surgical Technologies & Advanced Robotics
> > Brain and Mind Institute
> > Western University
> > London, ON, N6A 5B7
> > Canada
> >
> >
> >
> > ___
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> > 
> >
> >
> > 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
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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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[Freesurfer] Two Stage Longitudinal Model

[Timothy Hendrickson]

FreeSurfer Experts,

Hello I am attempting to perform a two stage longitudinal analysis. My
entire data set has two time points for each participant.
I understand that the subject order in the FSGD file should correspond with
the QDEC file run through long_mris_slopes.
In my case the FSGD file has half as many inputs as the QDEC file.

My question is would I take the covariates from TP1 and TP2 and take the
average to input into the FSGD file?

If that is the case is there anything wrong with performing the
long_qdec_table --qdec "qdec.table.dat --cross --out "cross.qdec.table.dat"
command and using that co-variate data to input into the FSGD file?

Respectfully,

-Tim

Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Mobile: 507-259-3434 (texts okay)
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[Freesurfer] Antwort: Re: TRACULA longitudinal stream: using multiple configuration files?

[j . oschwald]

Thank you, Michael!

-freesurfer-boun...@nmr.mgh.harvard.edu schrieb: -
An: Freesurfer support list 
Von: "Harms, Michael" 
Gesendet von: freesurfer-boun...@nmr.mgh.harvard.edu
Datum: 25.10.2016 16:03
Betreff: Re: [Freesurfer] TRACULA longitudinal stream: using multiple 
configuration files?


Hi,
I remember looking into this — all the time points for a given subject need to 
be specified in the same configuration file, otherwise you don’t get the 
longitudinal aspect of the processing.

cheers,
-MH

-- 
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.  Tel: 314-747-6173
St. Louis, MO  63110  Email: mha...@wustl.edu

From:  on behalf of 
"j.oschw...@psychologie.uzh.ch" 
Reply-To: Freesurfer support list 
Date: Tuesday, October 25, 2016 at 2:29 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] TRACULA longitudinal stream: using multiple configuration 
files?

Hi Freesurfer users

I wonder wether it makes a difference when using longitudinal TRACULA if all 
timepoints are run within one process (1 configuration file including all three 
timepoints) or if it is possible to split it into several independent processes 
(with several different configuration files - one per time point)?

Thank you for your help.
Jessica
 

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[Freesurfer] tmp directory not created

[Sneha Pandya]

Hi all,

I am running recon-all stream for ~200 subjects and after successful run of 
them I observed that for some of the patients recon-all ran successfully 
without error but it did not create "tmp" sub-folder. Can anyone please advice 
when recon-all stream does not create "tmp" folder and do I need to run these 
subjects again even after its successful completion?

Thanks,
Sneha

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[Freesurfer] mris_left_right_register not found

[Daya P]

Hi All,

I was looking to flip a label I created on the left hemisphere to the right
hemisphere and I read in previous messages that mris_left_right_register
and then mri_apply_reg might be an option.

I can find mri_apply_reg as a command but not mris_left_right_register. The
links to it previously posted are not available anymore.

Is there an updated link available?

Daiana
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