Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

[pablo najt]

Hi Jorge and FS experts,I have run again the analysis and still get the 
convergence problem.I am assuming the issue has to do with the preprocessing 
steps, as I had doubts on how to follow from the instructions if I am not using 
qdec and have a cross sectional design.
Instructions on lme in the wiki for preprocessing specify the following:
mris_preproc --qdec-long qdec.table.dat --target study_average --hemi lh --meas 
thickness --out lh.thickness.mghmri_surf2surf --hemi lh --s study_average 
--sval lh.thickness.mgh --tval lh.thickness_sm10.mgh --fwhm-trg 10 --cortex  
--noreshapeMy data -as I explained below- is cross section but I want to treat 
it as longitudinal as I want to analyse subjects belonging to the same family. 
Here is my 2 main questions: 1) for preprocessing should I follow instructions 
as it would be longitudinal data?2) Although my design does not allow using 
qdec (3 groups) do I still create a qdec table and follow literally the two 
instructions above ?Thank youPablo


Date: Fri, 16 Oct 2015 16:24:36 +
From: jbernal0...@yahoo.es
To: freesurfer@nmr.mgh.harvard.edu
CC: pablon...@hotmail.com
Subject: Re: [Freesurfer] A mixed effect model approach in within subject 
dataset {Disarmed}

Hi Pablo
Yes, too many locations at which the estimation algorithm didn't converge is 
problematic. That might mean that having two random effects is not appropriate 
for your data. You should try to run the command with just a single random 
effect for the intercept term:
lhstats = lme_mass_fit_vw(X, [1], lhY, ni, lhcortex, [], 4);
If the result still have too many non-convergence locations then something 
might be wrong with the ordering of the design matrix and its correspondence 
with the ordering of the ni vector or the ordering of the image data etc... You 
will need to check it thoroughly.
Cheers-Jorge





 De: pablo najt 
 Para: "freesurfer@nmr.mgh.harvard.edu"  
 Enviado: Viernes 16 de octubre de 2015 1:43
 Asunto: Re: [Freesurfer] A mixed effect model approach in within subject 
dataset {Disarmed}
   
Thanks you for the replies.Jorge and FS experts,I have run the analysis and 
first double checked that the sum of vectors of (ni) is equal to the number of 
rows in (X). Both are 140 which is the number of my subjects.The analysis gave 
the following 'error'(?) below:I looked up a previous thread coming across 
this. At that case you recommendedWould you recommend this afain>Aproximate 
percentage of fitted locations: 100%Warning: matlabpool will be removed in a 
future release.To query the size of an already started parallel pool, query the 
'NumWorkers'property of the pool.To check if a pool is already started use 
'isempty(gcp('nocreate'))'. Warning: matlabpool will be removed in a future 
release.To shutdown a parallel pool use 'delete(gcp('nocreate'))' instead. 
Parallel pool using the 'local' profile is shutting down.  Summary:Algorithm 
did not converge at 90.0637 percent of the total number of locations.Total 
elapsed time is 550.1023 minutes.Also almost all the time the screen showed the 
following message:144114: Algorithm did not converge. Initial and final 
likelihoods: -38.3408-1.5708i, -241.4153-1.570796i.Location 144113: Algorithm 
did not converge. Initial and final likelihoods: -5.5424-1.5708i, 
-133.8004-1.570796i.Location 144112: Algorithm did not converge. Initial and 
final likelihoods: -7.7571-1.5708i, -319.1378-1.570796i.Location 144111: 
Algorithm did not converge. Initial and final likelihoods: -16.8597-1.5708i, 
0.74448.Aproximate percentage of fitted locations: 100%So my two questions 
are:1. Is this problematic?2. Are there any fixes to this issue?Thank 
you,PabloDate: Thu, 15 Oct 2015 13:38:22 +From: jbernal0...@yahoo.esto: 
freesur...@nmr.mgh.harvard.eduCC: pablonajt@hotmail.comSubject: Re: 
[Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

Hi PabloThe error you are getting is because in your Matlab setup you can only 
request a maximum of 4 matlab parallel workers and by default lme requests 8. 
So you just need to modify your command like this: lhstats = lme_mass_fit_vw(X, 
[1 2], lhY, ni, lhcortex, [], 4);Please make sure that sum(ni) and length(X) 
give the same value before running the above command.Cheers-Jorge De: 
pablo najt  Para: Freesurfer support list 
  Enviado: Jueves 15 de octubre de 2015 7:18 
Asunto: Re: [Freesurfer] A mixed effect model approach in within subject 
dataset {Disarmed}   Thank you Martin.I am trying to run the following command 
line and get the error below. Would you have a suggestion to overcome this 
issue?Just in case I am also including a snapshot of my loaded variables at the 
bottom.Many thanks,Pablo>> lhstats = lme_mass_fit_vw(X, [1 

Re: [Freesurfer] MPRAGE SNR

[John Anderson]

Dear Jürgen

This really helps!

I highly appreciate your input on this.

 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

 
 

Sent: Monday, October 19, 2015 at 1:30 AM
From: JuergenHaenggi 
To: "Freesurfer support list" 
Subject: Re: [Freesurfer] MPRAGE SNR


Dear John
 

FS's QA tools provide the SNR 

see https://surfer.nmr.mgh.harvard.edu/fswiki/QATools

 

there is also a FS function called wm-anat-snr that can be used for that.

 

Hope this helps

Cheers

Jürgen


 

-
Jürgen Hänggi, Ph.D.
Division of Neuropsychology
Institute of Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25 
8050 Zurich, Switzerland
0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)       
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)                     
j.haen...@psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)   

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Am 18.10.2015 um 16:48 schrieb John Anderson:
 




Dear Experts,

Is there any tool in Freesurfer that can help to evaluate the SNR for T1 MPRAGE images directly ( i.e script). If not knidly can any help me to figure out the best way to dao it.

 

I highly appreciate your help!

 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419


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Re: [Freesurfer] -hippocampal-subfields-T1T2

[Eugenio Iglesias]

Hi Daniel, 
sorry for the late reply; I was on vacation. 
It seems that the T1-T2 registration failed. Can you please send me the .log 
files for the hippocampal subfields? They should be in the following directory: 
media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/scripts/
 
Cheers, 
Eugenio 

Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Daniele Orlandi"  
To: "Freesurfer support list"  
Sent: Monday, October 12, 2015 6:58:34 PM 
Subject: [Freesurfer] -hippocampal-subfields-T1T2 

Dear All, 
I'm trying to run the flag -hippocampal-subfields-T1T2 with the new FS v6.0 but 
I get the following error: 

>Fitting mesh to synthetic image from ASEG took 217.8633 seconds 
>Transforming points 
>Transforming points 
>ltaReadFile(/media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/mri/transforms/T1_to_T1+T2.v10.lta):
> can't open file 
>No such file or directory 
>ERROR: Reading transform from file 
>/media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/mri/transforms/T1_to_T1+T2.v10.lta
> 

Do you have any suggestion? 
thank you all for your collaboration 
Daniele 

___ 
Daniele Orlandi, PsyD, Research Assistant 
Laboratory of Epidemiology, Neuroimaging Alzheimer 
IRCCS Centro San Giovanni di Dio, Fatebenefratelli 
Via Pilastroni 4 
25125 Brescia - Italy 
tel: +39 030/3501563 
cell: +39 3495119685 
email: dorla...@fatebenefratelli.it ; daniele.orlandi@gmail.com 
( http://www.centroalzheimer.org/sito/chi_staff_e.php ) 



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Re: [Freesurfer] MPRAGE SNR

[Bruce Fischl]

Hi John

there is also a binary called mri_cnr that will compute the 
contrast-to-noise ratio (CNR), which is really the more interesting 
metric. It will also spit out the WM means+- std, and the ratio of these 
two can be used as an SNR measure.


cheers
Bruce


On Mon, 19 Oct 2015, John Anderson wrote:


Dear Jürgen
This really helps!
I highly appreciate your input on this.
 
Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
    Sent: Monday, October 19, 2015 at 1:30 AM
From: JuergenHaenggi 
To: "Freesurfer support list" 
Subject: Re: [Freesurfer] MPRAGE SNR
Dear John  
FS's QA tools provide the SNR 
see https://surfer.nmr.mgh.harvard.edu/fswiki/QATools
 
there is also a FS function called wm-anat-snr that can be used for that.
 
Hope this helps
Cheers
Jürgen
 
---
--
Jürgen Hänggi, Ph.D.
Division of Neuropsychology
Institute of Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25 
8050 Zurich, Switzerland
0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)       
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)                     
j.haen...@psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)   

This e-mail (and any attachment/s) contains confidential and/or privileged
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  Am 18.10.2015 um 16:48 schrieb John Anderson:
 
  Dear Experts,
Is there any tool in Freesurfer that can help to evaluate the SNR for
T1 MPRAGE images directly ( i.e script). If not knidly can any help me
to figure out the best way to dao it.
 
I highly appreciate your help!
 
Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
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HelpLine at
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Re: [Freesurfer] recon-all stripped brains

[Bruce Fischl]

Hi John

I guess you could run recon-all through to the skull stripping, then copy 
your skull-stripped volume to brainmask.mgz in the subject's mri dir, then 
restart recon-all from there.


cheers
Bruce


On Fri, 16 Oct 2015, John Anderson wrote:


Dear experts,
I want to run recon-all on a stripped brains ( T1 images after applying bet
tool).
Do I need to add any flags to the command recon -all -all subjid 
 
 

 
Bests,
John

 

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Re: [Freesurfer] MPRAGE SNR

[Bruce Fischl]

probably similar, although maybe Doug can comment. You probably want to run 
it on the orig.mgz as the intensity normalization can artificially increase 
the SNR (which is kind of the point)

Bruce


On Mon, 19 Oct 2015, John 
Anderson wrote:



Hi Bruce,
Thanks a lot!! this is really great!
I ran the command as the following :
 
mri_cnr subj_01/surf subj_01/mri/norm.mgz
processing MRI volume subj_01/mri/norm.mgz...
    white = 97.2+-9.5, gray = 69.0+-16.1, csf = 47.8+-16.5
    gray/white CNR = 2.291, gray/csf CNR = 0.848
lh CNR = 1.569
    white = 97.2+-9.3, gray = 69.4+-15.9, csf = 48.6+-17.0
    gray/white CNR = 2.278, gray/csf CNR = 0.798
rh CNR = 1.538
total CNR = 1.554
 
 
I noticed that the normal range for the SNR  (15-20) when using the command
"wm-anat-snr"
 
What is the normal range for cnr generated by the binary "mri_cnr"?
 
 
Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
    Sent: Monday, October 19, 2015 at 8:36 AM
From: "Bruce Fischl" 
To: "Freesurfer support list" 
Cc: j.haen...@psychologie.uzh.ch
Subject: Re: [Freesurfer] MPRAGE SNR
Hi John

there is also a binary called mri_cnr that will compute the
contrast-to-noise ratio (CNR), which is really the more interesting
metric. It will also spit out the WM means+- std, and the ratio of these
two can be used as an SNR measure.

cheers
Bruce


On Mon, 19 Oct 2015, John Anderson wrote:

> Dear Jürgen
> This really helps!
> I highly appreciate your input on this.
>  
> Bests,
> John Anderson
>
> Senior Research Associate
> Psychological and Brain Sciences Dept.
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834
> Fax: +1 (603) 646-1419
>     Sent: Monday, October 19, 2015 at 1:30 AM
> From: JuergenHaenggi 
> To: "Freesurfer support list" 
> Subject: Re: [Freesurfer] MPRAGE SNR
> Dear John  
> FS's QA tools provide the SNR 
> see https://surfer.nmr.mgh.harvard.edu/fswiki/QATools
>  
> there is also a FS function called wm-anat-snr that can be used for that.
>  
> Hope this helps
> Cheers
> Jürgen
>  
>---

> --
> Jürgen Hänggi, Ph.D.
> Division of Neuropsychology
> Institute of Psychology
> University of Zurich
> Binzmuehlestrasse 14, PO Box 25 
> 8050 Zurich, Switzerland
> 0041 44 635 73 97 (phone office)
> 0041 76 445 86 84 (phone mobile)       
> 0041 44 635 74 09 (fax office)
> BIN 4.D.04 (office room number)                     
> j.haen...@psychologie.uzh.ch (email)
> http://www.psychologie.uzh.ch/neuropsy/ (website)
> http://www.juergenhaenggi.ch (private website)   
>
> This e-mail (and any attachment/s) contains confidential and/or privileged
> information. If you are not the intended recipient (or have received this
> e-mail in error) please notify the sender immediately and destroy this
> e-mail. Any unauthorised copying, disclosure or distribution of the
> material in this e-mail is strictly forbidden.
>---

> --
>
>
>  
>   Am 18.10.2015 um 16:48 schrieb John Anderson:
>  
> Dear Experts,
> Is there any tool in Freesurfer that can help to evaluate the SNR for
> T1 MPRAGE images directly ( i.e script). If not knidly can any help me
> to figure out the best way to dao it.
>  
> I highly appreciate your help!
>  
> Bests,
> John Anderson
>
> Senior Research Associate
> Psychological and Brain Sciences Dept.
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834
> Fax: +1 (603) 646-1419
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> it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you
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Re: [Freesurfer] Volumes differ in acquisition paramaters

[Martin Reuter]

Hi Kasper,

if you use the same file formats and conversion tools across both time 
points, the images should be identical. Even after conversion to nii. 
Not sure why they are not.


Yes, both warnings are related to the acquisition parameters. The second 
should better say that header information is different or something like 
that. I see if I can improve that error message to be more specific in a 
future release.


Best, Martin

On 10/17/2015 08:59 AM, Kasper Jessen wrote:

Hi Bruce,

Thank you for your reply.

Initially a PAR/REC file was used to obtain an anat.nii file. This is 
used to create the [CROSS]. Two timepoints ([CROSS-1] and [CROSS-2]) 
was used to create the [BASE].


  * Is it because there is too many file formats, and if so, how
should this be managed? Is it possible to run freesurfer directly
from the PAR/REC file?
  * Is the “Image geometries differ across time” related to the
difference in acquisition parameters mentioned in the warning?

Best regards
Kasper Jessen

2015-10-10 16:12 GMT+02:00 Bruce Fischl >:


Hi Kasper

what was your input volume? The .02sec change in TR won't mean
anything,
although it is a bit surprising to see, as is the fact that the other
parameters (flip angle, TE, etc...) don't seem to be preserved. We
usually
read those right out of the dicom files if that is what you used
as input.
Not sure why we would preserve the TR but not the other parameters.

cheers
Bruce



On Sat, 10 Oct 2015, Kasper Jessen wrote:

>
> Dear Freesurfer group,
>
> When looking through the log after running recon-all, i have
noticed two
> different errors in the logs. The one being about 'volumes differ in
> acquisition parameters' and the other 'Image geometries differ
across time,
> maybe due to aquisition changes?'.
>
> Volumes differ in acquisition parameters
> v1acq fa=0.00 tr=10.032000 te=0.00 ti=0.00
> v2acq fa=0.00 tr=10.012000 te=0.00 ti=0.00
> WARNING: Image geometries differ across time, maybe due to
aquisition
> changes?
> This can potentially bias a longitudinal study! Will continue in
10s.
>
> What do the above errors mean and is it something we should be
worried
> about?
>
> Best regards,
> Kasper Jessen
> MD, PhD Student
>
>
>
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MD, PhD student
Center for neuropsychiatric Schizophrenia Research (CNSR)
Mental Health Centre Glostrup
Nordre Ringvej 29-67
2600 Glostrup
Tlf.: 24430136
E-mail: kaspe...@cnsr.dk  eller 
kasper.jes...@regionh.dk 



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Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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Re: [Freesurfer] MPRAGE SNR

[Harms, Michael]

Hi,

FWIW, I've looked at a number of these measures in 500+ subjects from HCP
data -- wm-anat-snr, pctsurfcon, G/W cnr, G/CSF cnr -- to see how they
relate to each other, and whether they correlate with mean cortical
thickness, white matter surface area, or number of SurfaceHoles (prior to
topology correction).

I didn't find much of note.  e.g., the highest correlations were:

r = -0.32 between mean cortical thickness and G/CSF cnr (from norm.mgz)
r = -0.25 between white surface area and wmanatsnr
r = -0.39 between SurfaceHoles and pctsurfcon (and same with G/W cnr from
norm.mgz)

Not surprisingly, pctsurfcon and G/W cnr are reasonably correlated (r =
0.49).

G/W cnr from norm.mgz and orig.mgz are correlated at r=0.80.
G/CSF cnr from norm.mgz and orig.mgz are correlated at r=0.97

In another context (but smaller number of subjects), I've looked to see if
these various snr, cnr measures from FS were related to manual quality
ratings, and the relationship was rather weak.

All-in-all, I haven't seen much that would indicate that these measures
can be used as a sort of "automated" QC measure.  Manual review of the
structurals and FS results is still needed.

That said, the structurals from the HCP 500 release were all of reasonably
good quality to begin with.  So, it is possible that these snr/cnr
measures might be more informative in identifying truly awful scans in a
clinical population with a wider variability in MPRAGE scan quality.

I'd certainly be interested in hearing from anyone if they have found that
to be the case in their data.

BTW: Average value for G/W cnr for the HCP 500 is 1.99 and 1.81 from
orig.mgz and norm.mgz respectively.
Average value for G/CSF cnr for the same is 0.78 and 0.79, respectively.

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  63110Email: mha...@wustl.edu




On 10/19/15 8:09 AM, "Bruce Fischl"  wrote:

probably similar, although maybe Doug can comment. You probably want to
run
it on the orig.mgz as the intensity normalization can artificially
increase
the SNR (which is kind of the point)
Bruce


On Mon, 19 Oct 2015, John
Anderson wrote:

> Hi Bruce,
> Thanks a lot!! this is really great!
> I ran the command as the following :
>
> mri_cnr subj_01/surf subj_01/mri/norm.mgz
> processing MRI volume subj_01/mri/norm.mgz...
> white = 97.2+-9.5, gray = 69.0+-16.1, csf = 47.8+-16.5
> gray/white CNR = 2.291, gray/csf CNR = 0.848
> lh CNR = 1.569
> white = 97.2+-9.3, gray = 69.4+-15.9, csf = 48.6+-17.0
> gray/white CNR = 2.278, gray/csf CNR = 0.798
> rh CNR = 1.538
> total CNR = 1.554
>
>
> I noticed that the normal range for the SNR  (15-20) when using the
>command
> "wm-anat-snr"
>
> What is the normal range for cnr generated by the binary "mri_cnr"?
>
>
> Bests,
> John Anderson
>
> Senior Research Associate
> Psychological and Brain Sciences Dept.
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834
> Fax: +1 (603) 646-1419
> Sent: Monday, October 19, 2015 at 8:36 AM
> From: "Bruce Fischl" 
> To: "Freesurfer support list" 
> Cc: j.haen...@psychologie.uzh.ch
> Subject: Re: [Freesurfer] MPRAGE SNR
> Hi John
>
> there is also a binary called mri_cnr that will compute the
> contrast-to-noise ratio (CNR), which is really the more interesting
> metric. It will also spit out the WM means+- std, and the ratio of these
> two can be used as an SNR measure.
>
> cheers
> Bruce
>
>
> On Mon, 19 Oct 2015, John Anderson wrote:
>
> > Dear Jürgen
> > This really helps!
> > I highly appreciate your input on this.
> >
> > Bests,
> > John Anderson
> >
> > Senior Research Associate
> > Psychological and Brain Sciences Dept.
> > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> > Phone: +1 (603) 646-9834
> > Fax: +1 (603) 646-1419
> > Sent: Monday, October 19, 2015 at 1:30 AM
> > From: JuergenHaenggi 
> > To: "Freesurfer support list" 
> > Subject: Re: [Freesurfer] MPRAGE SNR
> > Dear John
> > FS's QA tools provide the SNR
> > see https://surfer.nmr.mgh.harvard.edu/fswiki/QATools
> >
> > there is also a FS function called wm-anat-snr that can be used for
>that.
> >
> > Hope this helps
> > Cheers
> > Jürgen
> >
>
>>-
>>--
>
> > --
> > Jürgen Hänggi, Ph.D.
> > Division of Neuropsychology
> > Institute of Psychology
> > University of Zurich
> > Binzmuehlestrasse 14, PO Box 25
> > 8050 Zurich, Switzerland
> > 0041 44 635 73 97 (phone office)
> > 0041 76 445 86 84 (phone mobile)
> > 0041 44 635 74 09 (fax office)
> > BIN 4.D.04 (office 

[Freesurfer] BuildYourOwnMonteCarlo

[Joost Janssen]

Hi,

A question about building your own Monte Carlo.

here: https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo

it says: "If you want to restrict the correction to a smaller area to
reduce the severity of the correction, you can specify a mask or a label
and change the output folder".

Thus, if i have 2 anatomically distant (e.g. 1 frontal and 1 occipital) but
identically-sized (same # of vertices) cortical areas, only 1 MC for 1 area
needs to be created and can then be used with both areas? That is, only the
size of the area matters, not the location. Is that correct?

Thanks,
-joost
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Re: [Freesurfer] MPRAGE SNR

[Matt Glasser]

There is also the issue that grey and white matter are not truly a
homogeneous single intensity anatomically.

Peace,

Matt.

On 10/19/15, 9:23 AM, "Harms, Michael"

wrote:

>
>Hi,
>
>FWIW, I've looked at a number of these measures in 500+ subjects from HCP
>data -- wm-anat-snr, pctsurfcon, G/W cnr, G/CSF cnr -- to see how they
>relate to each other, and whether they correlate with mean cortical
>thickness, white matter surface area, or number of SurfaceHoles (prior to
>topology correction).
>
>I didn't find much of note.  e.g., the highest correlations were:
>
>r = -0.32 between mean cortical thickness and G/CSF cnr (from norm.mgz)
>r = -0.25 between white surface area and wmanatsnr
>r = -0.39 between SurfaceHoles and pctsurfcon (and same with G/W cnr from
>norm.mgz)
>
>Not surprisingly, pctsurfcon and G/W cnr are reasonably correlated (r =
>0.49).
>
>G/W cnr from norm.mgz and orig.mgz are correlated at r=0.80.
>G/CSF cnr from norm.mgz and orig.mgz are correlated at r=0.97
>
>In another context (but smaller number of subjects), I've looked to see if
>these various snr, cnr measures from FS were related to manual quality
>ratings, and the relationship was rather weak.
>
>All-in-all, I haven't seen much that would indicate that these measures
>can be used as a sort of "automated" QC measure.  Manual review of the
>structurals and FS results is still needed.
>
>That said, the structurals from the HCP 500 release were all of reasonably
>good quality to begin with.  So, it is possible that these snr/cnr
>measures might be more informative in identifying truly awful scans in a
>clinical population with a wider variability in MPRAGE scan quality.
>
>I'd certainly be interested in hearing from anyone if they have found that
>to be the case in their data.
>
>BTW: Average value for G/W cnr for the HCP 500 is 1.99 and 1.81 from
>orig.mgz and norm.mgz respectively.
>Average value for G/CSF cnr for the same is 0.78 and 0.79, respectively.
>
>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  63110Email: mha...@wustl.edu
>
>
>
>
>On 10/19/15 8:09 AM, "Bruce Fischl"  wrote:
>
>probably similar, although maybe Doug can comment. You probably want to
>run
>it on the orig.mgz as the intensity normalization can artificially
>increase
>the SNR (which is kind of the point)
>Bruce
>
>
>On Mon, 19 Oct 2015, John
>Anderson wrote:
>
>> Hi Bruce,
>> Thanks a lot!! this is really great!
>> I ran the command as the following :
>>
>> mri_cnr subj_01/surf subj_01/mri/norm.mgz
>> processing MRI volume subj_01/mri/norm.mgz...
>> white = 97.2+-9.5, gray = 69.0+-16.1, csf = 47.8+-16.5
>> gray/white CNR = 2.291, gray/csf CNR = 0.848
>> lh CNR = 1.569
>> white = 97.2+-9.3, gray = 69.4+-15.9, csf = 48.6+-17.0
>> gray/white CNR = 2.278, gray/csf CNR = 0.798
>> rh CNR = 1.538
>> total CNR = 1.554
>>
>>
>> I noticed that the normal range for the SNR  (15-20) when using the
>>command
>> "wm-anat-snr"
>>
>> What is the normal range for cnr generated by the binary "mri_cnr"?
>>
>>
>> Bests,
>> John Anderson
>>
>> Senior Research Associate
>> Psychological and Brain Sciences Dept.
>> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
>> Phone: +1 (603) 646-9834
>> Fax: +1 (603) 646-1419
>> Sent: Monday, October 19, 2015 at 8:36 AM
>> From: "Bruce Fischl" 
>> To: "Freesurfer support list" 
>> Cc: j.haen...@psychologie.uzh.ch
>> Subject: Re: [Freesurfer] MPRAGE SNR
>> Hi John
>>
>> there is also a binary called mri_cnr that will compute the
>> contrast-to-noise ratio (CNR), which is really the more interesting
>> metric. It will also spit out the WM means+- std, and the ratio of these
>> two can be used as an SNR measure.
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 19 Oct 2015, John Anderson wrote:
>>
>> > Dear Jürgen
>> > This really helps!
>> > I highly appreciate your input on this.
>> >
>> > Bests,
>> > John Anderson
>> >
>> > Senior Research Associate
>> > Psychological and Brain Sciences Dept.
>> > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
>> > Phone: +1 (603) 646-9834
>> > Fax: +1 (603) 646-1419
>> > Sent: Monday, October 19, 2015 at 1:30 AM
>> > From: JuergenHaenggi 
>> > To: "Freesurfer support list" 
>> > Subject: Re: [Freesurfer] MPRAGE SNR
>> > Dear John
>> > FS's QA tools provide the SNR
>> > see https://surfer.nmr.mgh.harvard.edu/fswiki/QATools
>> >
>> > there is also a FS function called wm-anat-snr that can be used for
>>that.
>> >
>> > Hope this helps
>> > Cheers
>> > Jürgen
>> >
>>

[Freesurfer] Viewing vitamin E capsules?

[Hutton, Seth]

Dear users,

I have been using FreeSurfer for a while now, but am working in a new lab and 
their goals fall outside of my realm of experience.
We are using both MRI imaging as well as FNIRs. We have multiple vitamin E 
capsules placed during both and would like to be able to view them in 
FreeSurfer so that we can better estimate the projected cortical localization 
of these capsules.
Using the generic recon-all -s -i -all we are unable to see our capsules, as 
they are most likely eliminated during the skull strip step. I see that I can 
change the threshold with "-wsmore", but am wondering if this is really the 
best way to accomplish what we are trying to do.
Is there any way to include our capsules without excluding the skull strip? If 
not could how would you recommend adjusting the threshold.
I tried excluding the skulls trip step with
recon-all -s -i -autorecon1 -noskullstrip
but then when I tried to view it using free view it was unable to open due to 
the lack of the brain mask.mgz.

Thank you so much for your time and consideration,
Seth H
**
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used for urgent or sensitive issues 
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Volumes differ in acquisition paramaters

[pablo najt]

Dear Martin and FS experts.I am having difficulty in loading my qdec.table.dat 
to Matlab.When I use the [command: Qdec = fReadQdec('qdec.table.dat'); ] Matlab 
only recognises a matrix of 140x1 cell, whereas instead it should recognise a 
140x4.I tried to import the table as 'table' from the gui interface but then I 
am getting error on the command: M = Qdec2num(Qdec,1) Any tips on how to load 
my table would be fabulous help.Thank youPabloTo: freesurfer@nmr.mgh.harvard.edu
From: mreu...@nmr.mgh.harvard.edu
Date: Mon, 19 Oct 2015 09:04:41 -0400
Subject: Re: [Freesurfer] Volumes differ in acquisition paramaters


  

  
  
Hi Kasper,



if you use the same file formats and conversion tools across both
time points, the images should be identical. Even after conversion
to nii. Not sure why they are not.



Yes, both warnings are related to the acquisition parameters. The
second should better say that header information is different or
something like that. I see if I can improve that error message to be
more specific in a future release.



Best, Martin



On 10/17/2015 08:59 AM, Kasper Jessen
  wrote:



  
Hi Bruce,


  
Thank you for your reply.


  Initially
a PAR/REC file was used to obtain an anat.nii file. This is
used to create the
[CROSS]. Two timepoints ([CROSS-1] and [CROSS-2]) was used
to create the [BASE]. 

  
Is it because there is too many file formats, and if so,
  how should this be managed? Is it possible to run
  freesurfer directly from the PAR/REC file?


Is the
“Image geometries differ across time” related to the
difference in acquisition parameters mentioned
  in the warning?
  

Best regards 
Kasper Jessen
  
  

2015-10-10 16:12 GMT+02:00 Bruce Fischl
  :

  Hi Kasper



what was your input volume? The .02sec change in TR won't
mean anything,

although it is a bit surprising to see, as is the fact that
the other

parameters (flip angle, TE, etc...) don't seem to be
preserved. We usually

read those right out of the dicom files if that is what you
used as input.

Not sure why we would preserve the TR but not the other
parameters.



cheers

Bruce


  





On Sat, 10 Oct 2015, Kasper Jessen wrote:



>

> Dear Freesurfer group,

>

> When looking through the log after running
recon-all, i have noticed two

> different errors in the logs. The one being about
'volumes differ in

> acquisition parameters' and the other 'Image
geometries differ across time,

> maybe due to aquisition changes?'.

>

> Volumes differ in acquisition parameters

> v1acq fa=0.00 tr=10.032000 te=0.00
ti=0.00

> v2acq fa=0.00 tr=10.012000 te=0.00
ti=0.00

> WARNING: Image geometries differ across time, maybe
due to aquisition

> changes?

> This can potentially bias a longitudinal study!
Will continue in 10s.

>

> What do the above errors mean and is it something
we should be worried

> about?

>

> Best regards,

> Kasper Jessen

> MD, PhD Student

>

>

>

  

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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 to you in error

but does not contain patient information, please contact the
sender and properly

dispose of the e-mail.



  







-- 

Re: [Freesurfer] recon-all stripped brains

[Douglas Greve]

It might just work to give recon-all skull stripped brains. I've done it 
before


On 10/19/15 8:38 AM, Bruce Fischl wrote:

Hi John

I guess you could run recon-all through to the skull stripping, then 
copy your skull-stripped volume to brainmask.mgz in the subject's mri 
dir, then restart recon-all from there.


cheers
Bruce


On Fri, 16 Oct 2015, John Anderson wrote:


Dear experts,
I want to run recon-all on a stripped brains ( T1 images after 
applying bet

tool).
Do I need to add any flags to the command recon -all -all subjid 




Bests,
John







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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] BuildYourOwnMonteCarlo

[Douglas Greve]

In theory that should work. I say "in theory" because there might be 
something unique to each area in terms of the distribution of the 
vertices across space. But I'm betting it will be safe to do. But why 
not run both simulations?


On 10/19/15 11:03 AM, Joost Janssen wrote:

Hi,

A question about building your own Monte Carlo.

here: https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo

it says: "If you want to restrict the correction to a smaller area to 
reduce the severity of the correction, you can specify a mask or a 
label and change the output folder".


Thus, if i have 2 anatomically distant (e.g. 1 frontal and 1 
occipital) but identically-sized (same # of vertices) cortical areas, 
only 1 MC for 1 area needs to be created and can then be used with 
both areas? That is, only the size of the area matters, not the 
location. Is that correct?


Thanks,
-joost


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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 to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Viewing vitamin E capsules?

[Bruce Fischl]

Hi Seth

do you really want to include the capsule within the brain mask? You can 
always view it and find its coordinate by visualizing the orig.mgz. If you 
really want it in the brainmask.mgz you can clone it back in using freeview 
or tkmedit


cheers
Bruce

On Mon, 19 Oct 2015, Hutton, Seth wrote:


Dear users,
I have been using FreeSurfer for a while now, but am working in a new lab
and their goals fall outside of my realm of experience. 
We are using both MRI imaging as well as FNIRs. We have multiple vitamin E
capsules placed during both and would like to be able to view them in
FreeSurfer so that we can better estimate the projected cortical
localization of these capsules. 
Using the generic recon-all -s -i -all we are unable to see our capsules, as
they are most likely eliminated during the skull strip step. I see that I
can change the threshold with "-wsmore", but am wondering if this is really
the best way to accomplish what we are trying to do.
Is there any way to include our capsules without excluding the skull strip?
If not could how would you recommend adjusting the threshold.
I tried excluding the skulls trip step with
recon-all -s -i -autorecon1 -noskullstrip
but then when I tried to view it using free view it was unable to open due
to the lack of the brain mask.mgz.

Thank you so much for your time and consideration,
Seth H

**
Electronic Mail is not secure, may not be read every day, and should not be
used for urgent or sensitive issues


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Volumes differ in acquisition paramaters

[Martin Reuter]

Hi Pablo,

maybe your file is not clean and contains strange symbols to separate 
coumns and rows?

Make sure columns are all separated by spaces.
You could load the table into exel or openoffice spreadsheet and then 
export as CSV with space (or you could also try tab) for the separation 
and no "" around values.


Best, Martin

On 10/19/2015 11:32 AM, pablo najt wrote:

Dear Martin and FS experts.
I am having difficulty in loading my qdec.table.dat to Matlab.
When I use the [command:/Qdec = fReadQdec('qdec.table.dat');/ ] Matlab 
only recognises a matrix of 140x1 cell, whereas instead it should 
recognise a 140x4.
I tried to import the table as 'table' from the gui interface but then 
I am getting error on the command: /M = Qdec2num(Qdec,1)/

Any tips on how to load my table would be fabulous help.
Thank you
Pablo

To: freesurfer@nmr.mgh.harvard.edu
From: mreu...@nmr.mgh.harvard.edu
Date: Mon, 19 Oct 2015 09:04:41 -0400
Subject: Re: [Freesurfer] Volumes differ in acquisition paramaters

Hi Kasper,

if you use the same file formats and conversion tools across both time 
points, the images should be identical. Even after conversion to nii. 
Not sure why they are not.


Yes, both warnings are related to the acquisition parameters. The 
second should better say that header information is different or 
something like that. I see if I can improve that error message to be 
more specific in a future release.


Best, Martin

On 10/17/2015 08:59 AM, Kasper Jessen wrote:

Hi Bruce,

Thank you for your reply.

Initially a PAR/REC file was used to obtain an anat.nii file. This
is used to create the [CROSS]. Two timepoints ([CROSS-1] and
[CROSS-2]) was used to create the [BASE].

  * Is it because there is too many file formats, and if so, how
should this be managed? Is it possible to run freesurfer
directly from the PAR/REC file?
  * Is the “Image geometries differ across time” related to the
difference in acquisition parameters mentioned in the warning?

Best regards
Kasper Jessen

2015-10-10 16:12 GMT+02:00 Bruce Fischl
>:

Hi Kasper

what was your input volume? The .02sec change in TR won't mean
anything,
although it is a bit surprising to see, as is the fact that
the other
parameters (flip angle, TE, etc...) don't seem to be
preserved. We usually
read those right out of the dicom files if that is what you
used as input.
Not sure why we would preserve the TR but not the other
parameters.

cheers
Bruce



On Sat, 10 Oct 2015, Kasper Jessen wrote:

>
> Dear Freesurfer group,
>
> When looking through the log after running recon-all, i have
noticed two
> different errors in the logs. The one being about 'volumes
differ in
> acquisition parameters' and the other 'Image geometries
differ across time,
> maybe due to aquisition changes?'.
>
> Volumes differ in acquisition parameters
> v1acq fa=0.00 tr=10.032000 te=0.00 ti=0.00
> v2acq fa=0.00 tr=10.012000 te=0.00 ti=0.00
> WARNING: Image geometries differ across time, maybe due to
aquisition
> changes?
> This can potentially bias a longitudinal study! Will
continue in 10s.
>
> What do the above errors mean and is it something we should
be worried
> about?
>
> Best regards,
> Kasper Jessen
> MD, PhD Student
>
>
>
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-- 
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MD, PhD student
Center for neuropsychiatric Schizophrenia Research (CNSR)
Mental Health Centre Glostrup
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2600 Glostrup
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Re: [Freesurfer] MPRAGE SNR

[Douglas Greve]

This has been my experience as well. Not much seems to predict which 
scans will need to be edited.

On 10/19/15 10:23 AM, Harms, Michael wrote:
> Hi,
>
> FWIW, I've looked at a number of these measures in 500+ subjects from HCP
> data -- wm-anat-snr, pctsurfcon, G/W cnr, G/CSF cnr -- to see how they
> relate to each other, and whether they correlate with mean cortical
> thickness, white matter surface area, or number of SurfaceHoles (prior to
> topology correction).
>
> I didn't find much of note.  e.g., the highest correlations were:
>
> r = -0.32 between mean cortical thickness and G/CSF cnr (from norm.mgz)
> r = -0.25 between white surface area and wmanatsnr
> r = -0.39 between SurfaceHoles and pctsurfcon (and same with G/W cnr from
> norm.mgz)
>
> Not surprisingly, pctsurfcon and G/W cnr are reasonably correlated (r =
> 0.49).
>
> G/W cnr from norm.mgz and orig.mgz are correlated at r=0.80.
> G/CSF cnr from norm.mgz and orig.mgz are correlated at r=0.97
>
> In another context (but smaller number of subjects), I've looked to see if
> these various snr, cnr measures from FS were related to manual quality
> ratings, and the relationship was rather weak.
>
> All-in-all, I haven't seen much that would indicate that these measures
> can be used as a sort of "automated" QC measure.  Manual review of the
> structurals and FS results is still needed.
>
> That said, the structurals from the HCP 500 release were all of reasonably
> good quality to begin with.  So, it is possible that these snr/cnr
> measures might be more informative in identifying truly awful scans in a
> clinical population with a wider variability in MPRAGE scan quality.
>
> I'd certainly be interested in hearing from anyone if they have found that
> to be the case in their data.
>
> BTW: Average value for G/W cnr for the HCP 500 is 1.99 and 1.81 from
> orig.mgz and norm.mgz respectively.
> Average value for G/CSF cnr for the same is 0.78 and 0.79, respectively.
>
> 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  63110Email: mha...@wustl.edu
>
>
>
>
> On 10/19/15 8:09 AM, "Bruce Fischl"  wrote:
>
> probably similar, although maybe Doug can comment. You probably want to
> run
> it on the orig.mgz as the intensity normalization can artificially
> increase
> the SNR (which is kind of the point)
> Bruce
>
>
> On Mon, 19 Oct 2015, John
> Anderson wrote:
>
>> Hi Bruce,
>> Thanks a lot!! this is really great!
>> I ran the command as the following :
>>
>> mri_cnr subj_01/surf subj_01/mri/norm.mgz
>> processing MRI volume subj_01/mri/norm.mgz...
>>  white = 97.2+-9.5, gray = 69.0+-16.1, csf = 47.8+-16.5
>>  gray/white CNR = 2.291, gray/csf CNR = 0.848
>> lh CNR = 1.569
>>  white = 97.2+-9.3, gray = 69.4+-15.9, csf = 48.6+-17.0
>>  gray/white CNR = 2.278, gray/csf CNR = 0.798
>> rh CNR = 1.538
>> total CNR = 1.554
>>
>>
>> I noticed that the normal range for the SNR  (15-20) when using the
>> command
>> "wm-anat-snr"
>>
>> What is the normal range for cnr generated by the binary "mri_cnr"?
>>
>>
>> Bests,
>> John Anderson
>>
>> Senior Research Associate
>> Psychological and Brain Sciences Dept.
>> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
>> Phone: +1 (603) 646-9834
>> Fax: +1 (603) 646-1419
>>  Sent: Monday, October 19, 2015 at 8:36 AM
>> From: "Bruce Fischl" 
>> To: "Freesurfer support list" 
>> Cc: j.haen...@psychologie.uzh.ch
>> Subject: Re: [Freesurfer] MPRAGE SNR
>> Hi John
>>
>> there is also a binary called mri_cnr that will compute the
>> contrast-to-noise ratio (CNR), which is really the more interesting
>> metric. It will also spit out the WM means+- std, and the ratio of these
>> two can be used as an SNR measure.
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 19 Oct 2015, John Anderson wrote:
>>
>>> Dear Jürgen
>>> This really helps!
>>> I highly appreciate your input on this.
>>>
>>> Bests,
>>> John Anderson
>>>
>>> Senior Research Associate
>>> Psychological and Brain Sciences Dept.
>>> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
>>> Phone: +1 (603) 646-9834
>>> Fax: +1 (603) 646-1419
>>>  Sent: Monday, October 19, 2015 at 1:30 AM
>>> From: JuergenHaenggi 
>>> To: "Freesurfer support list" 
>>> Subject: Re: [Freesurfer] MPRAGE SNR
>>> Dear John
>>> FS's QA tools provide the SNR
>>> see https://surfer.nmr.mgh.harvard.edu/fswiki/QATools
>>>
>>> there is also a FS function called wm-anat-snr that can be used for
>> that.
>>> Hope this helps
>>> Cheers
>>> Jürgen
>>>
>>> -
>>> --
>>> 

Re: [Freesurfer] MPRAGE SNR

[John Anderson]

Hi All,

Thank you very much for your comments!

 

Is it advisable to include SNR as a covariate when we use Qdec to run the final statistics on volumetrics, surfaces and cortical thickness?

Does it make sence ?

 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

 
 

Sent: Monday, October 19, 2015 at 11:48 AM
From: "Douglas Greve" 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] MPRAGE SNR

This has been my experience as well. Not much seems to predict which
scans will need to be edited.

On 10/19/15 10:23 AM, Harms, Michael wrote:
> Hi,
>
> FWIW, I've looked at a number of these measures in 500+ subjects from HCP
> data -- wm-anat-snr, pctsurfcon, G/W cnr, G/CSF cnr -- to see how they
> relate to each other, and whether they correlate with mean cortical
> thickness, white matter surface area, or number of SurfaceHoles (prior to
> topology correction).
>
> I didn't find much of note. e.g., the highest correlations were:
>
> r = -0.32 between mean cortical thickness and G/CSF cnr (from norm.mgz)
> r = -0.25 between white surface area and wmanatsnr
> r = -0.39 between SurfaceHoles and pctsurfcon (and same with G/W cnr from
> norm.mgz)
>
> Not surprisingly, pctsurfcon and G/W cnr are reasonably correlated (r =
> 0.49).
>
> G/W cnr from norm.mgz and orig.mgz are correlated at r=0.80.
> G/CSF cnr from norm.mgz and orig.mgz are correlated at r=0.97
>
> In another context (but smaller number of subjects), I've looked to see if
> these various snr, cnr measures from FS were related to manual quality
> ratings, and the relationship was rather weak.
>
> All-in-all, I haven't seen much that would indicate that these measures
> can be used as a sort of "automated" QC measure. Manual review of the
> structurals and FS results is still needed.
>
> That said, the structurals from the HCP 500 release were all of reasonably
> good quality to begin with. So, it is possible that these snr/cnr
> measures might be more informative in identifying truly awful scans in a
> clinical population with a wider variability in MPRAGE scan quality.
>
> I'd certainly be interested in hearing from anyone if they have found that
> to be the case in their data.
>
> BTW: Average value for G/W cnr for the HCP 500 is 1.99 and 1.81 from
> orig.mgz and norm.mgz respectively.
> Average value for G/CSF cnr for the same is 0.78 and 0.79, respectively.
>
> 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 63110Email: mha...@wustl.edu
>
>
>
>
> On 10/19/15 8:09 AM, "Bruce Fischl"  wrote:
>
> probably similar, although maybe Doug can comment. You probably want to
> run
> it on the orig.mgz as the intensity normalization can artificially
> increase
> the SNR (which is kind of the point)
> Bruce
>
>
> On Mon, 19 Oct 2015, John
> Anderson wrote:
>
>> Hi Bruce,
>> Thanks a lot!! this is really great!
>> I ran the command as the following :
>>
>> mri_cnr subj_01/surf subj_01/mri/norm.mgz
>> processing MRI volume subj_01/mri/norm.mgz...
>> white = 97.2+-9.5, gray = 69.0+-16.1, csf = 47.8+-16.5
>> gray/white CNR = 2.291, gray/csf CNR = 0.848
>> lh CNR = 1.569
>> white = 97.2+-9.3, gray = 69.4+-15.9, csf = 48.6+-17.0
>> gray/white CNR = 2.278, gray/csf CNR = 0.798
>> rh CNR = 1.538
>> total CNR = 1.554
>>
>>
>> I noticed that the normal range for the SNR (15-20) when using the
>> command
>> "wm-anat-snr"
>>
>> What is the normal range for cnr generated by the binary "mri_cnr"?
>>
>>
>> Bests,
>> John Anderson
>>
>> Senior Research Associate
>> Psychological and Brain Sciences Dept.
>> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
>> Phone: +1 (603) 646-9834
>> Fax: +1 (603) 646-1419
>> Sent: Monday, October 19, 2015 at 8:36 AM
>> From: "Bruce Fischl" 
>> To: "Freesurfer support list" 
>> Cc: j.haen...@psychologie.uzh.ch
>> Subject: Re: [Freesurfer] MPRAGE SNR
>> Hi John
>>
>> there is also a binary called mri_cnr that will compute the
>> contrast-to-noise ratio (CNR), which is really the more interesting
>> metric. It will also spit out the WM means+- std, and the ratio of these
>> two can be used as an SNR measure.
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 19 Oct 2015, John Anderson wrote:
>>
>>> Dear Jürgen
>>> This really helps!
>>> I highly appreciate your input on this.
>>>
>>> Bests,
>>> John Anderson
>>>
>>> Senior Research Associate
>>> Psychological and Brain Sciences Dept.
>>> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
>>> Phone: +1 (603) 646-9834
>>> Fax: +1 (603) 

Re: [Freesurfer] Viewing vitamin E capsules?

[dgw]

Why not just open the T1.mgz and load the FreeSurfer surfaces? Is there 
a more specific goal?

hth
d

On 10/19/15 10:56 AM, Hutton, Seth wrote:
> Dear users,
>
> I have been using FreeSurfer for a while now, but am working in a new
> lab and their goals fall outside of my realm of experience.
> We are using both MRI imaging as well as FNIRs. We have multiple vitamin
> E capsules placed during both and would like to be able to view them in
> FreeSurfer so that we can better estimate the projected cortical
> localization of these capsules.
> Using the generic recon-all -s -i -all we are unable to see our
> capsules, as they are most likely eliminated during the skull strip
> step. I see that I can change the threshold with "-wsmore", but am
> wondering if this is really the best way to accomplish what we are
> trying to do.
> Is there any way to include our capsules without excluding the skull
> strip? If not could how would you recommend adjusting the threshold.
> I tried excluding the skulls trip step with
> recon-all -s -i -autorecon1 -noskullstrip
> but then when I tried to view it using free view it was unable to open
> due to the lack of the brain mask.mgz.
>
> Thank you so much for your time and consideration,
> Seth H
>
> **
> Electronic Mail is not secure, may not be read every day, and should not
> be used for urgent or sensitive issues
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
>
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Re: [Freesurfer] MPRAGE SNR

[Bruce Fischl]

I think you would just be wasting your power
Bruce
On Mon, 19 Oct 2015, John 
Anderson wrote:



Hi All,
Thank you very much for your comments!
 
Is it advisable to include SNR as a covariate when we use Qdec to run the
final statistics on volumetrics, surfaces and cortical thickness?
Does it make sence ?
 
Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
    Sent: Monday, October 19, 2015 at 11:48 AM
From: "Douglas Greve" 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] MPRAGE SNR
This has been my experience as well. Not much seems to predict which
scans will need to be edited.

On 10/19/15 10:23 AM, Harms, Michael wrote:
> Hi,
>
> FWIW, I've looked at a number of these measures in 500+ subjects from HCP
> data -- wm-anat-snr, pctsurfcon, G/W cnr, G/CSF cnr -- to see how they
> relate to each other, and whether they correlate with mean cortical
> thickness, white matter surface area, or number of SurfaceHoles (prior to
> topology correction).
>
> I didn't find much of note. e.g., the highest correlations were:
>
> r = -0.32 between mean cortical thickness and G/CSF cnr (from norm.mgz)
> r = -0.25 between white surface area and wmanatsnr
> r = -0.39 between SurfaceHoles and pctsurfcon (and same with G/W cnr from
> norm.mgz)
>
> Not surprisingly, pctsurfcon and G/W cnr are reasonably correlated (r =
> 0.49).
>
> G/W cnr from norm.mgz and orig.mgz are correlated at r=0.80.
> G/CSF cnr from norm.mgz and orig.mgz are correlated at r=0.97
>
> In another context (but smaller number of subjects), I've looked to see if
> these various snr, cnr measures from FS were related to manual quality
> ratings, and the relationship was rather weak.
>
> All-in-all, I haven't seen much that would indicate that these measures
> can be used as a sort of "automated" QC measure. Manual review of the
> structurals and FS results is still needed.
>
> That said, the structurals from the HCP 500 release were all of reasonably
> good quality to begin with. So, it is possible that these snr/cnr
> measures might be more informative in identifying truly awful scans in a
> clinical population with a wider variability in MPRAGE scan quality.
>
> I'd certainly be interested in hearing from anyone if they have found that
> to be the case in their data.
>
> BTW: Average value for G/W cnr for the HCP 500 is 1.99 and 1.81 from
> orig.mgz and norm.mgz respectively.
> Average value for G/CSF cnr for the same is 0.78 and 0.79, respectively.
>
> 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 63110Email: mha...@wustl.edu
>
>
>
>
> On 10/19/15 8:09 AM, "Bruce Fischl"  wrote:
>
> probably similar, although maybe Doug can comment. You probably want to
> run
> it on the orig.mgz as the intensity normalization can artificially
> increase
> the SNR (which is kind of the point)
> Bruce
>
>
> On Mon, 19 Oct 2015, John
> Anderson wrote:
>
>> Hi Bruce,
>> Thanks a lot!! this is really great!
>> I ran the command as the following :
>>
>> mri_cnr subj_01/surf subj_01/mri/norm.mgz
>> processing MRI volume subj_01/mri/norm.mgz...
>> white = 97.2+-9.5, gray = 69.0+-16.1, csf = 47.8+-16.5
>> gray/white CNR = 2.291, gray/csf CNR = 0.848
>> lh CNR = 1.569
>> white = 97.2+-9.3, gray = 69.4+-15.9, csf = 48.6+-17.0
>> gray/white CNR = 2.278, gray/csf CNR = 0.798
>> rh CNR = 1.538
>> total CNR = 1.554
>>
>>
>> I noticed that the normal range for the SNR (15-20) when using the
>> command
>> "wm-anat-snr"
>>
>> What is the normal range for cnr generated by the binary "mri_cnr"?
>>
>>
>> Bests,
>> John Anderson
>>
>> Senior Research Associate
>> Psychological and Brain Sciences Dept.
>> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
>> Phone: +1 (603) 646-9834
>> Fax: +1 (603) 646-1419
>> Sent: Monday, October 19, 2015 at 8:36 AM
>> From: "Bruce Fischl" 
>> To: "Freesurfer support list" 
>> Cc: j.haen...@psychologie.uzh.ch
>> Subject: Re: [Freesurfer] MPRAGE SNR
>> Hi John
>>
>> there is also a binary called mri_cnr that will compute the
>> contrast-to-noise ratio (CNR), which is really the more interesting
>> metric. It will also spit out the WM means+- std, and the ratio of these
>> two can be used as an SNR measure.
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 19 Oct 2015, John Anderson wrote:
>>
>>> Dear Jürgen
>>> This really helps!
>>> I highly appreciate your input on this.
>>>
>>> Bests,
>>> John Anderson
>>>
>>> Senior Research Associate
>>> Psychological and Brain Sciences Dept.
>>> Dartmouth College, 419 Moore Hall, 

Re: [Freesurfer] converting surfaces into volumes or integrating them into volumes

[Douglas Greve]

In that case, you just need to mri_convert aparc+aseg.mgz aparc+aseg.nii


On 10/19/15 3:24 PM, Bruce Fischl wrote:
> Hi Boris
>
> the aparc*aseg.mgz files are probably want you want. They are the surface
> parcellations sampled into the volume. Of course you lose resolution when
> you sample a continuous surface into a discrete volume though.
>
> cheers
> Bruce
>
>
> On Mon, 19 Oct 2015, Boris Shabash wrote:
>
>> Hello FreeSurfer group
>>
>> How are you?
>>
>> I have currently started working with FS and would like to visualize some of 
>> the volume results. I have no issue visualizing the .mgz volumes produced 
>> since I can use mri_convert to convert them to .nii format and then 
>> visualize them using my software. However, I'd like to know if there is a 
>> way to convert the resulting surface labels (e.g. my_output/surf/rh.white or 
>> my_output/surf/rh.pial) into .nii files that I can also visualize or combine 
>> them with a resulting .mgz file into a single .nii file that contains the 
>> information for both volumes and the surfaces. Ideally I'd like to know if 
>> there is a way to combine them into a single file via the terminal.
>>
>> Please let me know if FS comes with a tool the allows for this process or if 
>> you know of any external tool.
>>
>>
>> Sincerely,
>> Boris
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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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 to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] converting surfaces into volumes or integrating them into volumes

[Bruce Fischl]

Hi Boris

the aparc*aseg.mgz files are probably want you want. They are the surface 
parcellations sampled into the volume. Of course you lose resolution when 
you sample a continuous surface into a discrete volume though.

cheers
Bruce


On Mon, 19 Oct 2015, Boris Shabash wrote:

> Hello FreeSurfer group
>
> How are you?
>
> I have currently started working with FS and would like to visualize some of 
> the volume results. I have no issue visualizing the .mgz volumes produced 
> since I can use mri_convert to convert them to .nii format and then visualize 
> them using my software. However, I'd like to know if there is a way to 
> convert the resulting surface labels (e.g. my_output/surf/rh.white or 
> my_output/surf/rh.pial) into .nii files that I can also visualize or combine 
> them with a resulting .mgz file into a single .nii file that contains the 
> information for both volumes and the surfaces. Ideally I'd like to know if 
> there is a way to combine them into a single file via the terminal.
>
> Please let me know if FS comes with a tool the allows for this process or if 
> you know of any external tool.
>
>
> Sincerely,
> Boris
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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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 to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] converting surfaces into volumes or integrating them into volumes

[Boris Shabash]

Hello FreeSurfer group

How are you?

I have currently started working with FS and would like to visualize some of 
the volume results. I have no issue visualizing the .mgz volumes produced since 
I can use mri_convert to convert them to .nii format and then visualize them 
using my software. However, I'd like to know if there is a way to convert the 
resulting surface labels (e.g. my_output/surf/rh.white or 
my_output/surf/rh.pial) into .nii files that I can also visualize or combine 
them with a resulting .mgz file into a single .nii file that contains the 
information for both volumes and the surfaces. Ideally I'd like to know if 
there is a way to combine them into a single file via the terminal.

Please let me know if FS comes with a tool the allows for this process or if 
you know of any external tool.


Sincerely,
Boris
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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 to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] converting surfaces into volumes or integrating them into volumes

[Douglas Greve]

Try mri_surf2vol. Run it with --help to get more docs

On 10/19/15 3:09 PM, Boris Shabash wrote:
> Hello FreeSurfer group
>
> How are you?
>
> I have currently started working with FS and would like to visualize some of 
> the volume results. I have no issue visualizing the .mgz volumes produced 
> since I can use mri_convert to convert them to .nii format and then visualize 
> them using my software. However, I'd like to know if there is a way to 
> convert the resulting surface labels (e.g. my_output/surf/rh.white or 
> my_output/surf/rh.pial) into .nii files that I can also visualize or combine 
> them with a resulting .mgz file into a single .nii file that contains the 
> information for both volumes and the surfaces. Ideally I'd like to know if 
> there is a way to combine them into a single file via the terminal.
>
> Please let me know if FS comes with a tool the allows for this process or if 
> you know of any external tool.
>
>
> Sincerely,
> Boris
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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[Freesurfer] patching 5.1

[Aaron Tanenbaum]

Hello All
Several years ago Freesurfer 5.1 was patched to resolve some issues.  I
just remember the patch resolved issues plaguing 5.1 and earlier. how does
one get the patch version. no where on the FTP server i can see patched
versions and instruction on performing a patch.
Aaron Tanenbaum
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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 to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] MPRAGE SNR

[Harms, Michael]

My experience, which appears to be consistent with Doug's, is that there is no substitute for reviewing the images and FS results manually.  Ultimately, it is a bit of a judgement call, and interacts with the goals/purposes of your study.




-- 
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: John Anderson 
Reply-To: "freesurfer@nmr.mgh.harvard.edu" 
Date: Monday, October 19, 2015 11:30 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Cc: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] MPRAGE SNR






Thanks MH,
Let's say that we have 100 MPRAGEs and we want to include them in a cross sectional analysis.
Depending on your experience, do you recommend any criterion to (include/ exclude) these images  in the analysis? As I see visualizing the images alone is not enough to say that the quality of the image is fine. Also calculating the SNR, CNR want help
 a lot!
 
any suggestions?
 
Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
 
 

Sent: Monday, October 19, 2015 at 12:24 PM
From: "Harms, Michael" 
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] MPRAGE SNR



 
At best that would probably be harmless (if you have a decent number of subjects), but unless SNR, CNR actually relates to those measures in some fashion, you aren't really accomplishing anything by including it as a covariate.  You certainly wouldn't
 be able to claim that including SNR as a covariate has somehow "controlled" for MPRAGE data quality because there doesn't appear to be much of a relationship in the first place.
 
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: John Anderson 
Reply-To: "freesurfer@nmr.mgh.harvard.edu" 
Date: Monday, October 19, 2015 10:57 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Cc: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] MPRAGE SNR
 



Hi All,
Thank you very much for your comments!
 
Is it advisable to include SNR as a covariate when we use Qdec to run the final statistics on volumetrics, surfaces and cortical thickness?
Does it make sence ?
 
Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
  
  

Sent: Monday, October 19, 2015 at 11:48 AM
From: "Douglas Greve" 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] MPRAGE SNR
This has been my experience as well. Not much seems to predict which
scans will need to be edited.

On 10/19/15 10:23 AM, Harms, Michael wrote:
> Hi,
>
> FWIW, I've looked at a number of these measures in 500+ subjects from HCP
> data -- wm-anat-snr, pctsurfcon, G/W cnr, G/CSF cnr -- to see how they
> relate to each other, and whether they correlate with mean cortical
> thickness, white matter surface area, or number of SurfaceHoles (prior to
> topology correction).
>
> I didn't find much of note. e.g., the highest correlations were:
>
> r = -0.32 between mean cortical thickness and G/CSF cnr (from norm.mgz)
> r = -0.25 between white surface area and wmanatsnr
> r = -0.39 between SurfaceHoles and pctsurfcon (and same with G/W cnr from
> norm.mgz)
>
> Not surprisingly, pctsurfcon and G/W cnr are reasonably correlated (r =
> 0.49).
>
> G/W cnr from norm.mgz and orig.mgz are correlated at r=0.80.
> G/CSF cnr from norm.mgz and orig.mgz are correlated at r=0.97
>
> In another context (but smaller number of subjects), I've looked to see if
> these various snr, cnr measures from FS were related to manual quality
> ratings, and the relationship was rather weak.
>
> All-in-all, I haven't seen much that would indicate that these measures
> can be used as a sort of "automated" QC measure. Manual review of the
> structurals and FS results is still needed.
>
> That said, the structurals from the HCP 500 release were all of reasonably
> good quality to begin with. So, it is possible that these snr/cnr
> measures might be more informative in identifying truly awful scans in a
> clinical population 

Re: [Freesurfer] MPRAGE SNR

[Harms, Michael]

At best that would probably be harmless (if you have a decent number of subjects), but unless SNR, CNR actually relates to those measures in some fashion, you aren't really accomplishing anything by including it as a covariate.  You certainly wouldn't
 be able to claim that including SNR as a covariate has somehow "controlled" for MPRAGE data quality because there doesn't appear to be much of a relationship in the first place.


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: John Anderson 
Reply-To: "freesurfer@nmr.mgh.harvard.edu" 
Date: Monday, October 19, 2015 10:57 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Cc: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] MPRAGE SNR






Hi All,
Thank you very much for your comments!
 
Is it advisable to include SNR as a covariate when we use Qdec to run the final statistics on volumetrics, surfaces and cortical thickness?
Does it make sence ?
 
Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
 
 

Sent: Monday, October 19, 2015 at 11:48 AM
From: "Douglas Greve" 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] MPRAGE SNR
This has been my experience as well. Not much seems to predict which
scans will need to be edited.

On 10/19/15 10:23 AM, Harms, Michael wrote:
> Hi,
>
> FWIW, I've looked at a number of these measures in 500+ subjects from HCP
> data -- wm-anat-snr, pctsurfcon, G/W cnr, G/CSF cnr -- to see how they
> relate to each other, and whether they correlate with mean cortical
> thickness, white matter surface area, or number of SurfaceHoles (prior to
> topology correction).
>
> I didn't find much of note. e.g., the highest correlations were:
>
> r = -0.32 between mean cortical thickness and G/CSF cnr (from norm.mgz)
> r = -0.25 between white surface area and wmanatsnr
> r = -0.39 between SurfaceHoles and pctsurfcon (and same with G/W cnr from
> norm.mgz)
>
> Not surprisingly, pctsurfcon and G/W cnr are reasonably correlated (r =
> 0.49).
>
> G/W cnr from norm.mgz and orig.mgz are correlated at r=0.80.
> G/CSF cnr from norm.mgz and orig.mgz are correlated at r=0.97
>
> In another context (but smaller number of subjects), I've looked to see if
> these various snr, cnr measures from FS were related to manual quality
> ratings, and the relationship was rather weak.
>
> All-in-all, I haven't seen much that would indicate that these measures
> can be used as a sort of "automated" QC measure. Manual review of the
> structurals and FS results is still needed.
>
> That said, the structurals from the HCP 500 release were all of reasonably
> good quality to begin with. So, it is possible that these snr/cnr
> measures might be more informative in identifying truly awful scans in a
> clinical population with a wider variability in MPRAGE scan quality.
>
> I'd certainly be interested in hearing from anyone if they have found that
> to be the case in their data.
>
> BTW: Average value for G/W cnr for the HCP 500 is 1.99 and 1.81 from
> orig.mgz and norm.mgz respectively.
> Average value for G/CSF cnr for the same is 0.78 and 0.79, respectively.
>
> 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 63110Email: mha...@wustl.edu
>
>
>
>
> On 10/19/15 8:09 AM, "Bruce Fischl"  wrote:
>
> probably similar, although maybe Doug can comment. You probably want to
> run
> it on the orig.mgz as the intensity normalization can artificially
> increase
> the SNR (which is kind of the point)
> Bruce
>
>
> On Mon, 19 Oct 2015, John
> Anderson wrote:
>
>> Hi Bruce,
>> Thanks a lot!! this is really great!
>> I ran the command as the following :
>>
>> mri_cnr subj_01/surf subj_01/mri/norm.mgz
>> processing MRI volume subj_01/mri/norm.mgz...
>> white = 97.2+-9.5, gray = 69.0+-16.1, csf = 47.8+-16.5
>> gray/white CNR = 2.291, gray/csf CNR = 0.848
>> lh CNR = 1.569
>> white = 97.2+-9.3, gray = 69.4+-15.9, csf = 48.6+-17.0
>> gray/white CNR = 2.278, gray/csf CNR = 0.798
>> rh CNR = 1.538
>> total CNR = 1.554
>>
>>
>> I noticed that the normal range for the SNR (15-20) when using the
>> command
>> "wm-anat-snr"
>>
>> What is the normal range for cnr generated by the binary "mri_cnr"?
>>
>>
>> Bests,
>> John 

Re: [Freesurfer] MPRAGE SNR

[John Anderson]

Thanks MH,

Let's say that we have 100 MPRAGEs and we want to include them in a cross sectional analysis.

Depending on your experience, do you recommend any criterion to (include/ exclude) these images  in the analysis? As I see visualizing the images alone is not enough to say that the quality of the image is fine. Also calculating the SNR, CNR want help a lot!

 

any suggestions?
 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

 
 

Sent: Monday, October 19, 2015 at 12:24 PM
From: "Harms, Michael" 
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] MPRAGE SNR




 

At best that would probably be harmless (if you have a decent number of subjects), but unless SNR, CNR actually relates to those measures in some fashion, you aren't really accomplishing anything by including it as a covariate.  You certainly wouldn't be able to claim that including SNR as a covariate has somehow "controlled" for MPRAGE data quality because there doesn't appear to be much of a relationship in the first place.

 

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: John Anderson 
Reply-To: "freesurfer@nmr.mgh.harvard.edu" 
Date: Monday, October 19, 2015 10:57 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Cc: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] MPRAGE SNR

 




Hi All,

Thank you very much for your comments!

 

Is it advisable to include SNR as a covariate when we use Qdec to run the final statistics on volumetrics, surfaces and cortical thickness?

Does it make sence ?

 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

  

  


Sent: Monday, October 19, 2015 at 11:48 AM
From: "Douglas Greve" 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] MPRAGE SNR

This has been my experience as well. Not much seems to predict which
scans will need to be edited.

On 10/19/15 10:23 AM, Harms, Michael wrote:
> Hi,
>
> FWIW, I've looked at a number of these measures in 500+ subjects from HCP
> data -- wm-anat-snr, pctsurfcon, G/W cnr, G/CSF cnr -- to see how they
> relate to each other, and whether they correlate with mean cortical
> thickness, white matter surface area, or number of SurfaceHoles (prior to
> topology correction).
>
> I didn't find much of note. e.g., the highest correlations were:
>
> r = -0.32 between mean cortical thickness and G/CSF cnr (from norm.mgz)
> r = -0.25 between white surface area and wmanatsnr
> r = -0.39 between SurfaceHoles and pctsurfcon (and same with G/W cnr from
> norm.mgz)
>
> Not surprisingly, pctsurfcon and G/W cnr are reasonably correlated (r =
> 0.49).
>
> G/W cnr from norm.mgz and orig.mgz are correlated at r=0.80.
> G/CSF cnr from norm.mgz and orig.mgz are correlated at r=0.97
>
> In another context (but smaller number of subjects), I've looked to see if
> these various snr, cnr measures from FS were related to manual quality
> ratings, and the relationship was rather weak.
>
> All-in-all, I haven't seen much that would indicate that these measures
> can be used as a sort of "automated" QC measure. Manual review of the
> structurals and FS results is still needed.
>
> That said, the structurals from the HCP 500 release were all of reasonably
> good quality to begin with. So, it is possible that these snr/cnr
> measures might be more informative in identifying truly awful scans in a
> clinical population with a wider variability in MPRAGE scan quality.
>
> I'd certainly be interested in hearing from anyone if they have found that
> to be the case in their data.
>
> BTW: Average value for G/W cnr for the HCP 500 is 1.99 and 1.81 from
> orig.mgz and norm.mgz respectively.
> Average value for G/CSF cnr for the same is 0.78 and 0.79, respectively.
>
> 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 63110Email: mha...@wustl.edu
>
>
>
>
> On 10/19/15 8:09 AM, "Bruce Fischl"  wrote:
>
> probably similar, although maybe Doug can comment. You probably want to
> run
> it on the orig.mgz as the