[Freesurfer] correction

[Oertel, Viola]

Dear Freesurfers, 
could you please give me detailed information about the Bonferroni or 
clusterwise correction we can do in Freesurfer? How much iterations? Is that 
cluster- oder voxelwise? Is there anywhere a detailed description about the 
correction options?
Best regards, 
Viola
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[Freesurfer] Correction

[Juergen Haenggi]

Dear Freesurfer users

In my former email, I meant that I can not change from bash to tcsh shell on
Mac OS X. Sorry!

Thanks
Regards 
Juergen

---
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Department of Neuropsychology
Institute of Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
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[Freesurfer] correction

[Jared Price]

Hi, this is Jared again at the Brigham.  Quick correction.  The error 
says "pbsubmit: Command not found." not "psubmit: Command not found."

Thanks
-Jared



Jared Price
Center for Neurological Imaging
Brigham and Women's Hospital
Harvard Medical School
1249 Boylston Street
Boston, MA 02115

617-525-6076
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[Freesurfer] FreeSurfer Correction

[Ghazal Kiani]

Hi,

We were wondering when viewing group data on the inflated brain using
FreeSurfer, if FreeSurfer applies any correction and how we c an control
the correction value?

Thanks,
Ghazal
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Re: [Freesurfer] correction

[Douglas N Greve]

Hi Viola,

there's some detailed info if you run
mri_glmfit-sim --help
mri_glmfit --help

mri_glmfit-sim runs mri_glmfit.

When you use mri_glmfit-sim with the --cache option, it uses simulations 
that are based on 10,000 iterations.

Here are some slides that give more detail
http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.groupanalysis.ppt

Here's the paper we reference
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/hayasaka.2003.ni.1014.clustersize.pdf

doug

Oertel, Viola wrote:
> Dear Freesurfers, 
> could you please give me detailed information about the Bonferroni or 
> clusterwise correction we can do in Freesurfer? How much iterations? Is that 
> cluster- oder voxelwise? Is there anywhere a detailed description about the 
> correction options?
> Best regards, 
> Viola
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>
>
>   

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gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422

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Re: [Freesurfer] FreeSurfer Correction

[Douglas N Greve]

I don't know what you mean. can you elaborate?

On 04/30/2015 06:41 PM, Ghazal Kiani wrote:
> Hi,
>
> We were wondering when viewing group data on the inflated brain using 
> FreeSurfer, if FreeSurfer applies any correction and how we c an 
> control the correction value?
>
> Thanks,
> Ghazal
>
>
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Fax: 617-726-7422

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Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] Correction: cerebellum volumes

[Rachel Steinhorn]

We'd like to obtain total cerebellar volumes.  There are errors within the
cerebellar segmentation as revealed in the aseg.mgz file.  Is there a
method Is there a method to manually edit the cerebellar segmentation?

Thank You,
Rachel Steinhorn
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[Freesurfer] correction for field dishomogeneity

[clelia pellicano]

Dear experts,

I was wondering how freesurfer corrects for field dishomogeneity.
As long as I know, it's automatically done by the software .
My concern is because a reviewer has made this comment (please find it
below):

"Authors used an old 3 T MRI without using the appropriate pipeline
provided by freesurfer to correct for field dysomogeneity"

We have run the standard pipeline provided to derive measures of cortical
thickness and deep grey matter nuclei volume (FreeSurfer version 5.3.0 ).

Here the MRI protocol used:
All participants were scanned on a 3-Tesla Philips Intera whole-body MRI
scanner. A T1-weighted three-dimensional magnetization-prepared rapid
acquisition gradient-echo (MPRAGE; time echo: 4.6 ms; time repetition:
9.7ms; field of view: 240 ms; voxel size= 1 x1 x 1 mm) was acquired.

Any clue about?

Thank you in advance.

BW

Clelia


.
Clelia Pellicano, MD
PhD Student in Clinical and Experimental Neurosciences and Psychiatry,
Department of Neuroscience, Mental Health and Sensory Organs, NESMOS,
Sapienza University
Via di Grottarossa 1035, 00189 Rome, Italy
phone +390633775579
fax +390633775900

Research Neurologist
Department of Clinical and Experimental Neurology
Santa Lucia Foundation IRCSS
Via Ardeatina 306, 00179, Rome, Italy
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[Freesurfer] correction for multiple comparisons

[Marie Schneider]

Dear FreeSurfer experts,

I have some questions about corrections for multiple comparisons in
FreeSurfer. I have two samples, one consisting of two groups and one
consisting of three groups.

I do the comparison with the sample of two groups in qdec. Correcting for
multiple comparisons, I get a significant result using FDR, but no
significant result using Monte Carlo simulation. How can that be?

I analyze the sample with the three groups by mri_glmfit. In your tutorial,
I only found how to correct for multiple comparisons with the Monte Carlo
simulation using the command line, but not how to correct with FDR using
the command line. Is there a possibility to do this? If not, how many
iterations are usual to use within the Monte Carlo simulation?

Any help is appreciated.

Thank you very much,

Marie
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[Freesurfer] Correction for Multiple Comparisons

[mdkrue...@uwalumni.com]

Hey all-

This may be a simple question to answer, but in an analysis looking at say
cortical thickness between Group 1 and Group 2 with say 3 continues
variables (age, anxiety, IQ) there would be a contrast matrix of 1 -1 0 0 0
. How does free surfer correctly remove the effects of the continues
variables?


-- 
Michael D. Kruepke
PhD - University of Illinois at Urbana-Champaign
BA - Psych - University of Wisconsin-Madison
mdkrue...@gmail.com
(262)-483-7449
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[Freesurfer] Correction for Multiple Comparisons

[mdkrue...@uwalumni.com]

Freesurfers-

When correcting for multiple comparisons using:


mri_glmfit-sim \
  --glmdir lh.gender_age.glmdir \
  --sim mc-z 5 4 mc-z.negative \
  --sim-sign neg --cwpvalthresh 0.4\
  --overwrite

What does the sign mean (ie - the neg, pos, abs). Also for the mc-z
simulation type do we no longer need to include the smoothness of our data
(FWMH)?

Michael D. Kruepke
PhD - University of Illinois at Urbana-Champaign
BA - Psych - University of Wisconsin-Madison
mdkrue...@gmail.com
(262)-483-7449
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[Freesurfer] Correction for multiple comparisons

[Yann Quidé]

External Email - Use Caution

Dear all,

Using Freesurfer 5.3, I would like to limit my whole-brain analyses to a mask I 
already defined (ie, small volume correction-like analysis).
To correct for multiple comparisons, I want to use the mri_glmfit-sim option. 
As I am looking within my own mask, I understand I need to run my own 
Monte-Carlo simulation. Would 10,000 permutations be sufficient?
Also, I am a bit confused on what is best practice when setting the cluster 
forming threshold. Should I use the mc-z=3 (that is p=0.001) or mc-z=1.3 (that 
is p=0.05)?
Here is an exemple of what I’m doing so far:

mri_glmfit-sim \
  --glmdir $STATS_DIR/lh.my_analysis.glmdir \
  --sim mc-z 1 3 mc-z.abs.3 \
  --sim-sign abs

Thanks for your time.

Yann

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[Freesurfer] correction for multiple comparisons

[Antonella Kis]

Hi Doug,

I would like to run the correction for multiple comparisons. I know glmfit-sim 
corrects for multiple comparisons. My question is: 


the corrections for multiple comparisons will be done while running 


mri_glmfit-sim \
--glmdir rh.age.glmdir \
--cache 2 neg \
--overwrite

or I need to add --cwpvalthresh .025 before --overwrite. I found on-line that  
setting a treshold = 2 means  p < 0.05 but adding --cwpvalthresh .025 will do 
the correction across 2 spaces: lh and rh: .025 = .05/2
Bonferroni Correction and will show only the clusters with p<.025. 
  

Is this right? So to run for multiple corrections in fact I will need to run: 


mri_glmfit-sim \
--glmdir rh.age.glmdir \
--cache 2 neg \
--cwpvalthresh .025
--overwrite

Please advise me.

Thank you for your time and help.
Antonella



From: Douglas N Greve 
To: Antonella Kis 
Cc: "freesurfer@nmr.mgh.harvard.edu" 
Sent: Monday, August 22, 2011 2:28 PM
Subject: Re: [Freesurfer] GLM or Qdec ?



Antonella Kis wrote:
> Dear FS experts,
>
> I finished running the GLM and I wonder what is the best way to 
> further analyse my data in order to see if there is any relation 
> between age (at seizure onset) and cortical thickness for my  patients 
> versus control group.
>
>
> 1).  Why when I overlay the sig.mgh in tksurfer lh inflated, I get 
> more clusters than the number of clusters obtained from mri_glmfit-sim?
When you look at it in tksurfer, you are looking at uncorrected data. 
glmfit-sim corrects for multiple comparisons. Some of the clusters don't 
survive.
>
> 2). What sig.mgh represents?
-log10(p)
>
> 3) What's the real significance of a  cluster (how a cluster is formed)?
It is based on the likelihood of getting a cluster of that size by 
chance given the search space (cortical surface area), smoothness 
(FWHM), and cluster-forming threshold (eg, p<.05).
>
> 4). Why my thickness value in clusters (eg cluster no. 1 which 
> coresponds to the posteriorcingulate) for subject no.1 is different 
> that the thickness value obtained for the same region in the 
> lh.aparc.stats while running recon-all?
>
> 5). After running the GLM should I use visualizing and plotting method 
> to further analyse my data  and load FSGD file 
> lh.gender_age.glmdir/y.fsgd?
>
> 6). Should  my ROI's be defined or be the same with my clusters?
I don't know what you mean by that.
>
> 7). What is the difference between GLM and Qdec? What method is the 
> best to analyse the relation between age  and cortical thickness for 
> my  patients versus control group?
They are the same statistically. They are just different ways to provide 
information about your design and contrasts. QDEC is graphical (point 
and click). mri_glmfit you create FSGD files and run it from the 
command-line. QDEC actually creates FSGD files and contrast files and 
runs mri_glmfit.
>
> 8). Why when analysing with Qdec I get more clusters? Are this 
> defining or representing the sig.mgh as in GLM?
They should give identical results when run in the same way. My guess is 
that you have created two different designs and so are getting different 
answers.
>
> 9). When using Qdec were I can find as an output of results  the 
> number of clusters and the cortical thickness value?
You'll have to run the correction for multiple comparisons (interface on 
the results page). This simply runs mri_glmfit-sim.

doug
>
>
> Thank you and have a great day!
> Antonella
>
>
>
> 
>
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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
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Re: [Freesurfer] correction for field dishomogeneity

[Bruce Fischl]

Hi Clelia

yes, we correct for field inhomogeneity. Presumably they mean the B1 
receive field, which is what is typically meant in structurals. If they 
mean B0, we don't typically correct (nor do most people for structural 
imaging - this is more of an issue for diffusion and functional MRI).

cheers
Bruce

On Fri, 3 Jul 2015, clelia 
pellicano wrote:

> Dear experts,
> 
> I was wondering how freesurfer corrects for field dishomogeneity.
> As long as I know, it's automatically done by the software .
> My concern is because a reviewer has made this comment (please find it
> below):
> 
> "Authors used an old 3 T MRI without using the appropriate pipeline provided
> by freesurfer to correct for field dysomogeneity"
> 
> We have run the standard pipeline provided to derive measures of cortical
> thickness and deep grey matter nuclei volume (FreeSurfer version 5.3.0 ).
> 
> Here the MRI protocol used:
> All participants were scanned on a 3-Tesla Philips Intera whole-body MRI
> scanner. A T1-weighted three-dimensional magnetization-prepared rapid
> acquisition gradient-echo (MPRAGE; time echo: 4.6 ms; time repetition:
> 9.7ms; field of view: 240 ms; voxel size= 1 x1 x 1 mm) was acquired.
> 
> Any clue about?
> 
> Thank you in advance.
> 
> BW
> 
> Clelia
> 
> 
> . Clelia Pellicano, MDPhD Student in Clinical and Experimental Neurosciences
> and Psychiatry,
> Department of Neuroscience, Mental Health and Sensory Organs, NESMOS,
> Sapienza University
> Via di Grottarossa 1035, 00189 Rome, Italy
> phone +390633775579
> fax +390633775900
> 
> Research Neurologist
> Department of Clinical and Experimental Neurology
> Santa Lucia Foundation IRCSS
> Via Ardeatina 306, 00179, Rome, Italy
> 
>
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Re: [Freesurfer] correction for field dishomogeneity

[clelia pellicano]

Hi Bruce,

thank you for your reply. Do you have any idea about what they could mean
saying "without using the appropriate pipeline provided by freesurfer"?
Thanks

BW

C
Il giorno 03/lug/2015 15:32, "Bruce Fischl"  ha
scritto:

> Hi Clelia
>
> yes, we correct for field inhomogeneity. Presumably they mean the B1
> receive field, which is what is typically meant in structurals. If they
> mean B0, we don't typically correct (nor do most people for structural
> imaging - this is more of an issue for diffusion and functional MRI).
>
> cheers
> Bruce
>
> On Fri, 3 Jul 2015, clelia
> pellicano wrote:
>
> > Dear experts,
> >
> > I was wondering how freesurfer corrects for field dishomogeneity.
> > As long as I know, it's automatically done by the software .
> > My concern is because a reviewer has made this comment (please find it
> > below):
> >
> > "Authors used an old 3 T MRI without using the appropriate pipeline
> provided
> > by freesurfer to correct for field dysomogeneity"
> >
> > We have run the standard pipeline provided to derive measures of cortical
> > thickness and deep grey matter nuclei volume (FreeSurfer version 5.3.0 ).
> >
> > Here the MRI protocol used:
> > All participants were scanned on a 3-Tesla Philips Intera whole-body MRI
> > scanner. A T1-weighted three-dimensional magnetization-prepared rapid
> > acquisition gradient-echo (MPRAGE; time echo: 4.6 ms; time repetition:
> > 9.7ms; field of view: 240 ms; voxel size= 1 x1 x 1 mm) was acquired.
> >
> > Any clue about?
> >
> > Thank you in advance.
> >
> > BW
> >
> > Clelia
> >
> >
> > . Clelia Pellicano, MDPhD Student in Clinical and Experimental
> Neurosciences
> > and Psychiatry,
> > Department of Neuroscience, Mental Health and Sensory Organs, NESMOS,
> > Sapienza University
> > Via di Grottarossa 1035, 00189 Rome, Italy
> > phone +390633775579
> > fax +390633775900
> >
> > Research Neurologist
> > Department of Clinical and Experimental Neurology
> > Santa Lucia Foundation IRCSS
> > Via Ardeatina 306, 00179, Rome, Italy
> >
> >
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>
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> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] correction for field dishomogeneity

[Bruce Fischl]

not sure. Did you use recon-all? If so, then you did use
"the appropriate pipeline provided by freesurfer"
On Fri, 3 Jul 
2015, clelia pellicano wrote:

> 
> Hi Bruce,
> 
> thank you for your reply. Do you have any idea about what they could mean
> saying "without using the appropriate pipeline provided by freesurfer"?
> Thanks
> 
> BW
> 
> C
> 
> Il giorno 03/lug/2015 15:32, "Bruce Fischl"  ha
> scritto:
>   Hi Clelia
>
>   yes, we correct for field inhomogeneity. Presumably they mean
>   the B1
>   receive field, which is what is typically meant in structurals.
>   If they
>   mean B0, we don't typically correct (nor do most people for
>   structural
>   imaging - this is more of an issue for diffusion and functional
>   MRI).
>
>   cheers
>   Bruce
>
>   On Fri, 3 Jul 2015, clelia
>   pellicano wrote:
>
>   > Dear experts,
>   >
>   > I was wondering how freesurfer corrects for field
>   dishomogeneity.
>   > As long as I know, it's automatically done by the software .
>   > My concern is because a reviewer has made this comment (please
>   find it
>   > below):
>   >
>   > "Authors used an old 3 T MRI without using the appropriate
>   pipeline provided
>   > by freesurfer to correct for field dysomogeneity"
>   >
>   > We have run the standard pipeline provided to derive measures
>   of cortical
>   > thickness and deep grey matter nuclei volume (FreeSurfer
>   version 5.3.0 ).
>   >
>   > Here the MRI protocol used:
>   > All participants were scanned on a 3-Tesla Philips Intera
>   whole-body MRI
>   > scanner. A T1-weighted three-dimensional
>   magnetization-prepared rapid
>   > acquisition gradient-echo (MPRAGE; time echo: 4.6 ms; time
>   repetition:
>   > 9.7ms; field of view: 240 ms; voxel size= 1 x1 x 1 mm) was
>   acquired.
>   >
>   > Any clue about?
>   >
>   > Thank you in advance.
>   >
>   > BW
>   >
>   > Clelia
>   >
>   >
>   > . Clelia Pellicano, MDPhD Student in Clinical and Experimental
>   Neurosciences
>   > and Psychiatry,
>   > Department of Neuroscience, Mental Health and Sensory Organs,
>   NESMOS,
>   > Sapienza University
>   > Via di Grottarossa 1035, 00189 Rome, Italy
>   > phone +390633775579
>   > fax +390633775900
>   >
>   > Research Neurologist
>   > Department of Clinical and Experimental Neurology
>   > Santa Lucia Foundation IRCSS
>   > Via Ardeatina 306, 00179, Rome, Italy
>   >
>   >
>   ___
>   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
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Re: [Freesurfer] correction for field dishomogeneity

[clelia pellicano]

I did it. Thank you very much.

C
Il giorno 03/lug/2015 18:51, "Bruce Fischl"  ha
scritto:

> not sure. Did you use recon-all? If so, then you did use
> "the appropriate pipeline provided by freesurfer"
> On Fri, 3 Jul
> 2015, clelia pellicano wrote:
>
> >
> > Hi Bruce,
> >
> > thank you for your reply. Do you have any idea about what they could mean
> > saying "without using the appropriate pipeline provided by freesurfer"?
> > Thanks
> >
> > BW
> >
> > C
> >
> > Il giorno 03/lug/2015 15:32, "Bruce Fischl" 
> ha
> > scritto:
> >   Hi Clelia
> >
> >   yes, we correct for field inhomogeneity. Presumably they mean
> >   the B1
> >   receive field, which is what is typically meant in structurals.
> >   If they
> >   mean B0, we don't typically correct (nor do most people for
> >   structural
> >   imaging - this is more of an issue for diffusion and functional
> >   MRI).
> >
> >   cheers
> >   Bruce
> >
> >   On Fri, 3 Jul 2015, clelia
> >   pellicano wrote:
> >
> >   > Dear experts,
> >   >
> >   > I was wondering how freesurfer corrects for field
> >   dishomogeneity.
> >   > As long as I know, it's automatically done by the software .
> >   > My concern is because a reviewer has made this comment (please
> >   find it
> >   > below):
> >   >
> >   > "Authors used an old 3 T MRI without using the appropriate
> >   pipeline provided
> >   > by freesurfer to correct for field dysomogeneity"
> >   >
> >   > We have run the standard pipeline provided to derive measures
> >   of cortical
> >   > thickness and deep grey matter nuclei volume (FreeSurfer
> >   version 5.3.0 ).
> >   >
> >   > Here the MRI protocol used:
> >   > All participants were scanned on a 3-Tesla Philips Intera
> >   whole-body MRI
> >   > scanner. A T1-weighted three-dimensional
> >   magnetization-prepared rapid
> >   > acquisition gradient-echo (MPRAGE; time echo: 4.6 ms; time
> >   repetition:
> >   > 9.7ms; field of view: 240 ms; voxel size= 1 x1 x 1 mm) was
> >   acquired.
> >   >
> >   > Any clue about?
> >   >
> >   > Thank you in advance.
> >   >
> >   > BW
> >   >
> >   > Clelia
> >   >
> >   >
> >   > . Clelia Pellicano, MDPhD Student in Clinical and Experimental
> >   Neurosciences
> >   > and Psychiatry,
> >   > Department of Neuroscience, Mental Health and Sensory Organs,
> >   NESMOS,
> >   > Sapienza University
> >   > Via di Grottarossa 1035, 00189 Rome, Italy
> >   > phone +390633775579
> >   > fax +390633775900
> >   >
> >   > Research Neurologist
> >   > Department of Clinical and Experimental Neurology
> >   > Santa Lucia Foundation IRCSS
> >   > Via Ardeatina 306, 00179, Rome, Italy
> >   >
> >   >
> >   ___
> >   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] correction for field dishomogeneity

[Falk Lüsebrink]

Hi Clelia,

I think the reviewer might refer to the -3T flag of recon-all which enables 
3T-specific NU intensity correction parameters and usage of a special atlas for 
Talairach alignment.

Best,
Falk

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von clelia pellicano
Gesendet: Freitag, 3. Juli 2015 18:55
An: Freesurfer support list
Betreff: Re: [Freesurfer] correction for field dishomogeneity


I did it. Thank you very much.

C
Il giorno 03/lug/2015 18:51, "Bruce Fischl" 
mailto:fis...@nmr.mgh.harvard.edu>> ha scritto:
not sure. Did you use recon-all? If so, then you did use
"the appropriate pipeline provided by freesurfer"
On Fri, 3 Jul
2015, clelia pellicano wrote:

>
> Hi Bruce,
>
> thank you for your reply. Do you have any idea about what they could mean
> saying "without using the appropriate pipeline provided by freesurfer"?
> Thanks
>
> BW
>
> C
>
> Il giorno 03/lug/2015 15:32, "Bruce Fischl" 
> mailto:fis...@nmr.mgh.harvard.edu>> ha
> scritto:
>   Hi Clelia
>
>   yes, we correct for field inhomogeneity. Presumably they mean
>   the B1
>   receive field, which is what is typically meant in structurals.
>   If they
>   mean B0, we don't typically correct (nor do most people for
>   structural
>   imaging - this is more of an issue for diffusion and functional
>   MRI).
>
>   cheers
>   Bruce
>
>   On Fri, 3 Jul 2015, clelia
>   pellicano wrote:
>
>   > Dear experts,
>   >
>   > I was wondering how freesurfer corrects for field
>   dishomogeneity.
>   > As long as I know, it's automatically done by the software .
>   > My concern is because a reviewer has made this comment (please
>   find it
>   > below):
>   >
>   > "Authors used an old 3 T MRI without using the appropriate
>   pipeline provided
>   > by freesurfer to correct for field dysomogeneity"
>   >
>   > We have run the standard pipeline provided to derive measures
>   of cortical
>   > thickness and deep grey matter nuclei volume (FreeSurfer
>   version 5.3.0 ).
>   >
>   > Here the MRI protocol used:
>   > All participants were scanned on a 3-Tesla Philips Intera
>   whole-body MRI
>   > scanner. A T1-weighted three-dimensional
>   magnetization-prepared rapid
>   > acquisition gradient-echo (MPRAGE; time echo: 4.6 ms; time
>   repetition:
>   > 9.7ms; field of view: 240 ms; voxel size= 1 x1 x 1 mm) was
>   acquired.
>   >
>   > Any clue about?
>   >
>   > Thank you in advance.
>   >
>   > BW
>   >
>   > Clelia
>   >
>   >
>   > . Clelia Pellicano, MDPhD Student in Clinical and Experimental
>   Neurosciences
>   > and Psychiatry,
>   > Department of Neuroscience, Mental Health and Sensory Organs,
>   NESMOS,
>   > Sapienza University
>   > Via di Grottarossa 1035, 00189 Rome, Italy
>   > phone +390633775579
>   > fax +390633775900
>   >
>   > Research Neurologist
>   > Department of Clinical and Experimental Neurology
>   > Santa Lucia Foundation IRCSS
>   > Via Ardeatina 306, 00179, Rome, Italy
>   >
>   >
>   ___
>   Freesurfer mailing list
>   Freesurfer@nmr.mgh.harvard.edu<mailto: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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[Freesurfer] Correction with white-matter-points

[Wrobel, Pawel]

Dear FreeSurfer Team!

We have a question concerning corrections with white-matter-points. 

We are currently working on a T1 data set. After performing 
Freesurfer-Segmentations several days ago, we corrected the intensity 
normalization in small regions (e.g. Gyrus temporalis superior) with WM-points, 
stricktly obeying the decription on the FreeSurfer-Website (wiki).
Afterwards We used the following command: recon-all -autorecon2-cp -autorecon3 
-subjid cp_before.
The results in 80 % of corrections (105 scans) became worse than the first 
segmentation. In some cases the pial surface "descends" and sticks to the white 
matter surface, leaving the gray matter untouched, as if FreeSurfer would not 
recognize it. In some other cases the WM border touches the brain surface, 
including gray matter in the white matter. Sometimes the pial or white matter 
surface makes little incisions or loops into another compartment.

We have been trying different approaches. We rerun the correction with an older 
FreeSurfer version (5.1.). We reinstalled the new version of FreeSurfer which 
we were using before (5.3). We tried it on different computers.

We will be very thankful for Your help!

Yours sincerely 

Pawel
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[Freesurfer] Correction with white-matter-points

[Wrobel, Pawel]

Dear FreeSurfer Team!

Last week I wrote about to the mailing list about problems occurring after the 
WM-point correction. Later I received a message in which You told me that You 
can help me if I upload the scan. Where and how can I do this?

Thank You for Your help!

Kind Regards

Pawel W.
Psychiatry and Neuroimaging Laboratory (PNL)
Brigham and Women's Hospital
  

 
 Message: 6
 Date: Tue, 14 Jul 2015 11:33:57 -0400 (EDT)
 From: Bruce Fischl 
 Subject: Re: [Freesurfer] Correction with white-matter-points
 To: Freesurfer support list 
 Message-ID:
 
 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
 
 Hi Pawel
 
 does this happen in both versions? If so, upload a bad subject and we 
 will take a look
 
 cheers
 Bruce
 On Tue, 14 Jul 2015, Wrobel, Pawel wrote:
 
 > Dear FreeSurfer Team!
 >
 > We have a question concerning corrections with white-matter-points.
 >
 > We are currently working on a T1 data set. After performing 
 > Freesurfer-Segmentations several days ago, we corrected the intensity 
 > normalization in small regions (e.g. Gyrus temporalis superior) with 
 > WM-points, stricktly obeying the decription on the FreeSurfer-Website (wiki).
 > Afterwards We used the following command: recon-all -autorecon2-cp 
 > -autorecon3 -subjid cp_before.
 > The results in 80 % of corrections (105 scans) became worse than the first 
 > segmentation. In some cases the pial surface "descends" and sticks to the 
 > white matter surface, leaving the gray matter untouched, as if FreeSurfer 
 > would not recognize it. In some other cases the WM border touches the brain 
 > surface, including gray matter in the white matter. Sometimes the pial or 
 > white matter surface makes little incisions or loops into another 
 > compartment.
 >
 > We have been trying different approaches. We rerun the correction with an 
 > older FreeSurfer version (5.1.). We reinstalled the new version of 
 > FreeSurfer which we were using before (5.3). We tried it on different 
 > computers.
 >
 > We will be very thankful for Your help!
 >
 > Yours sincerely
 >
 > Pawel
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[Freesurfer] Correction for multiple comparisons question

[Fotiadis, Panagiotis]

Hi Freesurfer experts,

I was wondering about three things concerning the use of the mri_glmfit-sim 
command:

1) I tried running it with the --2spaces flag in order to Bonferroni correct 
over the two hemispheres but it tells me that the specific flag is not 
recognized. Is there another way to correct over the two hemispheres?

2) I set the cluster-based threshold to 0.999 in order to see all of the 
clusters and varied the voxel-based threshold in order to see the differences 
that it would make on the results. Specifically, i set it to be 1.3, 2.0, 2.3, 
and 3.0. Between the four different occurring cluster summaries, there was only 
one common cluster that appeared in all four summaries. As expected, the number 
of voxels of the specific cluster was decreasing as its voxel-wise threshold 
was increasing. 

a)  However, the reported cluster-wise threshold  varied between 0.05 to 0.96 
in those four cases. Does this sound reasonable? Shouldn't the cluster wise p 
values of the same cluster-between the four cases-be less dispersed?

b)  If there is a cluster reported in only one of the four summaries (i.e. when 
the voxel-based threshold is 1.3) that say has a cluster-wise p value of 0.03, 
do I consider that significant or not, since it does not appear in any other 
summary with such a low cluster wise p value and since the only published p 
value is the cluster wise one?

Thank you in advance for your time,
Panagiotis Fotiadis
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[Freesurfer] Correction for multiple comparisons error

[Fotiadis, Panagiotis]

Hi!

I have been running the mri_glmfit-sim command to do the correction for 
multiple comparisons for my group analysis and for some voxel-based thresholds 
(not all) there is an error that comes up when reading the colortable from the 
annotation file:

reading colortable from annotation file...
colortable with 35 entries read (originally 
/space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt)
*** glibc detected *** mri_surfcluster: malloc(): memory corruption: 
0x06e61230 ***
*** glibc detected *** mri_surfcluster: malloc(): memory corruption: 
0x06e61230 ***

and then it gets stuck. Do you happen to know what might be causing this issue?

Thank you for your time,
Panos
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Re: [Freesurfer] correction for multiple comparisons

[Douglas N Greve]

they are two different correction schemes. If they gave the same answer, 
then it would not make sense to have both. the monte carlo tries to 
compute the probability of a cluster of the given size under the null 
hypothesis. FDR controls for the number of false positives relative to 
the total number of positives under the assumption that if any 5% of 
your positives are false, then you would not change your conclusion.

For monte carlo, we generally use 1 iterations. If you are using the 
whole hemisphere, then you can used the cached tables. See the 
"command-line" tutorial.

doug

On 06/08/2012 08:03 AM, Marie Schneider wrote:
> Dear FreeSurfer experts,
>
> I have some questions about corrections for multiple comparisons in 
> FreeSurfer. I have two samples, one consisting of two groups and one 
> consisting of three groups.
>
> I do the comparison with the sample of two groups in qdec. Correcting 
> for multiple comparisons, I get a significant result using FDR, but no 
> significant result using Monte Carlo simulation. How can that be?
>
> I analyze the sample with the three groups by mri_glmfit. In your 
> tutorial, I only found how to correct for multiple comparisons with 
> the Monte Carlo simulation using the command line, but not how to 
> correct with FDR using the command line. Is there a possibility to do 
> this? If not, how many iterations are usual to use within the Monte 
> Carlo simulation?
>
> Any help is appreciated.
>
> Thank you very much,
>
> Marie
>
>
> ___
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-- 
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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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] correction for multiple comparisons

[Marie Schneider]

Thank you very much for your answer.

Are 10 000 iterations also used when I am running a Monte Carlo simulation
in qdec?

Thanks, Marie

2012/6/9 Douglas N Greve 

> they are two different correction schemes. If they gave the same answer,
> then it would not make sense to have both. the monte carlo tries to
> compute the probability of a cluster of the given size under the null
> hypothesis. FDR controls for the number of false positives relative to
> the total number of positives under the assumption that if any 5% of
> your positives are false, then you would not change your conclusion.
>
> For monte carlo, we generally use 1 iterations. If you are using the
> whole hemisphere, then you can used the cached tables. See the
> "command-line" tutorial.
>
> doug
>
> On 06/08/2012 08:03 AM, Marie Schneider wrote:
> > Dear FreeSurfer experts,
> >
> > I have some questions about corrections for multiple comparisons in
> > FreeSurfer. I have two samples, one consisting of two groups and one
> > consisting of three groups.
> >
> > I do the comparison with the sample of two groups in qdec. Correcting
> > for multiple comparisons, I get a significant result using FDR, but no
> > significant result using Monte Carlo simulation. How can that be?
> >
> > I analyze the sample with the three groups by mri_glmfit. In your
> > tutorial, I only found how to correct for multiple comparisons with
> > the Monte Carlo simulation using the command line, but not how to
> > correct with FDR using the command line. Is there a possibility to do
> > this? If not, how many iterations are usual to use within the Monte
> > Carlo simulation?
> >
> > Any help is appreciated.
> >
> > Thank you very much,
> >
> > Marie
> >
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
> ___
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>
>
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> 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.
>
>
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Re: [Freesurfer] correction for multiple comparisons

[Douglas N Greve]

yes, though I would probably do it outside of qdec as it can take a 
while (hours or days)

On 06/12/2012 08:03 AM, Marie Schneider wrote:
> Thank you very much for your answer.
>
> Are 10 000 iterations also used when I am running a Monte Carlo 
> simulation in qdec?
>
> Thanks, Marie
>
> 2012/6/9 Douglas N Greve  >
>
> they are two different correction schemes. If they gave the same
> answer,
> then it would not make sense to have both. the monte carlo tries to
> compute the probability of a cluster of the given size under the null
> hypothesis. FDR controls for the number of false positives relative to
> the total number of positives under the assumption that if any 5% of
> your positives are false, then you would not change your conclusion.
>
> For monte carlo, we generally use 1 iterations. If you are
> using the
> whole hemisphere, then you can used the cached tables. See the
> "command-line" tutorial.
>
> doug
>
> On 06/08/2012 08:03 AM, Marie Schneider wrote:
> > Dear FreeSurfer experts,
> >
> > I have some questions about corrections for multiple comparisons in
> > FreeSurfer. I have two samples, one consisting of two groups and one
> > consisting of three groups.
> >
> > I do the comparison with the sample of two groups in qdec.
> Correcting
> > for multiple comparisons, I get a significant result using FDR,
> but no
> > significant result using Monte Carlo simulation. How can that be?
> >
> > I analyze the sample with the three groups by mri_glmfit. In your
> > tutorial, I only found how to correct for multiple comparisons with
> > the Monte Carlo simulation using the command line, but not how to
> > correct with FDR using the command line. Is there a possibility
> to do
> > this? If not, how many iterations are usual to use within the Monte
> > Carlo simulation?
> >
> > Any help is appreciated.
> >
> > Thank you very much,
> >
> > Marie
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
>
> ___
> 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.
>
>

-- 
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
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Re: [Freesurfer] Correction for Multiple Comparisons

[Douglas N Greve]

It includes them in the model as regressors, so, for example, the Group 
1 mean (beta) is computed simultaneously with the slope. Think of a 
bunch of dots that form a line. You fit it to y = x*m + y0. y0 is the 
intercept (ie, expected y at x=0). In your case you have two y0's (one 
for each group) and three m's (one for each covariate). By using [1 -1 0 
0 0], you are specifying that the intercepts be compared.
doug

On 06/12/2012 02:37 PM, mdkrue...@uwalumni.com wrote:
> Hey all-
>
> This may be a simple question to answer, but in an analysis looking at 
> say cortical thickness between Group 1 and Group 2 with say 3 
> continues variables (age, anxiety, IQ) there would be a contrast 
> matrix of 1 -1 0 0 0 . How does free surfer correctly remove the 
> effects of the continues variables?
>
> -- 
> Michael D. Kruepke
> PhD - University of Illinois at Urbana-Champaign
> BA - Psych - University of Wisconsin-Madison
> mdkrue...@gmail.com 
> (262)-483-7449
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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
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Re: [Freesurfer] Correction for Multiple Comparisons

[Douglas N Greve]

If you run it with --help, you will see this. let me know if this is not 
clear.

6. Select the threshold sign (--sim-sign). This is the sign of the
threshold used to create the clusters for cluster-wise correction
of multiple comparisons. Options are abs (unsigned), pos
(positive), and neg (negative). If you have an a priori hypothesis
(eg, group1 > group2), then choose positive. If you don not know
the sign, then use abs. Choosing a sign will yield stronger results
(ie, smaller p-values), but you will lose the other sign.

The FWHM is obtained from the data (glmdir/fwhm.dat)

doug



On 06/13/2012 02:04 PM, mdkrue...@uwalumni.com wrote:
> Freesurfers-
>
> When correcting for multiple comparisons using:
> mri_glmfit-sim \
>--glmdir lh.gender_age.glmdir \
>--sim mc-z 5 4 mc-z.negative \
>--sim-sign neg --cwpvalthresh 0.4\
>--overwrite
> What does the sign mean (ie - the neg, pos, abs). Also for the mc-z 
> simulation type do we no longer need to include the smoothness of our 
> data (FWMH)?
>
> Michael D. Kruepke
> PhD - University of Illinois at Urbana-Champaign
> BA - Psych - University of Wisconsin-Madison
> mdkrue...@gmail.com 
> (262)-483-7449
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] Correction for Multiple Comparisons

[mdkrue...@uwalumni.com]

doug-

thanks for all the help on this. another quick question:

when choosing the simulation type does the ending have to match the sim
sign? for instance i see examples with

--sim mc-z 1 3 mc-z.pos.3 --sim sign pos

or

--sim mc-z 1 3 mc-z.neg.3 --sim sign neg

I guess what i am asking is what does the first sign (in the mc-z.(SIGN).3
mean?

michael

On Wed, Jun 13, 2012 at 2:26 PM, Douglas N Greve
wrote:

> If you run it with --help, you will see this. let me know if this is not
> clear.
>
> 6. Select the threshold sign (--sim-sign). This is the sign of the
>threshold used to create the clusters for cluster-wise correction
>of multiple comparisons. Options are abs (unsigned), pos
>(positive), and neg (negative). If you have an a priori hypothesis
>(eg, group1 > group2), then choose positive. If you don not know
>the sign, then use abs. Choosing a sign will yield stronger results
>(ie, smaller p-values), but you will lose the other sign.
>
> The FWHM is obtained from the data (glmdir/fwhm.dat)
>
> doug
>
>
>
> On 06/13/2012 02:04 PM, mdkrue...@uwalumni.com wrote:
> > Freesurfers-
> >
> > When correcting for multiple comparisons using:
> > mri_glmfit-sim \
> >--glmdir lh.gender_age.glmdir \
> >--sim mc-z 5 4 mc-z.negative \
> >--sim-sign neg --cwpvalthresh 0.4\
> >--overwrite
> > What does the sign mean (ie - the neg, pos, abs). Also for the mc-z
> > simulation type do we no longer need to include the smoothness of our
> > data (FWMH)?
> >
> > Michael D. Kruepke
> > PhD - University of Illinois at Urbana-Champaign
> > BA - Psych - University of Wisconsin-Madison
> > mdkrue...@gmail.com 
> > (262)-483-7449
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
> ___
> 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.
>
>


-- 
Michael D. Kruepke
PhD - University of Illinois at Urbana-Champaign
BA - Psych - University of Wisconsin-Madison
mdkrue...@gmail.com
(262)-483-7449
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Re: [Freesurfer] correction for multiple comparisons

[Marie Schneider]

Thanks very much for your help and your advice.

Are there any publications which describe the principles of the Monte Carlo
simulation when used for correction of multiple comparisons?

-Marie




2012/6/12 Douglas N Greve 

> yes, though I would probably do it outside of qdec as it can take a while
> (hours or days)
>
>
> On 06/12/2012 08:03 AM, Marie Schneider wrote:
>
>> Thank you very much for your answer.
>>
>> Are 10 000 iterations also used when I am running a Monte Carlo
>> simulation in qdec?
>>
>> Thanks, Marie
>>
>> 2012/6/9 Douglas N Greve > gr...@nmr.mgh.harvard.**edu >>
>>
>>
>>they are two different correction schemes. If they gave the same
>>answer,
>>then it would not make sense to have both. the monte carlo tries to
>>compute the probability of a cluster of the given size under the null
>>hypothesis. FDR controls for the number of false positives relative to
>>the total number of positives under the assumption that if any 5% of
>>your positives are false, then you would not change your conclusion.
>>
>>For monte carlo, we generally use 1 iterations. If you are
>>using the
>>whole hemisphere, then you can used the cached tables. See the
>>"command-line" tutorial.
>>
>>doug
>>
>>On 06/08/2012 08:03 AM, Marie Schneider wrote:
>>> Dear FreeSurfer experts,
>>>
>>> I have some questions about corrections for multiple comparisons in
>>> FreeSurfer. I have two samples, one consisting of two groups and one
>>> consisting of three groups.
>>>
>>> I do the comparison with the sample of two groups in qdec.
>>Correcting
>>> for multiple comparisons, I get a significant result using FDR,
>>but no
>>> significant result using Monte Carlo simulation. How can that be?
>>>
>>> I analyze the sample with the three groups by mri_glmfit. In your
>>> tutorial, I only found how to correct for multiple comparisons with
>>> the Monte Carlo simulation using the command line, but not how to
>>> correct with FDR using the command line. Is there a possibility
>>to do
>>> this? If not, how many iterations are usual to use within the Monte
>>> Carlo simulation?
>>>
>>> Any help is appreciated.
>>>
>>> Thank you very much,
>>>
>>> Marie
>>>
>>>
>>> __**_
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> >
>>
>>> 
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer
>>
>>--
>>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: 
>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
>>
>> 
>> >
>>
>>__**_
>>Freesurfer mailing list
>>Freesurfer@nmr.mgh.harvard.edu > 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.
>>
>>
>>
> --
> 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: 
> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
>
>
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Re: [Freesurfer] correction for multiple comparisons

[Douglas N Greve]

Here are a couple
Hayasaka 2003 Neuroimage
Hagler 2006 Neuroimage
The Hagler reg is specifically for surfaces
doug


On 06/14/2012 03:13 AM, Marie Schneider wrote:
> Thanks very much for your help and your advice.
>
> Are there any publications which describe the principles of the Monte 
> Carlo simulation when used for correction of multiple comparisons?
>
> -Marie
>
>
>
>
> 2012/6/12 Douglas N Greve  >
>
> yes, though I would probably do it outside of qdec as it can take
> a while (hours or days)
>
>
> On 06/12/2012 08:03 AM, Marie Schneider wrote:
>
> Thank you very much for your answer.
>
> Are 10 000 iterations also used when I am running a Monte
> Carlo simulation in qdec?
>
> Thanks, Marie
>
> 2012/6/9 Douglas N Greve  
>  >>
>
>
>they are two different correction schemes. If they gave the
> same
>answer,
>then it would not make sense to have both. the monte carlo
> tries to
>compute the probability of a cluster of the given size
> under the null
>hypothesis. FDR controls for the number of false positives
> relative to
>the total number of positives under the assumption that if
> any 5% of
>your positives are false, then you would not change your
> conclusion.
>
>For monte carlo, we generally use 1 iterations. If you are
>using the
>whole hemisphere, then you can used the cached tables. See the
>"command-line" tutorial.
>
>doug
>
>On 06/08/2012 08:03 AM, Marie Schneider wrote:
> > Dear FreeSurfer experts,
> >
> > I have some questions about corrections for multiple
> comparisons in
> > FreeSurfer. I have two samples, one consisting of two groups
> and one
> > consisting of three groups.
> >
> > I do the comparison with the sample of two groups in qdec.
>Correcting
> > for multiple comparisons, I get a significant result using FDR,
>but no
> > significant result using Monte Carlo simulation. How can
> that be?
> >
> > I analyze the sample with the three groups by mri_glmfit. In
> your
> > tutorial, I only found how to correct for multiple
> comparisons with
> > the Monte Carlo simulation using the command line, but not
> how to
> > correct with FDR using the command line. Is there a possibility
>to do
> > this? If not, how many iterations are usual to use within
> the Monte
> > Carlo simulation?
> >
> > Any help is appreciated.
> >
> > Thank you very much,
> >
> > Marie
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
>  >
>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>--
>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:
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> 
>
>___
>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 cont

Re: [Freesurfer] Correction for multiple comparisons

[Douglas Greve]

On 6/6/18 7:14 AM, Yann Quidé wrote:
>  External Email - Use Caution
>
> Dear all,
>
> Using Freesurfer 5.3, I would like to limit my whole-brain analyses to a mask 
> I already defined (ie, small volume correction-like analysis).
> To correct for multiple comparisons, I want to use the mri_glmfit-sim option. 
> As I am looking within my own mask, I understand I need to run my own 
> Monte-Carlo simulation. Would 10,000 permutations be sufficient?
Yes, you can probably get away with 1000 even.
> Also, I am a bit confused on what is best practice when setting the cluster 
> forming threshold. Should I use the mc-z=3 (that is p=0.001) or mc-z=1.3 
> (that is p=0.05)?
For mc simulation, you probably need 3 (ie, p<.001). If you need to use 
a lower threshold because none of your voxels survive, then consider 
using permutation instead of mcz.

> Here is an exemple of what I’m doing so far:
>
> mri_glmfit-sim \
>--glmdir $STATS_DIR/lh.my_analysis.glmdir \
>--sim mc-z 1 3 mc-z.abs.3 \
>--sim-sign abs
>
> Thanks for your time.
>
> Yann
>
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Re: [Freesurfer] correction for multiple comparisons

[Douglas N Greve]

Yes, that is correct, you should use .025 if you are correcting for both 
hemispheres.
doug

Antonella Kis wrote:
>
> Hi Doug,
>
> I would like to run the correction for multiple comparisons. I know 
> glmfit-sim corrects for multiple comparisons. My question is:
>
> the corrections for multiple comparisons will be done while running
>
> mri_glmfit-sim \
> --glmdir rh.age.glmdir \
> --cache 2 neg \
> --overwrite
>
> or I need to add --cwpvalthresh .025 before --overwrite. I found 
> on-line that  setting a treshold = 2 means  p < 0.05 but adding 
> --cwpvalthresh .025 will do the correction across 2 spaces: lh and rh: 
> .025 = .05/2
> Bonferroni Correction and will show only the clusters with p<.025.
>  
> Is this right? So to run for multiple corrections in fact I will need 
> to run:
>
> mri_glmfit-sim \
> --glmdir rh.age.glmdir \
> --cache 2 neg \
> --cwpvalthresh .025
> --overwrite
>
> Please advise me.
>
> Thank you for your time and help.
> Antonella
> 
> *From:* Douglas N Greve 
> *To:* Antonella Kis 
> *Cc:* "freesurfer@nmr.mgh.harvard.edu" 
> *Sent:* Monday, August 22, 2011 2:28 PM
> *Subject:* Re: [Freesurfer] GLM or Qdec ?
>
>
>
> Antonella Kis wrote:
> > Dear FS experts,
> >
> > I finished running the GLM and I wonder what is the best way to
> > further analyse my data in order to see if there is any relation
> > between age (at seizure onset) and cortical thickness for my  patients
> > versus control group.
> >
> >
> > 1).  Why when I overlay the sig.mgh in tksurfer lh inflated, I get
> > more clusters than the number of clusters obtained from mri_glmfit-sim?
> When you look at it in tksurfer, you are looking at uncorrected data.
> glmfit-sim corrects for multiple comparisons. Some of the clusters don't
> survive.
> >
> > 2). What sig.mgh represents?
> -log10(p)
> >
> > 3) What's the real significance of a  cluster (how a cluster is formed)?
> It is based on the likelihood of getting a cluster of that size by
> chance given the search space (cortical surface area), smoothness
> (FWHM), and cluster-forming threshold (eg, p<.05).
> >
> > 4). Why my thickness value in clusters (eg cluster no. 1 which
> > coresponds to the posteriorcingulate) for subject no.1 is different
> > that the thickness value obtained for the same region in the
> > lh.aparc.stats while running recon-all?
> >
> > 5). After running the GLM should I use visualizing and plotting method
> > to further analyse my data  and load FSGD file
> > lh.gender_age.glmdir/y.fsgd?
> >
> > 6). Should  my ROI's be defined or be the same with my clusters?
> I don't know what you mean by that.
> >
> > 7). What is the difference between GLM and Qdec? What method is the
> > best to analyse the relation between age  and cortical thickness for
> > my  patients versus control group?
> They are the same statistically. They are just different ways to provide
> information about your design and contrasts. QDEC is graphical (point
> and click). mri_glmfit you create FSGD files and run it from the
> command-line. QDEC actually creates FSGD files and contrast files and
> runs mri_glmfit.
> >
> > 8). Why when analysing with Qdec I get more clusters? Are this
> > defining or representing the sig.mgh as in GLM?
> They should give identical results when run in the same way. My guess is
> that you have created two different designs and so are getting different
> answers.
> >
> > 9). When using Qdec were I can find as an output of results  the
> > number of clusters and the cortical thickness value?
> You'll have to run the correction for multiple comparisons (interface on
> the results page). This simply runs mri_glmfit-sim.
>
> doug
> >
> >
> > Thank you and have a great day!
> > Antonella
> >
> >
> >
> > 
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> -- 
> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
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>
>
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> e-mail
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Re: [Freesurfer] correction for multiple comparisons

[Antonella Kis]

Good morning Doug,

Thank you for your help.
I followed your advise and unfortunately I do not understand why after
adding the threshold 2 cwpvalthresh .025  in order to do the correction across 
lh and rh I still get in my clusters summary and clusters with  cwp>.01 as well 
as cwp> .025.
This is what I was running:

mri_glmfit-sim \
--glmdir rh.age.glmdir \
--cache 2 neg \
--cwpvalthresh .025 \
--overwrite 


And this is my output: 

  
  
  
  
  
 
  
  
  
  
  
  
 

  
  
  
  
  
   
# ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 
 
1 -6.24 104279 2004.41 6.4 -83.6 34.4 0.0001 0 0 3539 cuneus 
 
2 -5.71 56656 2923.03 24.4 25.4 37.1 0.0001 0 0 5020 superiorfrontal 
 
3 -4.89 156133 1826.82 5.1 -29.7 38.6 0.0001 0 0 4324 posteriorcingulate 
 
4 -4.57 117278 1917.42 43.2 43.4 -8.2 0.0001 0 0 3393 parsorbitalis 
 
5 -4.32 134603 910.13 10.5 45.7 -9.2 0.0009 0 0 1597 medialorbitofrontal 
 
6 -4.01 47845 1018.06 38.9 -73.9 34.6 0.0003 0 0 1802 inferiorparietal 
 
7 -3.97 12268 580.81 14.2 -51 63.3 0.0132 0.01 0.01 1415 superiorparietal 
 
8 -3.78 54798 871.02 53 -39.7 -5.1 0.0010 0 0 1969 bankssts 
 
9 -3.78 21941 555.51 45.8 -28.2 6.4 0.0175 0.02 0.02 1369 superiortemporal 
 
10 -2.91 86118 884.25 10.1 -98.9 11.7 0.0010 0 0 1089 lateraloccipital 
 
11 -2.86 13271 674.26 21.5 -65.4 -6.1 0.0056 0 0.01 722 lingual 
  
  
  
  
  
  
 
  
 
 
 
 
 
 
  
  
  
  
  
  
 
  
  
  
  
  
  
 
  
  
  
  
  
  
 
  
  
  
  
  
  
 
Is this right?

Please advise.

Thank you.
Antonella



From: Douglas N Greve 
To: Antonella Kis 
Cc: "freesurfer@nmr.mgh.harvard.edu" 
Sent: Tuesday, August 23, 2011 4:33 PM
Subject: Re: [Freesurfer] correction for multiple comparisons

Yes, that is correct, you should use .025 if you are correcting for both 
hemispheres.
doug

Antonella Kis wrote:
>
> Hi Doug,
>
> I would like to run the correction for multiple comparisons. I know 
> glmfit-sim corrects for multiple comparisons. My question is:
>
> the corrections for multiple comparisons will be done while running
>
> mri_glmfit-sim \
> --glmdir rh.age.glmdir \
> --cache 2 neg \
> --overwrite
>
> or I need to add --cwpvalthresh .025 before --overwrite. I found 
> on-line that  setting a treshold = 2 means  p < 0.05 but adding 
> --cwpvalthresh .025 will do the correction across 2 spaces: lh and rh: 
> .025 = .05/2
> Bonferroni Correction and will show only the clusters with p<.025.
>  
> Is this right? So to run for multiple corrections in fact I will need 
> to run:
>
> mri_glmfit-sim \
> --glmdir rh.age.glmdir \
> --cache 2 neg \
> --cwpvalthresh .025
> --overwrite
>
> Please advise me.
>
> Thank you for your time and help.
> Antonella
> 
> *From:* Douglas N Greve 
> *To:* Antonella Kis 
> *Cc:* "freesurfer@nmr.mgh.harvard.edu" 
> *Sent:* Monday, August 22, 2011 2:28 PM
> *Subject:* Re: [Freesurfer] GLM or Qdec ?
>
>
>
> Antonella Kis wrote:
> > Dear FS experts,
> >
> > I finished running the GLM and I wonder what is the best way to
> > further analyse my data in order to see if there is any relation
> > between age (at seizure onset) and cortical thickness for my  patients
> > versus control group.
> >
> >
> > 1).  Why when I overlay the sig.mgh in tksurfer lh inflated, I get
> > more clusters than the number of clusters obtained from mri_glmfit-sim?
> When you look at it in tksurfer, you are looking at uncorrected data.
> glmfit-sim corrects for multiple comparisons. Some of the clusters don't
> survive.
> >
> > 2). What sig.mgh represents?
> -log10(p)
> >
> > 3) What's the real significance of a  cluster (how a cluster is formed)?
> It is based on the likelihood of getting a cluster of that size by
> chance given the search space (cortical surface area), smoothness
> (FWHM), and cluster-forming threshold (eg, p<.05).
> >
> > 4). Why my thickness value in clusters (eg cluster no. 1 which
> > coresponds to the posteriorcingulate) for subject no.1 is different
> > that the thickness value obtained for the same region in the
> > lh.aparc.stats while running recon-all?
> >
> > 5). After running the GLM should I use visualizing and plotting method
> > to further analyse my data  and load FSGD file
> > lh.gender_age.glmdir/y.fsgd?
> >
> > 6). Should  my ROI's be defined or be the same with my clusters?
> I don't know what you mean by that.
> >
> > 7). What is the difference between GLM and Qdec? What method is the
> > best to analyse the relation between age  and cortical thickness for
> > my  patients versus control gro

Re: [Freesurfer] correction of pial surface...

[Allison Stevens]

It looks like there might be some wm that is not labeled as wm. If you fix 
this first (by adding wm to the wm.mgz or adding control points if it is 
an intensity problem), that should fix the pial surface.

-- 

On Wed, 24 Feb 2010, Gonzalo Rojas wrote:

> Hi:
>
>   How can I correct the pial surface in the image that I am sending attached 
> ?...
>
>   Sincerely,
>
>
>
>
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Re: [Freesurfer] correction of pial surface...

[Allison Stevens]

Gonzalo,
It's difficult to tell on just this one slice and I'm more used to viewing 
scans in the coronal plane. If you turn the aseg.mgz on, is that part of 
the subcortical gm? If not and you believe it to be cortical gm, let me 
know and we'll take a look.

Allison

--

On Wed, 24 Feb 2010, Gonzalo Rojas wrote:


Hi:

 Thanks you very much for your answer...

 I think that wm not labeled as wm is the problem shown in arrow 1... but 
how can I  fix the problem of arrow 2 ?...


 Sincerely,


Gonzalo Rojas Costa
Advanced Medical Image Processing Laboratory
Department of Radiology
Las Condes Clinic
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl

El 24-02-2010 14:55, Allison Stevens escribió:

 It looks like there might be some wm that is not labeled as wm. If you
 fix this first (by adding wm to the wm.mgz or adding control points if
 it is an intensity problem), that should fix the pial surface.



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Re: [Freesurfer] Correction with white-matter-points

[Bruce Fischl]

Hi Pawel

does this happen in both versions? If so, upload a bad subject and we 
will take a look

cheers
Bruce
On Tue, 14 Jul 2015, Wrobel, Pawel wrote:

> Dear FreeSurfer Team!
>
> We have a question concerning corrections with white-matter-points.
>
> We are currently working on a T1 data set. After performing 
> Freesurfer-Segmentations several days ago, we corrected the intensity 
> normalization in small regions (e.g. Gyrus temporalis superior) with 
> WM-points, stricktly obeying the decription on the FreeSurfer-Website (wiki).
> Afterwards We used the following command: recon-all -autorecon2-cp 
> -autorecon3 -subjid cp_before.
> The results in 80 % of corrections (105 scans) became worse than the first 
> segmentation. In some cases the pial surface "descends" and sticks to the 
> white matter surface, leaving the gray matter untouched, as if FreeSurfer 
> would not recognize it. In some other cases the WM border touches the brain 
> surface, including gray matter in the white matter. Sometimes the pial or 
> white matter surface makes little incisions or loops into another compartment.
>
> We have been trying different approaches. We rerun the correction with an 
> older FreeSurfer version (5.1.). We reinstalled the new version of FreeSurfer 
> which we were using before (5.3). We tried it on different computers.
>
> We will be very thankful for Your help!
>
> Yours sincerely
>
> Pawel
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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Re: [Freesurfer] Correction with white-matter-points

[Bruce Fischl]

Hi Pawel

you should look on the wiki for this type of info! Instructions are here:

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

cheers
Bruce
On 
Mon, 20 Jul 2015, Wrobel, Pawel wrote:

> Dear FreeSurfer Team!
>
> Last week I wrote about to the mailing list about problems occurring after 
> the WM-point correction. Later I received a message in which You told me that 
> You can help me if I upload the scan. Where and how can I do this?
>
> Thank You for Your help!
>
> Kind Regards
>
> Pawel W.
> Psychiatry and Neuroimaging Laboratory (PNL)
> Brigham and Women's Hospital
>
>
>
> Message: 6
> Date: Tue, 14 Jul 2015 11:33:57 -0400 (EDT)
> From: Bruce Fischl 
> Subject: Re: [Freesurfer] Correction with white-matter-points
> To: Freesurfer support list 
> Message-ID:
> 
> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>
> Hi Pawel
>
> does this happen in both versions? If so, upload a bad subject and we
> will take a look
>
> cheers
> Bruce
> On Tue, 14 Jul 2015, Wrobel, Pawel wrote:
>
> > Dear FreeSurfer Team!
> >
> > We have a question concerning corrections with white-matter-points.
> >
> > We are currently working on a T1 data set. After performing 
> > Freesurfer-Segmentations several days ago, we corrected the intensity 
> > normalization in small regions (e.g. Gyrus temporalis superior) with 
> > WM-points, stricktly obeying the decription on the FreeSurfer-Website 
> > (wiki).
> > Afterwards We used the following command: recon-all -autorecon2-cp 
> > -autorecon3 -subjid cp_before.
> > The results in 80 % of corrections (105 scans) became worse than the first 
> > segmentation. In some cases the pial surface "descends" and sticks to the 
> > white matter surface, leaving the gray matter untouched, as if FreeSurfer 
> > would not recognize it. In some other cases the WM border touches the brain 
> > surface, including gray matter in the white matter. Sometimes the pial or 
> > white matter surface makes little incisions or loops into another 
> > compartment.
> >
> > We have been trying different approaches. We rerun the correction with an 
> > older FreeSurfer version (5.1.). We reinstalled the new version of 
> > FreeSurfer which we were using before (5.3). We tried it on different 
> > computers.
> >
> > We will be very thankful for Your help!
> >
> > Yours sincerely
> >
> > Pawel
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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Re: [Freesurfer] Correction for multiple comparisons - qdec

[Douglas Greve]

You can try permutation, though it is often more constraining than those 
other two options. To do this, you'll need to run mri_glmfit-sim from 
the command line using the --sim perm option. Run it with --help to get 
examples


On 8/7/15 6:59 AM, pablo najt wrote:

Dear FS experts,
I have a question about running corrections for multiple comparisons. 
I am finding a fairly large cluster analyzing 2 groups on sulcal 
depth. However when I tried FDR or cluster wise correction the results 
do not seem to survive. As the result is on the region I was 
predicting I want to make sure there are no other options for 
correcting for multiple comparisons. I am including a figure of my 
result to give you an idea of the size of the cluster. Do you have any 
suggestions for trying alternative ways of correcting?

Thank you in advance,
Pablo



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Re: [Freesurfer] Correction for multiple comparisons question

[Douglas Greve]

Hi Panagiotis,

On 5/12/13 9:32 PM, Fotiadis, Panagiotis wrote:
> Hi Freesurfer experts,
>
> I was wondering about three things concerning the use of the mri_glmfit-sim 
> command:
>
> 1) I tried running it with the --2spaces flag in order to Bonferroni correct 
> over the two hemispheres but it tells me that the specific flag is not 
> recognized. Is there another way to correct over the two hemispheres?
What version are you using? You can just adjust the clusterwise 
threshold by dividing by 2 (eg, if you want a clusterwise threshold of 
.05, then set it to .025)
>
> 2) I set the cluster-based threshold to 0.999 in order to see all of the 
> clusters and varied the voxel-based threshold in order to see the differences 
> that it would make on the results. Specifically, i set it to be 1.3, 2.0, 
> 2.3, and 3.0. Between the four different occurring cluster summaries, there 
> was only one common cluster that appeared in all four summaries. As expected, 
> the number of voxels of the specific cluster was decreasing as its voxel-wise 
> threshold was increasing.
>
> a)  However, the reported cluster-wise threshold  varied between 0.05 to 0.96 
> in those four cases. Does this sound reasonable? Shouldn't the cluster wise p 
> values of the same cluster-between the four cases-be less dispersed?
I'm not sure what you mean here. At 3.0, the cluster may be very small 
and so could appear to be very insignificant.
>
> b)  If there is a cluster reported in only one of the four summaries (i.e. 
> when the voxel-based threshold is 1.3) that say has a cluster-wise p value of 
> 0.03, do I consider that significant or not, since it does not appear in any 
> other summary with such a low cluster wise p value and since the only 
> published p value is the cluster wise one?
In principle, it is significant. A lot of reviewers balk at such a 
liberal voxel-wise threshold since gaussian random fields breaks down at 
liberal thresholds. However, this uses simulations and not GRF. You 
should make sure the reviewers know this. There still might be some 
resistance since you could be picking up some low spatial frequency 
trends (ie, stuff that is not spatially gaussian) in addition to your 
true activation.

doug
>
> Thank you in advance for your time,
> Panagiotis Fotiadis
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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Re: [Freesurfer] Correction for multiple comparisons question

[Fotiadis, Panagiotis]

Thanks for the clarifications, Doug!

1) I am using FS stable version 5.0.0, so I'm assuming that the --2spaces flag 
has probably been implemented for the more recent FS versions. 

2) Thanks, that makes a lot more sense now.

In addition, since clusters are formed based on the number of neighboring 
voxels above the set voxel-based threshold, how is it possible to have reported 
(from the summary) clusters that have a cluster-wise p value higher than the 
voxel-based one? Isn't the cluster-wise p value of a cluster the maximum p 
value of all the contiguous voxels in that cluster?

Thanks again for all your help.
Panos





From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, May 13, 2013 12:22 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Correction for multiple comparisons question

Hi Panagiotis,

On 5/12/13 9:32 PM, Fotiadis, Panagiotis wrote:
> Hi Freesurfer experts,
>
> I was wondering about three things concerning the use of the mri_glmfit-sim 
> command:
>
> 1) I tried running it with the --2spaces flag in order to Bonferroni correct 
> over the two hemispheres but it tells me that the specific flag is not 
> recognized. Is there another way to correct over the two hemispheres?
What version are you using? You can just adjust the clusterwise
threshold by dividing by 2 (eg, if you want a clusterwise threshold of
.05, then set it to .025)
>
> 2) I set the cluster-based threshold to 0.999 in order to see all of the 
> clusters and varied the voxel-based threshold in order to see the differences 
> that it would make on the results. Specifically, i set it to be 1.3, 2.0, 
> 2.3, and 3.0. Between the four different occurring cluster summaries, there 
> was only one common cluster that appeared in all four summaries. As expected, 
> the number of voxels of the specific cluster was decreasing as its voxel-wise 
> threshold was increasing.
>
> a)  However, the reported cluster-wise threshold  varied between 0.05 to 0.96 
> in those four cases. Does this sound reasonable? Shouldn't the cluster wise p 
> values of the same cluster-between the four cases-be less dispersed?
I'm not sure what you mean here. At 3.0, the cluster may be very small
and so could appear to be very insignificant.
>
> b)  If there is a cluster reported in only one of the four summaries (i.e. 
> when the voxel-based threshold is 1.3) that say has a cluster-wise p value of 
> 0.03, do I consider that significant or not, since it does not appear in any 
> other summary with such a low cluster wise p value and since the only 
> published p value is the cluster wise one?
In principle, it is significant. A lot of reviewers balk at such a
liberal voxel-wise threshold since gaussian random fields breaks down at
liberal thresholds. However, this uses simulations and not GRF. You
should make sure the reviewers know this. There still might be some
resistance since you could be picking up some low spatial frequency
trends (ie, stuff that is not spatially gaussian) in addition to your
true activation.

doug
>
> Thank you in advance for your time,
> Panagiotis Fotiadis
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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Re: [Freesurfer] Correction for multiple comparisons question

[Douglas N Greve]

On 05/13/2013 11:11 AM, Fotiadis, Panagiotis wrote:
> Thanks for the clarifications, Doug!
>
> 1) I am using FS stable version 5.0.0, so I'm assuming that the --2spaces 
> flag has probably been implemented for the more recent FS versions.
>
> 2) Thanks, that makes a lot more sense now.
>
> In addition, since clusters are formed based on the number of neighboring 
> voxels above the set voxel-based threshold, how is it possible to have 
> reported (from the summary) clusters that have a cluster-wise p value higher 
> than the voxel-based one? Isn't the cluster-wise p value of a cluster the 
> maximum p value of all the contiguous voxels in that cluster?
The cluster-wise p-value is independent from the voxel-wise (ie, cluster 
forming) p-value. The clusterwise p-value is not the maximum of the 
p-values inside the cluster.
>
> Thanks again for all your help.
> Panos
>
>
>
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, May 13, 2013 12:22 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Correction for multiple comparisons question
>
> Hi Panagiotis,
>
> On 5/12/13 9:32 PM, Fotiadis, Panagiotis wrote:
>> Hi Freesurfer experts,
>>
>> I was wondering about three things concerning the use of the mri_glmfit-sim 
>> command:
>>
>> 1) I tried running it with the --2spaces flag in order to Bonferroni correct 
>> over the two hemispheres but it tells me that the specific flag is not 
>> recognized. Is there another way to correct over the two hemispheres?
> What version are you using? You can just adjust the clusterwise
> threshold by dividing by 2 (eg, if you want a clusterwise threshold of
> .05, then set it to .025)
>> 2) I set the cluster-based threshold to 0.999 in order to see all of the 
>> clusters and varied the voxel-based threshold in order to see the 
>> differences that it would make on the results. Specifically, i set it to be 
>> 1.3, 2.0, 2.3, and 3.0. Between the four different occurring cluster 
>> summaries, there was only one common cluster that appeared in all four 
>> summaries. As expected, the number of voxels of the specific cluster was 
>> decreasing as its voxel-wise threshold was increasing.
>>
>> a)  However, the reported cluster-wise threshold  varied between 0.05 to 
>> 0.96 in those four cases. Does this sound reasonable? Shouldn't the cluster 
>> wise p values of the same cluster-between the four cases-be less dispersed?
> I'm not sure what you mean here. At 3.0, the cluster may be very small
> and so could appear to be very insignificant.
>> b)  If there is a cluster reported in only one of the four summaries (i.e. 
>> when the voxel-based threshold is 1.3) that say has a cluster-wise p value 
>> of 0.03, do I consider that significant or not, since it does not appear in 
>> any other summary with such a low cluster wise p value and since the only 
>> published p value is the cluster wise one?
> In principle, it is significant. A lot of reviewers balk at such a
> liberal voxel-wise threshold since gaussian random fields breaks down at
> liberal thresholds. However, this uses simulations and not GRF. You
> should make sure the reviewers know this. There still might be some
> resistance since you could be picking up some low spatial frequency
> trends (ie, stuff that is not spatially gaussian) in addition to your
> true activation.
>
> doug
>> Thank you in advance for your time,
>> Panagiotis Fotiadis
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
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
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The informati

Re: [Freesurfer] Correction for multiple comparisons question

[Fotiadis, Panagiotis]

Great, thank you for your time!

Panos

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, May 13, 2013 11:56 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Correction for multiple comparisons question

On 05/13/2013 11:11 AM, Fotiadis, Panagiotis wrote:
> Thanks for the clarifications, Doug!
>
> 1) I am using FS stable version 5.0.0, so I'm assuming that the --2spaces 
> flag has probably been implemented for the more recent FS versions.
>
> 2) Thanks, that makes a lot more sense now.
>
> In addition, since clusters are formed based on the number of neighboring 
> voxels above the set voxel-based threshold, how is it possible to have 
> reported (from the summary) clusters that have a cluster-wise p value higher 
> than the voxel-based one? Isn't the cluster-wise p value of a cluster the 
> maximum p value of all the contiguous voxels in that cluster?
The cluster-wise p-value is independent from the voxel-wise (ie, cluster
forming) p-value. The clusterwise p-value is not the maximum of the
p-values inside the cluster.
>
> Thanks again for all your help.
> Panos
>
>
>
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, May 13, 2013 12:22 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Correction for multiple comparisons question
>
> Hi Panagiotis,
>
> On 5/12/13 9:32 PM, Fotiadis, Panagiotis wrote:
>> Hi Freesurfer experts,
>>
>> I was wondering about three things concerning the use of the mri_glmfit-sim 
>> command:
>>
>> 1) I tried running it with the --2spaces flag in order to Bonferroni correct 
>> over the two hemispheres but it tells me that the specific flag is not 
>> recognized. Is there another way to correct over the two hemispheres?
> What version are you using? You can just adjust the clusterwise
> threshold by dividing by 2 (eg, if you want a clusterwise threshold of
> .05, then set it to .025)
>> 2) I set the cluster-based threshold to 0.999 in order to see all of the 
>> clusters and varied the voxel-based threshold in order to see the 
>> differences that it would make on the results. Specifically, i set it to be 
>> 1.3, 2.0, 2.3, and 3.0. Between the four different occurring cluster 
>> summaries, there was only one common cluster that appeared in all four 
>> summaries. As expected, the number of voxels of the specific cluster was 
>> decreasing as its voxel-wise threshold was increasing.
>>
>> a)  However, the reported cluster-wise threshold  varied between 0.05 to 
>> 0.96 in those four cases. Does this sound reasonable? Shouldn't the cluster 
>> wise p values of the same cluster-between the four cases-be less dispersed?
> I'm not sure what you mean here. At 3.0, the cluster may be very small
> and so could appear to be very insignificant.
>> b)  If there is a cluster reported in only one of the four summaries (i.e. 
>> when the voxel-based threshold is 1.3) that say has a cluster-wise p value 
>> of 0.03, do I consider that significant or not, since it does not appear in 
>> any other summary with such a low cluster wise p value and since the only 
>> published p value is the cluster wise one?
> In principle, it is significant. A lot of reviewers balk at such a
> liberal voxel-wise threshold since gaussian random fields breaks down at
> liberal thresholds. However, this uses simulations and not GRF. You
> should make sure the reviewers know this. There still might be some
> resistance since you could be picking up some low spatial frequency
> trends (ie, stuff that is not spatially gaussian) in addition to your
> true activation.
>
> doug
>> Thank you in advance for your time,
>> Panagiotis Fotiadis
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

--
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.h

Re: [Freesurfer] Correction for multiple comparisons error

[Douglas Greve]

what is your cmd line? What version of FS are you using? What is the 
full terminal output?
doug


On 5/25/13 6:55 PM, Fotiadis, Panagiotis wrote:
> Hi!
>
> I have been running the mri_glmfit-sim command to do the correction for 
> multiple comparisons for my group analysis and for some voxel-based 
> thresholds (not all) there is an error that comes up when reading the 
> colortable from the annotation file:
>
> reading colortable from annotation file...
> colortable with 35 entries read (originally 
> /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt)
> *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 
> 0x06e61230 ***
> *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 
> 0x06e61230 ***
>
> and then it gets stuck. Do you happen to know what might be causing this 
> issue?
>
> Thank you for your time,
> Panos
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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Re: [Freesurfer] Correction for multiple comparisons error

[Fotiadis, Panagiotis]

Hey Doug,

I was wondering whether you had a chance to give this a look!

Thanks again,
Panos

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fotiadis, Panagiotis
Sent: Tuesday, May 28, 2013 1:38 PM
To: Douglas Greve; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Correction for multiple comparisons error

Hi Doug,

1)  My cmd line is:

mri_glmfit --y lh.Diseased_gender_age.thickness.10B.mgh --fsgd 
Diseased_gender_age.fsgd dods --C CAA_male-vs-female_age_slope.mtx --C 
CAA_male-vs-female.mtx --C CAA-vs-Control_age_slope.mtx --C CAA-vs-Control.mtx 
--C Males-vs-Females_age_slope.mtx --C Males-vs-Females.mtx --surf fsaverage lh 
--cortex --glmdir lh.Diseased_gender_age.glmdir

2) The FS version that I am using is the stable 5.0.0,

3) I have attached the full terminal output in this email.

Thank you for your time!
Panos

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, May 27, 2013 10:08 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Correction for multiple comparisons error

what is your cmd line? What version of FS are you using? What is the
full terminal output?
doug


On 5/25/13 6:55 PM, Fotiadis, Panagiotis wrote:
> Hi!
>
> I have been running the mri_glmfit-sim command to do the correction for 
> multiple comparisons for my group analysis and for some voxel-based 
> thresholds (not all) there is an error that comes up when reading the 
> colortable from the annotation file:
>
> reading colortable from annotation file...
> colortable with 35 entries read (originally 
> /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt)
> *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 
> 0x06e61230 ***
> *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 
> 0x06e61230 ***
>
> and then it gets stuck. Do you happen to know what might be causing this 
> issue?
>
> Thank you for your time,
> Panos
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] Correction for multiple comparisons error

[Douglas N Greve]

Can you send me the terminal output in a text file? A word doc is very 
inconvenient:).
doug

On 05/28/2013 01:38 PM, Fotiadis, Panagiotis wrote:
> Hi Doug,
>
> 1)  My cmd line is:
>
> mri_glmfit --y lh.Diseased_gender_age.thickness.10B.mgh --fsgd 
> Diseased_gender_age.fsgd dods --C CAA_male-vs-female_age_slope.mtx --C 
> CAA_male-vs-female.mtx --C CAA-vs-Control_age_slope.mtx --C 
> CAA-vs-Control.mtx --C Males-vs-Females_age_slope.mtx --C 
> Males-vs-Females.mtx --surf fsaverage lh --cortex --glmdir 
> lh.Diseased_gender_age.glmdir
>
> 2) The FS version that I am using is the stable 5.0.0,
>
> 3) I have attached the full terminal output in this email.
>
> Thank you for your time!
> Panos
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, May 27, 2013 10:08 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>
> what is your cmd line? What version of FS are you using? What is the
> full terminal output?
> doug
>
>
> On 5/25/13 6:55 PM, Fotiadis, Panagiotis wrote:
>> Hi!
>>
>> I have been running the mri_glmfit-sim command to do the correction for 
>> multiple comparisons for my group analysis and for some voxel-based 
>> thresholds (not all) there is an error that comes up when reading the 
>> colortable from the annotation file:
>>
>> reading colortable from annotation file...
>> colortable with 35 entries read (originally 
>> /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt)
>> *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 
>> 0x06e61230 ***
>> *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 
>> 0x06e61230 ***
>>
>> and then it gets stuck. Do you happen to know what might be causing this 
>> issue?
>>
>> Thank you for your time,
>> Panos
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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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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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Re: [Freesurfer] Correction for multiple comparisons error

[Douglas N Greve]

hmm, can't tell from that what is going on. Can you tar up 
lh.Diseased_gender_age.glmdir and drop it to me at our file drop (URL at 
the end of this email)?
doug

On 05/30/2013 03:57 PM, Fotiadis, Panagiotis wrote:
> Hey Doug,
>
> Of course, I attached it in txt format in this email!
>
> Best,
> Panos
>
>
> 
> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, May 30, 2013 2:55 PM
> To: Fotiadis, Panagiotis
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>
> Can you send me the terminal output in a text file? A word doc is very
> inconvenient:).
> doug
>
> On 05/28/2013 01:38 PM, Fotiadis, Panagiotis wrote:
>> Hi Doug,
>>
>> 1)  My cmd line is:
>>
>> mri_glmfit --y lh.Diseased_gender_age.thickness.10B.mgh --fsgd 
>> Diseased_gender_age.fsgd dods --C CAA_male-vs-female_age_slope.mtx --C 
>> CAA_male-vs-female.mtx --C CAA-vs-Control_age_slope.mtx --C 
>> CAA-vs-Control.mtx --C Males-vs-Females_age_slope.mtx --C 
>> Males-vs-Females.mtx --surf fsaverage lh --cortex --glmdir 
>> lh.Diseased_gender_age.glmdir
>>
>> 2) The FS version that I am using is the stable 5.0.0,
>>
>> 3) I have attached the full terminal output in this email.
>>
>> Thank you for your time!
>> Panos
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Monday, May 27, 2013 10:08 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>>
>> what is your cmd line? What version of FS are you using? What is the
>> full terminal output?
>> doug
>>
>>
>> On 5/25/13 6:55 PM, Fotiadis, Panagiotis wrote:
>>> Hi!
>>>
>>> I have been running the mri_glmfit-sim command to do the correction for 
>>> multiple comparisons for my group analysis and for some voxel-based 
>>> thresholds (not all) there is an error that comes up when reading the 
>>> colortable from the annotation file:
>>>
>>> reading colortable from annotation file...
>>> colortable with 35 entries read (originally 
>>> /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt)
>>> *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 
>>> 0x06e61230 ***
>>> *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 
>>> 0x06e61230 ***
>>>
>>> and then it gets stuck. Do you happen to know what might be causing this 
>>> issue?
>>>
>>> Thank you for your time,
>>> Panos
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> 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/
>

-- 
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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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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Re: [Freesurfer] Correction for multiple comparisons error

[Fotiadis, Panagiotis]

Definitely, just uploaded it!

Panos

From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Thursday, May 30, 2013 4:10 PM
To: Fotiadis, Panagiotis
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Correction for multiple comparisons error

hmm, can't tell from that what is going on. Can you tar up
lh.Diseased_gender_age.glmdir and drop it to me at our file drop (URL at
the end of this email)?
doug

On 05/30/2013 03:57 PM, Fotiadis, Panagiotis wrote:
> Hey Doug,
>
> Of course, I attached it in txt format in this email!
>
> Best,
> Panos
>
>
> 
> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, May 30, 2013 2:55 PM
> To: Fotiadis, Panagiotis
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>
> Can you send me the terminal output in a text file? A word doc is very
> inconvenient:).
> doug
>
> On 05/28/2013 01:38 PM, Fotiadis, Panagiotis wrote:
>> Hi Doug,
>>
>> 1)  My cmd line is:
>>
>> mri_glmfit --y lh.Diseased_gender_age.thickness.10B.mgh --fsgd 
>> Diseased_gender_age.fsgd dods --C CAA_male-vs-female_age_slope.mtx --C 
>> CAA_male-vs-female.mtx --C CAA-vs-Control_age_slope.mtx --C 
>> CAA-vs-Control.mtx --C Males-vs-Females_age_slope.mtx --C 
>> Males-vs-Females.mtx --surf fsaverage lh --cortex --glmdir 
>> lh.Diseased_gender_age.glmdir
>>
>> 2) The FS version that I am using is the stable 5.0.0,
>>
>> 3) I have attached the full terminal output in this email.
>>
>> Thank you for your time!
>> Panos
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Monday, May 27, 2013 10:08 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>>
>> what is your cmd line? What version of FS are you using? What is the
>> full terminal output?
>> doug
>>
>>
>> On 5/25/13 6:55 PM, Fotiadis, Panagiotis wrote:
>>> Hi!
>>>
>>> I have been running the mri_glmfit-sim command to do the correction for 
>>> multiple comparisons for my group analysis and for some voxel-based 
>>> thresholds (not all) there is an error that comes up when reading the 
>>> colortable from the annotation file:
>>>
>>> reading colortable from annotation file...
>>> colortable with 35 entries read (originally 
>>> /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt)
>>> *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 
>>> 0x06e61230 ***
>>> *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 
>>> 0x06e61230 ***
>>>
>>> and then it gets stuck. Do you happen to know what might be causing this 
>>> issue?
>>>
>>> Thank you for your time,
>>> Panos
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> 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/
>

--
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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Re: [Freesurfer] Correction for multiple comparisons error

[Douglas N Greve]

This is a problem with version 5.0 when you set the clusterwise pvalue 
to something close to 1. I re-rand it with .995 and it work. This is 
fixed in 5.3
doug


On 05/30/2013 04:23 PM, Fotiadis, Panagiotis wrote:
> Definitely, just uploaded it!
>
> Panos
> 
> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, May 30, 2013 4:10 PM
> To: Fotiadis, Panagiotis
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>
> hmm, can't tell from that what is going on. Can you tar up
> lh.Diseased_gender_age.glmdir and drop it to me at our file drop (URL at
> the end of this email)?
> doug
>
> On 05/30/2013 03:57 PM, Fotiadis, Panagiotis wrote:
>> Hey Doug,
>>
>> Of course, I attached it in txt format in this email!
>>
>> Best,
>> Panos
>>
>>
>> 
>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>> Sent: Thursday, May 30, 2013 2:55 PM
>> To: Fotiadis, Panagiotis
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>>
>> Can you send me the terminal output in a text file? A word doc is very
>> inconvenient:).
>> doug
>>
>> On 05/28/2013 01:38 PM, Fotiadis, Panagiotis wrote:
>>> Hi Doug,
>>>
>>> 1)  My cmd line is:
>>>
>>> mri_glmfit --y lh.Diseased_gender_age.thickness.10B.mgh --fsgd 
>>> Diseased_gender_age.fsgd dods --C CAA_male-vs-female_age_slope.mtx --C 
>>> CAA_male-vs-female.mtx --C CAA-vs-Control_age_slope.mtx --C 
>>> CAA-vs-Control.mtx --C Males-vs-Females_age_slope.mtx --C 
>>> Males-vs-Females.mtx --surf fsaverage lh --cortex --glmdir 
>>> lh.Diseased_gender_age.glmdir
>>>
>>> 2) The FS version that I am using is the stable 5.0.0,
>>>
>>> 3) I have attached the full terminal output in this email.
>>>
>>> Thank you for your time!
>>> Panos
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Monday, May 27, 2013 10:08 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>>>
>>> what is your cmd line? What version of FS are you using? What is the
>>> full terminal output?
>>> doug
>>>
>>>
>>> On 5/25/13 6:55 PM, Fotiadis, Panagiotis wrote:
>>>> Hi!
>>>>
>>>> I have been running the mri_glmfit-sim command to do the correction for 
>>>> multiple comparisons for my group analysis and for some voxel-based 
>>>> thresholds (not all) there is an error that comes up when reading the 
>>>> colortable from the annotation file:
>>>>
>>>> reading colortable from annotation file...
>>>> colortable with 35 entries read (originally 
>>>> /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt)
>>>> *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 
>>>> 0x06e61230 ***
>>>> *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 
>>>> 0x06e61230 ***
>>>>
>>>> and then it gets stuck. Do you happen to know what might be causing this 
>>>> issue?
>>>>
>>>> Thank you for your time,
>>>> Panos
>>>> ___
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> --
>> 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/
>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bu

Re: [Freesurfer] Correction for multiple comparisons error

[Fotiadis, Panagiotis]

Great, thanks!!

In addition, since I am applying the mri_glmfit (and mri_glmfit-sim) analysis 
on each hemisphere separately (lh.**.glmfit and rh.**.glmfit) do I 
still need to apply the correction over the two hemispheres (that is divide by 
2 the cluster wise threshold since in FS 5.0.0 the --2spaces flag does not 
apply)? 

Best,
Panos

From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Thursday, May 30, 2013 4:29 PM
To: Fotiadis, Panagiotis
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Correction for multiple comparisons error

This is a problem with version 5.0 when you set the clusterwise pvalue
to something close to 1. I re-rand it with .995 and it work. This is
fixed in 5.3
doug


On 05/30/2013 04:23 PM, Fotiadis, Panagiotis wrote:
> Definitely, just uploaded it!
>
> Panos
> 
> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, May 30, 2013 4:10 PM
> To: Fotiadis, Panagiotis
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>
> hmm, can't tell from that what is going on. Can you tar up
> lh.Diseased_gender_age.glmdir and drop it to me at our file drop (URL at
> the end of this email)?
> doug
>
> On 05/30/2013 03:57 PM, Fotiadis, Panagiotis wrote:
>> Hey Doug,
>>
>> Of course, I attached it in txt format in this email!
>>
>> Best,
>> Panos
>>
>>
>> 
>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>> Sent: Thursday, May 30, 2013 2:55 PM
>> To: Fotiadis, Panagiotis
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>>
>> Can you send me the terminal output in a text file? A word doc is very
>> inconvenient:).
>> doug
>>
>> On 05/28/2013 01:38 PM, Fotiadis, Panagiotis wrote:
>>> Hi Doug,
>>>
>>> 1)  My cmd line is:
>>>
>>> mri_glmfit --y lh.Diseased_gender_age.thickness.10B.mgh --fsgd 
>>> Diseased_gender_age.fsgd dods --C CAA_male-vs-female_age_slope.mtx --C 
>>> CAA_male-vs-female.mtx --C CAA-vs-Control_age_slope.mtx --C 
>>> CAA-vs-Control.mtx --C Males-vs-Females_age_slope.mtx --C 
>>> Males-vs-Females.mtx --surf fsaverage lh --cortex --glmdir 
>>> lh.Diseased_gender_age.glmdir
>>>
>>> 2) The FS version that I am using is the stable 5.0.0,
>>>
>>> 3) I have attached the full terminal output in this email.
>>>
>>> Thank you for your time!
>>> Panos
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Monday, May 27, 2013 10:08 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>>>
>>> what is your cmd line? What version of FS are you using? What is the
>>> full terminal output?
>>> doug
>>>
>>>
>>> On 5/25/13 6:55 PM, Fotiadis, Panagiotis wrote:
>>>> Hi!
>>>>
>>>> I have been running the mri_glmfit-sim command to do the correction for 
>>>> multiple comparisons for my group analysis and for some voxel-based 
>>>> thresholds (not all) there is an error that comes up when reading the 
>>>> colortable from the annotation file:
>>>>
>>>> reading colortable from annotation file...
>>>> colortable with 35 entries read (originally 
>>>> /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt)
>>>> *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 
>>>> 0x06e61230 ***
>>>> *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 
>>>> 0x06e61230 ***
>>>>
>>>> and then it gets stuck. Do you happen to know what might be causing this 
>>>> issue?
>>>>
>>>> Thank you for your time,
>>>> Panos
>>>> ___
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Correction for multiple comparisons error

[Douglas N Greve]

yes
On 05/30/2013 04:43 PM, Fotiadis, Panagiotis wrote:
> Great, thanks!!
>
> In addition, since I am applying the mri_glmfit (and mri_glmfit-sim) analysis 
> on each hemisphere separately (lh.**.glmfit and rh.**.glmfit) do I 
> still need to apply the correction over the two hemispheres (that is divide 
> by 2 the cluster wise threshold since in FS 5.0.0 the --2spaces flag does not 
> apply)?
>
> Best,
> Panos
> 
> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, May 30, 2013 4:29 PM
> To: Fotiadis, Panagiotis
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>
> This is a problem with version 5.0 when you set the clusterwise pvalue
> to something close to 1. I re-rand it with .995 and it work. This is
> fixed in 5.3
> doug
>
>
> On 05/30/2013 04:23 PM, Fotiadis, Panagiotis wrote:
>> Definitely, just uploaded it!
>>
>> Panos
>> 
>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>> Sent: Thursday, May 30, 2013 4:10 PM
>> To: Fotiadis, Panagiotis
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>>
>> hmm, can't tell from that what is going on. Can you tar up
>> lh.Diseased_gender_age.glmdir and drop it to me at our file drop (URL at
>> the end of this email)?
>> doug
>>
>> On 05/30/2013 03:57 PM, Fotiadis, Panagiotis wrote:
>>> Hey Doug,
>>>
>>> Of course, I attached it in txt format in this email!
>>>
>>> Best,
>>> Panos
>>>
>>>
>>> 
>>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>>> Sent: Thursday, May 30, 2013 2:55 PM
>>> To: Fotiadis, Panagiotis
>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>>>
>>> Can you send me the terminal output in a text file? A word doc is very
>>> inconvenient:).
>>> doug
>>>
>>> On 05/28/2013 01:38 PM, Fotiadis, Panagiotis wrote:
>>>> Hi Doug,
>>>>
>>>> 1)  My cmd line is:
>>>>
>>>> mri_glmfit --y lh.Diseased_gender_age.thickness.10B.mgh --fsgd 
>>>> Diseased_gender_age.fsgd dods --C CAA_male-vs-female_age_slope.mtx --C 
>>>> CAA_male-vs-female.mtx --C CAA-vs-Control_age_slope.mtx --C 
>>>> CAA-vs-Control.mtx --C Males-vs-Females_age_slope.mtx --C 
>>>> Males-vs-Females.mtx --surf fsaverage lh --cortex --glmdir 
>>>> lh.Diseased_gender_age.glmdir
>>>>
>>>> 2) The FS version that I am using is the stable 5.0.0,
>>>>
>>>> 3) I have attached the full terminal output in this email.
>>>>
>>>> Thank you for your time!
>>>> Panos
>>>> 
>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>>>> [gr...@nmr.mgh.harvard.edu]
>>>> Sent: Monday, May 27, 2013 10:08 PM
>>>> To: freesurfer@nmr.mgh.harvard.edu
>>>> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>>>>
>>>> what is your cmd line? What version of FS are you using? What is the
>>>> full terminal output?
>>>> doug
>>>>
>>>>
>>>> On 5/25/13 6:55 PM, Fotiadis, Panagiotis wrote:
>>>>> Hi!
>>>>>
>>>>> I have been running the mri_glmfit-sim command to do the correction for 
>>>>> multiple comparisons for my group analysis and for some voxel-based 
>>>>> thresholds (not all) there is an error that comes up when reading the 
>>>>> colortable from the annotation file:
>>>>>
>>>>> reading colortable from annotation file...
>>>>> colortable with 35 entries read (originally 
>>>>> /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt)
>>>>> *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 
>>>>> 0x06e61230 ***
>>>>> *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 
>>>>> 0x06e61230 ***
>>>>>
>>>>> and then it gets stuck. Do you happen to know what might be causing this 
>>>>> issue?
>>>>>
>>>>> Thank you fo

Re: [Freesurfer] Correction for multiple comparisons error

[Fotiadis, Panagiotis]

Great, thanks!
Panos

From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Thursday, May 30, 2013 4:47 PM
To: Fotiadis, Panagiotis
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Correction for multiple comparisons error

yes
On 05/30/2013 04:43 PM, Fotiadis, Panagiotis wrote:
> Great, thanks!!
>
> In addition, since I am applying the mri_glmfit (and mri_glmfit-sim) analysis 
> on each hemisphere separately (lh.**.glmfit and rh.**.glmfit) do I 
> still need to apply the correction over the two hemispheres (that is divide 
> by 2 the cluster wise threshold since in FS 5.0.0 the --2spaces flag does not 
> apply)?
>
> Best,
> Panos
> 
> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, May 30, 2013 4:29 PM
> To: Fotiadis, Panagiotis
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>
> This is a problem with version 5.0 when you set the clusterwise pvalue
> to something close to 1. I re-rand it with .995 and it work. This is
> fixed in 5.3
> doug
>
>
> On 05/30/2013 04:23 PM, Fotiadis, Panagiotis wrote:
>> Definitely, just uploaded it!
>>
>> Panos
>> 
>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>> Sent: Thursday, May 30, 2013 4:10 PM
>> To: Fotiadis, Panagiotis
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>>
>> hmm, can't tell from that what is going on. Can you tar up
>> lh.Diseased_gender_age.glmdir and drop it to me at our file drop (URL at
>> the end of this email)?
>> doug
>>
>> On 05/30/2013 03:57 PM, Fotiadis, Panagiotis wrote:
>>> Hey Doug,
>>>
>>> Of course, I attached it in txt format in this email!
>>>
>>> Best,
>>> Panos
>>>
>>>
>>> 
>>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>>> Sent: Thursday, May 30, 2013 2:55 PM
>>> To: Fotiadis, Panagiotis
>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>>>
>>> Can you send me the terminal output in a text file? A word doc is very
>>> inconvenient:).
>>> doug
>>>
>>> On 05/28/2013 01:38 PM, Fotiadis, Panagiotis wrote:
>>>> Hi Doug,
>>>>
>>>> 1)  My cmd line is:
>>>>
>>>> mri_glmfit --y lh.Diseased_gender_age.thickness.10B.mgh --fsgd 
>>>> Diseased_gender_age.fsgd dods --C CAA_male-vs-female_age_slope.mtx --C 
>>>> CAA_male-vs-female.mtx --C CAA-vs-Control_age_slope.mtx --C 
>>>> CAA-vs-Control.mtx --C Males-vs-Females_age_slope.mtx --C 
>>>> Males-vs-Females.mtx --surf fsaverage lh --cortex --glmdir 
>>>> lh.Diseased_gender_age.glmdir
>>>>
>>>> 2) The FS version that I am using is the stable 5.0.0,
>>>>
>>>> 3) I have attached the full terminal output in this email.
>>>>
>>>> Thank you for your time!
>>>> Panos
>>>> 
>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>>>> [gr...@nmr.mgh.harvard.edu]
>>>> Sent: Monday, May 27, 2013 10:08 PM
>>>> To: freesurfer@nmr.mgh.harvard.edu
>>>> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>>>>
>>>> what is your cmd line? What version of FS are you using? What is the
>>>> full terminal output?
>>>> doug
>>>>
>>>>
>>>> On 5/25/13 6:55 PM, Fotiadis, Panagiotis wrote:
>>>>> Hi!
>>>>>
>>>>> I have been running the mri_glmfit-sim command to do the correction for 
>>>>> multiple comparisons for my group analysis and for some voxel-based 
>>>>> thresholds (not all) there is an error that comes up when reading the 
>>>>> colortable from the annotation file:
>>>>>
>>>>> reading colortable from annotation file...
>>>>> colortable with 35 entries read (originally 
>>>>> /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt)
>>>>> *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 
>>>>> 0x06e61230 ***
>>>>> *** glibc detected *** mri_surfcluster: 

Re: [Freesurfer] Correction for multiple comparisons error

[Fotiadis, Panagiotis]

Sorry for the follow up email. If for instance I want to see any clusters that 
have a p value of 0.05 or less, I need to set the cluster wise p value in the 
mri_glmfit-sim command to 0.025 (to account for the correction over the two 
hemispheres). Then, suppose that a cluster is shown in the summary that has a p 
value of 0.015. Is that its actual p value, or is its actual p value (that is 
the value reported to the paper) 0.03? 

Thanks,
Panos

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fotiadis, Panagiotis
Sent: Thursday, May 30, 2013 4:50 PM
To: Douglas N Greve
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Correction for multiple comparisons error

Great, thanks!
Panos

From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Thursday, May 30, 2013 4:47 PM
To: Fotiadis, Panagiotis
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Correction for multiple comparisons error

yes
On 05/30/2013 04:43 PM, Fotiadis, Panagiotis wrote:
> Great, thanks!!
>
> In addition, since I am applying the mri_glmfit (and mri_glmfit-sim) analysis 
> on each hemisphere separately (lh.**.glmfit and rh.**.glmfit) do I 
> still need to apply the correction over the two hemispheres (that is divide 
> by 2 the cluster wise threshold since in FS 5.0.0 the --2spaces flag does not 
> apply)?
>
> Best,
> Panos
> 
> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, May 30, 2013 4:29 PM
> To: Fotiadis, Panagiotis
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>
> This is a problem with version 5.0 when you set the clusterwise pvalue
> to something close to 1. I re-rand it with .995 and it work. This is
> fixed in 5.3
> doug
>
>
> On 05/30/2013 04:23 PM, Fotiadis, Panagiotis wrote:
>> Definitely, just uploaded it!
>>
>> Panos
>> 
>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>> Sent: Thursday, May 30, 2013 4:10 PM
>> To: Fotiadis, Panagiotis
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>>
>> hmm, can't tell from that what is going on. Can you tar up
>> lh.Diseased_gender_age.glmdir and drop it to me at our file drop (URL at
>> the end of this email)?
>> doug
>>
>> On 05/30/2013 03:57 PM, Fotiadis, Panagiotis wrote:
>>> Hey Doug,
>>>
>>> Of course, I attached it in txt format in this email!
>>>
>>> Best,
>>> Panos
>>>
>>>
>>> 
>>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>>> Sent: Thursday, May 30, 2013 2:55 PM
>>> To: Fotiadis, Panagiotis
>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>>>
>>> Can you send me the terminal output in a text file? A word doc is very
>>> inconvenient:).
>>> doug
>>>
>>> On 05/28/2013 01:38 PM, Fotiadis, Panagiotis wrote:
>>>> Hi Doug,
>>>>
>>>> 1)  My cmd line is:
>>>>
>>>> mri_glmfit --y lh.Diseased_gender_age.thickness.10B.mgh --fsgd 
>>>> Diseased_gender_age.fsgd dods --C CAA_male-vs-female_age_slope.mtx --C 
>>>> CAA_male-vs-female.mtx --C CAA-vs-Control_age_slope.mtx --C 
>>>> CAA-vs-Control.mtx --C Males-vs-Females_age_slope.mtx --C 
>>>> Males-vs-Females.mtx --surf fsaverage lh --cortex --glmdir 
>>>> lh.Diseased_gender_age.glmdir
>>>>
>>>> 2) The FS version that I am using is the stable 5.0.0,
>>>>
>>>> 3) I have attached the full terminal output in this email.
>>>>
>>>> Thank you for your time!
>>>> Panos
>>>> 
>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>>>> [gr...@nmr.mgh.harvard.edu]
>>>> Sent: Monday, May 27, 2013 10:08 PM
>>>> To: freesurfer@nmr.mgh.harvard.edu
>>>> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>>>>
>>>> what is your cmd line? What version of FS are you using? What is the
>>>> full terminal output?
>>>> doug
>>>>
>>>>
>>>> On 5/25/13 6:55 PM, Fotiadis, Panagiotis wrote:
>>>>> Hi!
>>>>>
&

Re: [Freesurfer] Correction for multiple comparisons error

[Douglas N Greve]

you would report .03
doug


On 05/30/2013 05:10 PM, Fotiadis, Panagiotis wrote:
> Sorry for the follow up email. If for instance I want to see any clusters 
> that have a p value of 0.05 or less, I need to set the cluster wise p value 
> in the mri_glmfit-sim command to 0.025 (to account for the correction over 
> the two hemispheres). Then, suppose that a cluster is shown in the summary 
> that has a p value of 0.015. Is that its actual p value, or is its actual p 
> value (that is the value reported to the paper) 0.03?
>
> Thanks,
> Panos
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fotiadis, Panagiotis
> Sent: Thursday, May 30, 2013 4:50 PM
> To: Douglas N Greve
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>
> Great, thanks!
> Panos
> 
> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, May 30, 2013 4:47 PM
> To: Fotiadis, Panagiotis
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>
> yes
> On 05/30/2013 04:43 PM, Fotiadis, Panagiotis wrote:
>> Great, thanks!!
>>
>> In addition, since I am applying the mri_glmfit (and mri_glmfit-sim) 
>> analysis on each hemisphere separately (lh.**.glmfit and 
>> rh.**.glmfit) do I still need to apply the correction over the two 
>> hemispheres (that is divide by 2 the cluster wise threshold since in FS 
>> 5.0.0 the --2spaces flag does not apply)?
>>
>> Best,
>> Panos
>> 
>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>> Sent: Thursday, May 30, 2013 4:29 PM
>> To: Fotiadis, Panagiotis
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>>
>> This is a problem with version 5.0 when you set the clusterwise pvalue
>> to something close to 1. I re-rand it with .995 and it work. This is
>> fixed in 5.3
>> doug
>>
>>
>> On 05/30/2013 04:23 PM, Fotiadis, Panagiotis wrote:
>>> Definitely, just uploaded it!
>>>
>>> Panos
>>> 
>>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>>> Sent: Thursday, May 30, 2013 4:10 PM
>>> To: Fotiadis, Panagiotis
>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>>>
>>> hmm, can't tell from that what is going on. Can you tar up
>>> lh.Diseased_gender_age.glmdir and drop it to me at our file drop (URL at
>>> the end of this email)?
>>> doug
>>>
>>> On 05/30/2013 03:57 PM, Fotiadis, Panagiotis wrote:
>>>> Hey Doug,
>>>>
>>>> Of course, I attached it in txt format in this email!
>>>>
>>>> Best,
>>>> Panos
>>>>
>>>>
>>>> 
>>>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>>>> Sent: Thursday, May 30, 2013 2:55 PM
>>>> To: Fotiadis, Panagiotis
>>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>>> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>>>>
>>>> Can you send me the terminal output in a text file? A word doc is very
>>>> inconvenient:).
>>>> doug
>>>>
>>>> On 05/28/2013 01:38 PM, Fotiadis, Panagiotis wrote:
>>>>> Hi Doug,
>>>>>
>>>>> 1)  My cmd line is:
>>>>>
>>>>> mri_glmfit --y lh.Diseased_gender_age.thickness.10B.mgh --fsgd 
>>>>> Diseased_gender_age.fsgd dods --C CAA_male-vs-female_age_slope.mtx --C 
>>>>> CAA_male-vs-female.mtx --C CAA-vs-Control_age_slope.mtx --C 
>>>>> CAA-vs-Control.mtx --C Males-vs-Females_age_slope.mtx --C 
>>>>> Males-vs-Females.mtx --surf fsaverage lh --cortex --glmdir 
>>>>> lh.Diseased_gender_age.glmdir
>>>>>
>>>>> 2) The FS version that I am using is the stable 5.0.0,
>>>>>
>>>>> 3) I have attached the full terminal output in this email.
>>>>>
>>>>> Thank you for your time!
>>>>> Panos
>>>>> 
>>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>>>

Re: [Freesurfer] Correction for multiple comparisons error

[Fotiadis, Panagiotis]

Great, thank you for your help!

Panos

From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Thursday, May 30, 2013 5:39 PM
To: Fotiadis, Panagiotis
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Correction for multiple comparisons error

you would report .03
doug


On 05/30/2013 05:10 PM, Fotiadis, Panagiotis wrote:
> Sorry for the follow up email. If for instance I want to see any clusters 
> that have a p value of 0.05 or less, I need to set the cluster wise p value 
> in the mri_glmfit-sim command to 0.025 (to account for the correction over 
> the two hemispheres). Then, suppose that a cluster is shown in the summary 
> that has a p value of 0.015. Is that its actual p value, or is its actual p 
> value (that is the value reported to the paper) 0.03?
>
> Thanks,
> Panos
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fotiadis, Panagiotis
> Sent: Thursday, May 30, 2013 4:50 PM
> To: Douglas N Greve
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>
> Great, thanks!
> Panos
> 
> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, May 30, 2013 4:47 PM
> To: Fotiadis, Panagiotis
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>
> yes
> On 05/30/2013 04:43 PM, Fotiadis, Panagiotis wrote:
>> Great, thanks!!
>>
>> In addition, since I am applying the mri_glmfit (and mri_glmfit-sim) 
>> analysis on each hemisphere separately (lh.**.glmfit and 
>> rh.**.glmfit) do I still need to apply the correction over the two 
>> hemispheres (that is divide by 2 the cluster wise threshold since in FS 
>> 5.0.0 the --2spaces flag does not apply)?
>>
>> Best,
>> Panos
>> 
>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>> Sent: Thursday, May 30, 2013 4:29 PM
>> To: Fotiadis, Panagiotis
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>>
>> This is a problem with version 5.0 when you set the clusterwise pvalue
>> to something close to 1. I re-rand it with .995 and it work. This is
>> fixed in 5.3
>> doug
>>
>>
>> On 05/30/2013 04:23 PM, Fotiadis, Panagiotis wrote:
>>> Definitely, just uploaded it!
>>>
>>> Panos
>>> 
>>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>>> Sent: Thursday, May 30, 2013 4:10 PM
>>> To: Fotiadis, Panagiotis
>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>>>
>>> hmm, can't tell from that what is going on. Can you tar up
>>> lh.Diseased_gender_age.glmdir and drop it to me at our file drop (URL at
>>> the end of this email)?
>>> doug
>>>
>>> On 05/30/2013 03:57 PM, Fotiadis, Panagiotis wrote:
>>>> Hey Doug,
>>>>
>>>> Of course, I attached it in txt format in this email!
>>>>
>>>> Best,
>>>> Panos
>>>>
>>>>
>>>> 
>>>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>>>> Sent: Thursday, May 30, 2013 2:55 PM
>>>> To: Fotiadis, Panagiotis
>>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>>> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>>>>
>>>> Can you send me the terminal output in a text file? A word doc is very
>>>> inconvenient:).
>>>> doug
>>>>
>>>> On 05/28/2013 01:38 PM, Fotiadis, Panagiotis wrote:
>>>>> Hi Doug,
>>>>>
>>>>> 1)  My cmd line is:
>>>>>
>>>>> mri_glmfit --y lh.Diseased_gender_age.thickness.10B.mgh --fsgd 
>>>>> Diseased_gender_age.fsgd dods --C CAA_male-vs-female_age_slope.mtx --C 
>>>>> CAA_male-vs-female.mtx --C CAA-vs-Control_age_slope.mtx --C 
>>>>> CAA-vs-Control.mtx --C Males-vs-Females_age_slope.mtx --C 
>>>>> Males-vs-Females.mtx --surf fsaverage lh --cortex --glmdir 
>>>>> lh.Diseased_gender_age.glmdir
>>>>>
>>>>> 2) The FS version that I am using is the stable 5.0.0,
>>>>>
>>>>> 3) I have attached the full terminal output in this email.
>>>>>
&g

[Freesurfer] Correction multiple comparisons for parcelated areas

[Anita van Loenhoud]

Dear FreeSurfers,

I’m comparing two groups (patients (N=45) and controls (N=93)) on
cortical thickness using 34 parcelated areas in each hemisphere (i.e.
68 areas in total). When correcting for multiple comparisons using
Bonferroni, only one area remains significant. Bonferroni is quite
conservative (alpha needs to be lower than 0.05/68= 0.000735). Could
you recommend any other, more lenient correction statistics for my
data?

In a search through the literature, I encountered adjusted Bonferroni
or Benjamini-Hochberg as alternatives. Do you think these would be
useful statistics, or have I missed other, more appropriate ones?

Thanks a lot,

Anna

___
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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] Correction for Multiple Comparisons - Sign Question

[mdkrue...@uwalumni.com]

Freesurfers-

When choosing the simulation type does the ending have to match the sim
sign? for instance i see examples with

--sim mc-z 1 3 mc-z.pos.3 --sim sign pos

or

--sim mc-z 1 3 mc-z.neg.3 --sim sign neg

I guess what i am asking is what does the first sign (in the mc-z.(SIGN).3
mean?

michael

-- 
Michael D. Kruepke
PhD - University of Illinois at Urbana-Champaign
BA - Psych - University of Wisconsin-Madison
mdkrue...@gmail.com
(262)-483-7449
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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] Correction Needed for the Midline

[Maxime Perron]

External Email - Use Caution

Hi Freesurfer Experts,
 
About 2 weeks ago, I sent a question about the midline correction but have not 
yet received a feedback. I am wondering if someone had time to check my data or 
has an idea on how to correct the bad midline. 

I tried to correct the aseg.presurf.mgz (Freesurfer v.6.0.0) many times with 
different autorecon (wm, cp, noaseg); still, although the segmentation changes, 
the midline doesn’t follow the new segmentation.
 
Since 10 of my subjects show this error, a solution is much needed.
 
Many thanks for your help!
 
Best,
Maxime​

De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Maxime Perron 

Envoyé : 17 septembre 2018 10:00
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

External Email - Use Caution

Hi Freesurfer Experts,

I was wondering if you have had time to look at my data to correct my midline 
problems? Many of my subjects have this problem.

Best regards,
Maxime

De : Maxime Perron
Envoyé : 13 septembre 2018 22:29
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

Hi Bruce,

I upload my subject to the ftp site as you requested. In the file midline_MP, 
you will find a file named Freesurfer_S043_test in which I made modifications 
on the aseg.presurf. The other file is the participant without modification.

The problem of the midline is from the coronal slice 137 to 157. For example, 
Talairach: 1.9 4.6 14.3.

Thank you for all your help,
Maxime

> On Sep 13, 2018, at 10:08 AM, Bruce Fischl  wrote:
>
> Hi Maxime
>
> if you upload a gzipped tar file of the entire subject dir to our ftp site we 
> will take a look. Please include voxel coordinates of the spots you think are 
> inaccurate.
>
> cheers
> Bruce
> On Thu, 13 Sep 2018, Maxime Perron wrote:
>
>>   External Email - Use Caution
>>
>> Hi Freesurfer Experts,
>>
>> I tried to correct the midline with the information you provided me. Indeed, 
>> I tried to correct the aseg.presurf (Freesurfer v.6) using Freeview. 
>> Although parcelisation has changed, the midline has not changed. I launched 
>> several types of autorecon (-noaseg, -cp, -wm), but it didn't work. Do you 
>> have an idea?
>>
>> Best,
>> Maxime
>>
>>> On Aug 10, 2018, at 5:09 PM, Bruce Fischl  
>>> wrote:
>>>
>>> HI Maxime
>>>
>>> check the aseg labels and make sure they are correct (and fix them if not). 
>>> Probably a couple of left/right ventricle voxels are mislabeled
>>> Bruce
>>> On Fri, 10 Aug 2018, Maxime Perron wrote:
>>>
External Email - Use Caution
 Hello FreeSurfer Developers,

 I use Freesurfer 6 on macOS Sierra 10.12.6. In several subjects, I found 
 midline cutting error, that
 is the midline does not go through exactly the center of the brain in 
 coronal cut. For example, the
 midline is a little bit fuzzy and goes through an hemisphere than the 
 other (see attachment). I've
 searched in the mail list and ​I don't find the way to fix it. Does anyone 
 have any idea to fix it?
 Thank you,
 Maxime Perron
>>> ___
>>> 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.
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> ___
> 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] Correction Needed for the Midline

[Diamond, Bram Ryder]

Hi Maxime,


I'll take a look at your data and the issue you're having and get back to you 
after the weekend.


Best,

Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Maxime Perron 

Sent: Tuesday, September 25, 2018 1:14:08 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline

External Email - Use Caution

Hi Freesurfer Experts,

About 2 weeks ago, I sent a question about the midline correction but have not 
yet received a feedback. I am wondering if someone had time to check my data or 
has an idea on how to correct the bad midline.

I tried to correct the aseg.presurf.mgz (Freesurfer v.6.0.0) many times with 
different autorecon (wm, cp, noaseg); still, although the segmentation changes, 
the midline doesn’t follow the new segmentation.

Since 10 of my subjects show this error, a solution is much needed.

Many thanks for your help!

Best,
Maxime​

De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Maxime Perron 

Envoyé : 17 septembre 2018 10:00
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

External Email - Use Caution

Hi Freesurfer Experts,

I was wondering if you have had time to look at my data to correct my midline 
problems? Many of my subjects have this problem.

Best regards,
Maxime

De : Maxime Perron
Envoyé : 13 septembre 2018 22:29
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

Hi Bruce,

I upload my subject to the ftp site as you requested. In the file midline_MP, 
you will find a file named Freesurfer_S043_test in which I made modifications 
on the aseg.presurf. The other file is the participant without modification.

The problem of the midline is from the coronal slice 137 to 157. For example, 
Talairach: 1.9 4.6 14.3.

Thank you for all your help,
Maxime

> On Sep 13, 2018, at 10:08 AM, Bruce Fischl  wrote:
>
> Hi Maxime
>
> if you upload a gzipped tar file of the entire subject dir to our ftp site we 
> will take a look. Please include voxel coordinates of the spots you think are 
> inaccurate.
>
> cheers
> Bruce
> On Thu, 13 Sep 2018, Maxime Perron wrote:
>
>>   External Email - Use Caution
>>
>> Hi Freesurfer Experts,
>>
>> I tried to correct the midline with the information you provided me. Indeed, 
>> I tried to correct the aseg.presurf (Freesurfer v.6) using Freeview. 
>> Although parcelisation has changed, the midline has not changed. I launched 
>> several types of autorecon (-noaseg, -cp, -wm), but it didn't work. Do you 
>> have an idea?
>>
>> Best,
>> Maxime
>>
>>> On Aug 10, 2018, at 5:09 PM, Bruce Fischl  
>>> wrote:
>>>
>>> HI Maxime
>>>
>>> check the aseg labels and make sure they are correct (and fix them if not). 
>>> Probably a couple of left/right ventricle voxels are mislabeled
>>> Bruce
>>> On Fri, 10 Aug 2018, Maxime Perron wrote:
>>>
>>>>External Email - Use Caution
>>>> Hello FreeSurfer Developers,
>>>>
>>>> I use Freesurfer 6 on macOS Sierra 10.12.6. In several subjects, I found 
>>>> midline cutting error, that
>>>> is the midline does not go through exactly the center of the brain in 
>>>> coronal cut. For example, the
>>>> midline is a little bit fuzzy and goes through an hemisphere than the 
>>>> other (see attachment). I've
>>>> searched in the mail list and ​I don't find the way to fix it. Does anyone 
>>>> have any idea to fix it?
>>>> Thank you,
>>>> Maxime Perron
>>> ___
>>> 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.
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> _

Re: [Freesurfer] Correction Needed for the Midline

[Maxime Perron]

External Email - Use Caution

Hi Bram, 


Thank you very much for the reply, I'm glad you'll have some time to look at the issue. Please don't hesitate to contact me should anything specific be needed. I'll be happy to contribute!

Many thanks,
Maxime​
​

De : freesurfer-boun...@nmr.mgh.harvard.edu  de la part de Diamond, Bram Ryder 
Envoyé : 11 octobre 2018 13:18
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Midline
 



Hi Maxime,


I'll take a look at your data and the issue you're having and get back to you after the weekend.


Best,
Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu  on behalf of Maxime Perron 
Sent: Tuesday, September 25, 2018 1:14:08 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline
 


    External Email - Use Caution    

Hi Freesurfer Experts,
 
About 2 weeks ago, I sent a question about the midline correction but have not yet received a feedback. I am wondering if someone had time to check my data or has an idea on how to correct the bad midline.


I tried to correct the aseg.presurf.mgz (Freesurfer v.6.0.0) many times with different autorecon (wm, cp, noaseg); still, although the segmentation changes, the midline doesn’t follow the new segmentation.
 
Since 10 of my subjects show this error, a solution is much needed.
 
Many thanks for your help!
 
Best,
Maxime​

De : freesurfer-boun...@nmr.mgh.harvard.edu  de la part de Maxime Perron 
Envoyé : 17 septembre 2018 10:00
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

    External Email - Use Caution

Hi Freesurfer Experts,

I was wondering if you have had time to look at my data to correct my midline problems? Many of my subjects have this problem.

Best regards,
Maxime

De : Maxime Perron
Envoyé : 13 septembre 2018 22:29
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

Hi Bruce,

I upload my subject to the ftp site as you requested. In the file midline_MP, you will find a file named Freesurfer_S043_test in which I made modifications on the aseg.presurf. The other file is the participant without modification.

The problem of the midline is from the coronal slice 137 to 157. For example, Talairach: 1.9 4.6 14.3.

Thank you for all your help,
Maxime

> On Sep 13, 2018, at 10:08 AM, Bruce Fischl  wrote:
>
> Hi Maxime
>
> if you upload a gzipped tar file of the entire subject dir to our ftp site we will take a look. Please include voxel coordinates of the spots you think are inaccurate.
>
> cheers
> Bruce
> On Thu, 13 Sep 2018, Maxime Perron wrote:
>
>>   External Email - Use Caution
>>
>> Hi Freesurfer Experts,
>>
>> I tried to correct the midline with the information you provided me. Indeed, I tried to correct the aseg.presurf (Freesurfer v.6) using Freeview. Although parcelisation has changed, the midline has not changed. I launched several types of autorecon (-noaseg,
 -cp, -wm), but it didn't work. Do you have an idea?
>>
>> Best,
>> Maxime
>>
>>> On Aug 10, 2018, at 5:09 PM, Bruce Fischl  wrote:
>>>
>>> HI Maxime
>>>
>>> check the aseg labels and make sure they are correct (and fix them if not). Probably a couple of left/right ventricle voxels are mislabeled
>>> Bruce
>>> On Fri, 10 Aug 2018, Maxime Perron wrote:
>>>
>>>>    External Email - Use Caution
>>>> Hello FreeSurfer Developers,
>>>>
>>>> I use Freesurfer 6 on macOS Sierra 10.12.6. In several subjects, I found midline cutting error, that
>>>> is the midline does not go through exactly the center of the brain in coronal cut. For example, the
>>>> midline is a little bit fuzzy and goes through an hemisphere than the other (see attachment). I've
>>>> searched in the mail list and ​I don't find the way to fix it. Does anyone have any idea to fix it?
>>>> Thank you,
>>>> Maxime Perron
>>> ___
>>> 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 cont

Re: [Freesurfer] Correction Needed for the Midline

[Diamond, Bram Ryder]

Hi Maxime,

I'm having trouble finding your data - can you please use the filedrop instead?

https://gate.nmr.mgh.harvard.edu/filedrop2/

Thanks,
Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Maxime Perron 

Sent: Friday, October 12, 2018 11:17:07 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline


External Email - Use Caution

Hi Bram,

Thank you very much for the reply, I'm glad you'll have some time to look at 
the issue. Please don't hesitate to contact me should anything specific be 
needed. I'll be happy to contribute!

Many thanks,
Maxime​
​

De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Diamond, Bram Ryder 

Envoyé : 11 octobre 2018 13:18
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Midline


Hi Maxime,


I'll take a look at your data and the issue you're having and get back to you 
after the weekend.


Best,

Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Maxime Perron 

Sent: Tuesday, September 25, 2018 1:14:08 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline

External Email - Use Caution

Hi Freesurfer Experts,

About 2 weeks ago, I sent a question about the midline correction but have not 
yet received a feedback. I am wondering if someone had time to check my data or 
has an idea on how to correct the bad midline.

I tried to correct the aseg.presurf.mgz (Freesurfer v.6.0.0) many times with 
different autorecon (wm, cp, noaseg); still, although the segmentation changes, 
the midline doesn’t follow the new segmentation.

Since 10 of my subjects show this error, a solution is much needed.

Many thanks for your help!

Best,
Maxime​

De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Maxime Perron 

Envoyé : 17 septembre 2018 10:00
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

External Email - Use Caution

Hi Freesurfer Experts,

I was wondering if you have had time to look at my data to correct my midline 
problems? Many of my subjects have this problem.

Best regards,
Maxime

De : Maxime Perron
Envoyé : 13 septembre 2018 22:29
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

Hi Bruce,

I upload my subject to the ftp site as you requested. In the file midline_MP, 
you will find a file named Freesurfer_S043_test in which I made modifications 
on the aseg.presurf. The other file is the participant without modification.

The problem of the midline is from the coronal slice 137 to 157. For example, 
Talairach: 1.9 4.6 14.3.

Thank you for all your help,
Maxime

> On Sep 13, 2018, at 10:08 AM, Bruce Fischl  wrote:
>
> Hi Maxime
>
> if you upload a gzipped tar file of the entire subject dir to our ftp site we 
> will take a look. Please include voxel coordinates of the spots you think are 
> inaccurate.
>
> cheers
> Bruce
> On Thu, 13 Sep 2018, Maxime Perron wrote:
>
>>   External Email - Use Caution
>>
>> Hi Freesurfer Experts,
>>
>> I tried to correct the midline with the information you provided me. Indeed, 
>> I tried to correct the aseg.presurf (Freesurfer v.6) using Freeview. 
>> Although parcelisation has changed, the midline has not changed. I launched 
>> several types of autorecon (-noaseg, -cp, -wm), but it didn't work. Do you 
>> have an idea?
>>
>> Best,
>> Maxime
>>
>>> On Aug 10, 2018, at 5:09 PM, Bruce Fischl  
>>> wrote:
>>>
>>> HI Maxime
>>>
>>> check the aseg labels and make sure they are correct (and fix them if not). 
>>> Probably a couple of left/right ventricle voxels are mislabeled
>>> Bruce
>>> On Fri, 10 Aug 2018, Maxime Perron wrote:
>>>
>>>>External Email - Use Caution
>>>> Hello FreeSurfer Developers,
>>>>
>>>> I use Freesurfer 6 on macOS Sierra 10.12.6. In several subjects, I found 
>>>> midline cutting error, that
>>>> is the midline does not go through exactly the center of the brain in 
>>>> coronal cut. For example, the
>>>> midline is a little bit fuzzy and goes through an hemisphere than the 
>>>> other (see attachment). I've
>>>> searched in the mail list and ​I don't find the way to fix it. Does anyone 
>>>> have any idea to fix it?
>>>> Thank you,
>>>> Maxime Perron
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.n

Re: [Freesurfer] Correction Needed for the Midline

[Maxime Perron]

External Email - Use Caution
Hi Bram,


No worries.


Here is the link : http://gate.nmr.mgh.harvard.edu/filedrop2/?a=al9nxdabh5h


Thanks,
Maxime 




On Oct 16, 2018, at 1:11 PM, Diamond, Bram Ryder <brdiam...@mgh.harvard.edu> wrote:




Hi Maxime,


I'm having trouble finding your data - can you please use the filedrop instead?


https://gate.nmr.mgh.harvard.edu/filedrop2/


Thanks,
Bram





From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Maxime Perron <maxime.perro...@ulaval.ca>
Sent: Friday, October 12, 2018 11:17:07 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline
 


External
 Email - Use Caution


Hi Bram, 


Thank you very much for the reply, I'm glad you'll have some time to look at the issue. Please don't hesitate to contact me should anything specific be needed. I'll be happy to contribute!

Many thanks,
Maxime​
​ 

De : freesurfer-boun...@nmr.mgh.harvard.edu
 <freesurfer-boun...@nmr.mgh.harvard.edu> de la part de Diamond, Bram Ryder <brdiam...@mgh.harvard.edu>
Envoyé : 11 octobre 2018 13:18
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Midline
 



Hi Maxime,


I'll take a look at your data and the issue you're having and get back to you after the weekend.


Best,
Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu
 <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Maxime Perron <maxime.perro...@ulaval.ca>
Sent: Tuesday, September 25, 2018 1:14:08 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline
 


    External Email - Use Caution

Hi Freesurfer Experts,
 
About 2 weeks ago, I sent a question about the midline correction but have not yet received a feedback. I am wondering if someone had time to check my data or has an idea on how to correct the bad midline. 

I tried to correct the aseg.presurf.mgz (Freesurfer v.6.0.0) many times with different autorecon (wm, cp, noaseg); still, although the segmentation changes, the midline doesn’t follow the new segmentation.
 
Since 10 of my subjects show this error, a solution is much needed.
 
Many thanks for your help!
 
Best,
Maxime​

De : freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> de la part de Maxime Perron <maxime.perro...@ulaval.ca>
Envoyé : 17 septembre 2018 10:00
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

    External Email - Use Caution

Hi Freesurfer Experts,

I was wondering if you have had time to look at my data to correct my midline problems? Many of my subjects have this problem.

Best regards,
Maxime

De : Maxime Perron
Envoyé : 13 septembre 2018 22:29
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

Hi Bruce,

I upload my subject to the ftp site as you requested. In the file midline_MP, you will find a file named Freesurfer_S043_test in which I made modifications on the aseg.presurf. The other file is the participant without modification.

The problem of the midline is from the coronal slice 137 to 157. For example, Talairach: 1.9 4.6 14.3.

Thank you for all your help,
Maxime

> On Sep 13, 2018, at 10:08 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
>
> Hi Maxime
>
> if you upload a gzipped tar file of the entire subject dir to our ftp site we will take a look. Please include voxel coordinates of the spots you think are inaccurate.
>
> cheers
> Bruce
> On Thu, 13 Sep 2018, Maxime Perron wrote:
>
>>   External Email - Use Caution
>>
>> Hi Freesurfer Experts,
>>
>> I tried to correct the midline with the information you provided me. Indeed, I tried to correct the aseg.presurf (Freesurfer v.6) using Freeview. Although parcelisation has changed, the midline has not changed. I launched several types of autorecon (-noaseg,
 -cp, -wm), but it didn't work. Do you have an idea?
>>
>> Best,
>> Maxime
>>
>>> On Aug 10, 2018, at 5:09 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
>>>
>>> HI Maxime
>>>
>>> check the aseg labels and make sure they are correct (and fix them if not). Probably a couple of left/right ventricle voxels are mislabeled
>>> Bruce
>>> On Fri, 10 Aug 2018, Maxime Perron wrote:
>>>
>>>>    External Email - Use Caution
>>>> Hello FreeSurfer Developers,
>>>>
>>>> I use Freesurfer 6 on macOS Sierra 10.12.6. In several subjects, I found midline cutting error, that
&

Re: [Freesurfer] Correction Needed for the Midline

[Maxime Perron]

External Email - Use Caution
Sorry. Here are the good links : 


http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1maf5ah0hw0
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=abmzg2jvk9t


Maxime 


On Oct 16, 2018, at 2:22 PM, Maxime Perron <maxime.perro...@ulaval.ca> wrote:



External Email - Use Caution


Hi Bram,


No worries.


Here is the link : http://gate.nmr.mgh.harvard.edu/filedrop2/?a=al9nxdabh5h


Thanks,
Maxime 




On Oct 16, 2018, at 1:11 PM, Diamond, Bram Ryder <brdiam...@mgh.harvard.edu> wrote:




Hi Maxime,


I'm having trouble finding your data - can you please use the filedrop instead?


https://gate.nmr.mgh.harvard.edu/filedrop2/


Thanks,
Bram





From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Maxime Perron <maxime.perro...@ulaval.ca>
Sent: Friday, October 12, 2018 11:17:07 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline
 


External
 Email - Use Caution


Hi Bram, 


Thank you very much for the reply, I'm glad you'll have some time to look at the issue. Please don't hesitate to contact me should anything specific be needed. I'll be happy to contribute!

Many thanks,
Maxime​
​ 

De : freesurfer-boun...@nmr.mgh.harvard.edu
 <freesurfer-boun...@nmr.mgh.harvard.edu> de la part de Diamond, Bram Ryder <brdiam...@mgh.harvard.edu>
Envoyé : 11 octobre 2018 13:18
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Midline
 



Hi Maxime,


I'll take a look at your data and the issue you're having and get back to you after the weekend.


Best,
Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu
 <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Maxime Perron <maxime.perro...@ulaval.ca>
Sent: Tuesday, September 25, 2018 1:14:08 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline
 


    External Email - Use Caution

Hi Freesurfer Experts,
 
About 2 weeks ago, I sent a question about the midline correction but have not yet received a feedback. I am wondering if someone had time to check my data or has an idea on how to correct the bad midline. 

I tried to correct the aseg.presurf.mgz (Freesurfer v.6.0.0) many times with different autorecon (wm, cp, noaseg); still, although the segmentation changes, the midline doesn’t follow the new segmentation.
 
Since 10 of my subjects show this error, a solution is much needed.
 
Many thanks for your help!
 
Best,
Maxime​

De : freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> de la part de Maxime Perron <maxime.perro...@ulaval.ca>
Envoyé : 17 septembre 2018 10:00
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

    External Email - Use Caution

Hi Freesurfer Experts,

I was wondering if you have had time to look at my data to correct my midline problems? Many of my subjects have this problem.

Best regards,
Maxime

De : Maxime Perron
Envoyé : 13 septembre 2018 22:29
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

Hi Bruce,

I upload my subject to the ftp site as you requested. In the file midline_MP, you will find a file named Freesurfer_S043_test in which I made modifications on the aseg.presurf. The other file is the participant without modification.

The problem of the midline is from the coronal slice 137 to 157. For example, Talairach: 1.9 4.6 14.3.

Thank you for all your help,
Maxime

> On Sep 13, 2018, at 10:08 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
>
> Hi Maxime
>
> if you upload a gzipped tar file of the entire subject dir to our ftp site we will take a look. Please include voxel coordinates of the spots you think are inaccurate.
>
> cheers
> Bruce
> On Thu, 13 Sep 2018, Maxime Perron wrote:
>
>>   External Email - Use Caution
>>
>> Hi Freesurfer Experts,
>>
>> I tried to correct the midline with the information you provided me. Indeed, I tried to correct the aseg.presurf (Freesurfer v.6) using Freeview. Although parcelisation has changed, the midline has not changed. I launched several types of autorecon (-noaseg,
 -cp, -wm), but it didn't work. Do you have an idea?
>>
>> Best,
>> Maxime
>>
>>> On Aug 10, 2018, at 5:09 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
>>>
>>> HI Maxime
>>>
>>> check the aseg labels and make sure they are correct (and fix them if not). Probably a couple of left/right ventricle voxels are mislabeled
>>&g

Re: [Freesurfer] Correction Needed for the Midline

[Diamond, Bram Ryder]

Hi Maxime,


What did you edit in the aseg? It looks like the CC_* have been mislabeled.


Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Maxime Perron 

Sent: Tuesday, October 16, 2018 2:23:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline


External Email - Use Caution

Sorry. Here are the good links :

http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1maf5ah0hw0
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=abmzg2jvk9t

Maxime

On Oct 16, 2018, at 2:22 PM, Maxime Perron 
mailto:maxime.perro...@ulaval.ca>> wrote:


External Email - Use Caution

Hi Bram,

No worries.

Here is the link : http://gate.nmr.mgh.harvard.edu/filedrop2/?a=al9nxdabh5h

Thanks,
Maxime

On Oct 16, 2018, at 1:11 PM, Diamond, Bram Ryder 
mailto:brdiam...@mgh.harvard.edu>> wrote:


Hi Maxime,

I'm having trouble finding your data - can you please use the filedrop instead?

https://gate.nmr.mgh.harvard.edu/filedrop2/

Thanks,
Bram


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Maxime Perron 
mailto:maxime.perro...@ulaval.ca>>
Sent: Friday, October 12, 2018 11:17:07 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline

External Email - Use Caution

Hi Bram,

Thank you very much for the reply, I'm glad you'll have some time to look at 
the issue. Please don't hesitate to contact me should anything specific be 
needed. I'll be happy to contribute!

Many thanks,
Maxime​
​

De : 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 de la part de Diamond, Bram Ryder 
mailto:brdiam...@mgh.harvard.edu>>
Envoyé : 11 octobre 2018 13:18
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Midline

Hi Maxime,

I'll take a look at your data and the issue you're having and get back to you 
after the weekend.

Best,
Bram

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Maxime Perron 
mailto:maxime.perro...@ulaval.ca>>
Sent: Tuesday, September 25, 2018 1:14:08 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline

External Email - Use Caution

Hi Freesurfer Experts,

About 2 weeks ago, I sent a question about the midline correction but have not 
yet received a feedback. I am wondering if someone had time to check my data or 
has an idea on how to correct the bad midline.

I tried to correct the aseg.presurf.mgz (Freesurfer v.6.0.0) many times with 
different autorecon (wm, cp, noaseg); still, although the segmentation changes, 
the midline doesn’t follow the new segmentation.

Since 10 of my subjects show this error, a solution is much needed.

Many thanks for your help!

Best,
Maxime​

De : 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 de la part de Maxime Perron 
mailto:maxime.perro...@ulaval.ca>>
Envoyé : 17 septembre 2018 10:00
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

External Email - Use Caution

Hi Freesurfer Experts,

I was wondering if you have had time to look at my data to correct my midline 
problems? Many of my subjects have this problem.

Best regards,
Maxime

De : Maxime Perron
Envoyé : 13 septembre 2018 22:29
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

Hi Bruce,

I upload my subject to the ftp site as you requested. In the file midline_MP, 
you will find a file named Freesurfer_S043_test in which I made modifications 
on the aseg.presurf. The other file is the participant without modification.

The problem of the midline is from the coronal slice 137 to 157. For example, 
Talairach: 1.9 4.6 14.3.

Thank you for all your help,
Maxime

> On Sep 13, 2018, at 10:08 AM, Bruce Fischl 
> mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>
> Hi Maxime
>
> if you upload a gzipped tar file of the entire subject dir to our ftp site we 
> will take a look. Please include voxel coordinates of the spots you think are 
> inaccurate.
>
> cheers
> Bruce
> On Thu, 13 Sep 2018, Maxime Perron wrote:
>
>>   External Email - Use Caution
>>
>> Hi Freesurfer Experts,
>>
>> I tried to correct the midline with the information you provided me. Indeed, 
>> I tried to correct the aseg.presurf (Freesurfer v.6) using Freeview

Re: [Freesurfer] Correction Needed for the Midline

[Maxime Perron]

External Email - Use Caution
Hi Bram,

I modified the label of the lateral ventricules because they were mislabeled too (Freesurfer_S043_test). I didn't change the label of the CC_*. Do you think that can fix the middle line?
​ 

Thanks,
Maxime




De : freesurfer-boun...@nmr.mgh.harvard.edu  de la part de Diamond, Bram Ryder 
Envoyé : 16 octobre 2018 14:36
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Midline
 



Hi Maxime,


What did you edit in the
 aseg? It looks like the CC_* have been mislabeled.


Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu  on behalf of Maxime Perron 
Sent: Tuesday, October 16, 2018 2:23:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline
 



External Email - Use Caution

Sorry. Here are the good links : 


http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1maf5ah0hw0
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=abmzg2jvk9t


Maxime 


On Oct 16, 2018, at 2:22 PM, Maxime Perron <maxime.perro...@ulaval.ca> wrote:



External Email - Use Caution


Hi Bram,


No worries.


Here is the link : http://gate.nmr.mgh.harvard.edu/filedrop2/?a=al9nxdabh5h


Thanks,
Maxime 




On Oct 16, 2018, at 1:11 PM, Diamond, Bram Ryder <brdiam...@mgh.harvard.edu> wrote:




Hi Maxime,


I'm having trouble finding your data - can you please use the filedrop instead?


https://gate.nmr.mgh.harvard.edu/filedrop2/


Thanks,
Bram





From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Maxime Perron <maxime.perro...@ulaval.ca>
Sent: Friday, October 12, 2018 11:17:07 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline
 


External Email - Use Caution


Hi Bram, 


Thank you very much for the reply, I'm glad you'll have some time to look at the issue. Please don't hesitate to contact me should anything specific be needed. I'll be happy to contribute!

Many thanks,
Maxime​
​ 

De : freesurfer-boun...@nmr.mgh.harvard.edu
 <freesurfer-boun...@nmr.mgh.harvard.edu> de la part de Diamond, Bram Ryder <brdiam...@mgh.harvard.edu>
Envoyé : 11 octobre 2018 13:18
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Midline
 



Hi Maxime,


I'll take a look at your data and the issue you're having and get back to you after the weekend.


Best,
Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu
 <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Maxime Perron <maxime.perro...@ulaval.ca>
Sent: Tuesday, September 25, 2018 1:14:08 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline
 


    External Email - Use Caution

Hi Freesurfer Experts,
 
About 2 weeks ago, I sent a question about the midline correction but have not yet received a feedback. I am wondering if someone had time to check my data or has an idea on how to correct the bad midline. 

I tried to correct the aseg.presurf.mgz (Freesurfer v.6.0.0) many times with different autorecon (wm, cp, noaseg); still, although the segmentation changes, the midline doesn’t follow the new segmentation.
 
Since 10 of my subjects show this error, a solution is much needed.
 
Many thanks for your help!
 
Best,
Maxime​

De : freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> de la part de Maxime Perron <maxime.perro...@ulaval.ca>
Envoyé : 17 septembre 2018 10:00
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

    External Email - Use Caution

Hi Freesurfer Experts,

I was wondering if you have had time to look at my data to correct my midline problems? Many of my subjects have this problem.

Best regards,
Maxime

De : Maxime Perron
Envoyé : 13 septembre 2018 22:29
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

Hi Bruce,

I upload my subject to the ftp site as you requested. In the file midline_MP, you will find a file named Freesurfer_S043_test in which I made modifications on the aseg.presurf. The other file is the participant without modification.

The problem of the midline is from the coronal slice 137 to 157. For example, Talairach: 1.9 4.6 14.3.

Thank you for all your help,
Maxime

> On Sep 13, 2018, at 10:08 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
>
> Hi Maxime
>
> if you upload a gzipped tar file of the entire subject dir to our ftp site we will take a look. Please include voxel coordinates of the spots you think are inaccurate.
>
> cheers
> Bruce
> On Thu, 13 Sep 2018, Maxime P

Re: [Freesurfer] Correction Needed for the Midline

[Diamond, Bram Ryder]

Possibly - I would definitely start there. The surfaces are following the 
corpus callosum into the right hemisphere because the aseg labeling is off.


Best,

Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Maxime Perron 

Sent: Tuesday, October 16, 2018 2:48:46 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline


External Email - Use Caution

Hi Bram,

I modified the label of the lateral ventricules because they were mislabeled 
too (Freesurfer_S043_test). I didn't change the label of the CC_*. Do you think 
that can fix the middle line?
​

Thanks,
Maxime



De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Diamond, Bram Ryder 

Envoyé : 16 octobre 2018 14:36
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Midline


Hi Maxime,


What did you edit in the aseg? It looks like the CC_* have been mislabeled.


Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Maxime Perron 

Sent: Tuesday, October 16, 2018 2:23:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline


External Email - Use Caution

Sorry. Here are the good links :

http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1maf5ah0hw0
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=abmzg2jvk9t

Maxime

On Oct 16, 2018, at 2:22 PM, Maxime Perron 
mailto:maxime.perro...@ulaval.ca>> wrote:


External Email - Use Caution

Hi Bram,

No worries.

Here is the link : http://gate.nmr.mgh.harvard.edu/filedrop2/?a=al9nxdabh5h

Thanks,
Maxime

On Oct 16, 2018, at 1:11 PM, Diamond, Bram Ryder 
mailto:brdiam...@mgh.harvard.edu>> wrote:


Hi Maxime,

I'm having trouble finding your data - can you please use the filedrop instead?

https://gate.nmr.mgh.harvard.edu/filedrop2/

Thanks,
Bram


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Maxime Perron 
mailto:maxime.perro...@ulaval.ca>>
Sent: Friday, October 12, 2018 11:17:07 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline

External Email - Use Caution

Hi Bram,

Thank you very much for the reply, I'm glad you'll have some time to look at 
the issue. Please don't hesitate to contact me should anything specific be 
needed. I'll be happy to contribute!

Many thanks,
Maxime​
​

De : 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 de la part de Diamond, Bram Ryder 
mailto:brdiam...@mgh.harvard.edu>>
Envoyé : 11 octobre 2018 13:18
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Midline

Hi Maxime,

I'll take a look at your data and the issue you're having and get back to you 
after the weekend.

Best,
Bram

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Maxime Perron 
mailto:maxime.perro...@ulaval.ca>>
Sent: Tuesday, September 25, 2018 1:14:08 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline

External Email - Use Caution

Hi Freesurfer Experts,

About 2 weeks ago, I sent a question about the midline correction but have not 
yet received a feedback. I am wondering if someone had time to check my data or 
has an idea on how to correct the bad midline.

I tried to correct the aseg.presurf.mgz (Freesurfer v.6.0.0) many times with 
different autorecon (wm, cp, noaseg); still, although the segmentation changes, 
the midline doesn’t follow the new segmentation.

Since 10 of my subjects show this error, a solution is much needed.

Many thanks for your help!

Best,
Maxime​

De : 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 de la part de Maxime Perron 
mailto:maxime.perro...@ulaval.ca>>
Envoyé : 17 septembre 2018 10:00
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

External Email - Use Caution

Hi Freesurfer Experts,

I was wondering if you have had time to look at my data to correct my midline 
problems? Many of my subjects have this problem.

Best regards,
Maxime

De : Maxime Perron
Envoyé : 13 septembre 2018 22:29
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

Hi Bruce,

I upload my subject to the ftp site as you requested. In the file midline_MP, 
you will find a file named Freesurfer_S043_test in 

Re: [Freesurfer] Correction Needed for the Midline

[Maxime Perron]

External Email - Use Caution

There surely seems to be a link indeed; I'll look at where to correct the labeling and will give you feedback on the result. In the meantime, should you have any advice on such an optimal way, I'll be glad to hear it.

I'll keep you posted soon in all cases.

Many thanks for your help,
Maxime
​



De : freesurfer-boun...@nmr.mgh.harvard.edu  de la part de Diamond, Bram Ryder 
Envoyé : 16 octobre 2018 14:54
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Midline
 



Possibly - I would definitely start there. The surfaces are following the
corpus callosum into the right hemisphere because the aseg labeling is off.


Best,
Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu  on behalf of Maxime Perron 
Sent: Tuesday, October 16, 2018 2:48:46 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline
 




External Email - Use Caution

Hi Bram,

I modified the label of the lateral ventricules because they were mislabeled too (Freesurfer_S043_test). I didn't change the label of the CC_*. Do you think that can fix the middle line?
​ 

Thanks,
Maxime




De : freesurfer-boun...@nmr.mgh.harvard.edu  de la part de Diamond, Bram Ryder 
Envoyé : 16 octobre 2018 14:36
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Midline
 



Hi Maxime,


What did you edit in the
 aseg? It looks like the CC_* have been mislabeled.


Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu  on behalf of Maxime Perron 
Sent: Tuesday, October 16, 2018 2:23:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline
 



External Email - Use Caution

Sorry. Here are the good links : 


http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1maf5ah0hw0
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=abmzg2jvk9t


Maxime 


On Oct 16, 2018, at 2:22 PM, Maxime Perron <maxime.perro...@ulaval.ca> wrote:



External Email - Use Caution


Hi Bram,


No worries.


Here is the link : http://gate.nmr.mgh.harvard.edu/filedrop2/?a=al9nxdabh5h


Thanks,
Maxime 




On Oct 16, 2018, at 1:11 PM, Diamond, Bram Ryder <brdiam...@mgh.harvard.edu> wrote:




Hi Maxime,


I'm having trouble finding your data - can you please use the filedrop instead?


https://gate.nmr.mgh.harvard.edu/filedrop2/


Thanks,
Bram





From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Maxime Perron <maxime.perro...@ulaval.ca>
Sent: Friday, October 12, 2018 11:17:07 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline
 


External Email - Use Caution


Hi Bram, 


Thank you very much for the reply, I'm glad you'll have some time to look at the issue. Please don't hesitate to contact me should anything specific be needed. I'll be happy to contribute!

Many thanks,
Maxime​
​ 

De : freesurfer-boun...@nmr.mgh.harvard.edu
 <freesurfer-boun...@nmr.mgh.harvard.edu> de la part de Diamond, Bram Ryder <brdiam...@mgh.harvard.edu>
Envoyé : 11 octobre 2018 13:18
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Midline
 



Hi Maxime,


I'll take a look at your data and the issue you're having and get back to you after the weekend.


Best,
Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu
 <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Maxime Perron <maxime.perro...@ulaval.ca>
Sent: Tuesday, September 25, 2018 1:14:08 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline
 


    External Email - Use Caution

Hi Freesurfer Experts,
 
About 2 weeks ago, I sent a question about the midline correction but have not yet received a feedback. I am wondering if someone had time to check my data or has an idea on how to correct the bad midline. 

I tried to correct the aseg.presurf.mgz (Freesurfer v.6.0.0) many times with different autorecon (wm, cp, noaseg); still, although the segmentation changes, the midline doesn’t follow the new segmentation.
 
Since 10 of my subjects show this error, a solution is much needed.
 
Many thanks for your help!
 
Best,
Maxime​

De : freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> de la part de Maxime Perron <maxime.perro...@ulaval.ca>
Envoyé : 17 septembre 2018 10:00
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

    External Email - Use Caution

Hi Freesurfer Experts,

I was wondering if you have had time to look at my data to correct my midline problems? Man

Re: [Freesurfer] Correction for the Optic Nerve

[Bruce Fischl]

Hi Antonella,

it's hard to say just looking at a single slice. Why do you think you 
need to correct it?

Bruce
On Wed, 3 Aug 2011, Antonella Kis wrote:


Hi Bruce,

I will be very grateful if you or someone else  can give me an advise if I 
should do some corrections for the optic nerve in the following
slice.

Many thanks,
Antonella

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[Freesurfer] correction for behavioral varialbles in qdec

[Rosa Steimke]

HI,
i have a question regarding qdec. If i load a designfile with 4 variables, but 
than i only select 1 for analysis, does qdec then correct for the other 
variables that i did not select? or do i have to select them?
thanks in advance!!
rosa
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[Freesurfer] correction on question: offset in qdec GUI

[stdp82]

 Hi list,
I have a question, probably trivial, on OFFSET in qdec GUI. What's this? And 
what I can do using it?


Stefano --- Begin Message ---
 Hi list,
I have a question, probably trivial, on onset in qdec GUI. What's this? And 
what I can do using it?


Stefano


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Re: [Freesurfer] Correction multiple comparisons for parcelated areas

[Chris Watson]

You can use FDR correction.

On 08/14/2013 08:16 AM, Anita van Loenhoud wrote:

Dear FreeSurfers,

I’m comparing two groups (patients (N=45) and controls (N=93)) on
cortical thickness using 34 parcelated areas in each hemisphere (i.e.
68 areas in total). When correcting for multiple comparisons using
Bonferroni, only one area remains significant. Bonferroni is quite
conservative (alpha needs to be lower than 0.05/68= 0.000735). Could
you recommend any other, more lenient correction statistics for my
data?

In a search through the literature, I encountered adjusted Bonferroni
or Benjamini-Hochberg as alternatives. Do you think these would be
useful statistics, or have I missed other, more appropriate ones?

Thanks a lot,

Anna

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Re: [Freesurfer] Correction multiple comparisons for parcelated areas

[Douglas Greve]

Hi Anna, you can use FDR (ie, Ben-Hoc). You can also use gaussian random 
fields (GRF) to do voxel-wise or cluster-wise stats. In our 
implementation, we actually use a monte carlo simulation. Run mri_glmfit 
and spec the label you want to constrain your results to (--label), then 
run mri_glmfit-sim and specify that you want to do the simulation.
doug



On 8/14/13 8:16 AM, Anita van Loenhoud wrote:
> Dear FreeSurfers,
>
> I’m comparing two groups (patients (N=45) and controls (N=93)) on
> cortical thickness using 34 parcelated areas in each hemisphere (i.e.
> 68 areas in total). When correcting for multiple comparisons using
> Bonferroni, only one area remains significant. Bonferroni is quite
> conservative (alpha needs to be lower than 0.05/68= 0.000735). Could
> you recommend any other, more lenient correction statistics for my
> data?
>
> In a search through the literature, I encountered adjusted Bonferroni
> or Benjamini-Hochberg as alternatives. Do you think these would be
> useful statistics, or have I missed other, more appropriate ones?
>
> Thanks a lot,
>
> Anna
>
> ___
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>
>

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[Freesurfer] Correction of registration in preproc-sess stream

[Jörg Pfannmöller]

Dear freesurfers,

I have a simple question concerning the freesurfer 5.1 FSFAST preprocessing. In 
the preprocessing the functional images are registered to the anatomical ones 
using bbregister. This is the 3rd in a series of 8 preprocessing steps. If the 
preproc-sess registration fails it is possible to achieve a proper registration 
using various options of bbregister. Does it suffice to replace the register 
files created during the preprocessing with the ones received during the 
registration correction in order to attain proper preprocessed data or are 
there routines in steps 4 to 8 in the preprocessing which rely on the 
registration? 

Thanks in advance

 pfannmoe
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Re: [Freesurfer] Correction for Multiple Comparisons - Sign Question

[Douglas N Greve]

That is just the name. It must be different for each call so that the 
files are not overwritten. It does not have to match the sign, but it 
will  be less confusing if it does.
doug

On 06/18/2012 12:38 PM, mdkrue...@uwalumni.com wrote:
> Freesurfers-
>
> When choosing the simulation type does the ending have to match the 
> sim sign? for instance i see examples with
>
> --sim mc-z 1 3 mc-z.pos.3 --sim sign pos
>
> or
>
> --sim mc-z 1 3 mc-z.neg.3 --sim sign neg
>
> I guess what i am asking is what does the first sign (in the 
> mc-z.(SIGN).3 mean?
>
> michael
>
> -- 
> Michael D. Kruepke
> PhD - University of Illinois at Urbana-Champaign
> BA - Psych - University of Wisconsin-Madison
> mdkrue...@gmail.com 
> (262)-483-7449 
>
>
>
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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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] correction for behavioral varialbles in qdec

[Bruce Fischl]

Hi Rosa,

you have to select them.

cheers,
Bruce

On Tue, 4 Aug 2009, Rosa Steimke wrote:

>
> HI,
> i have a question regarding qdec. If i load a designfile with 4 variables, 
> but than i only select 1 for analysis, does qdec then correct for the other 
> variables that i did not select? or do i have to select them?
> thanks in advance!!
> rosa
>
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Re: [Freesurfer] correction for behavioral varialbles in qdec

[Rosa Steimke]

Thanks Bruce!!
now i wonder whether it is possible to get a table of all the significant 
blobbs that i found in qdec that gives the size and average p value or some 
other way to find this out?
rosa
 Original-Nachricht 
> Datum: Tue, 4 Aug 2009 08:13:01 -0400 (EDT)
> Von: Bruce Fischl 
> An: Rosa Steimke 
> CC: freesurfer@nmr.mgh.harvard.edu
> Betreff: Re: [Freesurfer] correction for behavioral varialbles in qdec

> Hi Rosa,
> 
> you have to select them.
> 
> cheers,
> Bruce
> 
> On Tue, 4 Aug 2009, Rosa Steimke wrote:
> 
> >
> > HI,
> > i have a question regarding qdec. If i load a designfile with 4
> variables, but than i only select 1 for analysis, does qdec then correct for 
> the
> other variables that i did not select? or do i have to select them?
> > thanks in advance!!
> > rosa
> >
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Re: [Freesurfer] correction for behavioral varialbles in qdec

[Douglas N Greve]

You can run mri_surfcluster on the sig.mgh for this kind of thing.

doug

Rosa Steimke wrote:
> Thanks Bruce!!
> now i wonder whether it is possible to get a table of all the significant 
> blobbs that i found in qdec that gives the size and average p value or some 
> other way to find this out?
> rosa
>  Original-Nachricht 
>   
>> Datum: Tue, 4 Aug 2009 08:13:01 -0400 (EDT)
>> Von: Bruce Fischl 
>> An: Rosa Steimke 
>> CC: freesurfer@nmr.mgh.harvard.edu
>> Betreff: Re: [Freesurfer] correction for behavioral varialbles in qdec
>> 
>
>   
>> Hi Rosa,
>>
>> you have to select them.
>>
>> cheers,
>> Bruce
>>
>> On Tue, 4 Aug 2009, Rosa Steimke wrote:
>>
>> 
>>> HI,
>>> i have a question regarding qdec. If i load a designfile with 4
>>>   
>> variables, but than i only select 1 for analysis, does qdec then correct for 
>> the
>> other variables that i did not select? or do i have to select them?
>> 
>>> thanks in advance!!
>>> rosa
>>>
>>>   
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>
>   

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Phone Number: 617-724-2358 
Fax: 617-726-7422

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[Freesurfer] Correction at the cluster level in Freesurfer

[Olivier Colliot]

Hi Freesurfers,

I was wondering if there exists a procedure in Freesurfer to have 
corrections for multiple comparisons at the cluster level (as in SPM for 
example).

Many thanks
Olivier

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Re: [Freesurfer] correction on question: offset in qdec GUI

[Bruce Fischl]

Hi Stefano

I believe it's the offset of the center of the color scale. So for 
example in the red/positive blue/negative one, the cross-over doesn't 
have to be at 0


cheers
Bruce
On Fri, 22 Mar 2013, std...@virgilio.it wrote:


 Hi list,
I have a question, probably trivial, on OFFSET in qdec GUI. What's this? And
what I can do using it?



Stefano

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Re: [Freesurfer] Correction of registration in preproc-sess stream

[Douglas N Greve]

They rely on the registration. What is failing? It is usually the 
initialization that fails. If you're using FSL, you can try using the 
SPM registration (though it's a little trickier to set up).
doug

On 06/04/2012 05:20 AM, Jörg Pfannmöller wrote:
> Dear freesurfers,
>
> I have a simple question concerning the freesurfer 5.1 FSFAST preprocessing. 
> In the preprocessing the functional images are registered to the anatomical 
> ones using bbregister. This is the 3rd in a series of 8 preprocessing steps. 
> If the preproc-sess registration fails it is possible to achieve a proper 
> registration using various options of bbregister. Does it suffice to replace 
> the register files created during the preprocessing with the ones received 
> during the registration correction in order to attain proper preprocessed 
> data or are there routines in steps 4 to 8 in the preprocessing which rely on 
> the registration?
>
> Thanks in advance
>
>   pfannmoe
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>
>

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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] Correction of registration in preproc-sess stream

[Jörg Pfannmöller]

Dear Doug,

indeed the initialization fails. I was able to initiate bbregister manually, 
giving a good registration result. Can you give me a hint how to 
modify the registration and keeping the preproc-sess stream intact?

Cheers

   pfannmoe
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Re: [Freesurfer] Correction of registration in preproc-sess stream

[Douglas N Greve]

You can try running register-sess outside of preproc-sess, something like
register-sess -s session -fsd bold -per-run -init-spm

before you do that, you need to have spm5 and matlab, and change your 
matlab/startup.m to add the spm5 path
path(path,'/usr/pubsw/common/spm/spm5');

doug

ps. Is this whole brain coverage or are you chopping off some of the brain


On 06/04/2012 11:36 AM, Jörg Pfannmöller wrote:
> Dear Doug,
>
> indeed the initialization fails. I was able to initiate bbregister manually, 
> giving a good registration result. Can you give me a hint how to
> modify the registration and keeping the preproc-sess stream intact?
>
> Cheers
>
> pfannmoe
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] Correction of registration in preproc-sess stream

[Jörg Pfannmöller]

Dear Doug,

I am having a partial field of view and a full brain scan. How can I integrate 
the results in the preproc-sess sequence in order to complete the preprocessing 
correctly?

Cheers pfannmoe


On Mon, 04 Jun 2012 11:42:32 -0400
Douglas N Greve  wrote:

> You can try running register-sess outside of preproc-sess, something like
> register-sess -s session -fsd bold -per-run -init-spm
> 
> before you do that, you need to have spm5 and matlab, and change your 
> matlab/startup.m to add the spm5 path
> path(path,'/usr/pubsw/common/spm/spm5');
> 
> doug
> 
> ps. Is this whole brain coverage or are you chopping off some of the brain
> 
> 
> On 06/04/2012 11:36 AM, Jörg Pfannmöller wrote:
> > Dear Doug,
> >
> > indeed the initialization fails. I was able to initiate bbregister 
> > manually, giving a good registration result. Can you give me a hint how to
> > modify the registration and keeping the preproc-sess stream intact?
> >
> > Cheers
> >
> > pfannmoe
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> 
> -- 
> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> ___
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> 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] Correction of registration in preproc-sess stream

[Douglas Greve]

You can't do directly from preproc-sess, but you can do it from 
register-sess if you have an additional whole brain acquisition in the 
same session. This can be any acquisition (BOLD, MPRAGE, low-b DTI, etc) 
as long as it is whole brain. If your anatomical was acquired in the 
same session, then it is even easier because you can run register-sess 
with the -init-header option (instead of using fsl or spm). This assumes 
that the subject did not move more than 5mm between EPI and MPRAGE 
(usually the case). Let me know if this works for you.
doug

On 6/5/12 6:03 AM, Jörg Pfannmöller wrote:
> Dear Doug,
>
> I am having a partial field of view and a full brain scan. How can I 
> integrate the results in the preproc-sess sequence in order to complete the 
> preprocessing correctly?
>
> Cheers pfannmoe
>
>
> On Mon, 04 Jun 2012 11:42:32 -0400
> Douglas N Greve  wrote:
>
>> You can try running register-sess outside of preproc-sess, something like
>> register-sess -s session -fsd bold -per-run -init-spm
>>
>> before you do that, you need to have spm5 and matlab, and change your
>> matlab/startup.m to add the spm5 path
>> path(path,'/usr/pubsw/common/spm/spm5');
>>
>> doug
>>
>> ps. Is this whole brain coverage or are you chopping off some of the brain
>>
>>
>> On 06/04/2012 11:36 AM, Jörg Pfannmöller wrote:
>>> Dear Doug,
>>>
>>> indeed the initialization fails. I was able to initiate bbregister 
>>> manually, giving a good registration result. Can you give me a hint how to
>>> modify the registration and keeping the preproc-sess stream intact?
>>>
>>> Cheers
>>>
>>>  pfannmoe
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>> -- 
>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>
>> ___
>> 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] Correction of registration in preproc-sess stream

[Jörg Pfannmöller]

Dear Doug,

I have tested the various options of register-sess. The result was a succesful 
registration of the functional 
to the anatomical image. This registration with register-sess is performed 
after preproc-sess failed to achieve 
a proper registration. The register.dof6.dat file is updated by register-sess. 
I would like to ask a last thing just in order to make it definite. Can I now 
use those data for example with selxavg3-sess in order to compute 
the activated areas for this subject?

Greets pfannmoe


On Tue, 05 Jun 2012 18:30:42 -0400
Douglas Greve  wrote:

> You can't do directly from preproc-sess, but you can do it from 
> register-sess if you have an additional whole brain acquisition in the 
> same session. This can be any acquisition (BOLD, MPRAGE, low-b DTI, etc) 
> as long as it is whole brain. If your anatomical was acquired in the 
> same session, then it is even easier because you can run register-sess 
> with the -init-header option (instead of using fsl or spm). This assumes 
> that the subject did not move more than 5mm between EPI and MPRAGE 
> (usually the case). Let me know if this works for you.
> doug
> 
> On 6/5/12 6:03 AM, Jörg Pfannmöller wrote:
> > Dear Doug,
> >
> > I am having a partial field of view and a full brain scan. How can I 
> > integrate the results in the preproc-sess sequence in order to complete the 
> > preprocessing correctly?
> >
> > Cheers pfannmoe
> >
> >
> > On Mon, 04 Jun 2012 11:42:32 -0400
> > Douglas N Greve  wrote:
> >
> >> You can try running register-sess outside of preproc-sess, something like
> >> register-sess -s session -fsd bold -per-run -init-spm
> >>
> >> before you do that, you need to have spm5 and matlab, and change your
> >> matlab/startup.m to add the spm5 path
> >> path(path,'/usr/pubsw/common/spm/spm5');
> >>
> >> doug
> >>
> >> ps. Is this whole brain coverage or are you chopping off some of the brain
> >>
> >>
> >> On 06/04/2012 11:36 AM, Jörg Pfannmöller wrote:
> >>> Dear Doug,
> >>>
> >>> indeed the initialization fails. I was able to initiate bbregister 
> >>> manually, giving a good registration result. Can you give me a hint how to
> >>> modify the registration and keeping the preproc-sess stream intact?
> >>>
> >>> Cheers
> >>>
> >>>  pfannmoe
> >>> ___
> >>> Freesurfer mailing list
> >>> Freesurfer@nmr.mgh.harvard.edu
> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>>
> >>>
> >> -- 
> >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> >>
> >> ___
> >> 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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-- 
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Re: [Freesurfer] Correction of registration in preproc-sess stream

[Douglas N Greve]

You should run preproc-sess again to make sure that all the files that 
need to be updated after the registration are properly updated. This 
should not change the registration -- it should just look at the time 
stamps of  the files and update any that need updating. However, if the 
files earlier in the stream were changed at some point, then it might 
try to regenerate the registration, so just in case make a backup of 
your registration files before running preproc-sess.
doug



On 06/27/2012 08:08 AM, Jörg Pfannmöller wrote:
> Dear Doug,
>
> I have tested the various options of register-sess. The result was a 
> succesful registration of the functional
> to the anatomical image. This registration with register-sess is performed 
> after preproc-sess failed to achieve
> a proper registration. The register.dof6.dat file is updated by 
> register-sess. I would like to ask a last thing just in order to make it 
> definite. Can I now use those data for example with selxavg3-sess in order to 
> compute
> the activated areas for this subject?
>
> Greets pfannmoe
>
>
> On Tue, 05 Jun 2012 18:30:42 -0400
> Douglas Greve  wrote:
>
>> You can't do directly from preproc-sess, but you can do it from
>> register-sess if you have an additional whole brain acquisition in the
>> same session. This can be any acquisition (BOLD, MPRAGE, low-b DTI, etc)
>> as long as it is whole brain. If your anatomical was acquired in the
>> same session, then it is even easier because you can run register-sess
>> with the -init-header option (instead of using fsl or spm). This assumes
>> that the subject did not move more than 5mm between EPI and MPRAGE
>> (usually the case). Let me know if this works for you.
>> doug
>>
>> On 6/5/12 6:03 AM, Jörg Pfannmöller wrote:
>>> Dear Doug,
>>>
>>> I am having a partial field of view and a full brain scan. How can I 
>>> integrate the results in the preproc-sess sequence in order to complete the 
>>> preprocessing correctly?
>>>
>>> Cheers pfannmoe
>>>
>>>
>>> On Mon, 04 Jun 2012 11:42:32 -0400
>>> Douglas N Greve   wrote:
>>>
 You can try running register-sess outside of preproc-sess, something like
 register-sess -s session -fsd bold -per-run -init-spm

 before you do that, you need to have spm5 and matlab, and change your
 matlab/startup.m to add the spm5 path
 path(path,'/usr/pubsw/common/spm/spm5');

 doug

 ps. Is this whole brain coverage or are you chopping off some of the brain


 On 06/04/2012 11:36 AM, Jörg Pfannmöller wrote:
> Dear Doug,
>
> indeed the initialization fails. I was able to initiate bbregister 
> manually, giving a good registration result. Can you give me a hint how to
> modify the registration and keeping the preproc-sess stream intact?
>
> Cheers
>
>   pfannmoe
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
 -- 
 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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 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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>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>

-- 
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
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Re: [Freesurfer] Correction of registration in preproc-sess stream

[Jörg Pfannmöller]

P.S.:I executed the following sequence to achieve the first level analysis with 
a correct registration.

preproc-sess -s session_id -fsd bold -sliceorder siemens -surface fsaverage 
lhrh -mni305 -fwhm 0 -per-run

register-sess -s session_id  -fsd bold -per-run -init-header

preproc-sess -s session_id -fsd bold -sliceorder siemens -surface fsaverage 
lhrh -mni305 -fwhm 0 -per-run -noreg -regfile 
session_id/bold/001/register.dof6.dat -force

selxavg3-sess -s session_id -analysis stim.sm0.lh -no-preproc


As far as I can see this is the right procedure. Do you agree or is there 
another or simpler way to correct the registration and proceed with a first 
level analysis?
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Re: [Freesurfer] Correction of registration in preproc-sess stream

[Douglas N Greve]

No, that looks correct.
doug

On 06/27/2012 12:05 PM, Jörg Pfannmöller wrote:
> P.S.:I executed the following sequence to achieve the first level analysis 
> with a correct registration.
>
> preproc-sess -s session_id -fsd bold -sliceorder siemens -surface fsaverage 
> lhrh -mni305 -fwhm 0 -per-run
>
> register-sess -s session_id  -fsd bold -per-run -init-header
>
> preproc-sess -s session_id -fsd bold -sliceorder siemens -surface fsaverage 
> lhrh -mni305 -fwhm 0 -per-run -noreg -regfile 
> session_id/bold/001/register.dof6.dat -force
>
> selxavg3-sess -s session_id -analysis stim.sm0.lh -no-preproc
>
>
> As far as I can see this is the right procedure. Do you agree or is there 
> another or simpler way to correct the registration and proceed with a first 
> level analysis?
> ___
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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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] Correction at the cluster level in Freesurfer

[Douglas N Greve]

Yes, we use simulation-based. Look at the group analysis tutorial. You 
will have to run mri_glmfit-sim (or run the script that QDEC creates).

doug

Olivier Colliot wrote:
> Hi Freesurfers,
>
> I was wondering if there exists a procedure in Freesurfer to have 
> corrections for multiple comparisons at the cluster level (as in SPM for 
> example).
>
> Many thanks
> Olivier
>
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>
>
>   

-- 
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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
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[Freesurfer] correction for multiple comparison: simulation vs grf vs cache

[john Anderson]

External Email - Use Caution

Hi Dr Greve,
I would like to correct surface based analyses of PET data for multiple 
comparisons. I ran group comparisons in three spaces. left and right 
hemispheres and subcortical.
I used the method --cache in mri_glmfit-sim to correct the analyses in eft and 
right hemispheres.
I used the method --grf in mri_glmfit-sim to correct the analyses in 
subcortical regions.
My questions are:

In one of your kind responses to a collegue here 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-January/035650.html
you had suggested  "If you want to use GRF, you should use smooth by twice the 
native voxel size. I would not go higher than .01 on the threshold".
Would you mind clarify what it means don;t go higher than .01 is this the cwp 
threshold? also smoothing by twice the native voxel is this means fwhm=2mm?

The methods --cache and --grf are giving me the expected results.. when  I 
should consider using simulation --perm ?

Thanks for any clarification
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Re: [Freesurfer] correction for multiple comparison: simulation vs grf vs cache

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

Hi John, I would recommend that you use permutation. See 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
In terms of the threshold, "not going higher than .01" means using 
between 0 and .01 (eg, don't use .05). For permutation, you can use 
whatever thershold you want.

On 1/23/19 8:46 AM, john Anderson wrote:
>
> External Email - Use Caution
>
> Hi Dr Greve,
> I would like to correct surface based analyses of PET data for 
> multiple comparisons. I ran group comparisons in three spaces. left 
> and right hemispheres and subcortical.
> I used the method --cache in mri_glmfit-sim to correct the analyses in 
> eft and right hemispheres.
> I used the method --grf in mri_glmfit-sim to correct the analyses in 
> subcortical regions.
> My questions are:
>
> In one of your kind responses to a collegue here 
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-January/035650.html
> you had suggested  "If you want to use GRF, you should use smooth by 
> twice the native voxel size. I would not go higher than .01 on the 
> threshold".
> Would you mind clarify what it means don;t go higher than .01 is this 
> the cwp threshold? also smoothing by twice the native voxel is this 
> means fwhm=2mm?
>
> The methods --cache and --grf are giving me the expected results.. 
> when  I should consider using simulation --perm ?
>
> Thanks for any clarification
> John
>
>
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[Freesurfer] Correction for head size - Total hippocampal volume and subfield volume

[New Fei Ho]

Hi,

I have two questions regarding ICV correction for total hippocampal volume
(from aseg.stats) and for hippocampal subfield volumes.

1) Total hippocampal volume: I am using the mri_label_volume script that
uses the atlas normalization factor as an estimate for total ICV two
T1-weighted scans (T1  = 1100ms, TE = 3.39ms, TR = 2530 ms, FOV = 256) and
a third T1-weighted (T1 = 1100ms, TE = 1.54ms, TR = 2200ms, FOV = 192)
conducted in the same session.
The pearson's correlation coefficient between the left hippocampal volume
of the 3 scans and their corrected volumes (35 healthy subjects) are .998,
.662 and .997.For the right hippocampal volumes, the coefficients are
.678, .995 and .893.

If the eTIV accounts for variances in head, are the r-values too high
(especially .998, .995)?

2) As for hippocampal subfield volume correction for head size, can I
similarly apply the same method, or would you recommend just using total
ICV (from aseg.stats) as a covariate?

Thanks,
New Fei
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Re: [Freesurfer] CORRECTION ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

[zkaufman]

Here is the proper link.

ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/fsaverage.tar.gz


>> Bruce,
>>
>> By "symlink from your /mnt/hgfs/mydata/fsaverage to
>> /usr/local/freesurfer/subjects/fsaverage" you mean "ln -s
>> /mnt/hgfs/mydata/fsaverage  /usr/local/freesurfer/subjects/fsaverage" ?
>> which fsaverage is the target ?
>>
>> Thanks,
>> Mahmoud
>>
>
> The "target" fsaverage is the one that came with the installation. Which
> you no longer have so I have created a link for you to download it again
> and put it back in your $SUBJECTS_DIR (see next answer).
>
>
>> On Fri, Sep 19, 2014 at 9:50 AM, Mahmoud  wrote:
>>
>>> Bruce,
>>>
>>> Thank you for your follow up and advice. Please let me know:
>>> 1- How to download the fsaverage again?
>
> Ive created a link for you to download it:
> ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/Linux_centos4_x86_64/fsaverage.tar.gz
>
>>> 2- should I do the symlink manually or it will be done by recon-all
>>> later ?
>
> Just extract the file above into your $SUBJECTS_DIR so that you have a
> $SUBJECTS_DIR/fsaverage directory and recon-all will take care of the
> rest.
>
>>> 3- What steps should I take before running the recon-all -all ? should
>>> I
>>> create any specific directory? set any permission ?
>
> None. Hopefully this will just work.
>
>
> -Zeke
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>
>

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[Freesurfer] Correction: TRACULA FS 7.2.0 Error: domainname: Command not found. Too many )’s.

[juergen.haenggi]

External Email - Use Caution

Dear TRACULA experts

I would like to correct my statement in my former email.
The "Error: domainname: Command not found. Too many )’s.“ also occurs if using 
TRACULA in FS 7.1.1, but trac-all does not stop (in contrast to FS 7.2.0), and 
therefore I wrongly claimed that this error does not occur in FS 7.1.1.

Because I would like to use the new features of TRACULA in FS 7.2.0 (thanks a 
lot to the developers), I am looking for a work around of this error.

Sorry, for posting this question again, but the solution proposed 
(https://secure-web.cisco.com/1zm53xsYIz9OTCov14EoLN5S3ILc_IPbOKLZjDIuBmZSHy-a9qEKlyvbY7g3_zY63DWaZVDBNGW30nXhS5tu_hMDtwS3GQQtK-fuHos9uLRYMuz_V4DljnKR0hueTQ1o7iChjjQByKj-E2ko9d1Mw6w_WuV9DFlRESmYrE7rdU4dCw-TELeeK4vssLsEDEIfssdjKDaYSZ76fWBTtpSxGKlAf49k_Nqggo7tWvMe9We7VPLZrN7Ypwq2IONzU0oqb4UF_sGIQyeO_Ptim_cefZg/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg70662.html)
 did not work.

Thanks in advance
Regards
Jürgen

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