[Freesurfer] Freeview automation

[Garikoitz Lerma-Usabiaga]

Hi list,
is it possible to automate Freeview automation from the command line?

I want to automatically render 3D images of the hippocampus (I have a
separate volume, based on hippo-subfields) and have an image for all
subjects for quality checking.

thanks!
Gari
___
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] Conversion

[Anna Josefson]

Dear FreeSurfer users!

 I am new to Freesurfer, and I have succesfully managed to run recon-all on
my data, for every subject.

Now I plan to use the output  - some of the different cortical and
subcortical brain structures as ROI's in my SPM analyses.

Then I would have to convert from freesurfer space to SPM space via the
coordinates.

And - I would also have to  convert from .mgz to .nii data format.

Does any have any tips on how to do this? Or a script?

Kind Regards,
Anna B. Josefson
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] Conversion

[Azeez Adebimpe]

use mri_convertcheck this 
linkhttps://surfer.nmr.mgh.harvard.edu/pub/docs/html/mri_convert.help.xml.html

Azeez Adebimpe


Date: Fri, 31 May 2013 13:23:20 +0200
From: anna.b.josef...@gmail.com
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Conversion

Dear FreeSurfer users!

 I am new to Freesurfer, and I have succesfully managed to run recon-all on my 
data, for every subject.

Now
 I plan to use the output  - some of the different cortical and 
subcortical brain structures as ROI's in my SPM analyses.

Then I would have to convert from freesurfer space to SPM space via the 
coordinates.

And - I would also have to  convert from .mgz to .nii data format.


Does any have any tips on how to do this? Or a script?

Kind Regards,
Anna B. Josefson

___
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


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] Editing after reconstruction

[Cristian Paz]

Hello FS-ers,

I have a beginner question.

I am wondering about editing. Since I have no  superior of me in my lab to
inspect or guide me in my freesurfer analyses - I get a bit worried that I
might oversee some important errors from recon-all.

If there is nothing that is strikingly wrong in the output from recon-all -
should I then expect my results to be good enough for group analyses?

If there is no error messages, and nothing that looks strange when I open
rsults in tkmedit (for a beginner)?

How often does a reconstruction from Freesurfer need to be
edited,(roughfly, on average) if you have a group of lets say 32 subjects ?

thank you so much for your help!

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


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

Re: [Freesurfer] Freeview automation

[Ruopeng Wang]

There is a screenshot option -ss from the command-line. Run 'freeview -h' will 
show you all the available options. 

Ruopeng

On May 31, 2013, at 6:16 AM, Garikoitz Lerma-Usabiaga  
wrote:

> Hi list, 
> is it possible to automate Freeview automation from the command line? 
> 
> I want to automatically render 3D images of the hippocampus (I have a 
> separate volume, based on hippo-subfields) and have an image for all subjects 
> for quality checking.
> 
> thanks!
> Gari 
> ___
> 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.

Re: [Freesurfer] TRACULA outputs out of expected range

[Ali Ezzati]

Thanks a lot Anastasia.

I had an extra volume at the end of file which was just an average of all other 
volumes (automatically generated by philips scanner). Removing that extra 
volume solved my problem.

Thank you again,
Ali Ezzati

From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: Friday, May 17, 2013 11:49 AM
To: Ali Ezzati
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] TRACULA outputs out of expected range

Hi Ali - The last row of your gradient table is "0 0 0". And yet, based on
the b-value table, it is supposed to correspond to a diffusion-weighted
volume with b=800. So there must have been a diffusion-encoding gradient
vector that was applied to acquire that volume, and you need to find out
what that gradient vector was and put it in that line.

Also, some of the lines in the gradient table follow the Xe-Y notation and
some don't. I don't know if this will cause a problem, it's possible that
it might depending on the platform. In any case, it's good to be
consistent to be safe.

Hope this helps,
a.y

On Mon, 6 May 2013, Ali Ezzati wrote:

> Hi Anastasia,
>
> I think I still have the previous problem of "out of range outputs". For 
> example: based on literature (& your previous TRACULA-bases articles) the 
> expected range of mean FA value is around 0.4-0.5, but the average FA for my 
> data is 0.7-0.8. The same is true with MD, RD, AD values. Comparative 
> analysis between groups is not promising too. This makes me think something 
> is going wrong with my analysis/settings, although I get no error during 
> processing.
>
> I can only think of settings in .dmricr or bvec file to be a source of error, 
> so I have attached a sample of them for one of the subjects to this email. I 
> would be grateful if you could take a look at them and let me know if they 
> are as expected.
>
> There are 3 .bvec files inside the "dmri" folder:
> 1- dwi_orig.mghdti.bvecs
> 2- bvecs.norot
> 3- bvecs
> The first 2 files are the same as my input .bvec file ("bvecs.norot" is 
> rotated to 3 rows instead of 3 columns).
> File 3 -"bevecs"- is different from the other 2 files.
>
>
> Thank you again for your help,
> Ali
> 
> From: Ali Ezzati
> Sent: Friday, May 03, 2013 11:54 AM
> To: Anastasia Yendiki
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] TRACULA outputs out of expected range
>
> Hi Anastasia,
>
> Thank you for your response. I think I figured out what was the problem:  The 
> delimiter for the 3 column .bvec file MUST be SPACE/TAB, otherwise the 
> program fails to reshape it correctly. In my case the delimiter was "," and 
> the program was reading only the 1st column of it.
>
> I have one more question:   I know that FA values might differ from study to 
> study and from MRI to MRI, but what is a reasonable range for that after 
> analysis with Tracula?  In your study (20011) the range was ~ 0.3-0.6. But 
> for in elderly population the average is around 0.2 higher. Does it sound 
> normal to you? I was not able to find any study using your method in elderly 
> population for comparison.
>
> Thank you,
> Ali
> 
> From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
> Sent: Tuesday, April 30, 2013 3:11 PM
> To: Ali Ezzati
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] TRACULA outputs out of expected range
>
> Hi Ali - This is unusual. It may have something to do with system
> settings. Can you send an example of the two versions of the bvecs files
> that have the different values?
>
> Thanks,
> a.y
>
> On Mon, 29 Apr 2013, Ali Ezzati wrote:
>
>> Hello Experts,
>> I would be grateful if you could help me with this problem:
>>
>> I was able to run all steps of TRACULA on several subjects without any error 
>> message, but all the final
>> outcomes (FA,MD,RD,AD values) are out of the expected range (i.e average FA 
>> values for all tracts are >1).
>>
>> I tried to identify the source of this problem... clearly FA values in 
>> "dmri/dtifit_FA", which is an output
>> of  "prep" step are all out of range. The only source of error that I can 
>> think of is .bvecs file. My input
>> .bvecs files are in 3 columns, exactly as described in the manual.
>>
>> There are two .bvecs file in the "dmri" folder. one is 
>> "dwi_orig.mghdti.bvecs" which is exactly the same as
>> my input .bvecs file and the other one's name is just "bvecs", which has 
>> completely different values. Could
>> this be the source of my problem? or something else is causing this.
>>
>> Thank you,
>> Ali
>>
>>
>>
>>
>
>
> 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

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.
>
> 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 
>> c

Re: [Freesurfer] mprage flag in recon-all

[Bruce Fischl]

Hi Caspar

it changes some parameters to the intensity normalization and segmentation 
to account for the lower SNR and increased CNR in the mprage. You'll need 
to look in the recon-all script for the details


cheers
Bruce


On Thu, 30 May 2013, Caspar M. Schwiedrzik wrote:


Hi!
Is there more documentation on what settings the mprage flag enables in
recon-all?
Specifically, I would be interested which individual steps it affects and
what  the parameters are for each of the steps.
Thanks!
Caspar


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


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

Re: [Freesurfer] Editing after reconstruction

[Bruce Fischl]

Hi Cris

it really depends on your data quality. If it's good then you might be 
fine most of the time. You should scroll through the slices in tkmedit with 
the surfaces overlaid to verify that they do indeed follow the gray/white 
and pial boundaries.


cheers
Bruce
On Fri, 31 May 2013, Cristian Paz wrote:


Hello FS-ers,

I have a beginner question.

I am wondering about editing. Since I have no  superior of me in my lab to
inspect or guide me in my freesurfer analyses - I get a bit worried that I
might oversee some important errors from recon-all.

If there is nothing that is strikingly wrong in the output from recon-all -
should I then expect my results to be good enough for group analyses?

If there is no error messages, and nothing that looks strange when I open
rsults in tkmedit (for a beginner)?

How often does a reconstruction from Freesurfer need to be edited,(roughfly,
on average) if you have a group of lets say 32 subjects ?

thank you so much for your help!

best regards,
Cris



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


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

Re: [Freesurfer] recon-all errors: v5.0.0; dataset 4

[Sudhin A. Shah]

On May 28, 2013, at 3:48 PM, Sudhin A. Shah wrote:

CORRECTING DEFECT 1 (vertices=33, convex hull=57)
After retessellation of defect 1, euler #=-41 (88676,260208,171491) : 
difference with theory (-61) = -20

CORRECTING DEFECT 2 (vertices=30163, convex hull=6211)
error in the retessellation
normal vector of length zero at vertex 88778 with 0 faces
vertex 88778 has 0 face
No such file or directory
Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 
5 19:39:49 UTC 2012 x86_64 GNU/Linux

recon-all -s IN387G exited with ERRORS at Thu May 16 05:11:49 EDT 2013

___
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


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

Re: [Freesurfer] recon-all errors: v5.0.0; dataset 4

[Bruce Fischl]

Hi Sudhin

have you looked at the defect to see what is causing it? It's very big, 
which is probably the root of the problem.


Bruce
On Fri, 31 May 2013, Sudhin A. 
Shah wrote:




On May 28, 2013, at 3:48 PM, Sudhin A. Shah wrote:

  CORRECTING DEFECT 1 (vertices=33, convex hull=57)
  After retessellation of defect 1, euler #=-41
  (88676,260208,171491) : difference with theory (-61) = -20 

  CORRECTING DEFECT 2 (vertices=30163, convex hull=6211)
  error in the retessellation 
  normal vector of length zero at vertex 88778 with 0 faces
  vertex 88778 has 0 face
  No such file or directory
  Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic
  #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux

  recon-all -s IN387G exited with ERRORS at Thu May 16 05:11:49
  EDT 2013

___
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


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] Conversion

[Douglas Greve]

Anna, if you need to get it back into the native anatomical space, see

http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat

You can use nii as the output format instead of mgz

doug


On 5/31/13 7:23 AM, Anna Josefson wrote:

Dear FreeSurfer users!

 I am new to Freesurfer, and I have succesfully managed to run 
recon-all on my data, for every subject.


Now I plan to use the output  - some of the different cortical and 
subcortical brain structures as ROI's in my SPM analyses.


Then I would have to convert from freesurfer space to SPM space via 
the coordinates.


And - I would also have to  convert from .mgz to .nii data format.

Does any have any tips on how to do this? Or a script?

Kind Regards,
Anna B. Josefson


___
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.

Re: [Freesurfer] Average for each voxel across all conditions

[Katie Bettencourt]

Yes, in each analysis directory there is a meanfunc.nii.

Maybe this summer I will switch to FS5, but I have a bunch of experiments
in 4.5 and am not 100% comfortable with the way the retinotopy analysis
needs to be done in FS5, which is a vital component of my work.

Katie


On Thu, May 30, 2013 at 4:50 PM, Douglas N Greve
wrote:

>
> Hi Katie, I don't remember what 4.5 outputs. Is there a "meanfunc"
> volume there? Itwould be much easier to support you if you were using
> version 5.x:)
> doug
>
> On 05/30/2013 04:36 PM, Katie Bettencourt wrote:
> > Hi,
> >
> > I have an experiment where I have 3 conditions in a FIR event related
> > analysis (running FS 4.5).  I need to get the mean activity level for
> > each voxel across all conditions across the run, so that I can
> > calculate percent signal change for each individual voxel.  Is this
> > available (I have analyzed each run separately) somewhere?
> >
> > Katie
> >
> >
> > ___
> > 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/
>
> ___
> 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


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] ventral DC

[Yang, Daniel]

Dear all,

in the aseg.volume, there is a term called 'ventral DC' and I am wondering what 
it is.

I looked up the previous posts and know DC = diencephalon, and it's a grab bag 
of stuff that cannot be resolved.

However, does anyone know what exactly ventral DC is?

Thanks!
Daniel

--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] Freeview automation

[Juan Eugenio Iglesias]

Ender asked me to forward you this:

I had to automate freeview recently.
Freeview can be used via command line.
For options please write
freeview -h
in the console / terminal.

An example command that produces a surface and overlays a map on it:
freeview -f lh.inflated:overlay=L.mgz -cam azimuth 180

Let me know if this helps.

Cheers,

E




On Fri, 2013-05-31 at 08:35 -0400, Ruopeng Wang wrote:
> There is a screenshot option -ss from the command-line. Run 'freeview -h' 
> will show you all the available options. 
> 
> Ruopeng
> 
> On May 31, 2013, at 6:16 AM, Garikoitz Lerma-Usabiaga  
> wrote:
> 
> > Hi list, 
> > is it possible to automate Freeview automation from the command line? 
> > 
> > I want to automatically render 3D images of the hippocampus (I have a 
> > separate volume, based on hippo-subfields) and have an image for all 
> > subjects for quality checking.
> > 
> > thanks!
> > Gari 
> > ___
> > 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
> 
> 

-- 
Juan Eugenio Iglesias, PhD
http://www.jeiglesias.com
igles...@nmr.mgh.harvard.edu
Athinoula A. Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, Massachusetts 2129
U.S.A.



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


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

Re: [Freesurfer] Freeview automation

[Garikoitz Lerma-Usabiaga]

Thanks!

I can visualize the 3D renders of interest with different colors, but from
"freeview -h" I couldn't get the following: is it possible to automatize
the "File > Save movie frames" option?

Thanks again!
Gari



On Fri, May 31, 2013 at 4:59 PM, Juan Eugenio Iglesias <
igles...@nmr.mgh.harvard.edu> wrote:

> Ender asked me to forward you this:
>
> I had to automate freeview recently.
> Freeview can be used via command line.
> For options please write
> freeview -h
> in the console / terminal.
>
> An example command that produces a surface and overlays a map on it:
> freeview -f lh.inflated:overlay=L.mgz -cam azimuth 180
>
> Let me know if this helps.
>
> Cheers,
>
> E
>
>
>
>
> On Fri, 2013-05-31 at 08:35 -0400, Ruopeng Wang wrote:
> > There is a screenshot option -ss from the command-line. Run 'freeview
> -h' will show you all the available options.
> >
> > Ruopeng
> >
> > On May 31, 2013, at 6:16 AM, Garikoitz Lerma-Usabiaga <
> gariko...@gmail.com> wrote:
> >
> > > Hi list,
> > > is it possible to automate Freeview automation from the command line?
> > >
> > > I want to automatically render 3D images of the hippocampus (I have a
> separate volume, based on hippo-subfields) and have an image for all
> subjects for quality checking.
> > >
> > > thanks!
> > > Gari
> > > ___
> > > 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
> >
> >
>
> --
> Juan Eugenio Iglesias, PhD
> http://www.jeiglesias.com
> igles...@nmr.mgh.harvard.edu
> Athinoula A. Martinos Center for Biomedical Imaging
> 149 Thirteenth Street, Suite 2301
> Charlestown, Massachusetts 2129
> U.S.A.
>
>
>
>
>
> 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


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] Importance of Segmentation/Parcellation edits with respect to cortical thickness

[Jonathan Holt]

Hi all,

We are using the parcellation of Desikan-Killiany

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

and creating labels for each structure in each hemisphere with:

mri_annotation2label --subject ${SUBJ} --hemi ${HEMI} --outdir
${SUBJ}/${SUBJ}_annotate

and making matlab text readable (via matlab load command) thickness
files with:

mris_convert -c ${HEMI}.thickkness ${HEMI}.white ${HEMI}.thickness.asc

Then we are reading in the ascii thickness files and the labels and creating
histograms (unit area) for each structure for each participant,
essentially following:

https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.HowcanIma
keahistogramofcorticalthickness.3F

We've dropped the zeros but also dropping values of thickness identically =
5mm.

The question is: How important are parcellation edits, that is how accurate are 
the generated segmentation labels, and should we be dedicating effort to 
ensuring they're accurate and possibly editing them if not (if so, what should 
be used as a guide/template?)

jon


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


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

Re: [Freesurfer] Freeview automation

[Ender Konukoglu]

Sure.

I couldn't find that option neither.

What I did was to semi-automatize.
I wrote a batch file to call freeview multiple times with different 
parameters.
Each time freeview pops up and I save the image/video. During this time 
the process in the terminal waits for me.

When I shut that window the next freeview window pops up and I do the same.

Ender


On 05/31/2013 11:05 AM, Garikoitz Lerma-Usabiaga wrote:

Thanks!

I can visualize the 3D renders of interest with different colors, but 
from "freeview -h" I couldn't get the following: is it possible to 
automatize the "File > Save movie frames" option?


Thanks again!
Gari



On Fri, May 31, 2013 at 4:59 PM, Juan Eugenio Iglesias 
mailto:igles...@nmr.mgh.harvard.edu>> 
wrote:


Ender asked me to forward you this:

I had to automate freeview recently.
Freeview can be used via command line.
For options please write
freeview -h
in the console / terminal.

An example command that produces a surface and overlays a map on it:
freeview -f lh.inflated:overlay=L.mgz -cam azimuth 180

Let me know if this helps.

Cheers,

E




On Fri, 2013-05-31 at 08:35 -0400, Ruopeng Wang wrote:
> There is a screenshot option -ss from the command-line. Run
'freeview -h' will show you all the available options.
>
> Ruopeng
>
> On May 31, 2013, at 6:16 AM, Garikoitz Lerma-Usabiaga
mailto:gariko...@gmail.com>> wrote:
>
> > Hi list,
> > is it possible to automate Freeview automation from the
command line?
> >
> > I want to automatically render 3D images of the hippocampus (I
have a separate volume, based on hippo-subfields) and have an
image for all subjects for quality checking.
> >
> > thanks!
> > Gari
> > ___
> > 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
>
>

--
Juan Eugenio Iglesias, PhD
http://www.jeiglesias.com
igles...@nmr.mgh.harvard.edu 
Athinoula A. Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, Massachusetts 2129
U.S.A.





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.

Re: [Freesurfer] Importance of Segmentation/Parcellation edits with respect to cortical thickness

[Bruce Fischl]

Hi Jon

the parcellation labels are usually pretty accurate, particularly since 
gyral borders are pretty arbitrary. I wouldn't touch them unless you see a 
dramatic and obvious failure (e.g. precentral gyrus labeled as 
post-central). This happens pretty rarely though
Bruce


On Fri, 31 May 
2013, Jonathan Holt wrote:

> Hi all,
> 
> We are using the parcellation of Desikan-Killiany
> 
> https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation
> 
> and creating labels for each structure in each hemisphere with:
> 
> mri_annotation2label --subject ${SUBJ} --hemi ${HEMI} --outdir
> ${SUBJ}/${SUBJ}_annotate
> 
> and making matlab text readable (via matlab load command) thickness
> files with:
> 
> mris_convert -c ${HEMI}.thickkness ${HEMI}.white ${HEMI}.thickness.asc
> 
> Then we are reading in the ascii thickness files and the labels and creating
> histograms (unit area) for each structure for each participant,
> essentially following:
> 
> https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.HowcanIma
> 
> keahistogramofcorticalthickness.3F
> 
> We've dropped the zeros but also dropping values of thickness identically =
> 5mm.
> 
> The question is: How important are parcellation edits, that is how accurate
> are the generated segmentation labels, and should we be dedicating effort to
> ensuring they're accurate and possibly editing them if not (if so, what
> should be used as a guide/template?)
> jon
> 
> 
> 
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] Freeview automation

[Garikoitz Lerma-Usabiaga]

Thanks Ender,
I am trying to make a command file with multiple commands too in order to
have snapshots from different views.

thanks for the help!
Gari


On Fri, May 31, 2013 at 5:13 PM, Ender Konukoglu  wrote:

>  Sure.
>
> I couldn't find that option neither.
>
> What I did was to semi-automatize.
> I wrote a batch file to call freeview multiple times with different
> parameters.
> Each time freeview pops up and I save the image/video. During this time
> the process in the terminal waits for me.
> When I shut that window the next freeview window pops up and I do the
> same.
>
> Ender
>
>
>
> On 05/31/2013 11:05 AM, Garikoitz Lerma-Usabiaga wrote:
>
> Thanks!
>
>  I can visualize the 3D renders of interest with different colors, but
> from "freeview -h" I couldn't get the following: is it possible to
> automatize the "File > Save movie frames" option?
>
>  Thanks again!
> Gari
>
>
>
> On Fri, May 31, 2013 at 4:59 PM, Juan Eugenio Iglesias <
> igles...@nmr.mgh.harvard.edu> wrote:
>
>> Ender asked me to forward you this:
>>
>> I had to automate freeview recently.
>> Freeview can be used via command line.
>> For options please write
>> freeview -h
>> in the console / terminal.
>>
>> An example command that produces a surface and overlays a map on it:
>> freeview -f lh.inflated:overlay=L.mgz -cam azimuth 180
>>
>> Let me know if this helps.
>>
>> Cheers,
>>
>> E
>>
>>
>>
>>
>> On Fri, 2013-05-31 at 08:35 -0400, Ruopeng Wang wrote:
>> > There is a screenshot option -ss from the command-line. Run 'freeview
>> -h' will show you all the available options.
>> >
>> > Ruopeng
>> >
>> > On May 31, 2013, at 6:16 AM, Garikoitz Lerma-Usabiaga <
>> gariko...@gmail.com> wrote:
>> >
>> > > Hi list,
>> > > is it possible to automate Freeview automation from the command line?
>> > >
>> > > I want to automatically render 3D images of the hippocampus (I have a
>> separate volume, based on hippo-subfields) and have an image for all
>> subjects for quality checking.
>> > >
>> > > thanks!
>> > > Gari
>> > > ___
>> > > 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
>> >
>> >
>>
>>  --
>> Juan Eugenio Iglesias, PhD
>> http://www.jeiglesias.com
>> igles...@nmr.mgh.harvard.edu
>> Athinoula A. Martinos Center for Biomedical Imaging
>> 149 Thirteenth Street, Suite 2301
>> Charlestown, Massachusetts 2129
>> U.S.A.
>>
>>
>>
>>
>>
>> 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 
> listfreesur...@nmr.mgh.harvard.eduhttps://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.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] ventral DC

[Bruce Fischl]

Hi Daniel
it's a bunch of things like substancia nigra, the subthalamic nucleus, 
LGN (I think), etc


Bruce
On Fri, 31 May 2013, Yang, Daniel wrote:


Dear all,

in the aseg.volume, there is a term called 'ventral DC' and I am wondering
what it is.

I looked up the previous posts and know DC = diencephalon, and it's a grab
bag of stuff that cannot be resolved.

However, does anyone know what exactly ventral DC is?

Thanks!
Daniel

-- 
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

___
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] Group Analysis

[Fotiadis, Panagiotis]

Hey Doug,

Sorry for the overwhelming amount of questions. I wanted to confirm something. 
Suppose you want to do group analysis between two groups say a healthy cohort 
vs a diseased cohort. Each cohort has ~40 and ~30 subjects each (different 
people), and you want to compare how for instance the cortical thickness 
decreases over age in the one group versus the other. Do you still set the 
contrast vector as [0 0 1 -1]  ([intercept 1 intercept 2 slope 1 slope 2]) and 
follow the analysis described in 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis or do you go 
on a different way since there are different subjects instead of one with 40 
(or 30) different longitudinal data for each cohort? Don't we need to correct 
the age slopes for the fact that we have 40 (and 30) different subjects in each 
cohort?

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


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

Re: [Freesurfer] Freeview automation

[Ruopeng Wang]

If you use '-ss' option, freeview will save a screenshot and close 
itself. For example:


freeview -v foo.mgz -ss foo.jpg

On 05/31/2013 11:13 AM, Ender Konukoglu wrote:

Sure.

I couldn't find that option neither.

What I did was to semi-automatize.
I wrote a batch file to call freeview multiple times with different 
parameters.
Each time freeview pops up and I save the image/video. During this 
time the process in the terminal waits for me.
When I shut that window the next freeview window pops up and I do the 
same.


Ender


On 05/31/2013 11:05 AM, Garikoitz Lerma-Usabiaga wrote:

Thanks!

I can visualize the 3D renders of interest with different colors, but 
from "freeview -h" I couldn't get the following: is it possible to 
automatize the "File > Save movie frames" option?


Thanks again!
Gari



On Fri, May 31, 2013 at 4:59 PM, Juan Eugenio Iglesias 
mailto:igles...@nmr.mgh.harvard.edu>> 
wrote:


Ender asked me to forward you this:

I had to automate freeview recently.
Freeview can be used via command line.
For options please write
freeview -h
in the console / terminal.

An example command that produces a surface and overlays a map on it:
freeview -f lh.inflated:overlay=L.mgz -cam azimuth 180

Let me know if this helps.

Cheers,

E




On Fri, 2013-05-31 at 08:35 -0400, Ruopeng Wang wrote:
> There is a screenshot option -ss from the command-line. Run
'freeview -h' will show you all the available options.
>
> Ruopeng
>
> On May 31, 2013, at 6:16 AM, Garikoitz Lerma-Usabiaga
mailto:gariko...@gmail.com>> wrote:
>
> > Hi list,
> > is it possible to automate Freeview automation from the
command line?
> >
> > I want to automatically render 3D images of the hippocampus
(I have a separate volume, based on hippo-subfields) and have an
image for all subjects for quality checking.
> >
> > thanks!
> > Gari
> > ___
> > 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
>
>

--
Juan Eugenio Iglesias, PhD
http://www.jeiglesias.com
igles...@nmr.mgh.harvard.edu 
Athinoula A. Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, Massachusetts 2129
U.S.A.





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



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


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

Re: [Freesurfer] Freeview automation

[Garikoitz Lerma-Usabiaga]

Thanks! it is working perfectly, I created a command file to take several
screenshots, for example:

[...]
-cam azimuth 90
-ss imagen6.png
-cam azimuth 90
-cam Elevation 90
-ss imagen7.png
-slice 127 180 127
-ss imagen8.png
-slice 127 80 127
-cam Elevation 180
-ss imagen9.png
-quit



On Fri, May 31, 2013 at 5:34 PM, Ruopeng Wang wrote:

>  If you use '-ss' option, freeview will save a screenshot and close
> itself. For example:
>
> freeview -v foo.mgz -ss foo.jpg
>
>
> On 05/31/2013 11:13 AM, Ender Konukoglu wrote:
>
> Sure.
>
> I couldn't find that option neither.
>
> What I did was to semi-automatize.
> I wrote a batch file to call freeview multiple times with different
> parameters.
> Each time freeview pops up and I save the image/video. During this time
> the process in the terminal waits for me.
> When I shut that window the next freeview window pops up and I do the
> same.
>
> Ender
>
>
> On 05/31/2013 11:05 AM, Garikoitz Lerma-Usabiaga wrote:
>
> Thanks!
>
>  I can visualize the 3D renders of interest with different colors, but
> from "freeview -h" I couldn't get the following: is it possible to
> automatize the "File > Save movie frames" option?
>
>  Thanks again!
> Gari
>
>
>
> On Fri, May 31, 2013 at 4:59 PM, Juan Eugenio Iglesias <
> igles...@nmr.mgh.harvard.edu> wrote:
>
>> Ender asked me to forward you this:
>>
>> I had to automate freeview recently.
>> Freeview can be used via command line.
>> For options please write
>> freeview -h
>> in the console / terminal.
>>
>> An example command that produces a surface and overlays a map on it:
>> freeview -f lh.inflated:overlay=L.mgz -cam azimuth 180
>>
>> Let me know if this helps.
>>
>> Cheers,
>>
>> E
>>
>>
>>
>>
>> On Fri, 2013-05-31 at 08:35 -0400, Ruopeng Wang wrote:
>> > There is a screenshot option -ss from the command-line. Run 'freeview
>> -h' will show you all the available options.
>> >
>> > Ruopeng
>> >
>> > On May 31, 2013, at 6:16 AM, Garikoitz Lerma-Usabiaga <
>> gariko...@gmail.com> wrote:
>> >
>> > > Hi list,
>> > > is it possible to automate Freeview automation from the command line?
>> > >
>> > > I want to automatically render 3D images of the hippocampus (I have a
>> separate volume, based on hippo-subfields) and have an image for all
>> subjects for quality checking.
>> > >
>> > > thanks!
>> > > Gari
>> > > ___
>> > > 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
>> >
>> >
>>
>>  --
>> Juan Eugenio Iglesias, PhD
>> http://www.jeiglesias.com
>> igles...@nmr.mgh.harvard.edu
>> Athinoula A. Martinos Center for Biomedical Imaging
>> 149 Thirteenth Street, Suite 2301
>> Charlestown, Massachusetts 2129
>> U.S.A.
>>
>>
>>
>>
>>
>> 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 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://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.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] Group Analysis

[Douglas N Greve]

Hi Panos, are you asking whether theunbalanced design will leadto one 
slope being different than another just because the numbers are 
different? That is not a problem. You can simply follow the instructions 
on the wiki.
doug



On 05/31/2013 11:26 AM, Fotiadis, Panagiotis wrote:
> Hey Doug,
>
> Sorry for the overwhelming amount of questions. I wanted to confirm 
> something. Suppose you want to do group analysis between two groups say a 
> healthy cohort vs a diseased cohort. Each cohort has ~40 and ~30 subjects 
> each (different people), and you want to compare how for instance the 
> cortical thickness decreases over age in the one group versus the other. Do 
> you still set the contrast vector as [0 0 1 -1]  ([intercept 1 intercept 2 
> slope 1 slope 2]) and follow the analysis described in 
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis or do you 
> go on a different way since there are different subjects instead of one with 
> 40 (or 30) different longitudinal data for each cohort? Don't we need to 
> correct the age slopes for the fact that we have 40 (and 30) different 
> subjects in each cohort?
>
> Thanks,
> Panos
> ___
> 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/

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


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

Re: [Freesurfer] ventral DC

[Yang, Daniel]

Hi Bruce and Thomas,

Thanks so much for your help! I think I have a better idea now.

Best,
Daniel

--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 5/31/13 11:23 AM, "Bruce Fischl" 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:

Hi Daniel
it's a bunch of things like substancia nigra, the subthalamic nucleus,
LGN (I think), etc

Bruce
On Fri, 31 May 2013, Yang, Daniel wrote:

Dear all,
in the aseg.volume, there is a term called 'ventral DC' and I am wondering
what it is.
I looked up the previous posts and know DC = diencephalon, and it's a grab
bag of stuff that cannot be resolved.
However, does anyone know what exactly ventral DC is?
Thanks!
Daniel
--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454



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


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] beta weights from FS-Fast analysis

[Douglas N Greve]

On 05/30/2013 04:37 PM, Joseph Dien wrote:
> Just to make sure I'm doing this right, I'm going to summarize what 
> I've taken away from your answers and to ask some new questions. In 
> order to present the results, I need two things:
>
> 1) A set of histograms (with error bars) for each cluster figure to 
> show the % signal change for each of the four contrasts of interest.
> The cache.th20.pos.y.ocn.dat file only gives it for the condition 
> where the cluster was significant so I can't use that.
> So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot 
> from the group level analysis to generate a mask for each cluster of 
> interest.
> Then I could extract the value of the voxels from each 
> subject's cespct file for each contrast, average them across the 
> cluster ROI, then average them across each subject, to generate the 
> histogram?
> This would suffice to give me the %age signal change?
> I would be doing these computations in Matlab using MRIread.
I don't understand. If you don't have a cluster for a contrast, how are 
you defining the cluster? From another contrast?

>
> 2) A results table with the headings:
>
> Cluster p (FWE corrected)
> Cluster size
> Peak Voxel p (FWE corrected)
> Peak Voxel T
> Peak Voxel Coords
> BA
> Anatomical Landmark
>
> I can get the first two from 
> the cache.th20.pos/neg.sig.cluster.summary files from the group level 
> analysis.
> I can get the peak voxel coordinates from the summary files as well.
> I can use this to get the peak voxel p from the group level sig.nii.gz 
> file.  Is this FWE corrected?  If not, how can I get this information?
What do you mean? The cluster p-value is corrected, why do you need the 
max p and why does it need to be corrected?
> I can use these coordinates to get the peak voxel T by getting the 
> value from the group level F.nii.gz file and taking its square root. 
>  How can I get the sign of the T statistic?
Same as the sign of gamma.mgh
> I can use the Lancaster transform to convert the MNI305 peak voxel 
> coordinates into the Atlas coordinates to look up the putative BA and 
> landmarks (unless there is a better way with Freesurfer?  I'm seeing 
> some references to some BA labels in the forum but it doesn't look 
> like this is a complete set yet?).
Some of the BA labels are in FS, but not nearly all of them
doug
>
> Sorry for all these questions!  I got some nice results from FSFAST 
> and would like to get them written up.
>
> Cheers!
>
> Joe
>
>
>
>
> On May 29, 2013, at 10:53 PM, Douglas Greve  > wrote:
>
>>
>> On 5/29/13 10:42 PM, Joseph Dien wrote:
>>>
>>> On May 29, 2013, at 11:40 AM, Douglas N Greve 
>>> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>>
 Hi Joe,

 On 05/29/2013 01:00 AM, Joseph Dien wrote:
> I need to extract the beta weights from a cluster identified with
> FS-Fast in order to compute percentage signal change.
>
> 1) I see a file called beta.nii.gz that appears to have the beta
> weight information.  It has a four dimensional structure and the
> fourth dimension appears to be the beta weights.  Is there an index
> somewhere as to which beta weight is which?  Or if not, how are they
> organized?
 For the first level analysis, the first N beta weights correspond 
 to the
 N conditions in the paradigm file. The rest are nuisance variables.
>
>>>
>>> Ah, very good!  In order to compute the percent signal change 
>>> statistic (I'm following the MarsBaR approach: 
>>> http://marsbar.sourceforge.net/faq.html#how-is-the-percent-signal-change-calculated)
>>>  
>>> I'm also going to need the beta weights for the session mean 
>>> regressors.  How are the nuisance regressors organized?
>> You can just use the meanfunc.nii.gz. Also, each contrasts is 
>> computed as the simple contrast (ces) and as a percent of the 
>> baseline at the voxel (cespct, cesvarpct).
>>>
> 2) In order to extract the cluster, it looks like I would
> use mri_label2vol to convert cache.th20.neg.sig.ocn.annot into a
> volume where the voxels are tagged with the number of the
> corresponding cluster.
 Is that  from a group analysis?
>
>>>
>>> Yes, that's right.
>>>
> I could then use that to generate masks to extract the information I
> need for each cluster from beta.nii.gz.
 If this is from a group analysis, then there should already be a file
 there (something.y.ocn.dat) that has a value for each subject in the
 rows and a value for each cluster in the columns.
>
>>>
>>> I see it.  Are these values already scaled as percent signal change? 
>>>  If so, that would be wonderful!  :)
>> Only if you specified it when you ran isxconcat-sess. Note that the 
>> "non-scaled" values are actually scaled to percent of grand mean 
>> intensity.
>>>
> Is that correct?
>
> 3) The final information that I would need is the canonical hrf shape
> generated by FSFAST for a single even

Re: [Freesurfer] beta weights from FS-Fast analysis

[Douglas N Greve]

On 05/31/2013 01:49 AM, Joseph Dien wrote:
> I was able to make more progress so I'm mostly good at this point but 
> I have a remaining question:
>
> I assume the contents of sig.nii.gz (which I assume are the vertex 
> p-values) are not FWE corrected.  Is it possible to get FWE-corrected 
> vertex p-values?  Or are only clusterwise corrections available?
There should be something like cache.th13.abs.sig.voxel.mgh which is 
corrected on a voxelwise basis (the th13 is just part of the name but it 
should be the same regardless of the threshold you choose)
doug
>
> Thanks again for your patience!
>
> Joe
>
> On May 30, 2013, at 4:37 PM, Joseph Dien  > wrote:
>
>> Just to make sure I'm doing this right, I'm going to summarize what 
>> I've taken away from your answers and to ask some new questions. In 
>> order to present the results, I need two things:
>>
>> 1) A set of histograms (with error bars) for each cluster figure to 
>> show the % signal change for each of the four contrasts of interest.
>> The cache.th20.pos.y.ocn.dat file only gives it for the condition 
>> where the cluster was significant so I can't use that.
>> So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot 
>> from the group level analysis to generate a mask for each cluster of 
>> interest.
>> Then I could extract the value of the voxels from each 
>> subject's cespct file for each contrast, average them across the 
>> cluster ROI, then average them across each subject, to generate the 
>> histogram?
>> This would suffice to give me the %age signal change?
>> I would be doing these computations in Matlab using MRIread.
>>
>> 2) A results table with the headings:
>>
>> Cluster p (FWE corrected)
>> Cluster size
>> Peak Voxel p (FWE corrected)
>> Peak Voxel T
>> Peak Voxel Coords
>> BA
>> Anatomical Landmark
>>
>> I can get the first two from 
>> the cache.th20.pos/neg.sig.cluster.summary files from the group level 
>> analysis.
>> I can get the peak voxel coordinates from the summary files as well.
>> I can use this to get the peak voxel p from the group 
>> level sig.nii.gz file.  Is this FWE corrected?  If not, how can I get 
>> this information?
>> I can use these coordinates to get the peak voxel T by getting the 
>> value from the group level F.nii.gz file and taking its square root. 
>>  How can I get the sign of the T statistic?
>> I can use the Lancaster transform to convert the MNI305 peak voxel 
>> coordinates into the Atlas coordinates to look up the putative BA and 
>> landmarks (unless there is a better way with Freesurfer?  I'm seeing 
>> some references to some BA labels in the forum but it doesn't look 
>> like this is a complete set yet?).
>>
>> Sorry for all these questions!  I got some nice results from FSFAST 
>> and would like to get them written up.
>>
>> Cheers!
>>
>> Joe
>>
>>
>>
>>
>> On May 29, 2013, at 10:53 PM, Douglas Greve 
>> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>
>>>
>>> On 5/29/13 10:42 PM, Joseph Dien wrote:

 On May 29, 2013, at 11:40 AM, Douglas N Greve 
 mailto:gr...@nmr.mgh.harvard.edu>> wrote:

> Hi Joe,
>
> On 05/29/2013 01:00 AM, Joseph Dien wrote:
>> I need to extract the beta weights from a cluster identified with
>> FS-Fast in order to compute percentage signal change.
>>
>> 1) I see a file called beta.nii.gz that appears to have the beta
>> weight information.  It has a four dimensional structure and the
>> fourth dimension appears to be the beta weights.  Is there an index
>> somewhere as to which beta weight is which?  Or if not, how are they
>> organized?
> For the first level analysis, the first N beta weights correspond 
> to the
> N conditions in the paradigm file. The rest are nuisance variables.
>>

 Ah, very good!  In order to compute the percent signal change 
 statistic (I'm following the MarsBaR approach: 
 http://marsbar.sourceforge.net/faq.html#how-is-the-percent-signal-change-calculated)
  
 I'm also going to need the beta weights for the session mean 
 regressors.  How are the nuisance regressors organized?
>>> You can just use the meanfunc.nii.gz. Also, each contrasts is 
>>> computed as the simple contrast (ces) and as a percent of the 
>>> baseline at the voxel (cespct, cesvarpct).

>> 2) In order to extract the cluster, it looks like I would
>> use mri_label2vol to convert cache.th20.neg.sig.ocn.annot into a
>> volume where the voxels are tagged with the number of the
>> corresponding cluster.
> Is that  from a group analysis?
>>

 Yes, that's right.

>> I could then use that to generate masks to extract the information I
>> need for each cluster from beta.nii.gz.
> If this is from a group analysis, then there should already be a file
> there (something.y.ocn.dat) that has a value for each subject in the
> rows and a value for each cluster in the columns.
>>

Re: [Freesurfer] white matter volume per lobe...

[Douglas N Greve]

don't know what's going on. Can you upload the subject to our file drop?
doug
On 05/30/2013 04:36 PM, Gonzalo Rojas Costa wrote:
> Hi Doug:
>
>The command is:
>
>   mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown
> --volmask --o mri/lobulitos.mgz --annot lobulos --wmparc-dmax 200
>
> and the terminal output is:
>
> mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown
> --volmask --o mri/lobulitos_2.mgz --annot lobulos --wmparc-dmax 200
>
> SUBJECTS_DIR /usr/local/freesurfer/subjects
> subject OAS1_0001_MR1
> outvol mri/lobulitos_2.mgz
> useribbon 0
> baseoffset 0
> labeling wm
> labeling hypo-intensities as wm
> dmaxctx 200.00
> RipUnknown 1
>
> Reading lh white surface
>   /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/lh.white
>
> Reading lh pial surface
>   /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/lh.pial
>
> Loading lh annotations from
> /usr/local/freesurfer/subjects/OAS1_0001_MR1/label/lh.lobulos.annot
> reading colortable from annotation file...
> colortable with 8 entries read (originally none)
>
> Reading rh white surface
>   /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/rh.white
>
> Reading rh pial surface
>   /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/rh.pial
>
> Loading rh annotations from
> /usr/local/freesurfer/subjects/OAS1_0001_MR1/label/rh.lobulos.annot
> reading colortable from annotation file...
> colortable with 8 entries read (originally none)
> Have color table for lh white annotation
> Have color table for rh white annotation
> Loading ribbon segmentation from
> /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/ribbon.mgz
> Loading filled from 
> /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/filled.mgz
> Ripping vertices labeled as unkown
> Ripped 7659 vertices from left hemi
> Ripped 7544 vertices from right hemi
>
> Building hash of lh white
>
> Building hash of lh pial
>
> Building hash of rh white
>
> Building hash of rh pial
>
> Loading aseg from /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/aseg.mgz
> ASeg Vox2RAS: ---
> -1.000   0.000   0.000   128.000;
>   0.000   0.000   1.000  -128.000;
>   0.000  -1.000   0.000   128.000;
>   0.000   0.000   0.000   1.000;
> -
>
> Labeling Slice
>0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  
> 19
>   20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  
> 39
>   40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  
> 59
>   60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  
> 79
>   80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  
> 99
> 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 
> 119
> 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 
> 139
> 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 
> 159
> 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 
> 179
> 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 
> 199
> 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 
> 219
> 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 
> 239
> 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 688931
> Used brute-force search on 139 voxels
> Fixing Parahip LH WM
>Found 0 clusters
> Fixing Parahip RH WM
>Found 0 clusters
> Writing output aseg to mri/lobulitos_2.mgz
>
>Sincerely,
>
>
> Gonzalo Rojas Costa
>
>
> On Thu, May 30, 2013 at 4:10 PM, Douglas N Greve
>  wrote:
>> can you send me your full command line as well as the terminal output?
>>
>> On 05/30/2013 02:26 PM, Gonzalo Rojas Costa wrote:
>>> Hi Doug:
>>>
>>> But, in the mri_aparc2aseg command, I test with the "--wmparc-dmax
>>> 200" option... I put that big value to test it, but I got the image
>>> that I sent you...
>>>
>>> Sincerely,
>>>
>>>
>>> Gonzalo Rojas Costa
> --
> Gonzalo Rojas Costa
> Laboratory for Advanced Medical Image Processing
> Department of Radiology
> Clínica las Condes
> Lo Fontecilla 441, Las Condes, Santiago, Chile.
> Tel: 56-2-2105170
> Cel: 56-9-97771785
> www.clc.cl
>
>

-- 
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/

___
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

Re: [Freesurfer] Cortical thickness

[Douglas N Greve]

There should be a file called something like cache.th13.abs.y.ocn.dat. 
This will have a column for each cluster and a row for each subject. The 
value in the row will be the input for each subject.
doug

On 05/30/2013 11:21 PM, Joshua deSouza wrote:
> Hello everyone,
>
> Please pardon my rather simple question
>
> I have done a GLM fit anlysis and have obtained a file sig.mgh alonf 
> with a few others after the analysis.As I know, I do not have to 
> create ROIs in order to do this. I also understand that doing a 
> multiple comparison analysis just compares the regions of importance 
> and evaluates them giving the most resilient cluster depending on the 
> threshold. So, this does not give a thickness estimate. I would like 
> to know how do I get the cortical thickness values from the results? 
> If so, can I do it after glmfit?
>
> And thanks Doug for your help in the other questions that I had prior 
> to this!
>
> Thank you
>
>
> ___
> 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/

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


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

Re: [Freesurfer] Group Analysis

[Fotiadis, Panagiotis]

Hey Doug,

Great, but besides the unbalanced numbers in each cohort, the fact that we have 
a cross sectional analysis instead of a longitudinal one doesn't matter right? 
Would it be correct to say that we still apply the same group analysis 
described in the wiki?

Thanks,
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: Friday, May 31, 2013 11:59 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Group Analysis

Hi Panos, are you asking whether theunbalanced design will leadto one
slope being different than another just because the numbers are
different? That is not a problem. You can simply follow the instructions
on the wiki.
doug



On 05/31/2013 11:26 AM, Fotiadis, Panagiotis wrote:
> Hey Doug,
>
> Sorry for the overwhelming amount of questions. I wanted to confirm 
> something. Suppose you want to do group analysis between two groups say a 
> healthy cohort vs a diseased cohort. Each cohort has ~40 and ~30 subjects 
> each (different people), and you want to compare how for instance the 
> cortical thickness decreases over age in the one group versus the other. Do 
> you still set the contrast vector as [0 0 1 -1]  ([intercept 1 intercept 2 
> slope 1 slope 2]) and follow the analysis described in 
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis or do you 
> go on a different way since there are different subjects instead of one with 
> 40 (or 30) different longitudinal data for each cohort? Don't we need to 
> correct the age slopes for the fact that we have 40 (and 30) different 
> subjects in each cohort?
>
> Thanks,
> Panos
> ___
> 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/

___
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.

Re: [Freesurfer] Group Analysis

[Douglas N Greve]

yes
doug
On 05/31/2013 12:16 PM, Fotiadis, Panagiotis wrote:
> Hey Doug,
>
> Great, but besides the unbalanced numbers in each cohort, the fact that we 
> have a cross sectional analysis instead of a longitudinal one doesn't matter 
> right? Would it be correct to say that we still apply the same group analysis 
> described in the wiki?
>
> Thanks,
> 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: Friday, May 31, 2013 11:59 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Group Analysis
>
> Hi Panos, are you asking whether theunbalanced design will leadto one
> slope being different than another just because the numbers are
> different? That is not a problem. You can simply follow the instructions
> on the wiki.
> doug
>
>
>
> On 05/31/2013 11:26 AM, Fotiadis, Panagiotis wrote:
>> Hey Doug,
>>
>> Sorry for the overwhelming amount of questions. I wanted to confirm 
>> something. Suppose you want to do group analysis between two groups say a 
>> healthy cohort vs a diseased cohort. Each cohort has ~40 and ~30 subjects 
>> each (different people), and you want to compare how for instance the 
>> cortical thickness decreases over age in the one group versus the other. Do 
>> you still set the contrast vector as [0 0 1 -1]  ([intercept 1 intercept 2 
>> slope 1 slope 2]) and follow the analysis described in 
>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis or do you 
>> go on a different way since there are different subjects instead of one with 
>> 40 (or 30) different longitudinal data for each cohort? Don't we need to 
>> correct the age slopes for the fact that we have 40 (and 30) different 
>> subjects in each cohort?
>>
>> Thanks,
>> Panos
>> ___
>> 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/
>
> ___
> 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/

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


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

Re: [Freesurfer] Group Analysis

[Fotiadis, Panagiotis]

Thanks!
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: Friday, May 31, 2013 12:22 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Group Analysis

yes
doug
On 05/31/2013 12:16 PM, Fotiadis, Panagiotis wrote:
> Hey Doug,
>
> Great, but besides the unbalanced numbers in each cohort, the fact that we 
> have a cross sectional analysis instead of a longitudinal one doesn't matter 
> right? Would it be correct to say that we still apply the same group analysis 
> described in the wiki?
>
> Thanks,
> 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: Friday, May 31, 2013 11:59 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Group Analysis
>
> Hi Panos, are you asking whether theunbalanced design will leadto one
> slope being different than another just because the numbers are
> different? That is not a problem. You can simply follow the instructions
> on the wiki.
> doug
>
>
>
> On 05/31/2013 11:26 AM, Fotiadis, Panagiotis wrote:
>> Hey Doug,
>>
>> Sorry for the overwhelming amount of questions. I wanted to confirm 
>> something. Suppose you want to do group analysis between two groups say a 
>> healthy cohort vs a diseased cohort. Each cohort has ~40 and ~30 subjects 
>> each (different people), and you want to compare how for instance the 
>> cortical thickness decreases over age in the one group versus the other. Do 
>> you still set the contrast vector as [0 0 1 -1]  ([intercept 1 intercept 2 
>> slope 1 slope 2]) and follow the analysis described in 
>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis or do you 
>> go on a different way since there are different subjects instead of one with 
>> 40 (or 30) different longitudinal data for each cohort? Don't we need to 
>> correct the age slopes for the fact that we have 40 (and 30) different 
>> subjects in each cohort?
>>
>> Thanks,
>> Panos
>> ___
>> 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/
>
> ___
> 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/

___
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.

Re: [Freesurfer] white matter volume per lobe...

[Gonzalo Rojas Costa]

Hi Douglas:

  The file is the OAS1_0001_MR1 case of OASIS-BRAINS database that I
re-processed using freesurfer 5.2.0...

  Sincerely,


Gonzalo Rojas Costa

On Fri, May 31, 2013 at 12:12 PM, Douglas N Greve
 wrote:
> don't know what's going on. Can you upload the subject to our file drop?
> doug
>
> On 05/30/2013 04:36 PM, Gonzalo Rojas Costa wrote:
>>
>> Hi Doug:
>>
>>The command is:
>>
>>   mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown
>> --volmask --o mri/lobulitos.mgz --annot lobulos --wmparc-dmax 200
>>
>> and the terminal output is:
>>
>> mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown
>> --volmask --o mri/lobulitos_2.mgz --annot lobulos --wmparc-dmax 200
>>
>> SUBJECTS_DIR /usr/local/freesurfer/subjects
>> subject OAS1_0001_MR1
>> outvol mri/lobulitos_2.mgz
>> useribbon 0
>> baseoffset 0
>> labeling wm
>> labeling hypo-intensities as wm
>> dmaxctx 200.00
>> RipUnknown 1
>>
>> Reading lh white surface
>>   /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/lh.white
>>
>> Reading lh pial surface
>>   /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/lh.pial
>>
>> Loading lh annotations from
>> /usr/local/freesurfer/subjects/OAS1_0001_MR1/label/lh.lobulos.annot
>> reading colortable from annotation file...
>> colortable with 8 entries read (originally none)
>>
>> Reading rh white surface
>>   /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/rh.white
>>
>> Reading rh pial surface
>>   /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/rh.pial
>>
>> Loading rh annotations from
>> /usr/local/freesurfer/subjects/OAS1_0001_MR1/label/rh.lobulos.annot
>> reading colortable from annotation file...
>> colortable with 8 entries read (originally none)
>> Have color table for lh white annotation
>> Have color table for rh white annotation
>> Loading ribbon segmentation from
>> /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/ribbon.mgz
>> Loading filled from
>> /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/filled.mgz
>> Ripping vertices labeled as unkown
>> Ripped 7659 vertices from left hemi
>> Ripped 7544 vertices from right hemi
>>
>> Building hash of lh white
>>
>> Building hash of lh pial
>>
>> Building hash of rh white
>>
>> Building hash of rh pial
>>
>> Loading aseg from
>> /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/aseg.mgz
>> ASeg Vox2RAS: ---
>> -1.000   0.000   0.000   128.000;
>>   0.000   0.000   1.000  -128.000;
>>   0.000  -1.000   0.000   128.000;
>>   0.000   0.000   0.000   1.000;
>> -
>>
>> Labeling Slice
>>0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17
>> 18  19
>>   20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37
>> 38  39
>>   40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57
>> 58  59
>>   60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77
>> 78  79
>>   80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97
>> 98  99
>> 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117
>> 118 119
>> 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137
>> 138 139
>> 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157
>> 158 159
>> 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177
>> 178 179
>> 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197
>> 198 199
>> 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217
>> 218 219
>> 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237
>> 238 239
>> 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx =
>> 688931
>> Used brute-force search on 139 voxels
>> Fixing Parahip LH WM
>>Found 0 clusters
>> Fixing Parahip RH WM
>>Found 0 clusters
>> Writing output aseg to mri/lobulitos_2.mgz
>>
>>Sincerely,
>>
>>
>> Gonzalo Rojas Costa
>>
>>
>> On Thu, May 30, 2013 at 4:10 PM, Douglas N Greve
>>  wrote:
>>>
>>> can you send me your full command line as well as the terminal output?
>>>
>>> On 05/30/2013 02:26 PM, Gonzalo Rojas Costa wrote:

 Hi Doug:

 But, in the mri_aparc2aseg command, I test with the "--wmparc-dmax
 200" option... I put that big value to test it, but I got the image
 that I sent you...

 Sincerely,


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

Re: [Freesurfer] Group Analysis

[Fotiadis, Panagiotis]

Hey Doug,

Is there any need to co-register the subjects (of the two cohorts) destined for 
group analysis to the fsaverage space first in order to be able to compare 
their cortical thickness on the same space, or does mri_glmfit do that?

Thanks again,
Panos

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fotiadis, Panagiotis
Sent: Friday, May 31, 2013 12:28 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Group Analysis

Thanks!
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: Friday, May 31, 2013 12:22 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Group Analysis

yes
doug
On 05/31/2013 12:16 PM, Fotiadis, Panagiotis wrote:
> Hey Doug,
>
> Great, but besides the unbalanced numbers in each cohort, the fact that we 
> have a cross sectional analysis instead of a longitudinal one doesn't matter 
> right? Would it be correct to say that we still apply the same group analysis 
> described in the wiki?
>
> Thanks,
> 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: Friday, May 31, 2013 11:59 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Group Analysis
>
> Hi Panos, are you asking whether theunbalanced design will leadto one
> slope being different than another just because the numbers are
> different? That is not a problem. You can simply follow the instructions
> on the wiki.
> doug
>
>
>
> On 05/31/2013 11:26 AM, Fotiadis, Panagiotis wrote:
>> Hey Doug,
>>
>> Sorry for the overwhelming amount of questions. I wanted to confirm 
>> something. Suppose you want to do group analysis between two groups say a 
>> healthy cohort vs a diseased cohort. Each cohort has ~40 and ~30 subjects 
>> each (different people), and you want to compare how for instance the 
>> cortical thickness decreases over age in the one group versus the other. Do 
>> you still set the contrast vector as [0 0 1 -1]  ([intercept 1 intercept 2 
>> slope 1 slope 2]) and follow the analysis described in 
>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis or do you 
>> go on a different way since there are different subjects instead of one with 
>> 40 (or 30) different longitudinal data for each cohort? Don't we need to 
>> correct the age slopes for the fact that we have 40 (and 30) different 
>> subjects in each cohort?
>>
>> Thanks,
>> Panos
>> ___
>> 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/
>
> ___
> 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/

___
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


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] Group Analysis

[Douglas N Greve]

mri_glmfit does not do it. Run mris_preproc. See the tutorial
doug



On 05/31/2013 01:13 PM, Fotiadis, Panagiotis wrote:
> Hey Doug,
>
> Is there any need to co-register the subjects (of the two cohorts) destined 
> for group analysis to the fsaverage space first in order to be able to 
> compare their cortical thickness on the same space, or does mri_glmfit do 
> that?
>
> Thanks again,
> Panos
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fotiadis, Panagiotis
> Sent: Friday, May 31, 2013 12:28 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Group Analysis
>
> Thanks!
> 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: Friday, May 31, 2013 12:22 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Group Analysis
>
> yes
> doug
> On 05/31/2013 12:16 PM, Fotiadis, Panagiotis wrote:
>> Hey Doug,
>>
>> Great, but besides the unbalanced numbers in each cohort, the fact that we 
>> have a cross sectional analysis instead of a longitudinal one doesn't matter 
>> right? Would it be correct to say that we still apply the same group 
>> analysis described in the wiki?
>>
>> Thanks,
>> 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: Friday, May 31, 2013 11:59 AM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Group Analysis
>>
>> Hi Panos, are you asking whether theunbalanced design will leadto one
>> slope being different than another just because the numbers are
>> different? That is not a problem. You can simply follow the instructions
>> on the wiki.
>> doug
>>
>>
>>
>> On 05/31/2013 11:26 AM, Fotiadis, Panagiotis wrote:
>>> Hey Doug,
>>>
>>> Sorry for the overwhelming amount of questions. I wanted to confirm 
>>> something. Suppose you want to do group analysis between two groups say a 
>>> healthy cohort vs a diseased cohort. Each cohort has ~40 and ~30 subjects 
>>> each (different people), and you want to compare how for instance the 
>>> cortical thickness decreases over age in the one group versus the other. Do 
>>> you still set the contrast vector as [0 0 1 -1]  ([intercept 1 intercept 2 
>>> slope 1 slope 2]) and follow the analysis described in 
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis or do 
>>> you go on a different way since there are different subjects instead of one 
>>> with 40 (or 30) different longitudinal data for each cohort? Don't we need 
>>> to correct the age slopes for the fact that we have 40 (and 30) different 
>>> subjects in each cohort?
>>>
>>> Thanks,
>>> Panos
>>> ___
>>> 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/
>>
>> ___
>> 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/
>
> ___
> 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.har

Re: [Freesurfer] Group Analysis

[Fotiadis, Panagiotis]

Thank you!

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: Friday, May 31, 2013 1:27 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Group Analysis

mri_glmfit does not do it. Run mris_preproc. See the tutorial
doug



On 05/31/2013 01:13 PM, Fotiadis, Panagiotis wrote:
> Hey Doug,
>
> Is there any need to co-register the subjects (of the two cohorts) destined 
> for group analysis to the fsaverage space first in order to be able to 
> compare their cortical thickness on the same space, or does mri_glmfit do 
> that?
>
> Thanks again,
> Panos
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fotiadis, Panagiotis
> Sent: Friday, May 31, 2013 12:28 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Group Analysis
>
> Thanks!
> 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: Friday, May 31, 2013 12:22 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Group Analysis
>
> yes
> doug
> On 05/31/2013 12:16 PM, Fotiadis, Panagiotis wrote:
>> Hey Doug,
>>
>> Great, but besides the unbalanced numbers in each cohort, the fact that we 
>> have a cross sectional analysis instead of a longitudinal one doesn't matter 
>> right? Would it be correct to say that we still apply the same group 
>> analysis described in the wiki?
>>
>> Thanks,
>> 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: Friday, May 31, 2013 11:59 AM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Group Analysis
>>
>> Hi Panos, are you asking whether theunbalanced design will leadto one
>> slope being different than another just because the numbers are
>> different? That is not a problem. You can simply follow the instructions
>> on the wiki.
>> doug
>>
>>
>>
>> On 05/31/2013 11:26 AM, Fotiadis, Panagiotis wrote:
>>> Hey Doug,
>>>
>>> Sorry for the overwhelming amount of questions. I wanted to confirm 
>>> something. Suppose you want to do group analysis between two groups say a 
>>> healthy cohort vs a diseased cohort. Each cohort has ~40 and ~30 subjects 
>>> each (different people), and you want to compare how for instance the 
>>> cortical thickness decreases over age in the one group versus the other. Do 
>>> you still set the contrast vector as [0 0 1 -1]  ([intercept 1 intercept 2 
>>> slope 1 slope 2]) and follow the analysis described in 
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis or do 
>>> you go on a different way since there are different subjects instead of one 
>>> with 40 (or 30) different longitudinal data for each cohort? Don't we need 
>>> to correct the age slopes for the fact that we have 40 (and 30) different 
>>> subjects in each cohort?
>>>
>>> Thanks,
>>> Panos
>>> ___
>>> 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/
>>
>> ___
>> 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/
>
> ___
> 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.

[Freesurfer] Difference between Original and Main surfaces?

[Jonathan Holt]

Always wondered, was never quite sure. I'm wondering why sometimes they
mirror each other and other times they shift away.

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


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

Re: [Freesurfer] Difference between Original and Main surfaces?

[Bruce Fischl]

the white surface uses information such as the surface normal and 
surface-based smoothing to refine the estimate of the gray/white boundary, 
so in general it is significantly more accurate. The orig is really just an 
initialization for the white

cheers
Bruce

On Fri, 31 May 2013, Jonathan Holt wrote:

> Always wondered, was never quite sure. I'm wondering why sometimes they
> mirror each other and other times they shift away.
> jon
> 
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] beta weights from FS-Fast analysis

[Joseph Dien]

On May 31, 2013, at 12:09 PM, Douglas N Greve  wrote:

> 
> On 05/30/2013 04:37 PM, Joseph Dien wrote:
>> Just to make sure I'm doing this right, I'm going to summarize what 
>> I've taken away from your answers and to ask some new questions. In 
>> order to present the results, I need two things:
>> 
>> 1) A set of histograms (with error bars) for each cluster figure to 
>> show the % signal change for each of the four contrasts of interest.
>> The cache.th20.pos.y.ocn.dat file only gives it for the condition 
>> where the cluster was significant so I can't use that.
>> So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot 
>> from the group level analysis to generate a mask for each cluster of 
>> interest.
>> Then I could extract the value of the voxels from each 
>> subject's cespct file for each contrast, average them across the 
>> cluster ROI, then average them across each subject, to generate the 
>> histogram?
>> This would suffice to give me the %age signal change?
>> I would be doing these computations in Matlab using MRIread.
> I don't understand. If you don't have a cluster for a contrast, how are 
> you defining the cluster? From another contrast?
> 

Well, what the reviewer told me to do is if I present a figure with a 
significant cluster for one condition, I should use that as an ROI to calculate 
the %age signal change for all four conditions and present it as a bar chart as 
part of the figure.  I think she wanted to be able to get a more qualitative 
sense of the data patterns.

>> 
>> 2) A results table with the headings:
>> 
>> Cluster p (FWE corrected)
>> Cluster size
>> Peak Voxel p (FWE corrected)
>> Peak Voxel T
>> Peak Voxel Coords
>> BA
>> Anatomical Landmark
>> 
>> I can get the first two from 
>> the cache.th20.pos/neg.sig.cluster.summary files from the group level 
>> analysis.
>> I can get the peak voxel coordinates from the summary files as well.
>> I can use this to get the peak voxel p from the group level sig.nii.gz 
>> file.  Is this FWE corrected?  If not, how can I get this information?
> What do you mean? The cluster p-value is corrected, why do you need the 
> max p and why does it need to be corrected?

Well, as I understand it, the drawback of clusterwise statistics is that while 
it assures you that the cluster passes muster as not being due to random chance 
(at 95% confidence), it doesn't provide any assurances at the voxel level (or 
in this case the vertex level) as it is likely that a cluster is composed of 
both signal and noise and you don't know which part is which.  So if a cluster 
covers both BA44 and BA45 (for example), you can't be sure whether the 
activation involves BA44, BA45, or both.  A voxelwise correction is more 
conservative but if it provides significance, it does allow for this kind of 
interpretation.

>> I can use these coordinates to get the peak voxel T by getting the 
>> value from the group level F.nii.gz file and taking its square root. 
>> How can I get the sign of the T statistic?
> Same as the sign of gamma.mgh

Ah, great!

>> I can use the Lancaster transform to convert the MNI305 peak voxel 
>> coordinates into the Atlas coordinates to look up the putative BA and 
>> landmarks (unless there is a better way with Freesurfer?  I'm seeing 
>> some references to some BA labels in the forum but it doesn't look 
>> like this is a complete set yet?).
> Some of the BA labels are in FS, but not nearly all of them
> doug

No problem!  I worked out that I can use the talairach.nii file made available 
by the Talairach Daemon folks.


>> 
>> Sorry for all these questions!  I got some nice results from FSFAST 
>> and would like to get them written up.
>> 
>> Cheers!
>> 
>> Joe
>> 
>> 
>> 
>> 
>> On May 29, 2013, at 10:53 PM, Douglas Greve > > wrote:
>> 
>>> 
>>> On 5/29/13 10:42 PM, Joseph Dien wrote:
 
 On May 29, 2013, at 11:40 AM, Douglas N Greve 
 mailto:gr...@nmr.mgh.harvard.edu>> wrote:
 
> Hi Joe,
> 
> On 05/29/2013 01:00 AM, Joseph Dien wrote:
>> I need to extract the beta weights from a cluster identified with
>> FS-Fast in order to compute percentage signal change.
>> 
>> 1) I see a file called beta.nii.gz that appears to have the beta
>> weight information.  It has a four dimensional structure and the
>> fourth dimension appears to be the beta weights.  Is there an index
>> somewhere as to which beta weight is which?  Or if not, how are they
>> organized?
> For the first level analysis, the first N beta weights correspond 
> to the
> N conditions in the paradigm file. The rest are nuisance variables.
>> 
 
 Ah, very good!  In order to compute the percent signal change 
 statistic (I'm following the MarsBaR approach: 
 http://marsbar.sourceforge.net/faq.html#how-is-the-percent-signal-change-calculated)
  
 I'm also going to need the beta weights for the session mean 
 regressors.

Re: [Freesurfer] beta weights from FS-Fast analysis

[Joseph Dien]

On May 31, 2013, at 12:11 PM, Douglas N Greve  wrote:

> 
> On 05/31/2013 01:49 AM, Joseph Dien wrote:
>> I was able to make more progress so I'm mostly good at this point but 
>> I have a remaining question:
>> 
>> I assume the contents of sig.nii.gz (which I assume are the vertex 
>> p-values) are not FWE corrected.  Is it possible to get FWE-corrected 
>> vertex p-values?  Or are only clusterwise corrections available?
> There should be something like cache.th13.abs.sig.voxel.mgh which is 
> corrected on a voxelwise basis (the th13 is just part of the name but it 
> should be the same regardless of the threshold you choose)
> doug

Excellent!  Thanks!  :)

>> 
>> Thanks again for your patience!
>> 
>> Joe
>> 
>> On May 30, 2013, at 4:37 PM, Joseph Dien > > wrote:
>> 
>>> Just to make sure I'm doing this right, I'm going to summarize what 
>>> I've taken away from your answers and to ask some new questions. In 
>>> order to present the results, I need two things:
>>> 
>>> 1) A set of histograms (with error bars) for each cluster figure to 
>>> show the % signal change for each of the four contrasts of interest.
>>> The cache.th20.pos.y.ocn.dat file only gives it for the condition 
>>> where the cluster was significant so I can't use that.
>>> So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot 
>>> from the group level analysis to generate a mask for each cluster of 
>>> interest.
>>> Then I could extract the value of the voxels from each 
>>> subject's cespct file for each contrast, average them across the 
>>> cluster ROI, then average them across each subject, to generate the 
>>> histogram?
>>> This would suffice to give me the %age signal change?
>>> I would be doing these computations in Matlab using MRIread.
>>> 
>>> 2) A results table with the headings:
>>> 
>>> Cluster p (FWE corrected)
>>> Cluster size
>>> Peak Voxel p (FWE corrected)
>>> Peak Voxel T
>>> Peak Voxel Coords
>>> BA
>>> Anatomical Landmark
>>> 
>>> I can get the first two from 
>>> the cache.th20.pos/neg.sig.cluster.summary files from the group level 
>>> analysis.
>>> I can get the peak voxel coordinates from the summary files as well.
>>> I can use this to get the peak voxel p from the group 
>>> level sig.nii.gz file.  Is this FWE corrected?  If not, how can I get 
>>> this information?
>>> I can use these coordinates to get the peak voxel T by getting the 
>>> value from the group level F.nii.gz file and taking its square root. 
>>> How can I get the sign of the T statistic?
>>> I can use the Lancaster transform to convert the MNI305 peak voxel 
>>> coordinates into the Atlas coordinates to look up the putative BA and 
>>> landmarks (unless there is a better way with Freesurfer?  I'm seeing 
>>> some references to some BA labels in the forum but it doesn't look 
>>> like this is a complete set yet?).
>>> 
>>> Sorry for all these questions!  I got some nice results from FSFAST 
>>> and would like to get them written up.
>>> 
>>> Cheers!
>>> 
>>> Joe
>>> 
>>> 
>>> 
>>> 
>>> On May 29, 2013, at 10:53 PM, Douglas Greve 
>>> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>> 
 
 On 5/29/13 10:42 PM, Joseph Dien wrote:
> 
> On May 29, 2013, at 11:40 AM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> 
>> Hi Joe,
>> 
>> On 05/29/2013 01:00 AM, Joseph Dien wrote:
>>> I need to extract the beta weights from a cluster identified with
>>> FS-Fast in order to compute percentage signal change.
>>> 
>>> 1) I see a file called beta.nii.gz that appears to have the beta
>>> weight information.  It has a four dimensional structure and the
>>> fourth dimension appears to be the beta weights.  Is there an index
>>> somewhere as to which beta weight is which?  Or if not, how are they
>>> organized?
>> For the first level analysis, the first N beta weights correspond 
>> to the
>> N conditions in the paradigm file. The rest are nuisance variables.
>>> 
> 
> Ah, very good!  In order to compute the percent signal change 
> statistic (I'm following the MarsBaR approach: 
> http://marsbar.sourceforge.net/faq.html#how-is-the-percent-signal-change-calculated)
>  
> I'm also going to need the beta weights for the session mean 
> regressors.  How are the nuisance regressors organized?
 You can just use the meanfunc.nii.gz. Also, each contrasts is 
 computed as the simple contrast (ces) and as a percent of the 
 baseline at the voxel (cespct, cesvarpct).
> 
>>> 2) In order to extract the cluster, it looks like I would
>>> use mri_label2vol to convert cache.th20.neg.sig.ocn.annot into a
>>> volume where the voxels are tagged with the number of the
>>> corresponding cluster.
>> Is that  from a group analysis?
>>> 
> 
> Yes, that's right.
> 
>>> I could then use that to generate masks to extract the information I
>>> need for each cluster f

Re: [Freesurfer] mprage flag in recon-all

[Caspar M. Schwiedrzik]

I only find flags for mri_normalize and mri_segment in recon-all, and I
have trouble reading the contents mri_normalize with a regular text editor.
caspar


2013/5/31 Bruce Fischl 

> Hi Caspar
>
> it changes some parameters to the intensity normalization and segmentation
> to account for the lower SNR and increased CNR in the mprage. You'll need
> to look in the recon-all script for the details
>
> cheers
> Bruce
>
>
>
> On Thu, 30 May 2013, Caspar M. Schwiedrzik wrote:
>
>  Hi!
>> Is there more documentation on what settings the mprage flag enables in
>> recon-all?
>> Specifically, I would be interested which individual steps it affects and
>> what  the parameters are for each of the steps.
>> Thanks!
>> Caspar
>>
>>
>>
>>
>
> 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


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] possible to display data obtained through mri_segment as heatmap?

[Salil Soman]

Dear Doug,

Thank you for your recent advise with using freesurfer to extract mean
values from non structural image data. Is there a way to generate an image
(e.g. heat map) displaying those values in free view?

Best wishes,

Sal
___
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] Release 5.2 vs 5.3

[Welsh, Robert]

Hi Bruce and others,

We started a rather extensive push of data through the linux 5.2 release of 
free surfer. We also use OS X at times and I was hoping to get a R5.2 for MAC 
but I see it's not available. One of the guys that works in my lab — Jon Holt — 
also said that 5.2 was no longer available and indicated he heard there may be 
issues with 5.2

So two questions:

1) we have > 100 subjects pushed through R5.2 and still working inside 5.2, are 
we in trouble? What's the advice. We have many FTE hours on the editing and 
would be very painful to go back (we already did with with 5.0 to 5.2 change).

2) are we safe using 5.3 in conjunction with 5.2?

Any other advice about versions etc. Given the amount of time it takes to push 
data through it is difficult to keep changing versions, plus from a publication 
view it would be a hard sale I think to reviewers to indicate we used multiple 
versions.

Thanks,

-Robert

-
Robert C. Welsh, Ph.D.
Assistant Professor
Department of Radiology
Department of Psychiatry
University of Michigan


**
Electronic Mail is not secure, may not be read every day, and should not be 
used for urgent or sensitive issues 
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] beta weights from FS-Fast analysis

[Douglas N Greve]

On 05/31/2013 02:45 PM, Joseph Dien wrote:
>
> On May 31, 2013, at 12:09 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>>
>> On 05/30/2013 04:37 PM, Joseph Dien wrote:
>>> Just to make sure I'm doing this right, I'm going to summarize what
>>> I've taken away from your answers and to ask some new questions. In
>>> order to present the results, I need two things:
>>>
>>> 1) A set of histograms (with error bars) for each cluster figure to
>>> show the % signal change for each of the four contrasts of interest.
>>> The cache.th20.pos.y.ocn.dat file only gives it for the condition
>>> where the cluster was significant so I can't use that.
>>> So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot
>>> from the group level analysis to generate a mask for each cluster of
>>> interest.
>>> Then I could extract the value of the voxels from each
>>> subject's cespct file for each contrast, average them across the
>>> cluster ROI, then average them across each subject, to generate the
>>> histogram?
>>> This would suffice to give me the %age signal change?
>>> I would be doing these computations in Matlab using MRIread.
>> I don't understand. If you don't have a cluster for a contrast, how are
>> you defining the cluster? From another contrast?
>>
>
> Well, what the reviewer told me to do is if I present a figure with a 
> significant cluster for one condition, I should use that as an ROI to 
> calculate the %age signal change for all four conditions and present 
> it as a bar chart as part of the figure.  I think she wanted to be 
> able to get a more qualitative sense of the data patterns.
If you have a cluster annotation (created by mri_glmfit-sim) then you 
can apply that to each contrast using mri_segstats with the --annot option.

>
>>>
>>> 2) A results table with the headings:
>>>
>>> Cluster p (FWE corrected)
>>> Cluster size
>>> Peak Voxel p (FWE corrected)
>>> Peak Voxel T
>>> Peak Voxel Coords
>>> BA
>>> Anatomical Landmark
>>>
>>> I can get the first two from
>>> the cache.th20.pos/neg.sig.cluster.summary files from the group level
>>> analysis.
>>> I can get the peak voxel coordinates from the summary files as well.
>>> I can use this to get the peak voxel p from the group level sig.nii.gz
>>> file.  Is this FWE corrected?  If not, how can I get this information?
>> What do you mean? The cluster p-value is corrected, why do you need the
>> max p and why does it need to be corrected?
>
> Well, as I understand it, the drawback of clusterwise statistics is 
> that while it assures you that the cluster passes muster as not being 
> due to random chance (at 95% confidence), it doesn't provide any 
> assurances at the voxel level (or in this case the vertex level) as it 
> is likely that a cluster is composed of both signal and noise and you 
> don't know which part is which.  So if a cluster covers both BA44 and 
> BA45 (for example), you can't be sure whether the activation involves 
> BA44, BA45, or both.  A voxelwise correction is more conservative but 
> if it provides significance, it does allow for this kind of 
> interpretation.
>
>>> I can use these coordinates to get the peak voxel T by getting the
>>> value from the group level F.nii.gz file and taking its square root.
>>> How can I get the sign of the T statistic?
>> Same as the sign of gamma.mgh
>
> Ah, great!
>
>>> I can use the Lancaster transform to convert the MNI305 peak voxel
>>> coordinates into the Atlas coordinates to look up the putative BA and
>>> landmarks (unless there is a better way with Freesurfer?  I'm seeing
>>> some references to some BA labels in the forum but it doesn't look
>>> like this is a complete set yet?).
>> Some of the BA labels are in FS, but not nearly all of them
>> doug
>
> No problem!  I worked out that I can use the talairach.nii file made 
> available by the Talairach Daemon folks.
>
>
>>>
>>> Sorry for all these questions!  I got some nice results from FSFAST
>>> and would like to get them written up.
>>>
>>> Cheers!
>>>
>>> Joe
>>>
>>>
>>>
>>>
>>> On May 29, 2013, at 10:53 PM, Douglas Greve 
>>> mailto:gr...@nmr.mgh.harvard.edu>
>>> > wrote:
>>>

 On 5/29/13 10:42 PM, Joseph Dien wrote:
>
> On May 29, 2013, at 11:40 AM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu> 
> > wrote:
>
>> Hi Joe,
>>
>> On 05/29/2013 01:00 AM, Joseph Dien wrote:
>>> I need to extract the beta weights from a cluster identified with
>>> FS-Fast in order to compute percentage signal change.
>>>
>>> 1) I see a file called beta.nii.gz that appears to have the beta
>>> weight information.  It has a four dimensional structure and the
>>> fourth dimension appears to be the beta weights.  Is there an index
>>> somewhere as to which beta weight is which?  Or if not, how are they
>>> organized?
>> For the first level analysis, the first N beta weights correspond

Re: [Freesurfer] possible to display data obtained through mri_segment as heatmap?

[Douglas N Greve]

Do you mean table data or data that you have on a map?
On 05/31/2013 03:20 PM, Salil Soman wrote:
> Dear Doug,
>
> Thank you for your recent advise with using freesurfer to extract mean 
> values from non structural image data. Is there a way to generate an 
> image (e.g. heat map) displaying those values in free view?
>
> Best wishes,
>
> Sal

-- 
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/

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


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

Re: [Freesurfer] possible to display data obtained through mri_segment as heatmap?

[Salil Soman]

I have been able to generate the table. I was asking about an actual image
(that could be visualized in freeview or something else).

Thank you.

-S


On Fri, May 31, 2013 at 12:25 PM, Douglas N Greve  wrote:

> Do you mean table data or data that you have on a map?
>
> On 05/31/2013 03:20 PM, Salil Soman wrote:
>
>> Dear Doug,
>>
>> Thank you for your recent advise with using freesurfer to extract mean
>> values from non structural image data. Is there a way to generate an image
>> (e.g. heat map) displaying those values in free view?
>>
>> Best wishes,
>>
>> Sal
>>
>
> --
> 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/ 
>
>
>
> 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


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] possible to display data obtained through mri_segment as heatmap?

[Douglas N Greve]

you can just specify an overlay on the freeview command line

On 05/31/2013 03:26 PM, Salil Soman wrote:
> I have been able to generate the table. I was asking about an actual 
> image (that could be visualized in freeview or something else).
>
> Thank you.
>
> -S
>
>
> On Fri, May 31, 2013 at 12:25 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Do you mean table data or data that you have on a map?
>
> On 05/31/2013 03:20 PM, Salil Soman wrote:
>
> Dear Doug,
>
> Thank you for your recent advise with using freesurfer to
> extract mean values from non structural image data. Is there a
> way to generate an image (e.g. heat map) displaying those
> values in free view?
>
> Best wishes,
>
> Sal
>
>
> -- 
> 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/
>
>
>
> 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: 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/

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

Re: [Freesurfer] mprage flag in recon-all

[Caspar M. Schwiedrzik]

yes, but recon-all just calls mri_segment with -mprage and mri_normalize
with -mprage.
I would like to know what -mprage does in these two functions, but i cannot
search them because they are executables, not scripts.
Caspar

2013/5/31 Harms, Michael 

>
>  Use any editor (even Word) with a search capacity, and search for the
> string 'mprage'.
> That will lead to you the variable internal to recon-all called
> "IsMPRAGE".  Searching for "IsMPRAGE" will then show you all in the stages
> that the -mprage flag affects.
>
>  cheers,
> -MH
>
>   --
> Michael Harms, Ph.D.
>  ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO  63110 Email: mha...@wustl.edu
>
>   From: "Caspar M. Schwiedrzik" 
> Date: Friday, May 31, 2013 2:14 PM
> To: "Freesurfer@nmr.mgh.harvard.edu" 
> Subject: Re: [Freesurfer] mprage flag in recon-all
>
>  I only find flags for mri_normalize and mri_segment in recon-all, and I
> have trouble reading the contents mri_normalize with a regular text editor.
> caspar
>
>
> 2013/5/31 Bruce Fischl 
>
>> Hi Caspar
>>
>> it changes some parameters to the intensity normalization and
>> segmentation to account for the lower SNR and increased CNR in the mprage.
>> You'll need to look in the recon-all script for the details
>>
>> cheers
>> Bruce
>>
>>
>>
>> On Thu, 30 May 2013, Caspar M. Schwiedrzik wrote:
>>
>>  Hi!
>>> Is there more documentation on what settings the mprage flag enables in
>>> recon-all?
>>> Specifically, I would be interested which individual steps it affects and
>>> what  the parameters are for each of the steps.
>>> Thanks!
>>> Caspar
>>>
>>>
>>>
>>>
>>
>>  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.
>>
>
>
>  --
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] mprage flag in recon-all

[Harms, Michael]

Sorry, I misinterpreted your question.  In that case, if you want more than the broad-brush description that Bruce provided, you'll likely need to download the source code and scour the c-code yourself to find the exact specifics.


cheers,
-MH




-- 
Michael Harms, Ph.D.

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






From: "Caspar M. Schwiedrzik" 
Date: Friday, May 31, 2013 2:50 PM
To: "Harms, Michael" , "Freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] mprage flag in recon-all




yes, but recon-all just calls mri_segment with -mprage and mri_normalize with -mprage.

I would like to know what -mprage does in these two functions, but i cannot search them because they are executables, not scripts.

Caspar

2013/5/31 Harms, Michael 






Use any editor (even Word) with a search capacity, and search for the string 'mprage'.
That will lead to you the variable internal to recon-all called "IsMPRAGE".  Searching for "IsMPRAGE" will then show you all in the stages that the -mprage flag affects.


cheers,
-MH




-- 
Michael Harms, Ph.D.

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







From: "Caspar M. Schwiedrzik" 
Date: Friday, May 31, 2013 2:14 PM
To: "Freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] mprage flag in recon-all






I only find flags for mri_normalize and mri_segment in recon-all, and I have trouble reading the contents mri_normalize with a regular text editor.

caspar


2013/5/31 Bruce Fischl 

Hi Caspar

it changes some parameters to the intensity normalization and segmentation to account for the lower SNR and increased CNR in the mprage. You'll need to look in the recon-all script for the details

cheers
Bruce




On Thu, 30 May 2013, Caspar M. Schwiedrzik wrote:


Hi!
Is there more documentation on what settings the mprage flag enables in
recon-all?
Specifically, I would be interested which individual steps it affects and
what  the parameters are for each of the steps.
Thanks!
Caspar








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.










 



The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient,
 be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return
 mail.









 



The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended
 recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone
 or return mail.


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


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

Re: [Freesurfer] mprage flag in recon-all

[Bruce Fischl]

mri_normalize is a binary so you can't, just recon-all.

On Fri, 31 May 2013, Caspar M. Schwiedrzik wrote:


I only find flags for mri_normalize and mri_segment in recon-all, and I have
trouble reading the contents mri_normalize with a regular text editor.
caspar


2013/5/31 Bruce Fischl 
  Hi Caspar

  it changes some parameters to the intensity normalization and
  segmentation to account for the lower SNR and increased CNR in
  the mprage. You'll need to look in the recon-all script for the
  details

  cheers
  Bruce


  On Thu, 30 May 2013, Caspar M. Schwiedrzik wrote:

Hi!
Is there more documentation on what settings the
mprage flag enables in
recon-all?
Specifically, I would be interested which individual
steps it affects and
what  the parameters are for each of the steps.
Thanks!
Caspar





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


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] Release 5.2 vs 5.3

[Bruce Fischl]

Hi Robert

I'm really sorry to hear it. I suspect that though that you would be better 
off rerunning everything through 5.3. It should be the case that all manual 
edits are retained and it's just compute time that you will have wasted. 
5.2 had a user-requested mod that made the surfaces inaccurate in some 
acquisitions, although not in our test suite, which of course is why we 
didn't catch it. We have announced the problem with 5.2 so I would worry 
that if you try to publish with it you will get yelled at by some reviewer.


Again, I'm sorry for the wasted time. We try hard to avoid this kind of 
problem, but our resources are quite finite and there's only so much 
testing we can do (and in this case, 5.2 passed all our internal tests).


Bruce


On Fri, 31 May 2013, Welsh, Robert wrote:


Hi Bruce and others,

We started a rather extensive push of data through the linux 5.2 release of
free surfer. We also use OS X at times and I was hoping to get a R5.2 for
MAC but I see it's not available. One of the guys that works in my lab — Jon
Holt — also said that 5.2 was no longer available and indicated he heard
there may be issues with 5.2

So two questions:

1) we have > 100 subjects pushed through R5.2 and still working inside 5.2,
are we in trouble? What's the advice. We have many FTE hours on the editing
and would be very painful to go back (we already did with with 5.0 to 5.2
change).

2) are we safe using 5.3 in conjunction with 5.2? 

Any other advice about versions etc. Given the amount of time it takes to
push data through it is difficult to keep changing versions, plus from a
publication view it would be a hard sale I think to reviewers to indicate we
used multiple versions.

Thanks,

-Robert

-
Robert C. Welsh, Ph.D.
Assistant Professor 
Department of Radiology
Department of Psychiatry
University of Michigan 


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


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


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

Re: [Freesurfer] beta weights from FS-Fast analysis

[Joseph Dien]

It looks like the corrected vertex p-values (ex: 
cache.th13.abs.sig.voxel.nii.gz) are only available for the surface-based lh 
and rh spaces.  For the subcortical volume-based analysis I don't see the 
corresponding corrected voxel p-values being available?

On May 31, 2013, at 2:46 PM, Joseph Dien  wrote:

> 
> On May 31, 2013, at 12:11 PM, Douglas N Greve  
> wrote:
> 
>> 
>> On 05/31/2013 01:49 AM, Joseph Dien wrote:
>>> I was able to make more progress so I'm mostly good at this point but 
>>> I have a remaining question:
>>> 
>>> I assume the contents of sig.nii.gz (which I assume are the vertex 
>>> p-values) are not FWE corrected.  Is it possible to get FWE-corrected 
>>> vertex p-values?  Or are only clusterwise corrections available?
>> There should be something like cache.th13.abs.sig.voxel.mgh which is 
>> corrected on a voxelwise basis (the th13 is just part of the name but it 
>> should be the same regardless of the threshold you choose)
>> doug
> 
> Excellent!  Thanks!  :)
> 
>>> 
>>> Thanks again for your patience!
>>> 
>>> Joe
>>> 
>>> On May 30, 2013, at 4:37 PM, Joseph Dien >> > wrote:
>>> 
 Just to make sure I'm doing this right, I'm going to summarize what 
 I've taken away from your answers and to ask some new questions. In 
 order to present the results, I need two things:
 
 1) A set of histograms (with error bars) for each cluster figure to 
 show the % signal change for each of the four contrasts of interest.
 The cache.th20.pos.y.ocn.dat file only gives it for the condition 
 where the cluster was significant so I can't use that.
 So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot 
 from the group level analysis to generate a mask for each cluster of 
 interest.
 Then I could extract the value of the voxels from each 
 subject's cespct file for each contrast, average them across the 
 cluster ROI, then average them across each subject, to generate the 
 histogram?
 This would suffice to give me the %age signal change?
 I would be doing these computations in Matlab using MRIread.
 
 2) A results table with the headings:
 
 Cluster p (FWE corrected)
 Cluster size
 Peak Voxel p (FWE corrected)
 Peak Voxel T
 Peak Voxel Coords
 BA
 Anatomical Landmark
 
 I can get the first two from 
 the cache.th20.pos/neg.sig.cluster.summary files from the group level 
 analysis.
 I can get the peak voxel coordinates from the summary files as well.
 I can use this to get the peak voxel p from the group 
 level sig.nii.gz file.  Is this FWE corrected?  If not, how can I get 
 this information?
 I can use these coordinates to get the peak voxel T by getting the 
 value from the group level F.nii.gz file and taking its square root. 
 How can I get the sign of the T statistic?
 I can use the Lancaster transform to convert the MNI305 peak voxel 
 coordinates into the Atlas coordinates to look up the putative BA and 
 landmarks (unless there is a better way with Freesurfer?  I'm seeing 
 some references to some BA labels in the forum but it doesn't look 
 like this is a complete set yet?).
 
 Sorry for all these questions!  I got some nice results from FSFAST 
 and would like to get them written up.
 
 Cheers!
 
 Joe
 
 
 
 
 On May 29, 2013, at 10:53 PM, Douglas Greve 
 mailto:gr...@nmr.mgh.harvard.edu>> wrote:
 
> 
> On 5/29/13 10:42 PM, Joseph Dien wrote:
>> 
>> On May 29, 2013, at 11:40 AM, Douglas N Greve 
>> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>> 
>>> Hi Joe,
>>> 
>>> On 05/29/2013 01:00 AM, Joseph Dien wrote:
 I need to extract the beta weights from a cluster identified with
 FS-Fast in order to compute percentage signal change.
 
 1) I see a file called beta.nii.gz that appears to have the beta
 weight information.  It has a four dimensional structure and the
 fourth dimension appears to be the beta weights.  Is there an index
 somewhere as to which beta weight is which?  Or if not, how are they
 organized?
>>> For the first level analysis, the first N beta weights correspond 
>>> to the
>>> N conditions in the paradigm file. The rest are nuisance variables.
 
>> 
>> Ah, very good!  In order to compute the percent signal change 
>> statistic (I'm following the MarsBaR approach: 
>> http://marsbar.sourceforge.net/faq.html#how-is-the-percent-signal-change-calculated)
>>  
>> I'm also going to need the beta weights for the session mean 
>> regressors.  How are the nuisance regressors organized?
> You can just use the meanfunc.nii.gz. Also, each contrasts is 
> computed as the simple contrast (ces) and as a percent of the 
> baseline at the voxel (cespct, cesvarpct).
>

Re: [Freesurfer] beta weights from FS-Fast analysis

[Douglas N Greve]

Oh, right, it is probably not there for subcortical. I don't know what I 
would have to do to write it out. It won't be something that happens 
before I get back from HBM. Can you remind me after HBM?
doug

On 05/31/2013 04:44 PM, Joseph Dien wrote:
> It looks like the corrected vertex p-values 
> (ex: cache.th13.abs.sig.voxel.nii.gz) are only available for the 
> surface-based lh and rh spaces.  For the subcortical volume-based 
> analysis I don't see the corresponding corrected voxel p-values being 
> available?
>
> On May 31, 2013, at 2:46 PM, Joseph Dien  > wrote:
>
>>
>> On May 31, 2013, at 12:11 PM, Douglas N Greve 
>> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>
>>>
>>> On 05/31/2013 01:49 AM, Joseph Dien wrote:
 I was able to make more progress so I'm mostly good at this point but
 I have a remaining question:

 I assume the contents of sig.nii.gz (which I assume are the vertex
 p-values) are not FWE corrected.  Is it possible to get FWE-corrected
 vertex p-values?  Or are only clusterwise corrections available?
>>> There should be something like cache.th13.abs.sig.voxel.mgh which is
>>> corrected on a voxelwise basis (the th13 is just part of the name 
>>> but it
>>> should be the same regardless of the threshold you choose)
>>> doug
>>
>> Excellent!  Thanks!  :)
>>

 Thanks again for your patience!

 Joe

 On May 30, 2013, at 4:37 PM, Joseph Dien >>> 
 > wrote:

> Just to make sure I'm doing this right, I'm going to summarize what
> I've taken away from your answers and to ask some new questions. In
> order to present the results, I need two things:
>
> 1) A set of histograms (with error bars) for each cluster figure to
> show the % signal change for each of the four contrasts of interest.
> The cache.th20.pos.y.ocn.dat file only gives it for the condition
> where the cluster was significant so I can't use that.
> So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot
> from the group level analysis to generate a mask for each cluster of
> interest.
> Then I could extract the value of the voxels from each
> subject's cespct file for each contrast, average them across the
> cluster ROI, then average them across each subject, to generate the
> histogram?
> This would suffice to give me the %age signal change?
> I would be doing these computations in Matlab using MRIread.
>
> 2) A results table with the headings:
>
> Cluster p (FWE corrected)
> Cluster size
> Peak Voxel p (FWE corrected)
> Peak Voxel T
> Peak Voxel Coords
> BA
> Anatomical Landmark
>
> I can get the first two from
> the cache.th20.pos/neg.sig.cluster.summary files from the group level
> analysis.
> I can get the peak voxel coordinates from the summary files as well.
> I can use this to get the peak voxel p from the group
> level sig.nii.gz file.  Is this FWE corrected?  If not, how can I get
> this information?
> I can use these coordinates to get the peak voxel T by getting the
> value from the group level F.nii.gz file and taking its square root.
> How can I get the sign of the T statistic?
> I can use the Lancaster transform to convert the MNI305 peak voxel
> coordinates into the Atlas coordinates to look up the putative BA and
> landmarks (unless there is a better way with Freesurfer?  I'm seeing
> some references to some BA labels in the forum but it doesn't look
> like this is a complete set yet?).
>
> Sorry for all these questions!  I got some nice results from FSFAST
> and would like to get them written up.
>
> Cheers!
>
> Joe
>
>
>
>
> On May 29, 2013, at 10:53 PM, Douglas Greve
> mailto:gr...@nmr.mgh.harvard.edu> 
> > wrote:
>
>>
>> On 5/29/13 10:42 PM, Joseph Dien wrote:
>>>
>>> On May 29, 2013, at 11:40 AM, Douglas N Greve
>>> mailto:gr...@nmr.mgh.harvard.edu> 
>>> > wrote:
>>>
 Hi Joe,

 On 05/29/2013 01:00 AM, Joseph Dien wrote:
> I need to extract the beta weights from a cluster identified with
> FS-Fast in order to compute percentage signal change.
>
> 1) I see a file called beta.nii.gz that appears to have the beta
> weight information.  It has a four dimensional structure and the
> fourth dimension appears to be the beta weights.  Is there an 
> index
> somewhere as to which beta weight is which?  Or if not, how 
> are they
> organized?
 For the first level analysis, the first N beta weights correspond
 to the
 N conditions in the paradigm file. The rest are nuisance variables.
>
>>>
>>> Ah, very good!  In order

[Freesurfer] CVS crashing consistently

[Graham Wideman]

Hi MGH folks,

I am attempting to download the source via CVS as described here:

http://freesurfer.net/fswiki/ReadOnlyCVS

using:

cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P 
-r release_5_3_0 dev

(ie: 5.3.0 source)

The CVS process is consistently stopping about 760 files into the process, with 
the final lines of output being:


cvs checkout: Updating dev/distribution/trctrain
U dev/distribution/trctrain/Makefile.am
Terminated with fatal signal 9


After the first attempt got stuck here, I attempted to run the checkout command 
again. CVS quickly displays a bunch of "Updating x" where x is all the 
directories already downloaded, then gets to trctrain and stops indefinitely. 
(I then killed it using Ctl-C)

I then created a new local directory and restarted from scratch. The checkout 
proceeded apace, and then got stuck at the same place (trctrain), with same 
failure message.

So... I'm thinking it might be something at your end, maybe disk problems in 
whatever files come next after the last one above?

FWIW, I'm using cvs as installed with Mint 15, which is 1.12.13-MirDebian-9 
(client/server)

-- Graham

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


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

Re: [Freesurfer] mprage flag in recon-all

[Bruce Fischl]

oh, my mistake. I thought it called them with specific parms. Sorry:

for mri_segment:

gray_hi = 99 ;   (same as --ghi 99)
wm_low = 89 ;(same as -wlo 89)


for mri_normalize:

intensity_below = 15 ; (same as -b 15)

cheers
Bruce


On Fri, 
31 May 2013, Caspar M. Schwiedrzik wrote:



yes, but recon-all just calls mri_segment with -mprage and mri_normalize
with -mprage.
I would like to know what -mprage does in these two functions, but i cannot
search them because they are executables, not scripts.
Caspar

2013/5/31 Harms, Michael 

Use any editor (even Word) with a search capacity, and search for the
string 'mprage'.
That will lead to you the variable internal to recon-all called
"IsMPRAGE".  Searching for "IsMPRAGE" will then show you all in the
stages that the -mprage flag affects.

cheers,
-MH

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

From: "Caspar M. Schwiedrzik" 
Date: Friday, May 31, 2013 2:14 PM
To: "Freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] mprage flag in recon-all

I only find flags for mri_normalize and mri_segment in recon-all, and
I have trouble reading the contents mri_normalize with a regular text
editor.
caspar


2013/5/31 Bruce Fischl 
  Hi Caspar

  it changes some parameters to the intensity normalization
  and segmentation to account for the lower SNR and
  increased CNR in the mprage. You'll need to look in the
  recon-all script for the details

  cheers
  Bruce


  On Thu, 30 May 2013, Caspar M. Schwiedrzik wrote:

Hi!
Is there more documentation on what settings
the mprage flag enables in
recon-all?
Specifically, I would be interested which
individual steps it affects and
what  the parameters are for each of the
steps.
Thanks!
Caspar





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.


 





The materials in this message are private and may contain Protected
Healthcare Information or other information of a sensitive nature. If
you are not the intended recipient, be advised that any unauthorized
use, disclosure, copying or the taking of any action in reliance on
the contents of this information is strictly prohibited. If you have
received this email in error, please immediately notify the sender via
telephone or return mail.



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


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

Re: [Freesurfer] mprage flag in recon-all

[Caspar M. Schwiedrzik]

thanks!
caspar


2013/5/31 Bruce Fischl :
> oh, my mistake. I thought it called them with specific parms. Sorry:
>
> for mri_segment:
>
> gray_hi = 99 ;   (same as --ghi 99)
> wm_low = 89 ;(same as -wlo 89)
>
>
> for mri_normalize:
>
> intensity_below = 15 ; (same as -b 15)
>
> cheers
> Bruce
>
>
>
> On Fri, 31 May 2013, Caspar M. Schwiedrzik wrote:
>
>> yes, but recon-all just calls mri_segment with -mprage and mri_normalize
>> with -mprage.
>> I would like to know what -mprage does in these two functions, but i
>> cannot
>> search them because they are executables, not scripts.
>> Caspar
>>
>> 2013/5/31 Harms, Michael 
>>
>> Use any editor (even Word) with a search capacity, and search for the
>> string 'mprage'.
>> That will lead to you the variable internal to recon-all called
>> "IsMPRAGE".  Searching for "IsMPRAGE" will then show you all in the
>> stages that the -mprage flag affects.
>>
>> cheers,
>> -MH
>>
>> --
>> Michael Harms, Ph.D.
>> ---
>> Conte Center for the Neuroscience of Mental Disorders
>> Washington University School of Medicine
>> Department of Psychiatry, Box 8134
>> 660 South Euclid Ave. Tel: 314-747-6173
>> St. Louis, MO  63110 Email: mha...@wustl.edu
>>
>> From: "Caspar M. Schwiedrzik" 
>> Date: Friday, May 31, 2013 2:14 PM
>> To: "Freesurfer@nmr.mgh.harvard.edu" 
>> Subject: Re: [Freesurfer] mprage flag in recon-all
>>
>> I only find flags for mri_normalize and mri_segment in recon-all, and
>> I have trouble reading the contents mri_normalize with a regular text
>> editor.
>> caspar
>>
>>
>> 2013/5/31 Bruce Fischl 
>>   Hi Caspar
>>
>>   it changes some parameters to the intensity normalization
>>   and segmentation to account for the lower SNR and
>>   increased CNR in the mprage. You'll need to look in the
>>   recon-all script for the details
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Thu, 30 May 2013, Caspar M. Schwiedrzik wrote:
>>
>> Hi!
>> Is there more documentation on what settings
>> the mprage flag enables in
>> recon-all?
>> Specifically, I would be interested which
>> individual steps it affects and
>> what  the parameters are for each of the
>> steps.
>> Thanks!
>> Caspar
>>
>>
>>
>>
>>
>> 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.
>>
>>
>>
>>
>>
>>
>> 
>>
>>
>>
>> The materials in this message are private and may contain Protected
>> Healthcare Information or other information of a sensitive nature. If
>> you are not the intended recipient, be advised that any unauthorized
>> use, disclosure, copying or the taking of any action in reliance on
>> the contents of this information is strictly prohibited. If you have
>> received this email in error, please immediately notify the sender via
>> telephone or return mail.
>>
>>
>>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] CVS crashing consistently

[Z K]

Hello Graham,

Thanks for the update. The read-only CVS server can be somewhat unstable 
at times, but this looks like a new error I have not seen before. I am 
looking into it now and will send an update when the issue is resolved.

-Zeke

On 05/31/2013 05:09 PM, Graham Wideman wrote:
> Hi MGH folks,
>
> I am attempting to download the source via CVS as described here:
>
> http://freesurfer.net/fswiki/ReadOnlyCVS
>
> using:
>
> cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P 
> -r release_5_3_0 dev
>
> (ie: 5.3.0 source)
>
> The CVS process is consistently stopping about 760 files into the process, 
> with the final lines of output being:
>
> 
> cvs checkout: Updating dev/distribution/trctrain
> U dev/distribution/trctrain/Makefile.am
> Terminated with fatal signal 9
> 
>
> After the first attempt got stuck here, I attempted to run the checkout 
> command again. CVS quickly displays a bunch of "Updating x" where x 
> is all the directories already downloaded, then gets to trctrain and stops 
> indefinitely. (I then killed it using Ctl-C)
>
> I then created a new local directory and restarted from scratch. The checkout 
> proceeded apace, and then got stuck at the same place (trctrain), with same 
> failure message.
>
> So... I'm thinking it might be something at your end, maybe disk problems in 
> whatever files come next after the last one above?
>
> FWIW, I'm using cvs as installed with Mint 15, which is 1.12.13-MirDebian-9 
> (client/server)
>
> -- Graham
>
> ___
> 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.

[Freesurfer] CVS crashing consistently: update

[Graham Wideman]

Hi MGH folks,

Update to previous report:

Review: Both of my attempts from scratch to CVS the 5.3.0 source failed after 
about 760 files, directory trctrain. CVS quit with fatal signal 9 error.

Previously when I tried to restart either of these, CVS would quickly run 
through all the up-to-date directories, then hang at trctrain, with no 
terminal, disk or network activity (as judged by router lights).

I have since let it sit there for probably 20 minutes, and suddenly the process 
came to life... downloading trctraindata.tar.gz (over 500 Meg).

So, I don't know if or why that large file was resulting in signal 9 error, but 
progress is now unjammed.

-- Graham

___
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.