[Freesurfer] TkmEdit Scripting SetBrushInfo Error

[Joerg Pfannmoeller]

Hi,

I am getting tzhe following an error if I use the following command in a 
tcl-script:

SetBrushInfo 3 1 2000 1 

The error is:

"Error: Parsing script file 
 
This error was encountered while running the script specified with the -tcl 
option. "


What is wrong?

Sincerely yours pfannmoe

 
___
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] One sample t-test in Qdec

[Buse Merve Ürgen]

Hello,

I would like to learn whether we can conduct one-sample t-test using Qdec.
I'm working on a single-case study, and I want to compare a single
subject's data with a group of controls (to see how this specific subject
is different from the group) in terms of volume, thickness and
meancurvature. As far as I know, we can do the analysis in Terminal, but I
would like to see & have the brain figure output (cluster by cluster) in
Qdec for one sample t-test as well. Is it possible?

Thanks in advance,

Buse.
___
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] Combining sagittal and axial T1 for volumetric analysis

[Tartaglia, Carmela]

I have patients and controls scanned on the same scanner but their data was 
acquired in different orientations. One group is sagittal and the other is 
axial. The sizes are 1X1X1 vs 1X1X1.2. Is it possible to combine these images 
for freesurfer analysis?

Thanks

carmela





This e-mail may contain confidential and/or privileged information for the sole 
use of the intended recipient. 
Any review or distribution by anyone other than the person for whom it was 
originally intended is strictly prohibited. 
If you have received this e-mail in error, please contact the sender and delete 
all copies. 
Opinions, conclusions or other information contained in this e-mail may not be 
that of the organization.


___
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] Combining sagittal and axial T1 for volumetric analysis

[Bruce Fischl]

Hi Carmela

are all controls scanned with one protocol and all patients with another? 
If so, combining them and interpreting the results is going to be 
difficult.

sorry
Bruce

On Wed, 5 Mar 2014, Tartaglia, Carmela wrote:

> I have patients and controls scanned on the same scanner but their data was 
> acquired in different orientations. One group is sagittal and the other is 
> axial. The sizes are 1X1X1 vs 1X1X1.2. Is it possible to combine these images 
> for freesurfer analysis?
>
> Thanks
>
> carmela
>
>
>
>
>
> This e-mail may contain confidential and/or privileged information for the 
> sole use of the intended recipient.
> Any review or distribution by anyone other than the person for whom it was 
> originally intended is strictly prohibited.
> If you have received this e-mail in error, please contact the sender and 
> delete all copies.
> Opinions, conclusions or other information contained in this e-mail may not 
> be that of the organization.
>
>
> ___
> 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] Is there a better direction for acquiring T1 structural scan? sagittal or axial

[Tartaglia, Carmela]

I am wondering if there is a preferred direction for acquiring T1 structural 
scan? sagittal or axial? and what is the rational?
Thanks
Carmela



This e-mail may contain confidential and/or privileged information for the sole 
use of the intended recipient. 
Any review or distribution by anyone other than the person for whom it was 
originally intended is strictly prohibited. 
If you have received this e-mail in error, please contact the sender and delete 
all copies. 
Opinions, conclusions or other information contained in this e-mail may not be 
that of the organization.


___
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] different thickness after converting wm.mgz in nifti and back

[Bruce Fischl]

Hi Karl

why is there any difference in either geometry or pixel values after 
converting back and forth? Can you send us your mri_convert command lines 
and screen output?


cheers
Bruce
On Wed, 5 Mar 2014, Koschutnig, Karl 
(karl.koschut...@uni-graz.at) wrote:



Dear experts,
our group decided to make all the white matter edits in brainvoyager (don't ask 
me why;-). So we converted the wm.mgz into nii and then into the brainvoyager 
format vmr, made the edits and the same way back into freesurfer. We started 
the recon-all -autorecon2-wm … and found massive reduction in the thickness. So 
far so bad.
To figure out the problem we started at the beginning of the conversion-mess 
and converted the wm.mgz into wm.nii and back into wm.mgz and found nearly the 
same reduction in the thickness. Finally, here comes my question. Is it 
possible that due to interpolation errors in the mri_convert routine this 
reduction can be explained?
PS: here is the output from mri_diff for the wm_orig.mgz and the converted one: 
Volumes differ in geometry row=1 col=1 diff=0.00 (5.96046e-08)
Please fin attached the reconstructed white matter surface (red = original, 
yellow = after converting the wm from nii in mgz and back)

thank you so much
best Karl___
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] Qdec failed

[Yinfei Li]

 Dear experts,

I have Freesurfer running quite well on Ubuntu for some time. But today when I 
tried to run the command ‘qdec’, I got the following error:

Qdec.bin: error while loading shared libraries: libXss.so.1: cannot open shared 
object file: No such file or directory

How do I fix this? Thank you.


Yinfei 
___
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] Freesurfer 5.3 and CentOS 5.10

[Weiner, Michael]

Thank you for the information, I wasn't sure if the centos4 build had mp
built into it. I will try this and forward the information on to the
researcher to see how their  runs can be improved.

Regards
Michael weiner 

-Original Message-
From: Z K [mailto:zkauf...@nmr.mgh.harvard.edu] 
Sent: Tuesday, March 04, 2014 1:17 PM
To: Weiner, Michael; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Freesurfer 5.3 and CentOS 5.10

Hello Michael,

Use the Freesurfer Centos4 build for your Centos5 platform. People who
want to take advantage of of multiple cores typically use the "-openmp
" flag when running recon-all. Theoretically the more cores
you use the faster the runtime, but we have found that that there is
little gain after 8 and when using that many we typically only see a 25%
decrease in the time it takes to run the entire recon-all stream.

You could try and get fancy by writing up a script and breaking up the
reson-all stream into parts and parrallelizing some of the processing of
the left and right hemispere... something along the lines of:

recon-all -s subj -autorecon1 -openmp 8
recon-all -s subj -autorecon2-volonly -openmp 8 recon-all -s subj
-autorecon2-perhemi -hemi rh -log recon-all-hemi rh.log -notify
rh-done.log -openmp 8 & recon-all -s subj -autorecon2-perhemi -hemi lh
-log recon-all-hemi-lh.log -notify lh-done.log -openmp 8 & while
(rh-done.log AND lh-done.log do not both exist) do
   sleep 1
end loop
recon-all -s subj -autorecon3 -openmp 8


-Zeke



On 03/03/2014 10:21 AM, Weiner, Michael wrote:
> I have recently upgraded our server from v5.0.0 to v5.3.0 running on 
> CentOS 5.10 and was a little surprised that there wasnt a version of 
> Freesurfer built for this platform but rather 4 and 6. I guess my main

> question is, was the version for centos4 built with openmpi at all? 
> THe server we are running Freesurfer on has 48 cores and we are trying

> to figure out how to make sure that while running Freesurfer we take 
> advantage of all these cores. Is there any documentation that i can 
> look at to help me in this endeavor or does anyone have any tips they
can share?
>
> Thank you in advance
> Michael Weiner
> Lead Analyst/UNIX Systems Administrator Lerner Research Institute 
> Computing Services Lerner Research Institute Cleveland Clinic
>
> ===
>
> Please consider the environment before printing this e-mail
>
> Cleveland Clinic is ranked as one of the top hospitals in America by 
> U.S.News & World Report (2013). Visit us online at 
> http://www.clevelandclinic.org for a complete listing of our services,

> staff and locations. Confidentiality Note: This message is intended 
> for use only by the individual or entity to which it is addressed and 
> may contain information that is privileged, confidential, and exempt 
> from disclosure under applicable law. If the reader of this message is

> not the intended recipient or the employee or agent responsible for 
> delivering the message to the intended recipient, you are hereby 
> notified that any dissemination, distribution or copying of this 
> communication is strictly prohibited. If you have received this 
> communication in error, please contact the sender immediately and 
> destroy the material in its entirety, whether electronic or hard copy.
> Thank you.
>
>
>
> ___
> 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.


===


 Please consider the environment before printing this e-mail

Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & 
World Report (2013).  
Visit us online at http://www.clevelandclinic.org for a complete listing of our 
services, staff and locations.


Confidentiality Note:  This message is intended for use only by the individual 
or entity to which it is addressed and may contain information that is 
privileged, confidential, and exempt from disclosure under applicable law.  If 
the reader of this message is not the intended recipient or the employee or 
agent responsible for delivering the message to the intended recipient, you are 
hereby notified that any dissemination, distribution or copying of this 
communication is strictly prohibited.  If you have received this communication 
in error,  please contact the sender immediately and destroy the material in 
its entirety, whether electronic or hard copy.  

Thank you.

___
Frees

Re: [Freesurfer] LGI in Qdec

[krista kelly]

Hi Marie,

It appears that the problem was the program that I was using to create the
. Qdecrc file. I was using Text Wrangler. I switched to TextMate and the
problem has been resolved.

Thanks so much for your help!
Krista


On Tue, Mar 4, 2014 at 8:27 PM, Marie Schaer  wrote:

>
>  Hi Krista,
>
>  Did you verify that your changes to .Qdecrc were properly saved? As long
> as the command more ~/.Qdecrc doesn't give you a line with MEASURE1 =
> pial_lgi, then you'll not have it in qdec menu. And version should not be
> an issue. How do you edit the .Qdecrc file? Did you check to see whether
> opening qdec had any effect on the line that you added (by running the
> command more ~/.Qdecrc before and after opening qdec)?
>
>  I need you to explain me a bit more how you did, otherwise it's
> difficult for me to help you.
>
>  Marie
>
>
>  On Mar 4, 2014, at 5:20 PM, krista kelly 
>  wrote:
>
>  Hi Marie,
>
>  Thanks for the the response. I've done that a few times and still, the
> lgi option does not come up in qdec as a measure. Could it be that I'm
> using an outdated version of Qdec? My freesurfer v is 5.3 so unless I need
> to update qdec on its own, I don't think that this is the problem. Any
> other ideas?
>
>  Best,
> Krista
>
>
> On Fri, Feb 28, 2014 at 4:16 PM, Marie Schaer wrote:
>
>>
>>  Hi Krista,
>>
>>  You need to add the following line in your .Qdecrc:
>>  MEASURE1 = pial_lgi
>>  and save the change.
>>
>>  I don't think it matters where you add it, I have it before all the
>> Qdec lines.
>>
>>  Then start qdec again, it should work. If not, check again the .Qdecrc
>> file, and look whether starting qdec erases the added line.
>>
>>  Let me know,
>>
>>  Marie
>>
>>  On Feb 28, 2014, at 1:09 PM, krista kelly 
>>   wrote:
>>
>>  Hi Marie,
>>
>>  The ?h.pial_lgi.fwhm?.fsaverage.mgh files in the surf folder are there. Here
>> is the output when I run more ~/.Qdecrc:
>>
>>  # This file is automatically generated by the application
>> # If you change any lines or add new lines, note that all
>> # coments and empty lines will be deleted. Every line has
>> # to be in format:
>> # key = value
>> #
>> Qdec1\Dialogs\ExitApplication = 0
>> Qdec1\Dialogs\SendErrorLog = 0
>> Qdec1\Geometry\MainPanelSize = 375
>> Qdec1\Geometry\MainPanelVisibility = 1
>> Qdec1\Geometry\SaveUserInterfaceGeometry = 1
>> Qdec1\Geometry\SecondaryPanelSize = 250
>> Qdec1\Geometry\SecondaryPanelVisibility = 0
>> Qdec1\Geometry\ViewPanelPosition = Right
>> Qdec1\Geometry\WindowGeometry = 900x700+787+1
>> Qdec1\MRU\File00 =
>> /Applications/freesurfer/subjects/qdec/qdec.tableNoBV45orBV46.dat
>> Qdec1\MRU\File00Cmd = LoadDataTable
>> Qdec1\RunTime\MostRecentVersionLaunched = 1.4
>> Qdec1\RunTime\PrintTargetDPI = 100.00
>> Qdec1\RunTime\ShowBalloonHelp = 1
>> Qdec1\RunTime\ShowSplashScreen = 1
>> Qdec1\RunTime\ToolbarFlatButtons = 1
>> Qdec1\RunTime\ToolbarFlatFrame = 1
>>
>>
>>  Thanks!
>> Krista
>>
>>
>> On Wed, Feb 26, 2014 at 7:12 PM, Marie Schaer wrote:
>>
>>>
>>>  Hi Krista,
>>>
>>>  Can you please run:
>>> more ~/.Qdecrc
>>> and copy paste the output for me?
>>>
>>>  The "rm: No match" issue in the qcache is not a problem, it's
>>> independent from the issue of listing lGI in the qdec menu. Even with the
>>> no match output in the qcache command, all the files should have been
>>> created properly (you can check that you have some files named
>>> ?h.pial_lgi.fwhm?.fsaverage.mgh in the surf folder of one of your subject
>>> if you want to be sure.
>>>
>>>  Let me know,
>>>
>>>  Marie
>>>
>>>  On Feb 25, 2014, at 6:55 PM, krista kelly 
>>> wrote:
>>>
>>>  Hi Marie,
>>>
>>>  I have tried adding the .Qdecrc file into the home folder as well but
>>> that does not work. The lgi measure is not appearing in the dropdown menu
>>> in the design tab in Qdec. Further, when I ran recon-all -qcache -measure
>>> pial_lgi, there were error messages saying 'rm: No match', although the
>>> -qcache exited without errors. Could this be the problem? If not, does
>>> anyone have any ideas?
>>>
>>>  Thanks!
>>> Krista
>>>
>>>
>>> On Mon, Feb 24, 2014 at 4:29 PM, Marie Schaer wrote:
>>>

 Hi Krista,

 Can you be more specific about what is not coming up? If lGI not listed
 in the menu of qdec, look at the following post:
 http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33427.html

 Otherwise can you describe more precisely the issue?

 Best,

 Marie

 On Feb 24, 2014, at 1:21 PM, krista kelly 
   wrote:

 > Hello,
 >
 > I followed instructions on how to incorporate the lgi_pial measure
 into QDec, however, it's not coming up when I go to choose this as a
 measure. I ran recon-all -s my_subject_id -qcache -measure pial_lgi and
 created a Qdecrc file in my $SUBJECTS_DIR directory. Does anyone have any
 insight as to why this may be occurring?
 >
 > Thanks,
 > Krista
  > ___
 > Freesu

Re: [Freesurfer] One sample t-test in Qdec

[Douglas N Greve]

Hi Buse, I think this is a two-sample t-test where the 2nd sample is 
your individual. You should be able to this in qdec
doug
On 03/05/2014 07:52 AM, Buse Merve Ürgen wrote:
> Hello,
>
> I would like to learn whether we can conduct one-sample t-test using 
> Qdec.
> I'm working on a single-case study, and I want to compare a single 
> subject's data with a group of controls (to see how this specific 
> subject is different from the group) in terms of volume, thickness and 
> meancurvature. As far as I know, we can do the analysis in Terminal, 
> but I would like to see & have the brain figure output (cluster by 
> cluster) in Qdec for one sample t-test as well. Is it possible?
>
> Thanks in advance,
>
> Buse.
>
>
> ___
> 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] Freesurfer 5.3 and CentOS 5.10

[Z K]

Micheal,

Im sorry but I sent you conflicting information.

The Centos4 build does NOT have openmp built into it. Our Centos4 builds 
use gcc version 3.4.6. It wasnt till gcc 4.2 that the gcc compiler 
implement openmp (v2.5)

Our CentOS6 build uses gcc 4.4.7 and does have openmp built into it. 
Sorry for the confusion.

-Zeke

On 03/05/2014 10:15 AM, Weiner, Michael wrote:
> Thank you for the information, I wasn't sure if the centos4 build had mp
> built into it. I will try this and forward the information on to the
> researcher to see how their  runs can be improved.
>
> Regards
> Michael weiner
>
> -Original Message-
> From: Z K [mailto:zkauf...@nmr.mgh.harvard.edu]
> Sent: Tuesday, March 04, 2014 1:17 PM
> To: Weiner, Michael; freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Freesurfer 5.3 and CentOS 5.10
>
> Hello Michael,
>
> Use the Freesurfer Centos4 build for your Centos5 platform. People who
> want to take advantage of of multiple cores typically use the "-openmp
> " flag when running recon-all. Theoretically the more cores
> you use the faster the runtime, but we have found that that there is
> little gain after 8 and when using that many we typically only see a 25%
> decrease in the time it takes to run the entire recon-all stream.
>
> You could try and get fancy by writing up a script and breaking up the
> reson-all stream into parts and parrallelizing some of the processing of
> the left and right hemispere... something along the lines of:
>
> recon-all -s subj -autorecon1 -openmp 8
> recon-all -s subj -autorecon2-volonly -openmp 8 recon-all -s subj
> -autorecon2-perhemi -hemi rh -log recon-all-hemi rh.log -notify
> rh-done.log -openmp 8 & recon-all -s subj -autorecon2-perhemi -hemi lh
> -log recon-all-hemi-lh.log -notify lh-done.log -openmp 8 & while
> (rh-done.log AND lh-done.log do not both exist) do
> sleep 1
> end loop
> recon-all -s subj -autorecon3 -openmp 8
>
>
> -Zeke
>
>
>
> On 03/03/2014 10:21 AM, Weiner, Michael wrote:
>> I have recently upgraded our server from v5.0.0 to v5.3.0 running on
>> CentOS 5.10 and was a little surprised that there wasnt a version of
>> Freesurfer built for this platform but rather 4 and 6. I guess my main
>
>> question is, was the version for centos4 built with openmpi at all?
>> THe server we are running Freesurfer on has 48 cores and we are trying
>
>> to figure out how to make sure that while running Freesurfer we take
>> advantage of all these cores. Is there any documentation that i can
>> look at to help me in this endeavor or does anyone have any tips they
> can share?
>>
>> Thank you in advance
>> Michael Weiner
>> Lead Analyst/UNIX Systems Administrator Lerner Research Institute
>> Computing Services Lerner Research Institute Cleveland Clinic
>>
>> ===
>>
>> Please consider the environment before printing this e-mail
>>
>> Cleveland Clinic is ranked as one of the top hospitals in America by
>> U.S.News & World Report (2013). Visit us online at
>> http://www.clevelandclinic.org for a complete listing of our services,
>
>> staff and locations. Confidentiality Note: This message is intended
>> for use only by the individual or entity to which it is addressed and
>> may contain information that is privileged, confidential, and exempt
>> from disclosure under applicable law. If the reader of this message is
>
>> not the intended recipient or the employee or agent responsible for
>> delivering the message to the intended recipient, you are hereby
>> notified that any dissemination, distribution or copying of this
>> communication is strictly prohibited. If you have received this
>> communication in error, please contact the sender immediately and
>> destroy the material in its entirety, whether electronic or hard copy.
>> Thank you.
>>
>>
>>
>> ___
>> 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.
>
>
> ===
>
>
>   Please consider the environment before printing this e-mail
>
> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News 
> & World Report (2013).
> Visit us online at http://www.clevelandclinic.org for a complete listing of 
> our services, staff and locations.
>
>
> Confidentiality Note:  This message is intended for use only by the 
> individual or entity to which it is addressed and may contain information 
> that is privileged, confidential, and exempt from disclosure under applic

Re: [Freesurfer] Freesurfer for rodents

[Douglas N Greve]

Hi Claudia, I don't know of anyone using it for rodents. In general, it 
is highly tuned to the parameters of the primate (mostly human) brain, 
and I think it would be quite difficult to adapt it to rodents. I'm 
cc'ing the FS list in case someone else has anything to add.
doug

On 03/05/2014 03:09 AM, Falfan-Melgoza, Claudia wrote:
> Dear Dr. Greve,
>
> I work at the Central Institute of Mental Health in Mannheim, Germany 
> and I am quite sure you have heard this question to no end but I would 
> like to ask you how viable would it be to use Freesurfer for rats and 
> mice?, I have read that providing an atlas of the rodent brain would 
> be the first step but as a first timer attempting to use Freesurfer I 
> am not quite sure that would cut it, or if the next steps in the 
> pipeline would need also a good amount of modification. And one last 
> question, do you know of other software that in your opinion could be 
> more suitable for rodents?
>
> I appreciate greatly your time and thank you very much in advance,
>
> Claudia Falfan-Melgoza
>
>
>
>
>
> Central Institute of Mental Health
> J5- 68159
> Mannheim, Germany

-- 
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] tkmedit edit voxel tcl script

[Joerg Pfannmoeller]

Hello,

if I have selected a voxel in a volume with tkmedit with a tcl script, how can 
I set the voxel value to 0.

Sincerely yours pfannmoe


___
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] extract pial_lgi from v1.thresh labels

[krista kelly]

Hello,

I would like to extract the pial_lgi data from Freesurfer's V1.thresh
labels but can't quite figure it out. I've tried adapting the commands from
the LGI Freesurfer tutorial as such:

mri_segstats --label-thresh BV20 lh V1.thresh.label --i
$SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats

I've also tried

mris_anatomical_stats -l lh.V1.thresh.label -f
BV20/stats/lh.V1.thresh.label.stats BV20 lh pial_lgi

but I've had no luck with either.

I would appreciate any help!

Thanks,
Krista
___
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] extract pial_lgi from v1.thresh labels

[Douglas N Greve]

try
mri_segstats --label-thresh .5 --label BV20 lh V1.thresh.label --i 
$SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats

On 03/05/2014 11:15 AM, krista kelly wrote:
> Hello,
>
> I would like to extract the pial_lgi data from Freesurfer's V1.thresh 
> labels but can't quite figure it out. I've tried adapting the commands 
> from the LGI Freesurfer tutorial as such:
>
> mri_segstats --label-thresh BV20 lh V1.thresh.label --i 
> $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats
>
> I've also tried
>
> mris_anatomical_stats -l lh.V1.thresh.label -f 
> BV20/stats/lh.V1.thresh.label.stats BV20 lh pial_lgi
>
> but I've had no luck with either.
>
> I would appreciate any help!
>
> Thanks,
> Krista
>
>
> ___
> 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] Problematic dilated ventricles

[Douglas N Greve]

It contains the volumes of the white matter parcellation. You can make a 
table with asegstats2table and specifying --stats=wmparc.stats
doug

On 03/05/2014 11:16 AM, Victor Kovac wrote:
> So, I assume the aseg.mgz contains the values represented in the 
> asegstats2table, but what values does the wmparc.mgz contain? Is this 
> where the output for the aparcstats2table comes from?
>
> Thanks!
> Victor
>
>
> On Tue, Mar 4, 2014 at 9:43 AM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> The wmparc is off because the surfaces are incorrect. The aseg
> does not
> have to follow the surfaces, but wmparc does
> doug
>
>
> On 03/03/2014 03:10 PM, Victor Kovac wrote:
> > Hi Bruce and Doug,
> >
> > "cp aseg.auto.mgz aseg.mgz" was my last step before running
> > -autorecon2-cp -autorecon3, as suggested by Bruce before, so I
> am not
> > sure what the problem could be. Since there seem to be problems
> > re-creating the pial/wm surfaces this way, would it be possible for
> > you to send the entire subject folder to me via GoogleDrive or some
> > other method?
> >
> > I also have another question: I have loaded a subject with tkmedit,
> > but the segmentation looks drastically improved when the
> -segmentation
> > is aseg.auto_noCCseg.mgz instead of -wmparc.mgz (images attached),
> > though the pial surface does not reflect this.
> >
> > Could you tell me why this is? And is it possible to get the pial/wm
> > surfaces to follow along the lines of the aseg.auto_noCCseg.mgz
> > segmentation? I am sorry if this is a naive question.
> >
> > Also: the images are from the original aseg.auto_noCCseg.mgz of this
> > subject (MPS2002-3), not the updated one you sent me, Bruce.
> >
> > Thank you!
> > Victor
> >
> >
> > On Mon, Mar 3, 2014 at 10:53 AM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
> >
> >
> > I think that it should. To be safe, I would "cp aseg.auto.mgz
> > aseg.mgz"
> > otherwise aseg.mgz will not  change (any differences will be
> > interpreted
> > as manual changes)
> > doug
> >
> >
> > On 03/02/2014 10:07 AM, Bruce Fischl wrote:
> > > Hi Victor
> > >
> > > hmmm, I'm not sure why that didn't work. Perhaps someone
> else can
> > > comment? Doug or Nick: if the aseg.mgz is recreated and you
> > start with
> > > -autorecon2-cp shouldn't it propagate the effects of the
> new aseg
> > > forward?
> > >
> > > cheers
> > > Bruce
> > >
> > >
> > > On Thu, 27 Feb 2014, Victor Kovac wrote:
> > >
> > >> Dear Bruce,
> > >> Have you had any time to try to analyze our subject
> MPS2002-3? I
> > >> believe you
> > >> mentioned you would give it a shot in your free time a
> couple of
> > >> months ago.
> > >>
> > >> Also, you were kind enough to analyze a subject for me,
> MPS1036-1,
> > >> and sent
> > >> me aseg.auto_noCCseg.new.mgz. I replaced the original
> file and
> > >> removed thee
> > >> "new" within the title, and then, to re-create the pial
> and wm
> > >> surfaces, I
> > >> ran:
> > >>
> > >> set mdir=$SUBJECTS_DIR/MPS1036-1/mri
> > >> mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz \
> > >> -lta $mdir/transforms/cc_up.lta  MPS1036-1
> > >> cp aseg.auto.mgz aseg.mgz
> > >>
> > >> and then: recon-all -autorecon2-cp -autorecon3, which I
> believe
> > >> starts the
> > >> recon-all pipeline at normalization2, as you suggested.
> > However, this
> > >> has
> > >> yielded no effect that I can see when I visualize the
> subject with
> > >>
> > >> tkmedit $proc brainmask.mgz lh.white -aux T1.mgz -aux-surface
> > rh.white
> > >> -segmentation wmparc.mgz
> $FREESURFER_HOME/FreeSurferColorLUT.txt
> > >>
> > >> Any advice would be greatly appreciated! Attached is the
> > >> recon-all.log for
> > >> this subject. Let me know if I should cc the group.
> > >>
> > >> Thank you.
> > >> Victor
> > >>
> > >>
> > >> On Tue, Jan 7, 2014 at 11:19 AM, Bruce Fischl
> > >>  
>  >>
> > >> wrote:
> > >>   Hi Victor
> > >>
> > >>   for each subject I think you want to run:
> > >>
> > >>
> > >>   set mdir=$SUBJECTS_DIR/$subject/mri
> > >>   mri_cc -aseg aseg.au

Re: [Freesurfer] extract pial_lgi from v1.thresh labels

[krista kelly]

Thanks Doug, but when I try this I get the following error: Option --label
unknown


On Wed, Mar 5, 2014 at 11:21 AM, Douglas N Greve
wrote:

>
> try
> mri_segstats --label-thresh .5 --label BV20 lh V1.thresh.label --i
> $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats
>
> On 03/05/2014 11:15 AM, krista kelly wrote:
> > Hello,
> >
> > I would like to extract the pial_lgi data from Freesurfer's V1.thresh
> > labels but can't quite figure it out. I've tried adapting the commands
> > from the LGI Freesurfer tutorial as such:
> >
> > mri_segstats --label-thresh BV20 lh V1.thresh.label --i
> > $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats
> >
> > I've also tried
> >
> > mris_anatomical_stats -l lh.V1.thresh.label -f
> > BV20/stats/lh.V1.thresh.label.stats BV20 lh pial_lgi
> >
> > but I've had no luck with either.
> >
> > I would appreciate any help!
> >
> > Thanks,
> > Krista
> >
> >
> > ___
> > 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.

Re: [Freesurfer] extract pial_lgi from v1.thresh labels

[Douglas N Greve]

sorry, it is --slabel
btw, there is documentation. If you run it without options it gives you 
a list of arguments as well as examples
doug
On 03/05/2014 11:32 AM, krista kelly wrote:
> Thanks Doug, but when I try this I get the following error: Option 
> --label unknown
>
>
> On Wed, Mar 5, 2014 at 11:21 AM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> try
> mri_segstats --label-thresh .5 --label BV20 lh V1.thresh.label --i
> $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats
>
> On 03/05/2014 11:15 AM, krista kelly wrote:
> > Hello,
> >
> > I would like to extract the pial_lgi data from Freesurfer's
> V1.thresh
> > labels but can't quite figure it out. I've tried adapting the
> commands
> > from the LGI Freesurfer tutorial as such:
> >
> > mri_segstats --label-thresh BV20 lh V1.thresh.label --i
> > $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats
> >
> > I've also tried
> >
> > mris_anatomical_stats -l lh.V1.thresh.label -f
> > BV20/stats/lh.V1.thresh.label.stats BV20 lh pial_lgi
> >
> > but I've had no luck with either.
> >
> > I would appreciate any help!
> >
> > Thanks,
> > Krista
> >
> >
> > ___
> > 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.
>
>

-- 
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] (no subject)

[Douglas N Greve]

*I would use BrainSegNotVent* found in aseg.stats. You can get more info 
here

http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats

doug

On 03/04/2014 10:57 AM, Hugh Pemberton wrote:
> Hi guys, just wondering what you'd say is the best measure for whole 
> brain volume? Cortex volume.. Cortical white matter volume.. Total 
> gray volume.. Intracranial volume.. etc.
> Cheers!
> Hugh
>
>
> ___
> 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] TkmEdit Scripting SetBrushInfo Error

[Joerg Pfannmoeller]

Allright, it works if I use those commands:

UpdateBrushInfo { inBrush inLow inHigh inNewValue inMode inCloneSource }
SetEditBrushConfiguration
___
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] extract pial_lgi from v1.thresh labels

[krista kelly]

Perfect, it works thanks!


On Wed, Mar 5, 2014 at 11:35 AM, Douglas N Greve
wrote:

> sorry, it is --slabel
> btw, there is documentation. If you run it without options it gives you a
> list of arguments as well as examples
> doug
>
> On 03/05/2014 11:32 AM, krista kelly wrote:
>
>> Thanks Doug, but when I try this I get the following error: Option
>> --label unknown
>>
>>
>> On Wed, Mar 5, 2014 at 11:21 AM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu > wrote:
>>
>>
>> try
>> mri_segstats --label-thresh .5 --label BV20 lh V1.thresh.label --i
>> $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats
>>
>> On 03/05/2014 11:15 AM, krista kelly wrote:
>> > Hello,
>> >
>> > I would like to extract the pial_lgi data from Freesurfer's
>> V1.thresh
>> > labels but can't quite figure it out. I've tried adapting the
>> commands
>> > from the LGI Freesurfer tutorial as such:
>> >
>> > mri_segstats --label-thresh BV20 lh V1.thresh.label --i
>> > $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats
>> >
>> > I've also tried
>> >
>> > mris_anatomical_stats -l lh.V1.thresh.label -f
>> > BV20/stats/lh.V1.thresh.label.stats BV20 lh pial_lgi
>> >
>> > but I've had no luck with either.
>> >
>> > I would appreciate any help!
>> >
>> > Thanks,
>> > Krista
>> >
>> >
>> > ___
>> > 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.
>>
>>
>>
> --
> 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] extract pial_lgi from v1.thresh labels

[krista kelly]

Hi again,

My apologies for the barrage of emails! I was able to do mri_segstats on V1
labels for pial_lgi using the following:

mri_segstats --label-thresh .5 --slabel $s lh
$SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i
$SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum
$SUBJECTS_DIR/$s/stats/lh.V1.thresh.label.LGI.stats

However, now I'm having trouble with bringing all of the data into one
table using aparcstats2table. I found online how to get the data for aparc
annotation (
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033069.html)
and tried to adapt to the labels. Here is what I've tried:

aparcstats2table --subjects BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28
BV29 BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44
BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 --hemi lh
--meas thickness --parc V1.thresh.label.LGI --tablefile
lh.V1.thresh.label.LGI.txt

I get the following output when I do this:

SUBJECTS_DIR : /Applications/freesurfer/subjects
Parsing the .stats files
Traceback (most recent call last):
  File "/Applications/freesurfer/bin/aparcstats2table", line 371, in

parc_measure_map = parsed.parse(options.meas)
  File "/Applications/freesurfer/bin/fsutils.py", line 207, in parse
val = float(strlist[self.measure_column_map[measure]])
ValueError: could not convert string to float: Seg

I've attached an example of the file created during mri_segstats in case
that helps.

Thanks!
Krista


On Wed, Mar 5, 2014 at 1:21 PM, krista kelly wrote:

> Perfect, it works thanks!
>
>
> On Wed, Mar 5, 2014 at 11:35 AM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> sorry, it is --slabel
>> btw, there is documentation. If you run it without options it gives you a
>> list of arguments as well as examples
>> doug
>>
>> On 03/05/2014 11:32 AM, krista kelly wrote:
>>
>>> Thanks Doug, but when I try this I get the following error: Option
>>> --label unknown
>>>
>>>
>>> On Wed, Mar 5, 2014 at 11:21 AM, Douglas N Greve <
>>> gr...@nmr.mgh.harvard.edu > wrote:
>>>
>>>
>>> try
>>> mri_segstats --label-thresh .5 --label BV20 lh V1.thresh.label --i
>>> $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats
>>>
>>> On 03/05/2014 11:15 AM, krista kelly wrote:
>>> > Hello,
>>> >
>>> > I would like to extract the pial_lgi data from Freesurfer's
>>> V1.thresh
>>> > labels but can't quite figure it out. I've tried adapting the
>>> commands
>>> > from the LGI Freesurfer tutorial as such:
>>> >
>>> > mri_segstats --label-thresh BV20 lh V1.thresh.label --i
>>> > $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats
>>> >
>>> > I've also tried
>>> >
>>> > mris_anatomical_stats -l lh.V1.thresh.label -f
>>> > BV20/stats/lh.V1.thresh.label.stats BV20 lh pial_lgi
>>> >
>>> > but I've had no luck with either.
>>> >
>>> > I would appreciate any help!
>>> >
>>> > Thanks,
>>> > Krista
>>> >
>>> >
>>> > ___
>>> > 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 >> harvard.edu>
>>>
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to
>>> whom it is
>>> addressed. If you believe this e-mail was sent to you in error and
>>> the e-mail
>>> contains patient information, please contact the Partners
>>> Compliance HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to
>>> you in error
>>> but does not contain patient information, please contact the
>>> sender and properly
>>> dispose of the e-mail.
>>>
>>>
>>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/

Re: [Freesurfer] extract pial_lgi from v1.thresh labels

[Douglas N Greve]

use asegstats2table (I know, it's confusing:)
doug


On 03/05/2014 01:42 PM, krista kelly wrote:
> Hi again,
>
> My apologies for the barrage of emails! I was able to do mri_segstats 
> on V1 labels for pial_lgi using the following:
>
> mri_segstats --label-thresh .5 --slabel $s lh 
> $SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i 
> $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum 
> $SUBJECTS_DIR/$s/stats/lh.V1.thresh.label.LGI.stats
>
> However, now I'm having trouble with bringing all of the data into one 
> table using aparcstats2table. I found online how to get the data for 
> aparc annotation 
> (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033069.html)
>  
> and tried to adapt to the labels. Here is what I've tried:
>
> aparcstats2table --subjects BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 
> BV28 BV29 BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 
> BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 
> MB18 --hemi lh --meas thickness --parc V1.thresh.label.LGI --tablefile 
> lh.V1.thresh.label.LGI.txt
>
> I get the following output when I do this:
>
> SUBJECTS_DIR : /Applications/freesurfer/subjects
> Parsing the .stats files
> Traceback (most recent call last):
>   File "/Applications/freesurfer/bin/aparcstats2table", line 371, in 
> 
> parc_measure_map = parsed.parse(options.meas)
>   File "/Applications/freesurfer/bin/fsutils.py", line 207, in parse
> val = float(strlist[self.measure_column_map[measure]])
> ValueError: could not convert string to float: Seg
>
> I've attached an example of the file created during mri_segstats in 
> case that helps.
>
> Thanks!
> Krista
>
>
> On Wed, Mar 5, 2014 at 1:21 PM, krista kelly  > wrote:
>
> Perfect, it works thanks!
>
>
> On Wed, Mar 5, 2014 at 11:35 AM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> sorry, it is --slabel
> btw, there is documentation. If you run it without options it
> gives you a list of arguments as well as examples
> doug
>
> On 03/05/2014 11:32 AM, krista kelly wrote:
>
> Thanks Doug, but when I try this I get the following
> error: Option --label unknown
>
>
> On Wed, Mar 5, 2014 at 11:21 AM, Douglas N Greve
>  
>  >> wrote:
>
>
> try
> mri_segstats --label-thresh .5 --label BV20 lh
> V1.thresh.label --i
> $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum
> lh.V1.thresh.label.stats
>
> On 03/05/2014 11:15 AM, krista kelly wrote:
> > Hello,
> >
> > I would like to extract the pial_lgi data from
> Freesurfer's
> V1.thresh
> > labels but can't quite figure it out. I've tried
> adapting the
> commands
> > from the LGI Freesurfer tutorial as such:
> >
> > mri_segstats --label-thresh BV20 lh V1.thresh.label --i
> > $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum
> lh.V1.thresh.label.stats
> >
> > I've also tried
> >
> > mris_anatomical_stats -l lh.V1.thresh.label -f
> > BV20/stats/lh.V1.thresh.label.stats BV20 lh pial_lgi
> >
> > but I've had no luck with either.
> >
> > I would appreciate any help!
> >
> > Thanks,
> > Krista
> >
> >
> > ___
> > 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
> 

[Freesurfer] freesurfer coordinates question

[David Phillips]

Hello,

Is there any way to extract a three dimensional coordinate representation of 
the different brain regions (i.e., their centroids) that freesurfer is 
estimating the cortical thickness of?

Any help is appreciated and apologies if this question has been answered before.

regards,
David
___
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] extract pial_lgi from v1.thresh labels

[krista kelly]

Thanks Doug! I did that and it worked, but now here's another problem: the
values that I obtained for V1, V2, and cortex for each subject are all the
same. For example, BV20 left hemisphere values for V1, V2, and cortex are
all 2.7241 (same thing happens for the right hemisphere). Maybe I can tell
you what I did step by step to see  if you can find where I went wrong.

First, I did a for loop to run mri_segstats for each participant for each
label per hemisphere (here is an example of V1):

foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31 BV32
BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08 MB09
MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 MB19 MB20) <>
mri_segstats --label-thresh .5 --slabel $s lh
$SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i
$SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum
$SUBJECTS_DIR/$s/stats/lh.V1.thresh.label.LGI.stats  <>
end <>

for left V2 I ran:

foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31 BV32
BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08 MB09
MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 MB19 MB20) <>
mri_segstats --label-thresh .5 --slabel $s lh
$SUBJECTS_DIR/$s/label/lh.V2.thresh.label --i
$SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum
$SUBJECTS_DIR/$s/stats/lh.V2.thresh.label.LGI.stats  <>
end <>

and for left cortex I ran:
foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31 BV32
BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08 MB09
MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 MB19 MB20) <>
mri_segstats --label-thresh .5 --slabel $s lh
$SUBJECTS_DIR/$s/label/lh.cortex --i $SUBJECTS_DIR/$s/surf/lh.pial_lgi
--sum $SUBJECTS_DIR/$s/stats/lh.cortex.LGI.stats
end <>


This is where the problem must be occurring since all files created during
these commands show the same files per hemisphere. I've attached three
files created during mri_segstats (left V1, V2, cortex.stats) for one
participant. I've also attached files created during asegstats2table to
show how all values are the same for each label for all participants (V1,
V2, cortex.LGI.txt).

If anyone has any insight into the problem, that would be great!

Best,
Krista


On Wed, Mar 5, 2014 at 1:54 PM, Douglas N Greve
wrote:

>
> use asegstats2table (I know, it's confusing:)
> doug
>
>
>
> On 03/05/2014 01:42 PM, krista kelly wrote:
>
>> Hi again,
>>
>> My apologies for the barrage of emails! I was able to do mri_segstats on
>> V1 labels for pial_lgi using the following:
>>
>> mri_segstats --label-thresh .5 --slabel $s lh
>> $SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i
>> $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum $SUBJECTS_DIR/$s/stats/lh.V1.
>> thresh.label.LGI.stats
>>
>> However, now I'm having trouble with bringing all of the data into one
>> table using aparcstats2table. I found online how to get the data for aparc
>> annotation (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/
>> 2013-September/033069.html) and tried to adapt to the labels. Here is
>> what I've tried:
>>
>> aparcstats2table --subjects BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28
>> BV29 BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44
>> BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 --hemi lh
>> --meas thickness --parc V1.thresh.label.LGI --tablefile
>> lh.V1.thresh.label.LGI.txt
>>
>> I get the following output when I do this:
>>
>> SUBJECTS_DIR : /Applications/freesurfer/subjects
>> Parsing the .stats files
>> Traceback (most recent call last):
>>   File "/Applications/freesurfer/bin/aparcstats2table", line 371, in
>> 
>> parc_measure_map = parsed.parse(options.meas)
>>   File "/Applications/freesurfer/bin/fsutils.py", line 207, in parse
>> val = float(strlist[self.measure_column_map[measure]])
>> ValueError: could not convert string to float: Seg
>>
>> I've attached an example of the file created during mri_segstats in case
>> that helps.
>>
>> Thanks!
>> Krista
>>
>>
>> On Wed, Mar 5, 2014 at 1:21 PM, krista kelly 
>> > krista.kell...@gmail.com>> wrote:
>>
>> Perfect, it works thanks!
>>
>>
>> On Wed, Mar 5, 2014 at 11:35 AM, Douglas N Greve
>> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>
>> sorry, it is --slabel
>> btw, there is documentation. If you run it without options it
>> gives you a list of arguments as well as examples
>> doug
>>
>> On 03/05/2014 11:32 AM, krista kelly wrote:
>>
>> Thanks Doug, but when I try this I get the following
>> error: Option --label unknown
>>
>>
>> On Wed, Mar 5, 2014 at 11:21 AM, Douglas N Greve
>> > 
>> >
>> >> wrote:
>>
>>
>> try
>> mri_segstats --label-thresh .5 --label BV20 lh
>> V1.thresh.label --i
>> $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum

[Freesurfer] Running Tracula on a cluster

[ebelleau]

Hello,

I plan on running a batch of subjects (around 80) on a computer cluster.

I am assuming that in the dmrirc configuration file, I can enter all of the 
subjects in subjlist?

However, do I have to add something to it to make sure that each subject gets 
sent to a different processor on the cluster?

I have attached my dmrirc file as well as the files needed for it to run on the 
cluster.

Thanks,

Emily

dmrirc.example
Description: Binary data


tracula-1.sbatch
Description: application/shellscript


tracula-1.sh
Description: application/shellscript
___
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] Running Tracula on a cluster

[Anastasia Yendiki]

Hi Emily - Which job management system does your cluster run on? Have you 
ever tried to run any of the FSL parallelized programs, like bedpostx, on 
your cluster?

a.y

On Wed, 5 Mar 2014, ebell...@uwm.edu wrote:

>
> Hello,
>
> I plan on running a batch of subjects (around 80) on a computer cluster.
>
> I am assuming that in the dmrirc configuration file, I can enter all of the 
> subjects in subjlist?
>
> However, do I have to add something to it to make sure that each subject gets 
> sent to a different processor on the cluster?
>
> I have attached my dmrirc file as well as the files needed for it to run on 
> the cluster.
>
> Thanks,
>
> Emily
___
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] Running Tracula on a cluster

[ebelleau]

Hi Anastasia,

We use SLURM.  

I have not personally yet run bedpost off of the cluster, but one of my 
colleagues was able to run his data off of our cluster ( the whole pathway 
including bedpost) without any problem. However he (Jon Wieser) made an 
individual dmrirc configuration file script for every subject and then made 
sure each one got assigned to a different processor in another script. 

Thanks,

Emily

- Original Message -
From: "Anastasia Yendiki" 
To: ebell...@uwm.edu
Cc: "freesurfer" 
Sent: Wednesday, March 5, 2014 3:02:14 PM
Subject: Re: [Freesurfer] Running Tracula on a cluster


Hi Emily - Which job management system does your cluster run on? Have you 
ever tried to run any of the FSL parallelized programs, like bedpostx, on 
your cluster?

a.y

On Wed, 5 Mar 2014, ebell...@uwm.edu wrote:

>
> Hello,
>
> I plan on running a batch of subjects (around 80) on a computer cluster.
>
> I am assuming that in the dmrirc configuration file, I can enter all of the 
> subjects in subjlist?
>
> However, do I have to add something to it to make sure that each subject gets 
> sent to a different processor on the cluster?
>
> I have attached my dmrirc file as well as the files needed for it to run on 
> the cluster.
>
> Thanks,
>
> Emily


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

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

Re: [Freesurfer] extract pial_lgi from v1.thresh labels

[Douglas N Greve]

Sorry, I gave you some bad advice. Only use --label-thresh with labels 
that have a statistic that is non-zero (this is the last column of the 
label file). Eg, in lh.V1.thresh.label, the stat is always 0 (but it is 
non-zero in lh.V1.label). The stat is the probability that the vertex is 
in the label, so you can choose the threshold based on that. The 
lh.V1.thresh.label is for when the stat is the max for V1 relative to 
the other labels (eg, V2). If you select thresh=.5, you may miss places 
where V1 is the most likely but still less than .5. I would probably use 
lh.V1.thresh.label (and then do not spec --label-thresh)

doug


On 03/05/2014 03:40 PM, krista kelly wrote:
> Thanks Doug! I did that and it worked, but now here's another problem: 
> the values that I obtained for V1, V2, and cortex for each subject are 
> all the same. For example, BV20 left hemisphere values for V1, V2, and 
> cortex are all 2.7241 (same thing happens for the right 
> hemisphere). Maybe I can tell you what I did step by step to see  if 
> you can find where I went wrong.
>
> First, I did a for loop to run mri_segstats for each participant for 
> each label per hemisphere (here is an example of V1):
>
> foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31 
> BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 
> MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 MB19 MB20) 
> <>
> mri_segstats --label-thresh .5 --slabel $s lh 
> $SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i 
> $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum 
> $SUBJECTS_DIR/$s/stats/lh.V1.thresh.label.LGI.stats  <>
> end <>
>
> for left V2 I ran:
>
> foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31 
> BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 
> MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 MB19 MB20) 
> <>
> mri_segstats --label-thresh .5 --slabel $s lh 
> $SUBJECTS_DIR/$s/label/lh.V2.thresh.label --i 
> $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum 
> $SUBJECTS_DIR/$s/stats/lh.V2.thresh.label.LGI.stats  <>
> end <>
>
> and for left cortex I ran:
> foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31 
> BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 
> MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 MB19 MB20) 
> <>
> mri_segstats --label-thresh .5 --slabel $s lh 
> $SUBJECTS_DIR/$s/label/lh.cortex --i $SUBJECTS_DIR/$s/surf/lh.pial_lgi 
> --sum $SUBJECTS_DIR/$s/stats/lh.cortex.LGI.stats
> end <>
>
>
> This is where the problem must be occurring since all files created 
> during these commands show the same files per hemisphere. I've 
> attached three files created during mri_segstats (left V1, V2, 
> cortex.stats) for one participant. I've also attached files created 
> during asegstats2table to show how all values are the same for each 
> label for all participants (V1, V2, cortex.LGI.txt).
>
> If anyone has any insight into the problem, that would be great!
>
> Best,
> Krista
>
>
> On Wed, Mar 5, 2014 at 1:54 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> use asegstats2table (I know, it's confusing:)
> doug
>
>
>
> On 03/05/2014 01:42 PM, krista kelly wrote:
>
> Hi again,
>
> My apologies for the barrage of emails! I was able to do
> mri_segstats on V1 labels for pial_lgi using the following:
>
> mri_segstats --label-thresh .5 --slabel $s lh
> $SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i
> $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum
> $SUBJECTS_DIR/$s/stats/lh.V1.thresh.label.LGI.stats
>
> However, now I'm having trouble with bringing all of the data
> into one table using aparcstats2table. I found online how to
> get the data for aparc annotation
> 
> (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033069.html)
> and tried to adapt to the labels. Here is what I've tried:
>
> aparcstats2table --subjects BV20 BV21 BV22 BV23 BV24 BV25 BV26
> BV27 BV28 BV29 BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38
> BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12
> MB13 MB14 MB15 MB16 MB17 MB18 --hemi lh --meas thickness
> --parc V1.thresh.label.LGI --tablefile lh.V1.thresh.label.LGI.txt
>
> I get the following output when I do this:
>
> SUBJECTS_DIR : /Applications/freesurfer/subjects
> Parsing the .stats files
> Traceback (most recent call last):
>   File "/Applications/freesurfer/bin/aparcstats2table", line
> 371, in 
> parc_measure_map = parsed.parse(options.meas)
>   File "/Applications/freesurfer/bin/fsutils.py", line 207, in
> parse
> val = float(strlist[self.measure_column_map[measure]])
> ValueError: could not convert string to float: Seg
>
> I've attached an example of the file created during
> mri_segstats in cas

[Freesurfer] Group comparisons

[Tudor Popescu]

Hello, I have some questions on doing group comparisons with thickness,
area and volume. Many thanks in advance for any help!

1) For a DOSS design with group and gender as categorical factors, I see
that an interaction contrast ("Is there a group-gender interaction in the
mean thickness?") still exists - but what does this contrast mean, given
that DOSS by definition doesn't allow for interactions?

2) it makes sense that measures such as thickness are analysed vertex-wise
in QDEC, however what does it mean when the dependent variable is area or
volume - measures that do not make physical sense for a single vertex but
only at the level of a region consisting of *several* vertices?

3) For values extracted from atlas regions with aparcstats2table, it seems
that the product of the extracted CT and area is in the same order of
magnitude as the extracted volume, but never really the same or even close
- why, when the volume of a region should theoretically be the product of
its surface area by its thickness?

Tudor
___
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] extract pial_lgi from v1.thresh labels

[krista kelly]

Thanks Doug! That fixed it. But now I have two numbers in each file, which
do I use (see also attached file)?

ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max
Range  1 0 124241 81007.3 Seg 2.7306 0.6613 1.4985 4.4779 2.9795  2 1
3540 2225.6 Seg0001 2.4966 0.3254 2.0502 3.0296 0.9794










On Wed, Mar 5, 2014 at 5:07 PM, Douglas N Greve
wrote:

>
> Sorry, I gave you some bad advice. Only use --label-thresh with labels
> that have a statistic that is non-zero (this is the last column of the
> label file). Eg, in lh.V1.thresh.label, the stat is always 0 (but it is
> non-zero in lh.V1.label). The stat is the probability that the vertex is in
> the label, so you can choose the threshold based on that. The
> lh.V1.thresh.label is for when the stat is the max for V1 relative to the
> other labels (eg, V2). If you select thresh=.5, you may miss places where
> V1 is the most likely but still less than .5. I would probably use
> lh.V1.thresh.label (and then do not spec --label-thresh)
>
> doug
>
>
>
> On 03/05/2014 03:40 PM, krista kelly wrote:
>
>> Thanks Doug! I did that and it worked, but now here's another problem:
>> the values that I obtained for V1, V2, and cortex for each subject are all
>> the same. For example, BV20 left hemisphere values for V1, V2, and cortex
>> are all 2.7241 (same thing happens for the right hemisphere). Maybe I can
>> tell you what I did step by step to see  if you can find where I went wrong.
>>
>> First, I did a for loop to run mri_segstats for each participant for each
>> label per hemisphere (here is an example of V1):
>>
>> foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31
>> BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08
>> MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 MB19 MB20) <>
>> mri_segstats --label-thresh .5 --slabel $s lh
>> $SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i
>> $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum 
>> $SUBJECTS_DIR/$s/stats/lh.V1.thresh.label.LGI.stats
>>  <>
>> end <>
>>
>> for left V2 I ran:
>>
>> foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31
>> BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08
>> MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 MB19 MB20) <>
>> mri_segstats --label-thresh .5 --slabel $s lh
>> $SUBJECTS_DIR/$s/label/lh.V2.thresh.label --i
>> $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum 
>> $SUBJECTS_DIR/$s/stats/lh.V2.thresh.label.LGI.stats
>>  <>
>> end <>
>>
>> and for left cortex I ran:
>> foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31
>> BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08
>> MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 MB19 MB20) <>
>> mri_segstats --label-thresh .5 --slabel $s lh 
>> $SUBJECTS_DIR/$s/label/lh.cortex
>> --i $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum $SUBJECTS_DIR/$s/stats/lh.
>> cortex.LGI.stats
>> end <>
>>
>>
>> This is where the problem must be occurring since all files created
>> during these commands show the same files per hemisphere. I've attached
>> three files created during mri_segstats (left V1, V2, cortex.stats) for one
>> participant. I've also attached files created during asegstats2table to
>> show how all values are the same for each label for all participants (V1,
>> V2, cortex.LGI.txt).
>>
>> If anyone has any insight into the problem, that would be great!
>>
>> Best,
>> Krista
>>
>>
>> On Wed, Mar 5, 2014 at 1:54 PM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu > wrote:
>>
>>
>> use asegstats2table (I know, it's confusing:)
>> doug
>>
>>
>>
>> On 03/05/2014 01:42 PM, krista kelly wrote:
>>
>> Hi again,
>>
>> My apologies for the barrage of emails! I was able to do
>> mri_segstats on V1 labels for pial_lgi using the following:
>>
>> mri_segstats --label-thresh .5 --slabel $s lh
>> $SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i
>> $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum
>> $SUBJECTS_DIR/$s/stats/lh.V1.thresh.label.LGI.stats
>>
>> However, now I'm having trouble with bringing all of the data
>> into one table using aparcstats2table. I found online how to
>> get the data for aparc annotation
>> (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/
>> 2013-September/033069.html)
>> and tried to adapt to the labels. Here is what I've tried:
>>
>> aparcstats2table --subjects BV20 BV21 BV22 BV23 BV24 BV25 BV26
>> BV27 BV28 BV29 BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38
>> BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12
>> MB13 MB14 MB15 MB16 MB17 MB18 --hemi lh --meas thickness
>> --parc V1.thresh.label.LGI --tablefile lh.V1.thresh.label.LGI.txt
>>
>> I get the following output when I do this:
>>
>> SUBJECTS_DIR : /Applications/freesurfer/subjects
>> Parsing the .stats files
>> 

Re: [Freesurfer] extract pial_lgi from v1.thresh labels

[Douglas N Greve]

Right, one more thing. add --excludeid 0

On 03/05/2014 05:59 PM, krista kelly wrote:
> Thanks Doug! That fixed it. But now I have two numbers in each file, 
> which do I use (see also attached file)?
>
> ColHeadersIndex   SegId   NVertices   Area_mm2StructName  
> Mean 
> StdDevMin Max Range
> 1 0   124241  81007.3 Seg 2.7306  0.6613  1.4985  
> 4.4779  2.9795  
> 2 1   35402225.6  Seg0001 2.4966  0.3254  2.0502  3.0296  
> 0.9794  
>
>   
>   
>   
>   
>   
>   
>   
>   
>   
>
>
>
> On Wed, Mar 5, 2014 at 5:07 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> Sorry, I gave you some bad advice. Only use --label-thresh with
> labels that have a statistic that is non-zero (this is the last
> column of the label file). Eg, in lh.V1.thresh.label, the stat is
> always 0 (but it is non-zero in lh.V1.label). The stat is the
> probability that the vertex is in the label, so you can choose the
> threshold based on that. The lh.V1.thresh.label is for when the
> stat is the max for V1 relative to the other labels (eg, V2). If
> you select thresh=.5, you may miss places where V1 is the most
> likely but still less than .5. I would probably use
> lh.V1.thresh.label (and then do not spec --label-thresh)
>
> doug
>
>
>
> On 03/05/2014 03:40 PM, krista kelly wrote:
>
> Thanks Doug! I did that and it worked, but now here's another
> problem: the values that I obtained for V1, V2, and cortex for
> each subject are all the same. For example, BV20 left
> hemisphere values for V1, V2, and cortex are all 2.7241 (same
> thing happens for the right hemisphere). Maybe I can tell you
> what I did step by step to see  if you can find where I went
> wrong.
>
> First, I did a for loop to run mri_segstats for each
> participant for each label per hemisphere (here is an example
> of V1):
>
> foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29
> BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41
> BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15
> MB16 MB17 MB18 MB19 MB20) <>
> mri_segstats --label-thresh .5 --slabel $s lh
> $SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i
> $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum
> $SUBJECTS_DIR/$s/stats/lh.V1.thresh.label.LGI.stats  <>
> end <>
>
> for left V2 I ran:
>
> foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29
> BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41
> BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15
> MB16 MB17 MB18 MB19 MB20) <>
> mri_segstats --label-thresh .5 --slabel $s lh
> $SUBJECTS_DIR/$s/label/lh.V2.thresh.label --i
> $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum
> $SUBJECTS_DIR/$s/stats/lh.V2.thresh.label.LGI.stats  <>
> end <>
>
> and for left cortex I ran:
> foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29
> BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41
> BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15
> MB16 MB17 MB18 MB19 MB20) <>
> mri_segstats --label-thresh .5 --slabel $s lh
> $SUBJECTS_DIR/$s/label/lh.cortex --i
> $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum
> $SUBJECTS_DIR/$s/stats/lh.cortex.LGI.stats
> end <>
>
>
> This is where the problem must be occurring since all files
> created during these commands show the same files per
> hemisphere. I've attached three files created during
> mri_segstats (left V1, V2, cortex.stats) for one participant.
> I've also attached files created during asegstats2table to
> show how all values are the same for each label for all
> participants (V1, V2, cortex.LGI.txt).
>
> If anyone has any insight into the problem, that would be great!
>
> Best,
> Krista
>
>
> On Wed, Mar 5, 2014 at 1:54 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
>
>
> use asegstats2table (I know, it's confusing:)
> doug
>
>
>
> On 03/05/2014 01:42 PM, krista kelly wrote:
>
> Hi again,
>
> My apologies for the barrage of emails! I was able to do
> mri_segstats on V1 labels for pial_lgi using the
> following:
>
> mri_segstats --label-thresh .5 --slabel $s lh
> $SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i
> $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum
> $SUBJECTS_DIR/$s/stats/lh.V1.thresh.label.LGI.stats
>
> However

Re: [Freesurfer] extract pial_lgi from v1.thresh labels

[Douglas N Greve]

not sure what you mean, those are not mutually exclusive

On 03/05/2014 06:05 PM, krista kelly wrote:
> Ok thanks!
>
> Also, for the lh.cortex pial_lgi, should I stick to --label-thresh .5 
> rather than --slabel?
>
>
> On Wed, Mar 5, 2014 at 5:59 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> Right, one more thing. add --excludeid 0
>
>
> On 03/05/2014 05:59 PM, krista kelly wrote:
>
> Thanks Doug! That fixed it. But now I have two numbers in each
> file, which do I use (see also attached file)?
>
> ColHeaders  Index   SegId   NVertices   Area_mm2  
>  StructName  Mean StdDev Min Max Range
> 1   0   124241  81007.3 Seg 2.7306  0.6613
>  1.4985  4.4779  2.9795
> 2   1   35402225.6  Seg0001 2.4966  0.3254
>  2.0502  3.0296  0.9794
>
>
>
>
>
>
>
>
>
>
>
>
>
> On Wed, Mar 5, 2014 at 5:07 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
>
>
> Sorry, I gave you some bad advice. Only use --label-thresh
> with
> labels that have a statistic that is non-zero (this is the
> last
> column of the label file). Eg, in lh.V1.thresh.label, the
> stat is
> always 0 (but it is non-zero in lh.V1.label). The stat is the
> probability that the vertex is in the label, so you can
> choose the
> threshold based on that. The lh.V1.thresh.label is for
> when the
> stat is the max for V1 relative to the other labels (eg,
> V2). If
> you select thresh=.5, you may miss places where V1 is the most
> likely but still less than .5. I would probably use
> lh.V1.thresh.label (and then do not spec --label-thresh)
>
> doug
>
>
>
> On 03/05/2014 03:40 PM, krista kelly wrote:
>
> Thanks Doug! I did that and it worked, but now here's
> another
> problem: the values that I obtained for V1, V2, and
> cortex for
> each subject are all the same. For example, BV20 left
> hemisphere values for V1, V2, and cortex are all
> 2.7241 (same
> thing happens for the right hemisphere). Maybe I can
> tell you
> what I did step by step to see  if you can find where
> I went
> wrong.
>
> First, I did a for loop to run mri_segstats for each
> participant for each label per hemisphere (here is an
> example
> of V1):
>
> foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27
> BV28 BV29
> BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40
> BV41
> BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14
> MB15
> MB16 MB17 MB18 MB19 MB20) <>
> mri_segstats --label-thresh .5 --slabel $s lh
> $SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i
> $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum
> $SUBJECTS_DIR/$s/stats/lh.V1.thresh.label.LGI.stats
>  <>
> end <>
>
> for left V2 I ran:
>
> foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27
> BV28 BV29
> BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40
> BV41
> BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14
> MB15
> MB16 MB17 MB18 MB19 MB20) <>
> mri_segstats --label-thresh .5 --slabel $s lh
> $SUBJECTS_DIR/$s/label/lh.V2.thresh.label --i
> $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum
> $SUBJECTS_DIR/$s/stats/lh.V2.thresh.label.LGI.stats
>  <>
> end <>
>
> and for left cortex I ran:
> foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27
> BV28 BV29
> BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40
> BV41
> BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14
> MB15
> MB16 MB17 MB18 MB19 MB20) <>
> mri_segstats --label-thresh .5 --slabel $s lh
> $SUBJECTS_DIR/$s/label/lh.cortex --i
> $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum
> $SUBJECTS_DIR/$s/stats/lh.cortex.LGI.stats
> end <>
>
>
> This is where the problem must be occurring since all
> files
> created during these commands show the same files per
> hemisphere. I've attached three files created during
> mri_segstats (left V1, V2, cortex.stats) for one
> participant.
>

[Freesurfer] Surface area in aparc stats

[沈庄明]

Hi all,
   I need to know how is the SurfArea in ?h.aparc.stats calculated by 
FreeSurfer? Since each cortical parcellation has its own thickness in 3D space, 
does the surface area computation consider both the exterior surface (i.e. the 
surface separating the gray matter and the background) and the interior surface 
(i.e. the surface separating the gray matter and the white matter)? 
   Thanks!


Zhuangming Shen







___
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] Surface area in aparc stats

[Douglas Greve]

By default, the surface area is computed from the white surface (ie, 
boundary between WM and GM). It is possible to compute it from the pial 
surface (ie, boundary between GM and background)

doug


On 3/5/14 9:14 PM, ??? wrote:

Hi all,
   I need to know how is the SurfArea in ?h.aparc.stats calculated by 
FreeSurfer? Since each cortical parcellation has its own thickness in 
3D space, does the surface area computation consider both the exterior 
surface (i.e. the surface separating the gray matter and the 
background) and the interior surface (i.e. the surface separating the 
gray matter and the white matter)?

   Thanks!

Zhuangming Shen








___
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 comparisons

[Douglas Greve]

On 3/5/14 5:25 PM, Tudor Popescu wrote:
Hello, I have some questions on doing group comparisons with 
thickness, area and volume. Many thanks in advance for any help!


1) For a DOSS design with group and gender as categorical factors, I 
see that an interaction contrast ("Is there a group-gender interaction 
in the mean thickness?") still exists - but what does this contrast 
mean, given that DOSS by definition doesn't allow for interactions?
Are you using QDEC? If so, don't use the DOSS as the contrasts are 
incorrect. It is possible to have an interaction among the categorical 
factors with a DOSS.


2) it makes sense that measures such as thickness are analysed 
vertex-wise in QDEC, however what does it mean when the dependent 
variable is area or volume - measures that do not make physical sense 
for a single vertex but only at the level of a region consisting of 
*several* vertices?
The interpretation is a little more difficult. Each vertex is assigned 
an area equal to the average of the triangles adjacent to it. This is 
just a value that can be mapped to a common space like any other value 
(eg, thickness) (but there is a special jacobain correction to account 
for stretching or compression). Smoothing reduces the effect of having 
different sized triangles. One can think of it like this: in the common 
space (fsaverage) image having a patch of a certain size. When you 
mapped that patch back to each individual, how big would that patch be? 
You could then do group statistics on that number. In this way you could 
analyze the entire hemisphere. Now imagine doing this but making the 
patch smaller and smaller.


3) For values extracted from atlas regions with aparcstats2table, it 
seems that the product of the extracted CT and area is in the same 
order of magnitude as the extracted volume, but never really the same 
or even close -- why, when the volume of a region should theoretically 
be the product of its surface area by its thickness?
It is an issue of how it is computed. Sum(CT*Area) != Sum(CT)*Sum(Area). 
When computing volume, CT*Area is computed for each vertex then summed 
across vertices.

doug



Tudor


___
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] Surface area in aparc stats

[Douglas Greve]

Hi Zhuangming, please remember to post to the list. Thanks! I don't 
understand your question. What do you mean by the exterior, anterior, 
posterior, etc, surfaces?



On 3/5/14 11:56 PM, 沈庄明 wrote:

Hi Doug,
Thank you for your prompting response. Do you mean the computation 
only calculate exterior surface of the cortical region ? The other 
five surface (i.e. anterior, posterior, left, right, interior) are 
excluded ?

Thanks!

Zhuangming


-原始邮件-
*发件人:* "Douglas Greve" mailto:gr...@nmr.mgh.harvard.edu>>
*发送时间:* 2014年3月6日 星期四
*收件人:* freesurfer@nmr.mgh.harvard.edu

*抄送:*
*主题:* Re: [Freesurfer] Surface area in aparc stats


By default, the surface area is computed from the white surface
(ie, boundary between WM and GM). It is possible to compute it
from the pial surface (ie, boundary between GM and background)
doug


On 3/5/14 9:14 PM, 沈庄明 wrote:

Hi all,
I need to know how is the SurfArea in ?h.aparc.stats calculated
by FreeSurfer? Since each cortical parcellation has its own
thickness in 3D space, does the surface area computation consider
both the exterior surface (i.e. the surface separating the gray
matter and the background) and the interior surface (i.e. the
surface separating the gray matter and the white matter)?
Thanks!

Zhuangming Shen








___
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.