[Freesurfer] How to transfer a reconstructed pial surface file into a 256*256*256 matlab matrix file?

[Yunxin Wang]

Hi dear all,

I'm new here and I've a simple question that how could I transfer the
reconstructed pial surface file(like lh.pial) into a 256*256*256 matlab
matrix used in later fast marching process?

Any suggestion will be appreciated!
Thank guys.

Best,
Yunxin Wang
___
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] Mapping data into segmented atlas

[Oscar Sotolongo Grau]

Hi Freesurfers,

I had run Freesurfer over a set of MRIs, extracted the volumes for
different ROIs and correlated with another biomarkers using R. Now I
want to represent the obtained correlations for the segmented ROIs into
a brain template. 


Is there some automated way to do that with Freesurfer? or maybe with
another tool?



-- 
O. Sotolongo, 
http://dfmf.uned.es/~osotolongo
Tf. +34 652 575 178

Fundació ACE. Institut Català de Neurociències Aplicades.
http://www.fundacioace.com




___
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] How to transfer a reconstructed pial surface file into a 256*256*256 matlab matrix file?

[Bruce Fischl]

Hi Yunxin

the surface lives in a continuum and is 2D. Do you mean filling the space 
between the ?h.white and ?h.pial surfaces? We do that as part of 
recon-all and create ribbon volumes in the mri dir

cheers
Bruce


On Mon, 5 Aug 2013, Yunxin Wang wrote:


Hi dear all,
I'm new here and I've a simple question that how could I transfer the 
reconstructed pial surface file(like lh.pial) into a
256*256*256 matlab matrix used in later fast marching process?

Any suggestion will be appreciated!
Thank guys.

Best,
Yunxin Wang



___
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] Controlling for shape (and size) of a ROI in co-registration

[pfotiad]

Hi FS Community,

Is there a way to control for the size and shape of a ROI when applying
co-registration? For instance, I drew a ROI in a scan through freesurfer,
and then when I coregistered that ROI to another scan, the resulting ROI
had a different shape and number of voxels compared to the original ROI.
IS there a way to control for that?

Thank you for your time.

Best,
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] Trac-all question

[Anastasia Yendiki]

Hi Alan - On the tutorial page you need to follow the directions under "If 
you are not at an organized course", and $TUTORIAL_DATA is whatever 
directory you have downloaded the tutorial data in.


Please address questions to the list and not to me personally, as other 
people may have the same issue and this way the answers get archived.


Thanks,
a.y

On Mon, 5 Aug 2013, Alan Francis wrote:


Hi Anastasia:

Sorry about being a pest. One more question. I am running the Tutorial data
to get a better understanding of Tracula. When I type $TUTORIAL_DATA,  it
keeps saying Undefined variable. Could you please help me.

Thanks,

Alan

csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D
ATA/diffusion_recons] : setenv FREESURFER_HOME
/usr/local/freesurfer/stable5_3_0/
csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D
ATA/diffusion_recons] : source $FREESURFER_HOME/Set
SetUpFreeSurfer.csh* SetUpFreeSurfer.sh* 
csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D
ATA/diffusion_recons] : source $FREESURFER_HOME/SetUpFreeSurfer.csh
 freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer/stable5_3_0/
FSFAST_HOME   /usr/local/freesurfer/stable5_3_0//fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/stable5_3_0//subjects
MNI_DIR   /usr/local/freesurfer/stable5_3_0//mni
FSL_DIR   /usr/pubsw/packages/fsl/current
csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D
ATA/diffusion_recons] : setenv SUBJECTS_DIR $TUTORIAL_DATA/d
$TUTORIAL_DATA/ not found

csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D
ATA/diffusion_recons] : setenv SUBJECTS_DIR /autofs/space/d
dali_001/ dali_002/ dali_003/
csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D
ATA/diffusion_recons] : setenv 
SUBJECTS_DIR/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_DA
TA/diffusion_recons/
csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D
ATA/diffusion_recons] : gedit
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial &
TUTORIAL_DATA: Undefined variable.
csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D
ATA/diffusion_recons] : gedit
/TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial &
[1] 32742
csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/TUTORIAL_D
ATA/diffusion_recons] : trac-all -prep -c
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial
TUTORIAL_DATA: Undefined variable.



On Fri, Aug 2, 2013 at 7:16 PM, Alan Francis 
wrote:
  thanks again.


On Fri, Aug 2, 2013 at 3:51 PM, Anastasia Yendiki
 wrote:

  It can have any name you want. You just have to type the
  right name next to the "-c ..."

  On Fri, 2 Aug 2013, Alan Francis wrote:

Sorry. I have another question. Should I name
the config file dmrirc.txt or
is there any other name?
thank you so much,

Alan


On Fri, Aug 2, 2013 at 2:45 PM, Alan Francis

wrote:
      Thanks Anastasia.


On Fri, Aug 2, 2013 at 2:26 PM, Anastasia
Yendiki
 wrote:

      Hi Alan - All the "set ..." commands for
tracula need to
      be in a configuration file. You then
pass that
      configuration file as an argument to the
"-c" option of
      trac-all. See tutorial:
             
     
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

      Hope this helps,
      a.y

      On Fri, 2 Aug 2013, Alan Francis wrote:

      Hi Anastasia and others:
      I have been trying to run Trac all on
five brains.
      It keeps giving me the
      error message:

      ERROR: run list is longer than subject
list

      My run list is equal to the subject
list: Here is
      the environment:

      Thanks for your help,

      Alan
      Martinos Center for Biomedical Imaging

     
__

      
     
freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
      

      Setting up environment for
FreeSurfer/FS-FAST (and
      FSL)
      FREESURFER_HOME  
/usr/local/freesurfer/stable5_3_0/
      

Re: [Freesurfer] Controlling for shape (and size) of a ROI in co-registration

[Bruce Fischl]

Hi Panos,

not unless you want to restrict the registration to be rigid (6 dofs)

cheers
Bruce
On 
Mon, 
5 Aug 2013, pfot...@nmr.mgh.harvard.edu wrote:

> Hi FS Community,
>
> Is there a way to control for the size and shape of a ROI when applying
> co-registration? For instance, I drew a ROI in a scan through freesurfer,
> and then when I coregistered that ROI to another scan, the resulting ROI
> had a different shape and number of voxels compared to the original ROI.
> IS there a way to control for that?
>
> Thank you for your time.
>
> Best,
> Panos
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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] Fwd: TR,TE,TI,FA variability w/ mri_ca_train

[Mark Plantz]

-- Forwarded message --
From: Mark Plantz 
Date: Mon, Aug 5, 2013 at 11:32 AM
Subject: Re: [Freesurfer] TR,TE,TI,FA variability w/ mri_ca_train
To: Bruce Fischl 


thank you. Would the command simply be something like this: mri_modify -tr
0 -te 0 -ti 0 -fa 0   ?


On Thu, Aug 1, 2013 at 1:41 PM, Bruce Fischl wrote:

> Hi Mark
>
> the formatting got messed up so I can't parse your table. You can get
> around this using mri_modify, and just setting everything to 0. As for the
> effects, look at the images and see what you think.
>
> cheers
> Bruce
>
>
> On Thu, 1 Aug 2013, Mark Plantz wrote:
>
>  Hello freesurfers,
>> I currently have a series of images with various TR,TE,TI,FA values. I
>> would like to use mri_ca_train to create a .gca atlas based on these
>> segmented volumes. Unfortunately, they all have slightly different control
>> parameters (TR,TE,TI,FA). Is there any way around this problem, or would
>> it
>> be best to break the subjects into multiple groups with the same control
>> parameters?
>>
>> Here are the various parameters: [each row is a subject]
>>
>> TR
>> TE
>> TI
>> flip angle
>> 9.38
>> 3.86
>> 450
>> 12
>> 9.34
>> 3.86
>> 450
>> 12
>> 9.38
>> 3.86
>> 450
>> 12
>> 9.38
>> 3.86
>> 450
>> 12
>> 9.34
>> 3.86
>> 450
>> 12
>> 9.44
>> 3.87
>> 450
>> 12
>> 9.39
>> 3.86
>> 450
>> 12
>> 2065.98
>> 7.61
>> 886.92
>> 90
>> 9.45
>> 3.89
>> 450
>> 12
>> 9.41
>> 3.87
>> 450
>> 12
>> 9.41
>> 3.87
>> 450
>> 12
>> 9.42
>> 3.91
>> 450
>> 12
>> 9.38
>> 3.86
>> 450
>> 12
>> 9.38
>> 3.86
>> 450
>> 12
>> 9.44
>> 3.86
>> 450
>> 12
>> 9.44
>> 3.86
>> 450
>> 12
>> 9.38
>> 3.86
>> 450
>> 12
>> 9.38
>> 3.86
>> 450
>> 12
>> 9.38
>> 3.86
>> 450
>> 12
>> 9.34
>> 3.86
>> 450
>> 12
>> 9.34
>> 3.86
>> 450
>> 12
>> 9.39
>> 3.86
>> 450
>> 12
>> 1900
>> 2.6
>> 900
>> 9
>> 1900
>> 2.6
>> 900
>> 9
>> 1900
>> 2.6
>> 900
>> 9
>> 9.41
>> 3.87
>> 450
>> 12
>> 9.41
>> 3.87
>> 450
>> 12
>> 9.41
>> 3.87
>> 450
>> 12
>> 1900
>> 2.6
>> 900
>> 9
>> 9.41
>> 3.87
>> 450
>> 12
>> 1900
>> 2.6
>> 900
>> 9
>> 1900
>> 2.6
>> 900
>> 9
>>
>> Thank you in advance.
>>
>> -Mark
>>
>>
>>
>>
>
> 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] TR,TE,TI,FA variability w/ mri_ca_train

[Mark Plantz]

For some reason, when I run that command, I get the following output:

Input volume  is : seg_mov
Output volume is : seg_mov_2

There are no errors, but when I check "mri_info" of the output file, the
TR, TE, etc. values are still non-zero. Any ideas what could cause that to
happen?

Thanks!

MP


On Mon, Aug 5, 2013 at 11:35 AM, Bruce Fischl wrote:

> yes, I think so
>
> On Mon, 5 Aug 2013, Mark Plantz wrote:
>
>  thank you. Would the command simply be something like this: mri_modify
>> -tr 0 -te 0 -ti 0 -fa 0   ?
>>
>>
>> On Thu, Aug 1, 2013 at 1:41 PM, Bruce Fischl 
>> wrote:
>>   Hi Mark
>>
>>   the formatting got messed up so I can't parse your table. You can
>> get around this using mri_modify, and just setting
>>   everything to 0. As for the effects, look at the images and see
>> what you think.
>>
>>   cheers
>>   Bruce
>>
>>   On Thu, 1 Aug 2013, Mark Plantz wrote:
>>
>> Hello freesurfers,
>> I currently have a series of images with various
>> TR,TE,TI,FA values. I
>> would like to use mri_ca_train to create a .gca atlas based
>> on these
>> segmented volumes. Unfortunately, they all have slightly
>> different control
>> parameters (TR,TE,TI,FA). Is there any way around this
>> problem, or would it
>> be best to break the subjects into multiple groups with the
>> same control
>> parameters?
>>
>> Here are the various parameters: [each row is a subject]
>>
>> TR
>> TE
>> TI
>> flip angle
>> 9.38
>> 3.86
>> 450
>> 12
>> 9.34
>> 3.86
>> 450
>> 12
>> 9.38
>> 3.86
>> 450
>> 12
>> 9.38
>> 3.86
>> 450
>> 12
>> 9.34
>> 3.86
>> 450
>> 12
>> 9.44
>> 3.87
>> 450
>> 12
>> 9.39
>> 3.86
>> 450
>> 12
>> 2065.98
>> 7.61
>> 886.92
>> 90
>> 9.45
>> 3.89
>> 450
>> 12
>> 9.41
>> 3.87
>> 450
>> 12
>> 9.41
>> 3.87
>> 450
>> 12
>> 9.42
>> 3.91
>> 450
>> 12
>> 9.38
>> 3.86
>> 450
>> 12
>> 9.38
>> 3.86
>> 450
>> 12
>> 9.44
>> 3.86
>> 450
>> 12
>> 9.44
>> 3.86
>> 450
>> 12
>> 9.38
>> 3.86
>> 450
>> 12
>> 9.38
>> 3.86
>> 450
>> 12
>> 9.38
>> 3.86
>> 450
>> 12
>> 9.34
>> 3.86
>> 450
>> 12
>> 9.34
>> 3.86
>> 450
>> 12
>> 9.39
>> 3.86
>> 450
>> 12
>> 1900
>> 2.6
>> 900
>> 9
>> 1900
>> 2.6
>> 900
>> 9
>> 1900
>> 2.6
>> 900
>> 9
>> 9.41
>> 3.87
>> 450
>> 12
>> 9.41
>> 3.87
>> 450
>> 12
>> 9.41
>> 3.87
>> 450
>> 12
>> 1900
>> 2.6
>> 900
>> 9
>> 9.41
>> 3.87
>> 450
>> 12
>> 1900
>> 2.6
>> 900
>> 9
>> 1900
>> 2.6
>> 900
>> 9
>>
>> Thank you in advance.
>>
>> -Mark
>>
>>
>>
>>
>>
>> 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 conta

Re: [Freesurfer] TR,TE,TI,FA variability w/ mri_ca_train

[Bruce Fischl]

can you send us the full command line and screen output of what you ran?
On 
Mon, 5 Aug 2013, Mark Plantz wrote:



For some reason, when I run that command, I get the following output:
Input volume  is : seg_mov
Output volume is : seg_mov_2

There are no errors, but when I check "mri_info" of the output file, the TR, 
TE, etc. values are still non-zero. Any ideas what
could cause that to happen?

Thanks!

MP


On Mon, Aug 5, 2013 at 11:35 AM, Bruce Fischl  
wrote:
  yes, I think so
  On Mon, 5 Aug 2013, Mark Plantz wrote:

thank you. Would the command simply be something like this: 
mri_modify -tr 0 -te 0 -ti 0 -fa 0
  ?


On Thu, Aug 1, 2013 at 1:41 PM, Bruce Fischl 
 wrote:
      Hi Mark

      the formatting got messed up so I can't parse your table. You 
can get around this using
mri_modify, and just setting
      everything to 0. As for the effects, look at the images and 
see what you think.

      cheers
      Bruce

      On Thu, 1 Aug 2013, Mark Plantz wrote:

            Hello freesurfers,
                I currently have a series of images with various 
TR,TE,TI,FA values. I
            would like to use mri_ca_train to create a .gca atlas 
based on these
            segmented volumes. Unfortunately, they all have 
slightly different control
            parameters (TR,TE,TI,FA). Is there any way around this 
problem, or would it
            be best to break the subjects into multiple groups with 
the same control
            parameters?

            Here are the various parameters: [each row is a subject]

            TR
            TE
            TI
            flip angle
            9.38
            3.86
            450
            12
            9.34
            3.86
            450
            12
            9.38
            3.86
            450
            12
            9.38
            3.86
            450
            12
            9.34
            3.86
            450
            12
            9.44
            3.87
            450
            12
            9.39
            3.86
            450
            12
            2065.98
            7.61
            886.92
            90
            9.45
            3.89
            450
            12
            9.41
            3.87
            450
            12
            9.41
            3.87
            450
            12
            9.42
            3.91
            450
            12
            9.38
            3.86
            450
            12
            9.38
            3.86
            450
            12
            9.44
            3.86
            450
            12
            9.44
            3.86
            450
            12
            9.38
            3.86
            450
            12
            9.38
            3.86
            450
            12
            9.38
            3.86
            450
            12
            9.34
            3.86
            450
            12
            9.34
            3.86
            450
            12
            9.39
            3.86
            450
            12
            1900
            2.6
            900
            9
            1900
            2.6
            900
            9
            1900
            2.6
            900
            9
            9.41
            3.87
            450
            12
            9.41
            3.87
            450
            12
            9.41
            3.87
 

[Freesurfer] wmparc.stats

[Yang, Daniel]

Dear FreeSurfer Experts,

I'm looking at stats/wmparc.stats, and there are some inconsistencies between 
subjects. I am wondering what might be the cause.

For one subject (say subject 1), part of the information appears to be:

# NRows 66
# NTableCols 10
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName normMean normStdDev 
normMin normMax normRange
  1 3001  1869 1869.0  wm-lh-bankssts   101.6999 
9.144569.   127.58.
  2 3003  1776 1776.0  wm-lh-caudalmiddlefrontal 98.1676 
8.507475.   125.50.
  3 3005   710  710.0  wm-lh-cuneus 103.7088
10.149378.   134.56.
  4 3006   106  106.0  wm-lh-entorhinal  84.5902 
9.035855.96.41.

For the other subject (subject 2), it appears to be:

# NRows 70
# NTableCols 10
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName normMean normStdDev 
normMin normMax normRange
  1 3001  1012 1012.0  wm-lh-bankssts93.6101
10.097171.   130.59.
  2 3002  1732 1732.0  wm-lh-caudalanteriorcingulate104.3373
10.687158.   126.68.
  3 3003  4743 4743.0  wm-lh-caudalmiddlefrontal 95.2809
11.513966.   117.51.
  4 3005  1488 1488.0  wm-lh-cuneus  91.9310
10.199564.   126.62.
  5 3006   398  398.0  wm-lh-entorhinal  75.3343 
9.066455.   101.46.

Thus, in subject 1, there is no estimate for 3002, 
wm-lh-caudalanteriorcingulate, and the NRows is different.

Could you please help? Both are analyzed by FreeSurfer 5.1.0.

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] TR,TE,TI,FA variability w/ mri_ca_train

[Mark Plantz]

Command and output:

dhcp-165-124-23-213:Desktop IngvalsonLab$ mri_modify -tr 0 -te 0 -ti 0 -fa
0 seg.mgz seg_new.mgz
Input volume  is : seg.mgz
Output volume is : seg_new.mgz
dhcp-165-124-23-213:Desktop IngvalsonLab$

Then, I checked the mri_info for each of the files (input and output)


   - *input info (seg.mgz):*

   Volume information for seg.mgz
  type: MGH
dimensions: 256 x 256 x 256
   voxel sizes: 1., 1., 1.
  type: FLOAT (3)
   fov: 256.000
   dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 2065.98 msec, TE: 7.61 msec, TI: 886.92 msec, flip angle:
90.00 degrees
   nframes: 1
   PhEncDir: UNKNOWN
ras xform present
xform info: x_r =  -1., y_r =  -0., z_r =   0., c_r =
4.4739
  : x_a =  -0., y_a =   0., z_a =   1., c_a =
6.3212
  : x_s =   0., y_s =  -1., z_s =  -0., c_s =
2.7581

talairach xfm :
/Applications/freesurfer/subjects/CMH-7263/mri/transforms/talairach.xfm
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.  -0.   0.   132.4739
   -0.   0.   1.  -121.6788
0.  -1.  -0.   130.7581
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.   0.   0.   132.4739
   -0.  -0.  -1.   130.7581
   -0.   1.  -0.   121.6788
0.   0.   0. 1.



   - *info for output (seg_new.mgz)*

Volume information for seg_new.mgz
  type: MGH
dimensions: 256 x 256 x 256
   voxel sizes: 1., 1., 1.
  type: FLOAT (3)
   fov: 256.000
   dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 2065.98 msec, TE: 7.61 msec, TI: 886.92 msec, flip angle:
90.00 degrees
   nframes: 1
   PhEncDir: UNKNOWN
ras xform present
xform info: x_r =  -1., y_r =  -0., z_r =   0., c_r =
4.4739
  : x_a =  -0., y_a =   0., z_a =   1., c_a =
6.3212
  : x_s =   0., y_s =  -1., z_s =  -0., c_s =
2.7581

talairach xfm :
/Applications/freesurfer/subjects/CMH-7263/mri/transforms/talairach.xfm
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.  -0.   0.   132.4739
   -0.   0.   1.  -121.6788
0.  -1.  -0.   130.7581
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.   0.   0.   132.4739
   -0.  -0.  -1.   130.7581
   -0.   1.  -0.   121.6788
0.   0.   0. 1.






On Mon, Aug 5, 2013 at 11:41 AM, Bruce Fischl wrote:

> can you send us the full command line and screen output of what you ran?
>
> On Mon, 5 Aug 2013, Mark Plantz wrote:
>
>  For some reason, when I run that command, I get the following output:
>> Input volume  is : seg_mov
>> Output volume is : seg_mov_2
>>
>> There are no errors, but when I check "mri_info" of the output file, the
>> TR, TE, etc. values are still non-zero. Any ideas what
>> could cause that to happen?
>>
>> Thanks!
>>
>> MP
>>
>>
>> On Mon, Aug 5, 2013 at 11:35 AM, Bruce Fischl 
>> wrote:
>>   yes, I think so
>>   On Mon, 5 Aug 2013, Mark Plantz wrote:
>>
>> thank you. Would the command simply be something like this:
>> mri_modify -tr 0 -te 0 -ti 0 -fa 0
>>   ?
>>
>>
>> On Thu, Aug 1, 2013 at 1:41 PM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu> wrote:
>>   Hi Mark
>>
>>   the formatting got messed up so I can't parse your
>> table. You can get around this using
>> mri_modify, and just setting
>>   everything to 0. As for the effects, look at the images
>> and see what you think.
>>
>>   cheers
>>   Bruce
>>
>>   On Thu, 1 Aug 2013, Mark Plantz wrote:
>>
>> Hello freesurfers,
>> I currently have a series of images with
>> various TR,TE,TI,FA values. I
>> would like to use mri_ca_train to create a .gca
>> atlas based on these
>> segmented volumes. Unfortunately, they all have
>> slightly different control
>> parameters (TR,TE,TI,FA). Is there any way around
>> this problem, or would it
>> be best to break the subjects into multiple
>> groups with the same control
>> parameters?
>>
>> Here are the various parameters: [each row is a
>

[Freesurfer] Monte Carlo

[Peter Boulos]

Good afternoon,

I am getting much different results in my QDEC before and after running
monte carlo cluster correction. Upon initially running the QDEC I have what
appears to be a significant group difference in the prefrontal region that
does not show up after I run the Monte Carlo but at the same time there
appears to be no result in the postcentral gyrus region prior to running
the Monte Carlo but after running it, there is a huge result in that
region. Is there something I missed?

Peter
___
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] hemispheric masks?

[John Richey]

Dear freesurfer experts, 

I was wondering whether there is an existing mask for the left and right 
hemispheres for fsaverage.  I can't seem to find any documentation of this, but 
perhaps I am missing something? 

Thanks in advance, 
John.




___
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] hemispheric masks?

[Douglas Greve]

It is stored as a label, see fsaverage/label/?h.cortex.label
doug

On 8/5/13 1:14 PM, John Richey wrote:

Dear freesurfer experts,

I was wondering whether there is an existing mask for the left and 
right hemispheres for fsaverage.  I can't seem to find any 
documentation of this, but perhaps I am missing something?


Thanks in advance,
John.






___
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] trac-preproc

[Alan Francis]

Hi All:

When I ran trac-preproc I got an error that read s as follows:

trac-preproc exited with ERRORS at Mon Aug  5 13:12:53 EDT 2013. I do have
a bvec.txt and bval file in each directory.

thanks for your help,

Alan


The following are the messages:

csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data]
:
trac-all -prep -c
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc
INFO: SUBJECTS_DIR is
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons
INFO: Diffusion root is
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/
Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0
trac-preproc -c
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/scripts/dmrirc.local
-log
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/scripts/trac-all.log
-cmd
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/scripts/trac-all.cmd
#-
/usr/local/freesurfer/stable5_3_0//bin/trac-preproc
#-
#@# Image corrections Mon Aug  5 13:12:10 EDT 2013
mri_convert
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/Diffusion_Recons/20080424_182054563000-12-01DTIValeras012a001.nii
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/dmri/dwi_orig.nii.gz
mri_convert
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/Diffusion_Recons/20080424_182054563000-12-01DTIValeras012a001.nii
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/dmri/dwi_orig.nii.gz

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/Diffusion_Recons/20080424_182054563000-12-01DTIValeras012a001.nii...
TR=7570.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.989696, 0.0161603, 0.142271)
j_ras = (0.0163, 0.999867, -0.000183368)
k_ras = (0.142255, -0.00213754, 0.989828)
writing to
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/dmri/dwi_orig.nii.gz...
cp
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/bvecs.txt
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/dmri/dwi_orig.mghdti.bvecs
cp: cannot stat
`/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/bvecs.txt':
No such file or directory
Linux cerebro 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013
x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Mon Aug  5 13:12:53 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.

Re: [Freesurfer] TR,TE,TI,FA variability w/ mri_ca_train

[Bruce Fischl]

Oh, I see. It checks against zero to see if things are specified. I'll 
fix that, but in the meantime why don't yo uset everything to 1 instead 
of 0

On Mon, 5 Aug 2013, Mark Plantz wrote:


Command and output:

dhcp-165-124-23-213:Desktop IngvalsonLab$ mri_modify -tr 0 -te 0 -ti 0 -fa 0 
seg.mgz seg_new.mgz
Input volume  is : seg.mgz
Output volume is : seg_new.mgz
dhcp-165-124-23-213:Desktop IngvalsonLab$ 

Then, I checked the mri_info for each of the files (input and output)

 *  input info (seg.mgz):
           Volume information for seg.mgz
          type: MGH
    dimensions: 256 x 256 x 256
   voxel sizes: 1., 1., 1.
          type: FLOAT (3)
           fov: 256.000
           dof: 0
        xstart: -128.0, xend: 128.0
        ystart: -128.0, yend: 128.0
        zstart: -128.0, zend: 128.0
            TR: 2065.98 msec, TE: 7.61 msec, TI: 886.92 msec, flip angle: 90.00 
degrees
       nframes: 1
       PhEncDir: UNKNOWN
ras xform present
    xform info: x_r =  -1., y_r =  -0., z_r =   0., c_r =     4.4739
              : x_a =  -0., y_a =   0., z_a =   1., c_a =     6.3212
              : x_s =   0., y_s =  -1., z_s =  -0., c_s =     2.7581

talairach xfm : 
/Applications/freesurfer/subjects/CMH-7263/mri/transforms/talairach.xfm
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
               -1.  -0.   0.   132.4739
               -0.   0.   1.  -121.6788
                0.  -1.  -0.   130.7581
                0.   0.   0.     1.

voxel-to-ras determinant -1

ras to voxel transform:
               -1.   0.   0.   132.4739
               -0.  -0.  -1.   130.7581
               -0.   1.  -0.   121.6788
                0.   0.   0.     1.


 *  info for output (seg_new.mgz)
        Volume information for seg_new.mgz
          type: MGH
    dimensions: 256 x 256 x 256
   voxel sizes: 1., 1., 1.
          type: FLOAT (3)
           fov: 256.000
           dof: 0
        xstart: -128.0, xend: 128.0
        ystart: -128.0, yend: 128.0
        zstart: -128.0, zend: 128.0
            TR: 2065.98 msec, TE: 7.61 msec, TI: 886.92 msec, flip angle: 90.00 
degrees
       nframes: 1
       PhEncDir: UNKNOWN
ras xform present
    xform info: x_r =  -1., y_r =  -0., z_r =   0., c_r =     4.4739
              : x_a =  -0., y_a =   0., z_a =   1., c_a =     6.3212
              : x_s =   0., y_s =  -1., z_s =  -0., c_s =     2.7581

talairach xfm : 
/Applications/freesurfer/subjects/CMH-7263/mri/transforms/talairach.xfm
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
               -1.  -0.   0.   132.4739
               -0.   0.   1.  -121.6788
                0.  -1.  -0.   130.7581
                0.   0.   0.     1.

voxel-to-ras determinant -1

ras to voxel transform:
               -1.   0.   0.   132.4739
               -0.  -0.  -1.   130.7581
               -0.   1.  -0.   121.6788
                0.   0.   0.     1.






On Mon, Aug 5, 2013 at 11:41 AM, Bruce Fischl  
wrote:
  can you send us the full command line and screen output of what you ran?
  On Mon, 5 Aug 2013, Mark Plantz wrote:

For some reason, when I run that command, I get the following 
output:
Input volume  is : seg_mov
Output volume is : seg_mov_2

There are no errors, but when I check "mri_info" of the output 
file, the TR, TE, etc. values are still
non-zero. Any ideas what
could cause that to happen?

Thanks!

MP


On Mon, Aug 5, 2013 at 11:35 AM, Bruce Fischl 
 wrote:
      yes, I think so
      On Mon, 5 Aug 2013, Mark Plantz wrote:

            thank you. Would the command simply be something like 
this: mri_modify -tr 0 -te 0 -ti 0 -fa
0
              ?


            On Thu, Aug 1, 2013 at 1:41 PM, Bruce Fischl 
 wrote:
                  Hi Mark

                  the formatting got messed up so I can't parse 
your table. You can get around this
using
            mri_modify, and just setting
                  everything to 0. As for the effects, look at the 
images and see what you think.

                  cheers
                  Bruce

                  On Thu, 1 Aug 2013, Mark Plantz wrote:

                        Hello freesurfers,
                            I currently have a series of images 
with various TR,TE,TI,FA values. I
                        would like to use mri_ca_train to create a 
.gca atlas based on these
                        seg

Re: [Freesurfer] trac-preproc

[Anastasia Yendiki]

The error says:
`/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/bvecs.txt': 
No such file or directory


Does this file exist?

On Mon, 5 Aug 2013, Alan Francis wrote:


Hi All:

When I ran trac-preproc I got an error that read s as follows:

trac-preproc exited with ERRORS at Mon Aug  5 13:12:53 EDT 2013. I do have a 
bvec.txt and bval file in each directory.

thanks for your help,

Alan


The following are the messages:

csh::alanf@cerebro 
[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data] : trac-all 
-prep -c
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc
INFO: SUBJECTS_DIR is 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons
INFO: Diffusion root is 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/
Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0
trac-preproc -c 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/scripts/dmrirc.local
 -log
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/scripts/trac-all.log
 -cmd
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/scripts/trac-all.cmd
#-
/usr/local/freesurfer/stable5_3_0//bin/trac-preproc
#-
#@# Image corrections Mon Aug  5 13:12:10 EDT 2013
mri_convert 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/Diffusion_Recons/20080424_182054563000-12-01DTIValeras012a001.nii
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/dmri/dwi_orig.nii.gz
mri_convert 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/Diffusion_Recons/20080424_182054563000-12-01DTIValeras012a001.nii
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/Diffusion_Recons/20080424_182054563000-12-01DTIValeras012a001.nii...
TR=7570.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.989696, 0.0161603, 0.142271)
j_ras = (0.0163, 0.999867, -0.000183368)
k_ras = (0.142255, -0.00213754, 0.989828)
writing to 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/dmri/dwi_orig.nii.gz...
cp 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/bvecs.txt
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_101/dmri/dwi_orig.mghdti.bvecs
cp: cannot stat 
`/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/bvecs.txt':
 No such file or directory
Linux cerebro 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 
x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Mon Aug  5 13:12:53 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.

Re: [Freesurfer] long_mris_slopes sign of do-rate

[Martin Reuter]

Hi Vincent,

yes, it is tp2-tp1 / time_delta

so thinning is negative, thickening positive. I'll correct the help 
text, the tutorial is right.

It knows about the time point ordering because of the time column.

Best, Martin

On 08/02/2013 09:04 PM, vbrun...@nmr.mgh.harvard.edu wrote:
> Dear Freesurfer experts,
>
> I have followed the LongitudinalTutorial with two time points + two
> groups and now, after looking at the output of the qdec analysis, I just
> want to make sure I haven't made a sign error as for the control group
> the difference is as expected around 0 but for the experimental group I
> see negative values (= thinning?) all over the place which seems weird,
> just want to make sure I got this right:
>
> I set the time variable to 0 for the baseline scan and to 1 for the
> after-intervention-scan. Is it correct that for do-rate the calculation
> is then only  -  and not the other
> way around?
> I ask because in the long_mris_slopes -help it says that do-rate would
> yield the "thinning in mm/time" and if this means that a positive value
> stands for thinning then this would contradict what I understood from
> the Tutorial where it says for the rate "thick2-thick1" is calculated,
> so a positive value should mean "thickening".
>
> Also, how does long_mris_slopes know which one is tp1 and which one is
> tp2? I assume it takes the first entry in the fsid column of
> long.qdec.table.dat as tp1 and the second entry below as tp2?
>
> Hm, I see no other possibilities of making a sign error during the whole
> process, did anyone report a similar issue?
>
> Thanks for your help! Best,
> Vincent
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu
reu...@mit.edu
Web  : http://reuter.mit.edu

___
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] trac-preproc

[Alan Francis]

Hi Anastasia:

Yes this file does exist but it did not have the *.txt suffix. Maybe I will
change the suffix and run this again.

thanks,

Alan


On Mon, Aug 5, 2013 at 1:57 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> The error says:
> `/autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_**
> Data/diffusion_recons/bvecs.**txt': No such file or directory
>
> Does this file exist?
>
>
> On Mon, 5 Aug 2013, Alan Francis wrote:
>
>  Hi All:
>>
>> When I ran trac-preproc I got an error that read s as follows:
>>
>> trac-preproc exited with ERRORS at Mon Aug  5 13:12:53 EDT 2013. I do
>> have a bvec.txt and bval file in each directory.
>>
>> thanks for your help,
>>
>> Alan
>>
>>
>> The following are the messages:
>>
>> csh::alanf@cerebro [/autofs/space/dali_003/users/**
>> BW_project_DTI/FreeSurfer_5.3_**Data] : trac-all -prep -c
>> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_**
>> Data/diffusion_recons/dmrirc
>> INFO: SUBJECTS_DIR is /autofs/space/dali_003/users/**
>> BW_project_DTI/FreeSurfer_5.3_**Data/diffusion_recons
>> INFO: Diffusion root is /autofs/space/dali_003/users/**
>> BW_project_DTI/FreeSurfer_5.3_**Data/diffusion_recons/
>> Actual FREESURFER_HOME /autofs/cluster/freesurfer/**
>> centos6_x86_64/stable5_3_0
>> trac-preproc -c /autofs/space/dali_003/users/**
>> BW_project_DTI/FreeSurfer_5.3_**Data/diffusion_recons//BW_101/**scripts/dmrirc.local
>> -log
>> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_**
>> Data/diffusion_recons//BW_101/**scripts/trac-all.log -cmd
>> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_**
>> Data/diffusion_recons//BW_101/**scripts/trac-all.cmd
>> #-**
>> /usr/local/freesurfer/stable5_**3_0//bin/trac-preproc
>> #-**
>> #@# Image corrections Mon Aug  5 13:12:10 EDT 2013
>> mri_convert /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_
>> **Data/diffusion_recons//BW_101/**Diffusion_Recons/20080424_**
>> 182054563000-12-**01DTIValeras012a001.nii
>> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_**
>> Data/diffusion_recons//BW_101/**dmri/dwi_orig.nii.gz
>> mri_convert /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_
>> **Data/diffusion_recons//BW_101/**Diffusion_Recons/20080424_**
>> 182054563000-12-**01DTIValeras012a001.nii
>> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_**
>> Data/diffusion_recons//BW_101/**dmri/dwi_orig.nii.gz
>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>> reading from
>> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_**
>> Data/diffusion_recons//BW_101/**Diffusion_Recons/20080424_**
>> 182054563000-12-**01DTIValeras012a001.nii...
>> TR=7570.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-0.989696, 0.0161603, 0.142271)
>> j_ras = (0.0163, 0.999867, -0.000183368)
>> k_ras = (0.142255, -0.00213754, 0.989828)
>> writing to /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_*
>> *Data/diffusion_recons//BW_101/**dmri/dwi_orig.nii.gz...
>> cp /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_**
>> Data/diffusion_recons/bvecs.**txt
>> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_**
>> Data/diffusion_recons//BW_101/**dmri/dwi_orig.mghdti.bvecs
>> cp: cannot stat `/autofs/space/dali_003/users/**
>> BW_project_DTI/FreeSurfer_5.3_**Data/diffusion_recons/bvecs.**txt': No
>> such file or directory
>> Linux cerebro 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC
>> 2013 x86_64 x86_64 x86_64 GNU/Linux
>>
>> trac-preproc exited with ERRORS at Mon Aug  5 13:12:53 EDT 2013
>>
>>
>>
>>
>>
>>
>
> 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] longitudinal stream percentage change

[Martin Reuter]

Hi Bastian,

actually (see other mail today) it computes percent thickening per year 
as it is the slope of the linear fit into the measurements (thickness 
with respect to age or time). If the slope is negative, there is thinning.

The results (within subject and on fsaverage) have signs so they always 
reflect both thinning or thickening. And usually due to noise you'll 
find regions in an individual subject that go both ways.
So when you look at the within subject results (on the base anatomy) you 
should see both blue and red regions. that should be also true for when 
looking at the same map on fsaverage (it is just mapped there, should 
not change the sign, only the location a little).

Best, Martin

On 08/02/2013 05:31 AM, Bastian Cheng wrote:
> Dear freesurfer-experts,
>
> I have successfully done a longitudinal analysis on cortical thickness
> changes over 2 timepoints (0 and 1 year).
>
> My question is:
>
> If I look at the -individual- overlays of perc. change (i.e. pc1fit),
> only positive values are shown.
> whereas at the -fsaverage- view, positve AND negative values are shown
> (i.e. thinning and thickening)
>
> I understood that long_mris_slopes calculates the "percent thinning per year".
> But is there a way to show both sides of the histogramm (i.e. from -2
> to +2) also on the -individual- overlay?
>
> This might be a naive question, however, any help is greatly appreciated!
>
> Bastian.
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu
reu...@mit.edu
Web  : http://reuter.mit.edu

___
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] longitudinal stream percentage change

[Martin Reuter]

By the way, smoothing can remove the thickening (if there is only a 
little and mainly thinning ).

Best, Martin

On 08/05/2013 02:18 PM, Martin Reuter wrote:
> Hi Bastian,
>
> actually (see other mail today) it computes percent thickening per year
> as it is the slope of the linear fit into the measurements (thickness
> with respect to age or time). If the slope is negative, there is thinning.
>
> The results (within subject and on fsaverage) have signs so they always
> reflect both thinning or thickening. And usually due to noise you'll
> find regions in an individual subject that go both ways.
> So when you look at the within subject results (on the base anatomy) you
> should see both blue and red regions. that should be also true for when
> looking at the same map on fsaverage (it is just mapped there, should
> not change the sign, only the location a little).
>
> Best, Martin
>
> On 08/02/2013 05:31 AM, Bastian Cheng wrote:
>> Dear freesurfer-experts,
>>
>> I have successfully done a longitudinal analysis on cortical thickness
>> changes over 2 timepoints (0 and 1 year).
>>
>> My question is:
>>
>> If I look at the -individual- overlays of perc. change (i.e. pc1fit),
>> only positive values are shown.
>> whereas at the -fsaverage- view, positve AND negative values are shown
>> (i.e. thinning and thickening)
>>
>> I understood that long_mris_slopes calculates the "percent thinning per 
>> year".
>> But is there a way to show both sides of the histogramm (i.e. from -2
>> to +2) also on the -individual- overlay?
>>
>> This might be a naive question, however, any help is greatly appreciated!
>>
>> Bastian.
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>

-- 
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu
reu...@mit.edu
Web  : http://reuter.mit.edu

___
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] Best way to generate Complete Stats Table

[Salil Soman]

Dear Doug and Bruce,

Thank you for your emails. I have also run the -hippo-subfields option on
my freesurfer processing. How do I extract those values as tables as well?

Best wishes,

Sal


On Sun, Aug 4, 2013 at 11:10 AM, Bruce Fischl wrote:

> try asegstats2table
>
> cheers
> Bruce
>
> On Sun, 4 Aug 2013, Salil Soman wrote:
>
>  Hi,
>> I have a large dataset for which I run freesurfer and confirmed that the
>> apar+aseg.mgz file is satisfactory. Can someone please recommend the best
>> way to aggregate all of the volumes/other values generated by freesurfer
>> into a single table for this dataset? (e.g. subjects as Rows and values by
>> columns).
>>
>> Best wishes,
>>
>> Sla
>>
>>
>>
>
> 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.
>
>


-- 
Salil Soman, MD, MS
Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory
Fellow - Palo Alto War Related Illness and Injury Study Center
WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System
___
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] trac-preproc

[Anastasia Yendiki]

Hi Alan - The file doesn't need to have an extension, .txt or other. But 
you do need to set bvecfile to the full name of the file, including the 
extension, if it has one.


a.y

On Mon, 5 Aug 2013, Alan Francis wrote:


Hi Anastasia:

Yes this file does exist but it did not have the *.txt suffix. Maybe I will
change the suffix and run this again.

thanks,

Alan


On Mon, Aug 5, 2013 at 1:57 PM, Anastasia Yendiki
 wrote:

  The error says:
`/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
  recons/bvecs.txt': No such file or directory

Does this file exist?

On Mon, 5 Aug 2013, Alan Francis wrote:

  Hi All:

  When I ran trac-preproc I got an error that read s as
  follows:

  trac-preproc exited with ERRORS at Mon Aug  5 13:12:53 EDT
  2013. I do have a bvec.txt and bval file in each
  directory.

  thanks for your help,

  Alan


  The following are the messages:

  csh::alanf@cerebro
  [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data]
  : trac-all -prep -c
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
  econs/dmrirc
  INFO: SUBJECTS_DIR 
is/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
  econs
  INFO: Diffusion root 
is/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
  econs/
  Actual FREESURFER_HOME
  /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0
  trac-preproc 
-c/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
  econs//BW_101/scripts/dmrirc.local -log
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
  econs//BW_101/scripts/trac-all.log -cmd
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
  econs//BW_101/scripts/trac-all.cmd
  #-
  /usr/local/freesurfer/stable5_3_0//bin/trac-preproc
  #-
  #@# Image corrections Mon Aug  5 13:12:10 EDT 2013
  
mri_convert/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs//BW_101/Diffusion_Recons/20080424_182054563000-12-01DTIValera
  s012a001.nii
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
  econs//BW_101/dmri/dwi_orig.nii.gz
  
mri_convert/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs//BW_101/Diffusion_Recons/20080424_182054563000-12-01DTIValera
  s012a001.nii
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
  econs//BW_101/dmri/dwi_orig.nii.gz
  $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter
  Exp $
  reading from
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs//BW_101/Diffusion_Recons/20080424_182054563000-12-01DTIValera
  s012a001.nii...
  TR=7570.00, TE=0.00, TI=0.00, flip angle=0.00
  i_ras = (-0.989696, 0.0161603, 0.142271)
  j_ras = (0.0163, 0.999867, -0.000183368)
  k_ras = (0.142255, -0.00213754, 0.989828)
  writing 
to/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
  econs//BW_101/dmri/dwi_orig.nii.gz...
  
cp/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
  econs/bvecs.txt
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
  econs//BW_101/dmri/dwi_orig.mghdti.bvecs
  cp: cannot 
stat`/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
  recons/bvecs.txt': No such file or directory
  Linux cerebro 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13
  00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

  trac-preproc exited with ERRORS at Mon Aug  5 13:12:53 EDT
  2013







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] tksurfer and mountain lion problem / question

[Salil Soman]

Hi,

I can run freeview using my current install on Mountain Lion, however when
I run tkmedit or tksurfer I get the following error:

GLUT: Fatal Error in tksurfer.bin: could not open display: :0.0

my /etc/profile has the setting export DISPLAY=:0.0  for a different
program. Is there settings I should add / change to allow tkmedit or
tksurfer to run?

Thanks!

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.

Re: [Freesurfer] Controlling for shape (and size) of a ROI in co-registration

[pfotiad]

I see, thanks Bruce!

> Hi Panos,
>
> not unless you want to restrict the registration to be rigid (6 dofs)
>
> cheers
> Bruce
> On
> Mon,
> 5 Aug 2013, pfot...@nmr.mgh.harvard.edu wrote:
>
>> Hi FS Community,
>>
>> Is there a way to control for the size and shape of a ROI when applying
>> co-registration? For instance, I drew a ROI in a scan through
>> freesurfer,
>> and then when I coregistered that ROI to another scan, the resulting ROI
>> had a different shape and number of voxels compared to the original ROI.
>> IS there a way to control for that?
>>
>> Thank you for your time.
>>
>> Best,
>> Panos
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>
>
>

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


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] Best way to generate Complete Stats Table

[Douglas Greve]

Good question:). It does not look like we are currently creating a stats 
file for the subfields, which means you will have to do it yourself. You 
can do it with something like


cd $SUBJECTS_DIR/subject
mri_segstats --seg mri/hippsubfieldseg.mgz --sum stats/hipposub.stats 
--pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask 
mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm 
--in-intensity-units MR --subject subject --surf-wm-vol --etiv --ctab 
$FREESURFERHOME/FreeSurferColorLUT.txt


You can then run asegstats2table specifying hipposub.stats as the stats file

doug




On 8/5/13 3:39 PM, Salil Soman wrote:

Dear Doug and Bruce,

Thank you for your emails. I have also run the -hippo-subfields option 
on my freesurfer processing. How do I extract those values as tables 
as well?


Best wishes,

Sal


On Sun, Aug 4, 2013 at 11:10 AM, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:


try asegstats2table

cheers
Bruce

On Sun, 4 Aug 2013, Salil Soman wrote:

Hi,
I have a large dataset for which I run freesurfer and
confirmed that the
apar+aseg.mgz file is satisfactory. Can someone please
recommend the best
way to aggregate all of the volumes/other values generated by
freesurfer
into a single table for this dataset? (e.g. subjects as Rows
and values by
columns).

Best wishes,

Sla




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.




--
Salil Soman, MD, MS
Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory
Fellow - Palo Alto War Related Illness and Injury Study Center
WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care 
System


___
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] Best way to generate Complete Stats Table

[Salil Soman]

Thank you!

-Sal


On Mon, Aug 5, 2013 at 2:22 PM, Douglas Greve wrote:

>
> Good question:). It does not look like we are currently creating a stats
> file for the subfields, which means you will have to do it yourself. You
> can do it with something like
>
> cd $SUBJECTS_DIR/subject
> mri_segstats --seg mri/hippsubfieldseg.mgz --sum stats/hipposub.stats --pv
> mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask
> mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm
> --in-intensity-units MR --subject subject  --surf-wm-vol --etiv --ctab
> $FREESURFERHOME/FreeSurferColorLUT.txt
>
> You can then run asegstats2table specifying hipposub.stats as the stats
> file
>
> doug
>
>
>
>
>
> On 8/5/13 3:39 PM, Salil Soman wrote:
>
> Dear Doug and Bruce,
>
>  Thank you for your emails. I have also run the -hippo-subfields option
> on my freesurfer processing. How do I extract those values as tables as
> well?
>
>  Best wishes,
>
>  Sal
>
>
> On Sun, Aug 4, 2013 at 11:10 AM, Bruce Fischl 
> wrote:
>
>> try asegstats2table
>>
>> cheers
>> Bruce
>>
>> On Sun, 4 Aug 2013, Salil Soman wrote:
>>
>>  Hi,
>>> I have a large dataset for which I run freesurfer and confirmed that the
>>> apar+aseg.mgz file is satisfactory. Can someone please recommend the best
>>> way to aggregate all of the volumes/other values generated by freesurfer
>>> into a single table for this dataset? (e.g. subjects as Rows and values
>>> by
>>> columns).
>>>
>>> Best wishes,
>>>
>>> Sla
>>>
>>>
>>>
>>
>>   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.
>>
>>
>
>
>  --
>  Salil Soman, MD, MS
> Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory
> Fellow - Palo Alto War Related Illness and Injury Study Center
> WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care
> System
>
>
>


-- 
Salil Soman, MD, MS
Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory
Fellow - Palo Alto War Related Illness and Injury Study Center
WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System
___
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] Error with recon-all: You are trying to re-run an existing subject

[Joseph Andreano]

Hi All,

I'm trying to use recon-all on some structural data, and when I drop the
command (specifically, recon-all -i
/cluster/iaslab/SPAR/mri/recon/3danat/003/001.mgz -subjid
SPAR_016_130708), I get this error message:

ERROR: You are trying to re-run an existing subject with (possibly) new
input data (-i).  If this is truly new input data, you should delete the
subject folder and re-run, or specify a different subject name.  If you
are continuing an analysis of an existing subject, then omit all -i flags.

I have tried all the options suggested in the error message, and none
work.  I can't delete the subject folder, because no such folder exists. 
I tried running the command with a different subject name, and although
the command appeared to complete without error, no folder with the new
name was created, and no files were generated.  I tried removing the -i
flags, and I got this: ERROR: nothing to do.

Any suggestions?

Thanks,
Joe Andreano


_

Joseph M. Andreano, PhD
Postdoctoral Researcher
Interdisciplinary Affective
   Science Laboratory
Massachusetts General Hospital
_
___
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] wmparc.stats

[Douglas Greve]

That is a little strange. Can you look at the wmparc.mgz to see if it is 
there? Also look at the aparc+aseg.mgz to see how big the cortical 
region for caudalanteriorcingulate is. The wmparc is based on the aparc 
part of aparc+aseg.

doug




On 8/5/13 12:49 PM, Yang, Daniel wrote:

Dear FreeSurfer Experts,

I'm looking at stats/wmparc.stats, and there are some inconsistencies 
between subjects. I am wondering what might be the cause.


For one subject (say subject 1), part of the information appears to be:

# NRows66
# NTableCols 10
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName normMean 
normStdDev normMin normMax normRange
  1 3001  1869 1869.0  wm-lh-bankssts   
101.6999 9.1445  69.   127.58.
  2 3003  1776 1776.0  wm-lh-caudalmiddlefrontal 
98.1676 8.5074  75.   125.50.
  3 3005   710  710.0  wm-lh-cuneus 
103.708810.1493  78.   134.56.
  4 3006   106  106.0  wm-lh-entorhinal 
 84.5902 9.0358  55.96.41.


For the other subject (subject 2), it appears to be:

# NRows 70
# NTableCols 10
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName normMean 
normStdDev normMin normMax normRange
  1 3001  1012 1012.0  wm-lh-bankssts   
 93.610110.0971  71.   130.59.
  2 3002  1732 1732.0  wm-lh-caudalanteriorcingulate   
 104.337310.6871  58.   126.68.
  3 3003  4743 4743.0  wm-lh-caudalmiddlefrontal 
95.280911.5139  66.   117.51.
  4 3005  1488 1488.0  wm-lh-cuneus 
 91.931010.1995  64.   126.62.
  5 3006   398  398.0  wm-lh-entorhinal 
 75.3343 9.0664  55.   101.46.


Thus, in subject 1, there is no estimate for 3002, 
wm-lh-caudalanteriorcingulate, and the NRows is different.


Could you please help? Both are analyzed by FreeSurfer 5.1.0.

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


___
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] Error with recon-all: You are trying to re-run an existing subject

[Bruce Fischl]

Hi Joe

try adding -all to the end. You need to specify a directive for it to 
carry out

cheers
Bruce
On Mon, 5 Aug 2013, Joseph Andreano wrote:

> Hi All,
>
> I'm trying to use recon-all on some structural data, and when I drop the
> command (specifically, recon-all -i
> /cluster/iaslab/SPAR/mri/recon/3danat/003/001.mgz -subjid
> SPAR_016_130708), I get this error message:
>
> ERROR: You are trying to re-run an existing subject with (possibly) new
> input data (-i).  If this is truly new input data, you should delete the
> subject folder and re-run, or specify a different subject name.  If you
> are continuing an analysis of an existing subject, then omit all -i flags.
>
> I have tried all the options suggested in the error message, and none
> work.  I can't delete the subject folder, because no such folder exists.
> I tried running the command with a different subject name, and although
> the command appeared to complete without error, no folder with the new
> name was created, and no files were generated.  I tried removing the -i
> flags, and I got this: ERROR: nothing to do.
>
> Any suggestions?
>
> Thanks,
> Joe Andreano
>
>
> _
>
> Joseph M. Andreano, PhD
> Postdoctoral Researcher
> Interdisciplinary Affective
>   Science Laboratory
> Massachusetts General Hospital
> _
> ___
> 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] Monte Carlo

[Douglas Greve]

Something is going wrong. Can you carefully document the key strokes and 
mouse clicks you used?

doug



On 8/5/13 1:08 PM, Peter Boulos wrote:

Good afternoon,

I am getting much different results in my QDEC before and after 
running monte carlo cluster correction. Upon initially running the 
QDEC I have what appears to be a significant group difference in the 
prefrontal region that does not show up after I run the Monte Carlo 
but at the same time there appears to be no result in the postcentral 
gyrus region prior to running the Monte Carlo but after running it, 
there is a huge result in that region. Is there something I missed?


Peter


___
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] Error with recon-all: You are trying to re-run an existing subject

[Douglas Greve]

are you looking in the right place? Look in $SUBJECTS_DIR, not the 
current directory
doug


On 8/5/13 5:45 PM, Joseph Andreano wrote:
> Hi All,
>
> I'm trying to use recon-all on some structural data, and when I drop the
> command (specifically, recon-all -i
> /cluster/iaslab/SPAR/mri/recon/3danat/003/001.mgz -subjid
> SPAR_016_130708), I get this error message:
>
> ERROR: You are trying to re-run an existing subject with (possibly) new
> input data (-i).  If this is truly new input data, you should delete the
> subject folder and re-run, or specify a different subject name.  If you
> are continuing an analysis of an existing subject, then omit all -i flags.
>
> I have tried all the options suggested in the error message, and none
> work.  I can't delete the subject folder, because no such folder exists.
> I tried running the command with a different subject name, and although
> the command appeared to complete without error, no folder with the new
> name was created, and no files were generated.  I tried removing the -i
> flags, and I got this: ERROR: nothing to do.
>
> Any suggestions?
>
> Thanks,
> Joe Andreano
>
>
> _
>
> Joseph M. Andreano, PhD
> Postdoctoral Researcher
> Interdisciplinary Affective
> Science Laboratory
> Massachusetts General Hospital
> _
> ___
> 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] Mapping data into segmented atlas

[Douglas Greve]

There is not an automated tool.  I would do it in matlab, loading in the 
segmentation, for each seg find the voxels in the segmentation and set 
their values equal to your computed value. You can use MRIread.m and 
MRIwrite.m


doug


On 8/5/13 6:37 AM, Oscar Sotolongo Grau wrote:

Mapping data into segmented atlas

Hi Freesurfers,

I had run Freesurfer over a set of MRIs, extracted the volumes for
different ROIs and correlated with another biomarkers using R. Now I
want to represent the obtained correlations for the segmented ROIs into
a brain template.


Is there some automated way to do that with Freesurfer? or maybe with
another tool?



--
O. Sotolongo, 
http://dfmf.uned.es/~osotolongo 
Tf. +34 652 575 178

Fundació ACE. Institut Català de Neurociències Aplicades.
http://www.fundacioace.com






___
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] Group thickness means

[Worker, Amanda]

Hello,



I just have a quick question about how to find the group mean of a significant 
cluster found in thickness analysis in QDEC. I have run comparison of a number 
of clinical groups with healthy controls and found several clusters of 
significant thinning. In the stats table generated by QDEC I can see individual 
subjects mean thickness but I'm not sure how to get the group mean? If you 
could help with this it would be much appreciated.



Thank you in advance.



Amanda
___
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] tksurfer and mountain lion problem / question

[zkaufman]

Hello Sal,

I tried setting my display to :0.0 and was able to get the tkmedit program
to open on my Mac Mountain Lion machine so Im not exactly sure why yours
is having difficulty. Have you installed XQuartz?

http://xquartz.macosforge.org/landing/

If you already have XQuartz installed I would go ahead and try commenting
out the DISPLAY variable setting in the /etc/profile file and reopen a
terminal and see if that works.

-Zeke



> Hi,
>
> I can run freeview using my current install on Mountain Lion, however when
> I run tkmedit or tksurfer I get the following error:
>
> GLUT: Fatal Error in tksurfer.bin: could not open display: :0.0
>
> my /etc/profile has the setting export DISPLAY=:0.0  for a different
> program. Is there settings I should add / change to allow tkmedit or
> tksurfer to run?
>
> Thanks!
>
> Sal
> ___
> 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] Binary mask

[pfotiad]

Hi FS Community,

Is there a way to create a binary mask of everything that is inside the
cortical ribbon of a subject (including the cortical ribbon)?
I ran:
mri_binarize --i aseg.mgz --match 3 --match 42 --o test.mgz which gave me
a binary mask of the cerebral cortex, but I was wondering whether there is
a way to create a binary mask of the cerebral cortex as well as everything
inside of it.
Thank you for your time.

Best,
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] Group thickness means

[Douglas Greve]

You should setup contrasts to test the group mean for each group 
separately in addition to your contrast of interest. I'm actually not 
sure whether QDEC will do this for you or not. Then


cd glmdir/group1contrast
mri_segstats --annot fsaverage lh 
../contrast-of-interest/cache.th13.abs.sig.ocn.annot --i gamma.mgh --sum 
yourcluster.summary.dat.


The "Mean" column will be the mean thickness

doug





On 8/5/13 6:19 PM, Worker, Amanda wrote:


Hello,

I just have a quick question about how to find the group mean of a 
significant cluster found in thickness analysis in QDEC. I have run 
comparison of a number of clinical groups with healthy controls and 
found several clusters of significant thinning. In the stats table 
generated by QDEC I can see individual subjects mean thickness but I'm 
not sure how to get the group mean? If you could help with this it 
would be much appreciated.


Thank you in advance.

Amanda



___
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] Binary mask

[Douglas Greve]

by "everything inside" you mean subcortical white matter and gray 
matter? If so, look at ribbon.mgz
doug




On 8/5/13 6:25 PM, pfot...@nmr.mgh.harvard.edu wrote:
> Hi FS Community,
>
> Is there a way to create a binary mask of everything that is inside the
> cortical ribbon of a subject (including the cortical ribbon)?
> I ran:
> mri_binarize --i aseg.mgz --match 3 --match 42 --o test.mgz which gave me
> a binary mask of the cerebral cortex, but I was wondering whether there is
> a way to create a binary mask of the cerebral cortex as well as everything
> inside of it.
> Thank you for your time.
>
> Best,
> Panos
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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


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] dPSD and ev duration

[Douglas Greve]

Hi Ella, sorry for the delay. The VRF gets reduced by a factor roughly 
equal to TR/dPSD, so 5 in your case. Whether this matters depends on how 
you eventually want to analyze the data. If you are going to assume a 
shape to the HRF (eg, using SPM or FSL), then it won't make much 
difference since the realized VRF will be 5 times your 4.5 which puts 
you in a good range. If you plan to analyze using an FIR (ie, don't 
assume a shape), then you might want to add some runs to boost the power.


doug


On 7/29/13 4:06 PM, Ella Hinton wrote:


Hi Doug
Thanks for your email. I gave your suggestion a try  - reduced the 
dPSD to 0.5 (as well as adjusted the PSDMAX, and no. of volumes to 
reflect the new TR - see full command line below).  Unfortunately the 
efficiency is way down (0.03) and the VRF you previously suggested 
should be between 20-40 is 4.5!  I now wonder if Optseq is trying to 
tell me this is now a bad design!!


Would be very grateful for any ideas for improvement?

optseq2 --ntp 240 --tr 2.5 --psdwin 0 20 0.5 --ev hf 3 50 --ev lf 3 50 
--ev nf 3 50 --nkeep 3 --o test14 --nsearch 1 --focb 100


many thanks
Ella


Date: Sun, 28 Jul 2013 23:33:07 -0400
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] dPSD and ev duration

Hi Ella, it has an internal clock that events have to be syncrhonized 
to. Try setting the dPSD to 0.5

doug



On 7/28/13 4:05 PM, Ella Hinton wrote:

Hi

Quick question - why must the duration of the EVs be an integer
multiple of the dPSD, which is also tied to the TR? I have event
duration of 3 seconds, but would like to reduce my TR from 3 down
to 2.5, but I can't seem to input the correct numbers for optseq
to help me.

thanks in advance
Ella


___
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 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] Group thickness means

[Worker, Amanda]

Hello,



I just have a quick question about how to find the group mean of a significant 
cluster found in thickness analysis in QDEC. I have run comparison of a number 
of clinical groups with healthy controls and found several clusters of 
significant thinning. In the stats table generated by QDEC I can see individual 
subjects mean thickness but I'm not sure how to get the group mean? If you 
could help with this it would be much appreciated.



Thank you in advance.



Amanda
___
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] function that do the same step like qcache?

[Douglas Greve]

The argument to --src_type should be the input file (eg, lh.curv, 
lh.sulc, lh.thickness). The --trgsurfval should be the name of the 
output file and --trg_type should be curv


doug

On 7/30/13 3:25 AM, fatma zribi wrote:

Dear Bruce,

I try to execute this command to smooth and resample data but I have 
one message of error:


mri_surf2surf --srcsubject s000_open_brain_sanlm_+TIR_normlalized 
--srcsurfval curv --src_type curv --trgsubject avg_all_subjects_SD 
--trgsurfval curv --hemi lh --fwhm-src 15 --trg_type smoothed.source.15


the error is: ERROR: could not determine type of curv

thank you for your help,

With best regards,

Fatma


2013/7/29 Bruce Fischl >


can you cc the list so that others can answer or see the answer?
You need to specify the source and target subjects with
--srcsubject and --trgsubject


cheers
Bruce


On Mon, 29 Jul 2013, fatma zribi wrote:

mri_surf2surf --hemi lh --s
s000_open_brain_sanlm_+TIR_normlalized --sval curv --src_type
curv --fwhm 10 --trg_type curv --tval
curv.10


2013/7/29 Bruce Fischl mailto:fis...@nmr.mgh.harvard.edu>>
  what is your full command line? You can smooth and map
with it (use -fwhm-src or fwhm-trg to smooth in either the
  source or target space)
  On Mon, 29 Jul 2013, fatma zribi wrote:

Dear Bruce,
I have tried mri-surf2surf, it makes the result
(smoothed curv for example) with the same dimension of
the subject. But I would
like a smoothed file with the dimesion of fsaverage.

Thank you for your help.

With best regards,

Fatma


2013/7/29 Bruce Fischl mailto:fis...@nmr.mgh.harvard.edu>>
  Hi Fatma

  you can use mri_surf2surf within subject I
believe, but Doug can confirm (although he's traveling
so it may be a
  bit). You can also do it interactively in
tksurfer.

  cheers
  Bruce


  On Mon, 29 Jul 2013, fatma zribi wrote:

Dear Bruce,

Would you mind tell me if there is a
function of freesurfer  that I can use to do the same
step of
qcache to smooth and
interpolate in the fsaverage one subject
with mri_surf2surf I can smooth only
or align one subject with an average.
thank you for you help.
with best regards,
Fatma




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] funcroi-table-sess error

[Douglas Greve]

Hi Alex, are you running it from the project folder? It is looking for a 
folder called "log" in the current directory. It should be creating this 
folder (bug). So, if you run it from the project folder, the log folder 
will be there. Or can create a log folder in your current directory 
(mkdir log)

doug

On 7/30/13 2:03 PM, Alexandra Tanner wrote:
> Dear Doug and Freesurfers,
>
> I am attempting to run funcroi-table-sess on a set of subjects but keep
> getting an error message I've never seen before:
>
> funcroi-table-sess -roi
> /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/ctx.lh.insula.aparc+aseg_2vFix.roicfg
> -sf
> /cluster/roffman/users/Stable5_PerRun/Subject_Files/30_ActiveFolateAndPlacebo_PostPrePAIRED
> -c Cond2vFix -o
> /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/18ActiveFolate_12Placebo_PreAndPost_7Tpost/ctx_lh_insula_aparc+aseg_2vFix
>
>
> log/funcroi-table-sess.log
> log/funcroi-table-sess.log: No such file or directory.
>
>
> Funcroi-sess ran without error, as did funcroi-config. I've run this
> analysis many times in the past and have never had this problem so I am at
> a loss as to what is going wrong. Any help would be greatly appreciated!
>
> Thanks,
> Alex
>
>
>
>

___
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] functional ROI-based structural statistics?

[Yang, Daniel]

Dear FreeSurfer Experts,

Theoretically, if you have a set of functional ROIs, is it possible to derive 
the cortical thickness, white surface area, and gray matter volume of those 
functional ROIs in FreeSurfer?

Many 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] wmparc.stats

[Yang, Daniel]

I check the recon-all.log. It appears that the cortical region for 
caudalanteriorcongulate for this subject is very small..

table columns are:
 number of vertices
 total surface area (mm^2)
 total gray matter volume (mm^3)
 average cortical thickness +- standard deviation (mm)
 integrated rectified mean curvature
 integrated rectified Gaussian curvature
 folding index
 intrinsic curvature index
 structure name

597390747  1.952 0.684 0.137 0.104  395 2.7  bankssts
29 18 42  2.705 0.791 0.131 0.0400 0.1  
caudalanteriorcingulate

Daniel

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

On 8/5/13 5:52 PM, "Douglas Greve" 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:

That is a little strange. Can you look at the wmparc.mgz to see if it is there? 
Also look at the aparc+aseg.mgz to see how big the cortical region for 
caudalanteriorcingulate is. The wmparc is based on the aparc part of aparc+aseg.
doug




On 8/5/13 12:49 PM, Yang, Daniel wrote:
Dear FreeSurfer Experts,

I'm looking at stats/wmparc.stats, and there are some inconsistencies between 
subjects. I am wondering what might be the cause.

For one subject (say subject 1), part of the information appears to be:

# NRows 66
# NTableCols 10
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName normMean normStdDev 
normMin normMax normRange
  1 3001  1869 1869.0  wm-lh-bankssts   101.6999 
9.144569.   127.58.
  2 3003  1776 1776.0  wm-lh-caudalmiddlefrontal 98.1676 
8.507475.   125.50.
  3 3005   710  710.0  wm-lh-cuneus 103.7088
10.149378.   134.56.
  4 3006   106  106.0  wm-lh-entorhinal  84.5902 
9.035855.96.41.

For the other subject (subject 2), it appears to be:

# NRows 70
# NTableCols 10
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName normMean normStdDev 
normMin normMax normRange
  1 3001  1012 1012.0  wm-lh-bankssts93.6101
10.097171.   130.59.
  2 3002  1732 1732.0  wm-lh-caudalanteriorcingulate104.3373
10.687158.   126.68.
  3 3003  4743 4743.0  wm-lh-caudalmiddlefrontal 95.2809
11.513966.   117.51.
  4 3005  1488 1488.0  wm-lh-cuneus  91.9310
10.199564.   126.62.
  5 3006   398  398.0  wm-lh-entorhinal  75.3343 
9.066455.   101.46.

Thus, in subject 1, there is no estimate for 3002, 
wm-lh-caudalanteriorcingulate, and the NRows is different.

Could you please help? Both are analyzed by FreeSurfer 5.1.0.

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.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.