[Freesurfer] Segmentation Algo

[Saurabh Thakur]

Hello Freesurfer expert,

I am new to freesurfer.

I wanted to know which algorithm is used for segmentation in freesurfer.

Thanks in advanced,

cheers
Saurabh Thakur,
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[Freesurfer] Freeview not working

[Saurabh Thakur]

Hi all,

My freeview is not working.

//=//

saurabh@saurabh-Precision-WorkStation-T3500:/usr/local/freesurfer$ freeview
freeview.bin: error while loading shared libraries: libXss.so.1: cannot
open shared object file: No such file or directory
saurabh@saurabh-Precision-WorkStation-T3500:/usr/local/freesurfer$

/=//

please suggest wht is going wrong.

Thanks in advance,

cheers
Saurabh Thakur,
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[Freesurfer] scuba running problem.

[Saurabh Thakur]

Hello Friends,

I m facing problem in freeview and scuba.

can anyone help me in this matter.
//==//
saurabh@saurabh-Precision-WorkStation-T3500:/$ cd $FREESURFER_HOME
saurabh@saurabh-Precision-WorkStation-T3500:/usr/local/freesurfer$

saurabh@saurabh-Precision-WorkStation-T3500:/usr/local/freesurfer$ scuba -v
$SUBJECTS_DIR/bert/mri/T1

Error starting scuba:

   File: tkUtils.tcl

   scuba could not be loaded because a support file was missing.
   Please check your installation. Make sure that the
   FREESURFER_HOME environment variable is set.

//==//


Thanks  in advance.

cheers
Saurabh Thakur,
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Re: [Freesurfer] Segmentation Algo

[Bruce Fischl]

Hi Saurabh

there are a number of different segmentatons in FreeSurfer (cortical, 
subcortical, hippocampal), all of which are documenented at:

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

cheers
Bruce

On Mon, 10 Feb 2014, Saurabh Thakur wrote:

> Hello Freesurfer expert,
> 
> I am new to freesurfer.
> 
> I wanted to know which algorithm is used for segmentation in freesurfer.
> 
> Thanks in advanced,
> 
> cheers
> Saurabh Thakur,
> 
> 
> 
> 
> 
>
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Re: [Freesurfer] scuba running problem.

[Bruce Fischl]

Hi Saurabh

scuba is deprecated - we haven't used it in years. Ruopeng or someone 
will answer your freeview question when they get a chance.


cheers
Bruce
On Mon, 10 Feb 
2014, Saurabh Thakur wrote:



Hello Friends,

I m facing problem in freeview and scuba.

can anyone help me in this matter.
//==//
saurabh@saurabh-Precision-WorkStation-T3500:/$ cd $FREESURFER_HOME
saurabh@saurabh-Precision-WorkStation-T3500:/usr/local/freesurfer$

saurabh@saurabh-Precision-WorkStation-T3500:/usr/local/freesurfer$ scuba -v
$SUBJECTS_DIR/bert/mri/T1

Error starting scuba:

   File: tkUtils.tcl

   scuba could not be loaded because a support file was missing.
   Please check your installation. Make sure that the
   FREESURFER_HOME environment variable is set.

//==//


Thanks  in advance.

cheers
Saurabh Thakur,





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Re: [Freesurfer] scuba running problem.

[Saurabh Thakur]

Oh...is it so
Bruce Thanks a lot for info.


cheers
Saurabh Thakur,






On Mon, Feb 10, 2014 at 6:55 PM, Bruce Fischl wrote:

> Hi Saurabh
>
> scuba is deprecated - we haven't used it in years. Ruopeng or someone will
> answer your freeview question when they get a chance.
>
> cheers
> Bruce
>
> On Mon, 10 Feb 2014, Saurabh Thakur wrote:
>
>  Hello Friends,
>>
>> I m facing problem in freeview and scuba.
>>
>> can anyone help me in this matter.
>> //==//
>> saurabh@saurabh-Precision-WorkStation-T3500:/$ cd $FREESURFER_HOME
>> saurabh@saurabh-Precision-WorkStation-T3500:/usr/local/freesurfer$
>>
>> saurabh@saurabh-Precision-WorkStation-T3500:/usr/local/freesurfer$ scuba
>> -v
>> $SUBJECTS_DIR/bert/mri/T1
>>
>> Error starting scuba:
>>
>>File: tkUtils.tcl
>>
>>scuba could not be loaded because a support file was missing.
>>Please check your installation. Make sure that the
>>FREESURFER_HOME environment variable is set.
>>
>> //==//
>>
>>
>> Thanks  in advance.
>>
>> cheers
>> Saurabh Thakur,
>>
>>
>>
>>
>>
>>
>>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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[Freesurfer] How to combine attached commands into one run

[Erik Lindberg]

Dear Freesufers,


I want to use the following commands in my recon-all to try to improve my
output some difficult images:

-gentle to mri_normalize

and

 -min_border_white 85 -min_gray_at_white_border 80

So far I only managed to do this by making one step at a time. I was
wondering if there is a way to combine these commands so I do not have to
run it step by step.
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[Freesurfer] QDEC Error

[pfotiad]

Hi FS community,

After I open QDEC, when I try to load my qdec data table, QDEC crashes for
some reason. The error message that comes out at the terminal is:

Returned Error on line 1:
missing close-brace
Stack trace:
missing close-brace
while executing
".vtkKWLoadSaveDialog5.vtkKWFileBrowserWidget0.vtkKWSplitFrame0.vtkKWFrame2.vtkKWSplitFrame0.vtkKWFrame0.vtkKWDirectoryExplorer0.vtkKWTreeWithScrollbar..."



X Error of failed request:  BadAlloc (insufficient resources for operation)
  Major opcode of failed request:  53 (X_CreatePixmap)
  Serial number of failed request:  611512
  Current serial number in output stream:  611810
Exit 1


I was wondering whether you know why is this happening. I am using FS v5.3
and my OS is Linux Centos 6.5.

Thanks in advance,
Panos


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Re: [Freesurfer] Freeview not working

[Z K]

Saurabh,

What is the output when you type "locate libXss.so.1" (without quotes) 
on the command line?

-Zeke

On 02/10/2014 05:17 AM, Saurabh Thakur wrote:
> Hi all,
>
> My freeview is not working.
>
> //=//
>
> saurabh@saurabh-Precision-WorkStation-T3500:/usr/local/freesurfer$ freeview
> freeview.bin: error while loading shared libraries: libXss.so.1: cannot
> open shared object file: No such file or directory
> saurabh@saurabh-Precision-WorkStation-T3500:/usr/local/freesurfer$
>
> /=//
>
> please suggest wht is going wrong.
>
> Thanks in advance,
>
> cheers
> Saurabh Thakur,
>
>
>
>
>
>
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[Freesurfer] Erasing, adding voxels in Freeview

[Denker, Alexander (NIH/NIMH) [F]]

Hi all,

This is probably a very elementary error in my use of Freeview, but I have been 
having trouble adding voxels to scans. I set the eraser value to "0", but when 
I draw, the voxel still shows up as a black box instead of grey. Am I not 
setting the right values or am I just in the wrong viewing mode?

Thanks!
Alexander

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[Freesurfer] Fwd: Edit hyperintense regions in aseg.mgz file in long or base?

[Linn Christin Bonaventure Norbom]

-- Forwarded message --
From: Linn Christin Bonaventure Norbom 
Date: Mon, Feb 10, 2014 at 4:06 PM
Subject: Edit hyperintense regions in aseg.mgz file in long or base?
To: Bruce Fischl 


Hi everyone,

I am registering hyperintense lesions as "lh-lesion" or "rh-lesion" and I
was wondering if it is better to do this as the base or the long stage. I
see that the freesurfer wiki page says I can do it at both stages depending
on the problem, but I was not sure if lesion registration counted as
"incorrect labeling" or "correcting the volume of importaint structures".

Thank you in advance!

Regards Linn Norbom
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Re: [Freesurfer] setting the useRealRAS bit

[Lilla Zollei]

Doug, mris_convert does not read / write that information either.

On Sun, 9 Feb 2014, Bruce Fischl wrote:

> really? I didn't realize that as I don't use them much. Doug: do you have 
> something like MRISread?
>
> On Sun, 9 Feb 2014, Lilla Zollei wrote:
>
>> 
>> Those .m files only give me a set of coordinates. They do not seem to be 
>> accessing any matrices or the required bit. Should this information be 
>> included at the beginning of each surface file?
>> Lilla
>> 
>> On Sun, 9 Feb 2014, Bruce Fischl wrote:
>> 
>>> Hi Lilla
>>> there is read_surf.m and write_surf.m, but I guess you will need to figure 
>>> out how to get the right ras2vox matrix into them
>>> cheers
>>> Bruce
>>> On Sun, 9 Feb 2014, Lilla Zollei wrote:
>>> 
 
 Hi,
 
 I have some FS-style surface files that were created using outside tools
 (from McGill). Due to some recent changes in FreeView they do not display
 properly though as the useRealRAS bit in the header is not set to 1. Do 
 we
 have any C / Matlab code that I could use to change that?
 
 Thanks, Lilla
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>>> 
>>> 
>>> 
>> 
>> 
>> 
>
>
>
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[Freesurfer] Color Bar options

[Jonathan Holt]

Hi all,

Would someone kindly point me toward color bar options, specifically for 
thickness maps. The color bar that appears by default includes negative values, 
and the bit with positive thickness values is very compressed.

For reference I’m looking at surfaces in freeview brought up by 

freeview -f 
SUBJ_ID/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
 


jon


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Re: [Freesurfer] Color Bar options

[Ruopeng Wang]

Hi Jon,

The range of color bar is automatically set by the internal color bar 
component that is used to display it. There is no option to change it at 
this point. I'll take note on that for future update.

Best,
Ruopeng

On 02/10/2014 11:49 AM, Jonathan Holt wrote:
> Hi all,
>
> Would someone kindly point me toward color bar options, specifically for 
> thickness maps. The color bar that appears by default includes negative 
> values, and the bit with positive thickness values is very compressed.
>
> For reference I’m looking at surfaces in freeview brought up by
>
> freeview -f 
> SUBJ_ID/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0
>
>
> jon
>
>
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>

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[Freesurfer] Fwd: OHBM Glass Brain Award: Call for Nominations

[Douglas N Greve]

FYI


 Original Message 
Subject:OHBM Glass Brain Award: Call for Nominations
Date:   Mon, 10 Feb 2014 11:18:43 -0600
From:   i...@humanbrainmapping.org
Reply-To:   i...@humanbrainmapping.org
To: gr...@nmr.mgh.harvard.edu





*ORGANIZATION FOR HUMAN BRAIN MAPPING
GLASS BRAIN AWARD*
/A lifetime achievement award in the field of human brain mapping/

Dear OHBM Member,

The Organization for Human Brain Mapping Council is excited to announce 
that OHBM has established an award to recognize and reward a lifetime of 
achievement by gifted and talented researchers using neuroimaging to 
discover original and influential findings to the organization of the 
human brain.

*Aw**a**r**d Criteria*

 1. Nominee must be visibly engaged in OHBM activities
 2. Nominee must have evidence of extraordinary lifetime accomplishments
in the field of human brain mapping and hold the promise of future
major contributions to the field
 3. The nominee must be over the age of 40
 4. The nominee must be present to accept the award given out at the
Annual Meeting
 5. No self-nominations are allowed

*Nomination Process*
Nominations for the Glass Brain Award should include a letter of 
nomination (no self-nominations are accepted) outlining the nominee’s 
lifetime accomplishments as well as a curriculum vita of the nominee. 
Additional letters of support are not required but will add to the 
strength of the nomination.  Nominators are required to collate all 
nomination materials into one single Adobe Acrobat PDF document to be 
emailed to OHBM at i...@humanbrainmapping.org 
. Deadline for nominations is March 
14, 2014.

*Rev**i**e**w Process*
The OHBM Council is charged with the selection of the Glass Brain Award 
recipient and will meet in mid-March to review the award criteria and 
discuss each nominee. The Council will then vote electronically on their 
top ranked candidates.  If needed, the Council will meet again to 
discuss any split decisions and make a final selection.  The award 
recipient will be notified electronically in April.

*Aw**a**rd*
The award recipient will be provided with an OHBM Glass Brain Award, 
gratis Annual Meeting registration, coach travel and two nights lodging 
at the host hotel.

We look forward to your involvement in the nomination process.  Please 
contact the OHBM Executive Office at i...@humanbrainmapping.org 
 with any questions.

Sincerely,

JoAnn Taie
Executive Director
Organization for Human Brain Mapping (OHBM)



Organization for Human Brain Mapping (OHBM)
5841 Cedar Lake Road, Suite 204
Minneapolis, MN 55416 USA
i...@humanbrainmapping.org 
www.humanbrainmapping.org 

To opt out of OHBM emails, contact the OHBM Executive Office at 
i...@humanbrainmapping.org .



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Re: [Freesurfer] PET Partial volume correction

[Douglas N Greve]

I can when I have a beta version! I'm actively working on putting the 
programs together into a package. Check back in a month or so.
doug




On 02/08/2014 03:41 PM, Jonathan DuBois wrote:
> Hi Doug,
>
> Thanks for replying. We are currently working on this analysis, is 
> there anyway you could provide a beta version of the PVC code?
>
> Thanks,
> Jonathan

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Erasing, adding voxels in Freeview

[Ruopeng Wang]

Hi Alexander,

Eraser value is used for erasing. Brush value is used for drawing. To 
erase, just hold shift key and press left mouse button.

Best,
Ruopeng

On 02/10/2014 10:23 AM, Denker, Alexander (NIH/NIMH) [F] wrote:
> Hi all,
>
> This is probably a very elementary error in my use of Freeview, but I have 
> been having trouble adding voxels to scans. I set the eraser value to "0", 
> but when I draw, the voxel still shows up as a black box instead of grey. Am 
> I not setting the right values or am I just in the wrong viewing mode?
>
> Thanks!
> Alexander
>
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>

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Re: [Freesurfer] Erasing, adding voxels in Freeview

[Louis Nicholas Vinke]

Hi Alexander,
If you are editing FS recons, then you should keep the eraser value set to 
"1" so that the edits can be detected by recon-all.
-Louis

On Mon, 10 Feb 2014, Ruopeng Wang wrote:

> Hi Alexander,
>
> Eraser value is used for erasing. Brush value is used for drawing. To
> erase, just hold shift key and press left mouse button.
>
> Best,
> Ruopeng
>
> On 02/10/2014 10:23 AM, Denker, Alexander (NIH/NIMH) [F] wrote:
>> Hi all,
>>
>> This is probably a very elementary error in my use of Freeview, but I have 
>> been having trouble adding voxels to scans. I set the eraser value to "0", 
>> but when I draw, the voxel still shows up as a black box instead of grey. Am 
>> I not setting the right values or am I just in the wrong viewing mode?
>>
>> Thanks!
>> Alexander
>>
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>>
>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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Re: [Freesurfer] Erasing, adding voxels in Freeview

[Denker, Alexander (NIH/NIMH) [F]]

So if I keep the value of the eraser at "1" then what do I need to change to 
add the voxels? It seems that no matter what value I put for drawing/erasing, I 
click and get a black box drawn on the screen. It seems that I am not combining 
button-clicks or values for the eraser and adding correctly.

Thank you



Sent with Good (www.good.com)


-Original Message-
From: Louis Nicholas Vinke 
[vi...@nmr.mgh.harvard.edu]
Sent: Monday, February 10, 2014 02:04 PM Eastern Standard Time
To: Denker, Alexander (NIH/NIMH) [F]
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Erasing, adding voxels in Freeview


Hi Alexander,
If you are editing FS recons, then you should keep the eraser value set to
"1" so that the edits can be detected by recon-all.
-Louis

On Mon, 10 Feb 2014, Ruopeng Wang wrote:

> Hi Alexander,
>
> Eraser value is used for erasing. Brush value is used for drawing. To
> erase, just hold shift key and press left mouse button.
>
> Best,
> Ruopeng
>
> On 02/10/2014 10:23 AM, Denker, Alexander (NIH/NIMH) [F] wrote:
>> Hi all,
>>
>> This is probably a very elementary error in my use of Freeview, but I have 
>> been having trouble adding voxels to scans. I set the eraser value to "0", 
>> but when I draw, the voxel still shows up as a black box instead of grey. Am 
>> I not setting the right values or am I just in the wrong viewing mode?
>>
>> Thanks!
>> Alexander
>>
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>>
>>
>
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Re: [Freesurfer] Erasing, adding voxels in Freeview

[Louis Nicholas Vinke]

In terms of FS editing, you should be only adding voxels which have a 
value of 255 to the wm.mgz (or cloning voxels into the brainmask.mgz).  If 
you are segmenting or drawing labels then select the color LUT for the 
colormap and then select the name of the structure you are segmenting. 
Are you using the left mouse button to draw voxels?


If the colormap is set to grayscale and you are trying to draw in voxels 
with a very low value (<40) then you will probably have to adjust the 
min/max settings before they are visible by eye.  Alternatively, you could 
switch the colormap to Jet or Heat, but that may make it difficult to edit 
in general.


On Mon, 10 Feb 2014, Denker, Alexander (NIH/NIMH) [F] wrote:


So if I keep the value of the eraser at "1" then what do I need to change to add
the voxels? It seems that no matter what value I put for drawing/erasing, I 
click
and get a black box drawn on the screen. It seems that I am not combining
button-clicks or values for the eraser and adding correctly.

Thank you



Sent with Good (www.good.com)


-Original Message-
From: Louis Nicholas Vinke [vi...@nmr.mgh.harvard.edu]
Sent: Monday, February 10, 2014 02:04 PM Eastern Standard Time
To: Denker, Alexander (NIH/NIMH) [F]
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Erasing, adding voxels in Freeview

Hi Alexander,
If you are editing FS recons, then you should keep the eraser value set to
"1" so that the edits can be detected by recon-all.
-Louis

On Mon, 10 Feb 2014, Ruopeng Wang wrote:

> Hi Alexander,
>
> Eraser value is used for erasing. Brush value is used for drawing. To
> erase, just hold shift key and press left mouse button.
>
> Best,
> Ruopeng
>
> On 02/10/2014 10:23 AM, Denker, Alexander (NIH/NIMH) [F] wrote:
>> Hi all,
>>
>> This is probably a very elementary error in my use of Freeview, but I have 
been
having trouble adding voxels to scans. I set the eraser value to "0", but when I
draw, the voxel still shows up as a black box instead of grey. Am I not setting 
the
right values or am I just in the wrong viewing mode?
>>
>> Thanks!
>> Alexander
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
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>
>
>


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Re: [Freesurfer] FDR question

[pfotiad]

Hi FS community,

I was wondering if anyone had a chance to give this a look.

Thanks in advance,
Panos


> Hi FS community,
>
> I am doing a cortical thickness comparison between a diseased and a
> healthy group. After running the mri_glmfit command for both hemispheres,
> I project the uncorrected significance map and there are a number of
> significant clusters showing (if you consider the p value to be at most
> 0.05). However, instead of using the clusterwise Correction for Multiple
> Comparisons, I wanted to use FDR to see what the results would look like,
> and I had a few questions regarding the whole process:
>
> 1) Are Tksurfer and QDEC the only tools in FS that I can apply the FDR
correction
> with, or are there any other ways?
>
> 2) In Tksurfer, I tried using the "Set Threshold Using FDR" tool, and when
> I set the rate from 0.88 to 0.87 it bumps up the minimum threshold from
> 1.37 to 3.24 hence resulting in no significant clusters for rates less
> than 0.88. Does that sound normal?
>
> Thanks in advance!
> Panos
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Re: [Freesurfer] Fwd: trac-all -path error

[Jon Wieser]

Hi Anastasia,
thanks for the information.we are able to process the DTI data successfully. 
we had 24 subjects which crashed during either the -perp or -path stage.
I viewed the alignments between the FA and the alignement segmentations (flirt 
and bbr alignments),  which ever alignment is better. I modify the dmrirc file 
to use that alignment and rerun trac-all , starting at the -prep stage
all but 2 were successfuly processed with  my method, that the dti tracts  look 
good in freeview
i didn't realign the registration using  tkregister,  because the anatomies are 
poor and lo res, making this realignment difficult
 thanks again!

JOn

- Original Message -
From: "Anastasia Yendiki" 
To: "Jon Wieser" 
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Thursday, February 6, 2014 3:16:16 PM
Subject: Re: [Freesurfer] Fwd: trac-all -path  error


We've generally seen better results with BBR, which is why it became the 
default setting.

On Thu, 6 Feb 2014, Jon Wieser wrote:

> HI Anastasia,
>
> I ran it again with the flirt registration and it finished ok.
> We did not have a specific reason for running it both ways. we are using the 
> default setting for the dmrirc file.
> do you recommend one method over the other?
>
> thanks again
> Jon
>
> - Original Message -
> From: "Anastasia Yendiki" 
> To: "Jon Wieser" 
> Cc: "freesurfer" 
> Sent: Thursday, February 6, 2014 3:07:12 PM
> Subject: Re: [Freesurfer] Fwd: trac-all -path  error
>
>
> That's entirely up to you, and whether you had a specific reason for
> running it both ways.
>
> If you want to fix the bbr registration manually, check the trac-all.log
> file for a command at the end of bbregister, where it says "To check
> results, run".
>
> On Thu, 6 Feb 2014, Jon Wieser wrote:
>
>> Hi Anastasia,
>> We used both flirt and bbr registration in the dmrirc file,   the Aparc+seg 
>> I just showedd you was from  the BBR resitration.  I looked at the flirt 
>> registration.  it looks OK.
>> should I rerun tracula using only the flirt registration?
>> Jon
>>
>> - Original Message -
>> From: "Anastasia Yendiki" 
>> To: "Jon Wieser" 
>> Cc: "freesurfer" 
>> Sent: Thursday, February 6, 2014 11:00:25 AM
>> Subject: Re: [Freesurfer] Fwd: trac-all -path  error
>>
>>
>> So there's your culprit. You need to fix the intra-subject
>> (diffusion-to-T1) registration. Did you use flirt or bbregister for that?
>>
>> On Thu, 6 Feb 2014, Jon Wieser wrote:
>>
>>> Hi Anastasia,
>>> I looked at the dlabel/diff/Aparc+aseg overlayed on the 
>>> dmri/dtifit_FA.nii.gz
>>> the alignemenst is way off (in freeview, in the coronal view, the aparc+seg 
>>> is rotated 45 degrees anti-clockwise),  and parts of the FA map in the L 
>>> ILF area are missing.  the original DTI is not missing data in these areas. 
>>> I have attached screenshots
>>> Jon
>>>
>>>
>>>
>>> - Original Message -
>>> From: "Anastasia Yendiki" 
>>> To: "Jon Wieser" 
>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>> Sent: Wednesday, February 5, 2014 6:35:12 PM
>>> Subject: Re: [Freesurfer] Fwd: trac-all -path  error
>>>
>>>
>>> Hi Jon - You need to look at the aparc+aseg after it has been mapped to
>>> diffusion space. It's possible that it looks fine in its original space
>>> but then maybe something goes wrong with the registration. So you should
>>> look at the aparc+aseg and aparc+aseg_mask files from the tracula
>>> dlabel/diff directory. These are in diffusion space and you can overlay
>>> them on the FA map to see if there's anything strange in the ILF area.
>>>
>>> Hope this helps,
>>> a.y
>>>
>>> On Tue, 14 Jan 2014, Jon Wieser wrote:
>>>
 Hi anastasia
 I looked at the brainmask and the aparc+aseg.  I did see anything missing  
 in the area of the left ILF.
 I have attached the files.  can you take a look at them?
 Thanks
 JOn

 - Original Message -
 From: "Anastasia Yendiki" 
 To: "Jon Wieser" 
 Cc: "freesurfer" 
 Sent: Friday, January 10, 2014 6:15:23 PM
 Subject: Re: [Freesurfer] Fwd: trac-all -path  error


 Hi Jon - Have you checked the brain mask and aparc+aseg for this subject?
 Anything missing there that might affect the left ILF?

 a.y

 On Wed, 8 Jan 2014, Jon Wieser wrote:

>
> Dear freesurfer experts
> I'm getting the following error when runing trac-all -c 
> dmrirc_single_subject -path
>
>
> Loading initial proposal SD's from 
> /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/Data/MRI/N1084/data/freesurfer/dlabel/diff/lh.ilf_AS_avg23_mni_flt_cpts_5_std.txt
> Processing pathway 3 of 18...
> Initializing MCMC
> Segmentation fault
> Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun  7 
> 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
>
>
> I have attached the trac-all.log and trac-all.error   files
>
> I am running tracula 5.3
>


 The information in this e-mail is intended o

[Freesurfer] creating specific files

[Borzello, Mia]

Hi Freesurfers,

I was wondering if there was a way to kind of fill in the blanks for a Surfer 
Output folder. I am working with an old data set, and it seem that some of the 
files are empty (0 bytes), "rh.pial" for example. Is there a way to pass the 
SurferOutput folder in and recreate what's missing?

Thanks,
Mia
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Re: [Freesurfer] creating specific files

[Bruce Fischl]

Hi Mia

delete the 0 length files and run recon-all -make all -s 

cheers
Bruce
On Mon, 
10 Feb 2014, Borzello, Mia wrote:



Hi Freesurfers, 
I was wondering if there was a way to kind of fill in the blanks for a
Surfer Output folder. I am working with an old data set, and it seem that
some of the files are empty (0 bytes), "rh.pial" for example. Is there a way
to pass the SurferOutput folder in and recreate what's missing?

Thanks, 
Mia

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Re: [Freesurfer] Tracula version and download problem

[Anastasia Yendiki]

Hi Clive - These are not stats in the volume or on the surface, so 
mri_glmfit doesn't apply. If you want to do group analyses along a tract 
on a table produced by trac-all -stat, you should import the table in any 
software that you use for statistics (matlab, SPSS, etc).


Best,
a.y

On Mon, 10 Feb 2014, Clive Wong wrote:


Dear Anastasia,
Thanks very much. I have already downloaded the file. The wiki page was also 
down a few hours ago, but it's ok now.

And I am interested in the tracula group stat. How could I use mri_glmfit on 
the text file? And can I use the QDEC (or the
contrast generated by QDEC) to do the glm?

Thanks
Clive


On Mon, Feb 10, 2014 at 6:13 AM, Anastasia Yendiki 
 wrote:

  Hi Clive - Yes, you can use the recent tracula update on top your already 
processed data. The new update only
  adds new functionality to trac-all, without changing any of the existing 
functionality in 5.3.

  Did you try downloading the update from here?
  http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

  a.y

  On Sun, 9 Feb 2014, Clive Wong wrote:

Hi,
I just want to confirm, is that I can use the new trac-all with the 
data
processed in the original FS5.3 trac-all?

And, I just want to download the new trac-all, but I have problem 
to connect
to the ftp server. I can login to the server, but it does not 
response to
any command. Please advise. 

Best,
Clive




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Re: [Freesurfer] Fwd: trac-all -path error

[Anastasia Yendiki]

Hi Jon - Glad to hear you could get around the registration issue. If the 
anatomical images are poor, then it makes sense that you'd encounter 
issues with bbregister, as bbregister relies on the surfaces that are 
derived exactly from those anatomical images.


Best,
a.y

On Mon, 10 Feb 2014, Jon Wieser wrote:


Hi Anastasia,
thanks for the information.we are able to process the DTI data successfully.
we had 24 subjects which crashed during either the -perp or -path stage.
I viewed the alignments between the FA and the alignement segmentations (flirt 
and bbr alignments),  which ever alignment is better. I modify the dmrirc file 
to use that alignment and rerun trac-all , starting at the -prep stage
all but 2 were successfuly processed with  my method, that the dti tracts  look 
good in freeview
i didn't realign the registration using  tkregister,  because the anatomies are 
poor and lo res, making this realignment difficult
 thanks again!

JOn

- Original Message -
From: "Anastasia Yendiki" 
To: "Jon Wieser" 
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Thursday, February 6, 2014 3:16:16 PM
Subject: Re: [Freesurfer] Fwd: trac-all -path  error


We've generally seen better results with BBR, which is why it became the
default setting.

On Thu, 6 Feb 2014, Jon Wieser wrote:


HI Anastasia,

I ran it again with the flirt registration and it finished ok.
We did not have a specific reason for running it both ways. we are using the 
default setting for the dmrirc file.
do you recommend one method over the other?

thanks again
Jon

- Original Message -
From: "Anastasia Yendiki" 
To: "Jon Wieser" 
Cc: "freesurfer" 
Sent: Thursday, February 6, 2014 3:07:12 PM
Subject: Re: [Freesurfer] Fwd: trac-all -path  error


That's entirely up to you, and whether you had a specific reason for
running it both ways.

If you want to fix the bbr registration manually, check the trac-all.log
file for a command at the end of bbregister, where it says "To check
results, run".

On Thu, 6 Feb 2014, Jon Wieser wrote:


Hi Anastasia,
We used both flirt and bbr registration in the dmrirc file,   the Aparc+seg I 
just showedd you was from  the BBR resitration.  I looked at the flirt 
registration.  it looks OK.
should I rerun tracula using only the flirt registration?
Jon

- Original Message -
From: "Anastasia Yendiki" 
To: "Jon Wieser" 
Cc: "freesurfer" 
Sent: Thursday, February 6, 2014 11:00:25 AM
Subject: Re: [Freesurfer] Fwd: trac-all -path  error


So there's your culprit. You need to fix the intra-subject
(diffusion-to-T1) registration. Did you use flirt or bbregister for that?

On Thu, 6 Feb 2014, Jon Wieser wrote:


Hi Anastasia,
I looked at the dlabel/diff/Aparc+aseg overlayed on the dmri/dtifit_FA.nii.gz
the alignemenst is way off (in freeview, in the coronal view, the aparc+seg is 
rotated 45 degrees anti-clockwise),  and parts of the FA map in the L ILF area 
are missing.  the original DTI is not missing data in these areas. I have 
attached screenshots
Jon



- Original Message -
From: "Anastasia Yendiki" 
To: "Jon Wieser" 
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, February 5, 2014 6:35:12 PM
Subject: Re: [Freesurfer] Fwd: trac-all -path  error


Hi Jon - You need to look at the aparc+aseg after it has been mapped to
diffusion space. It's possible that it looks fine in its original space
but then maybe something goes wrong with the registration. So you should
look at the aparc+aseg and aparc+aseg_mask files from the tracula
dlabel/diff directory. These are in diffusion space and you can overlay
them on the FA map to see if there's anything strange in the ILF area.

Hope this helps,
a.y

On Tue, 14 Jan 2014, Jon Wieser wrote:


Hi anastasia
I looked at the brainmask and the aparc+aseg.  I did see anything missing  in 
the area of the left ILF.
I have attached the files.  can you take a look at them?
Thanks
JOn

- Original Message -
From: "Anastasia Yendiki" 
To: "Jon Wieser" 
Cc: "freesurfer" 
Sent: Friday, January 10, 2014 6:15:23 PM
Subject: Re: [Freesurfer] Fwd: trac-all -path  error


Hi Jon - Have you checked the brain mask and aparc+aseg for this subject?
Anything missing there that might affect the left ILF?

a.y

On Wed, 8 Jan 2014, Jon Wieser wrote:



Dear freesurfer experts
I'm getting the following error when runing trac-all -c dmrirc_single_subject 
-path


Loading initial proposal SD's from 
/BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/Data/MRI/N1084/data/freesurfer/dlabel/diff/lh.ilf_AS_avg23_mni_flt_cpts_5_std.txt
Processing pathway 3 of 18...
Initializing MCMC
Segmentation fault
Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun  7 
16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386


I have attached the trac-all.log and trac-all.error   files

I am running tracula 5.3




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Re: [Freesurfer] Tracula version and download problem

[Clive Wong]

Thanks Anastasia. I ask that because in the tracula stat page, it
saids *"Measures
can be extracted from these files to be analyzed further, e.g., for
tract-based group analysis. Specifically, the text files can be converted
into a table using the command tractstats2table and then used for doing GLM
analyses with mri_glmfit or any other statistical software (SPSS, Excel,
Statview etc.)"*. So I think I may reuse the GLM matrix.

Best,
Clive


On Tue, Feb 11, 2014 at 8:29 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Clive - These are not stats in the volume or on the surface, so
> mri_glmfit doesn't apply. If you want to do group analyses along a tract on
> a table produced by trac-all -stat, you should import the table in any
> software that you use for statistics (matlab, SPSS, etc).
>
> Best,
> a.y
>
>
> On Mon, 10 Feb 2014, Clive Wong wrote:
>
>  Dear Anastasia,
>> Thanks very much. I have already downloaded the file. The wiki page was
>> also down a few hours ago, but it's ok now.
>>
>> And I am interested in the tracula group stat. How could I use mri_glmfit
>> on the text file? And can I use the QDEC (or the
>> contrast generated by QDEC) to do the glm?
>>
>> Thanks
>> Clive
>>
>>
>> On Mon, Feb 10, 2014 at 6:13 AM, Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu> wrote:
>>
>>   Hi Clive - Yes, you can use the recent tracula update on top your
>> already processed data. The new update only
>>   adds new functionality to trac-all, without changing any of the
>> existing functionality in 5.3.
>>
>>   Did you try downloading the update from here?
>>   http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates
>>
>>   a.y
>>
>>   On Sun, 9 Feb 2014, Clive Wong wrote:
>>
>> Hi,
>> I just want to confirm, is that I can use the new trac-all
>> with the data
>> processed in the original FS5.3 trac-all?
>>
>> And, I just want to download the new trac-all, but I have
>> problem to connect
>> to the ftp server. I can login to the server, but it does not
>> response to
>> any command. Please advise.
>>
>> Best,
>> Clive
>>
>>
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>>
>>
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Re: [Freesurfer] Freeview not working

[Saurabh Thakur]

Hello Zeke,

There was some packages missing.

I have updated it,so now its working.

Really thanks for the your help.

cheers
Saurabh Thakur,






On Mon, Feb 10, 2014 at 8:50 PM, Z K  wrote:

> Saurabh,
>
> What is the output when you type "locate libXss.so.1" (without quotes)
> on the command line?
>
> -Zeke
>
> On 02/10/2014 05:17 AM, Saurabh Thakur wrote:
> > Hi all,
> >
> > My freeview is not working.
> >
> > //=//
> >
> > saurabh@saurabh-Precision-WorkStation-T3500:/usr/local/freesurfer$
> freeview
> > freeview.bin: error while loading shared libraries: libXss.so.1: cannot
> > open shared object file: No such file or directory
> > saurabh@saurabh-Precision-WorkStation-T3500:/usr/local/freesurfer$
> >
> > /=//
> >
> > please suggest wht is going wrong.
> >
> > Thanks in advance,
> >
> > cheers
> > Saurabh Thakur,
> >
> >
> >
> >
> >
> >
> > ___
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> >
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
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Re: [Freesurfer] Choi's parcellation expansion inquiry

[Thomas Yeo]

Hi Sooyun,

It is possible that tri-linear might work better, but I have to caution
that you will get non-integer values. Have you tried mri_label2vol?
According to Doug in the last email, mri_label2vol might work better than
mri_vol2vol.

My suggestion is to first verify whether the transformation from Choi
parcellation to the subject's native space is good enough. To do that,
instead of transforming the Choi parcellation, try transforming the MNI152
template accompanying the Choi's parcellation (NOT the FSL MNI152
template). If the transformed MNI152 template does not match your subject's
native anatomy to your liking, then you need to improve the transformations.

Again, can you clarify where you are obtaining the transformation matrices?
Recall that I previously told you that to convert the Choi's parcellation
to the MNI152 template from FSL, you should just use mri_vol2vol, rather
than FIRST. The command is as follows: "mri_vol2vol --mov
original_choi_MNI152_parcellation.nii.gz --targ
$FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --regheader --o
FSL_choi_MNI152_parcellation.nii.gz --no-save-reg --interp nearest". And
the reason is that the Choi volume is in exactly the SAME space as the
$FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz, it's just that the header
information is different. Therefore the "regheader" flag takes care of that.

Cheers,
Thomas


On Tue, Feb 11, 2014 at 2:03 PM, 조수연  wrote:

>  Hi, Thomas.
>
>
>
>
>
> I have circled the unmasked regions in the image with a red brush tool.
> The yellow-red regions are the FreeSurfer space->MNI152 space->Subject
> space transformed Choi's loose mask files, and the blue regions are the
> subject's subcortical areas. My current ROI is the caudate and the putamen.
> As you can see, there are multiple regions where the labels aren't big
> enough to cover my subject data. I checked the original Choi's
> parcellations in the original space and the MNI152 space but it's hard to
> check whether the label in the specific location of my interest is missing
> or not because the voxel numbers and dementions are different per space,
> thus is hard to get the specific coordinates that lacks mask.
>
> I discussed with my lab members and concluded maybe the problem lies when
> we are transferring the image from one space to another in that we used the
> nearest neighbour when applying the transformation matrix. We are planning
> to use tri-lear for interpolation instead so that the achieved image has a
> looser intensity specificaton, so that it helps us to specify the lables of
> the subject's regions which are not covered by Choi's masks. Hope this
> helps.
>
> If you have any suggestions as of how to morph Choi's images best to our
> subject's fit, please do inform me. Thanks!
>
>
>
> Best regards, Sooyun.
>
>
>
>
>
> ---원본메일---
> 보낸사람 : Thomas Yeo 
> 받는사람: 조수연
> 참 조: freesurfer 
> 보낸날짜: 2014-02-11 00:11:48 GMT +0900 (ROK)
> 제목: Re: [Freesurfer] Choi's parcellation expansion inquiry
>
>
> Hi Sooyun,
>
> Which is the sky blue region you are referring to? Can you place your
> fslview cursor in the location where you think is missing the label?
>
> Can you visually inspect the original Choi's parcellation to see if the
> label is also missing at the corresponding MNI152 location? If the label is
> not missing, then perhaps your transformation is not doing its job, which I
> suspect might be the problem since the loose mask in Choi's parcellation is
> already pretty loose.
>
> Regards,
> Thomas
>
>
> On Mon, Feb 10, 2014 at 12:20 PM, 조수연  wrote:
>
>>  Hi, all.
>>
>> I'm trying to apply Choi's parcellations onto my subjects' data. I used
>> the 7-Network loose mask but it turns out that even the loose mask isn't
>> capable of covering up the ROI.
>>
>> Is there a way I can further "expand" the loose mask and make it "looser"?
>>
>> The uncovered areas of my subject's image are colored skyblue. The rest
>> are parcellated segments of Choi's image.
>>
>> FYI Choi's FreeSurfer grid images were linearly transformed by concat
>> matrix which shifts FreeSurfer grid to Standard MNI152 grid to our
>> subject's grid.
>>
>>
>>
>> Thanks.
>>
>>
>>
>> Best regards, Sooyun.
>>
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>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
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>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
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