[Freesurfer] aparc+aseg labels

[Sarosh, Cyrus]

Hello,

I was hoping somebody could help me out. I am trying to create a label file for 
the aparc+aseg file. All I'm wanting is the pixel value and the label. I know 
there is the FreeSurferColorLUT.txt file which contains this information, but 
looking at this file I can tell that all of these labels aren't included in 
every file, so I'm trying to create a file like this for each individual MR I 
use only containing the labels needed for each individual scan. I don't know if 
this is possible, but hopefully it is and somebody could give me the commands 
to use to generate this file? Thanks for your help.

Cyrus

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[Freesurfer] Edits to aparc+aseg.mgz

[Sarosh, Cyrus]

Hello FreeSurfer Users,


I looked for a possible solution to my problem in the Mail Archive and found 
this article referring to almost the exact same problem I am having: 
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06314.html. 
Basically, pieces of the subarachnoid space/pia mater/arachnoid/dura 
mater/skull are being segmented as the cortex in certain slices and this occurs 
when it is physically adjacent to the gray matter. Besides this point 
everything else seems to be running smooth. In the related article I found that 
this may be caused by the MR parameters so I will give you the acquisition 
information that I know. The acquisitions are SPGRs, taken on either a GE 3T or 
1.5T and the resolution is 1mm isotropic. Any solutions besides going through 
each series slice by slice and making corrections would be greatly appreciated.



Thanks,

Cyrus
**
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used for urgent or sensitive issues 
___
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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.

Re: [Freesurfer] Edits to aparc+aseg.mgz

[Sarosh, Cyrus]

Doug,

I looked at the surface files by using the command -tkmedit (subject ID) 
brainmask.mgz -surfs -aseg. I also viewed the same surfs using the T1.mgz file. 
The pial surface (red line) does identify the dura as part of the cortex, but 
it doesn't look as bad as the aseg.mgz vois made it appear.

Cyrus

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Monday, August 13, 2012 4:13 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz

Hi Cyrus, this may or may not be a problem. The cortical label in aseg.mgz is 
not used for this reason. Usually, the surface-based method will exclude the 
dura in these situations. Are the surfaces accurate or are they including dura 
as well? BTW, you should not be editing the 
aparc+aseg.mgz.
doug

On 08/13/2012 01:04 PM, Sarosh, Cyrus wrote:
>
> Hello FreeSurfer Users,
>
> I looked for a possible solution to my problem in the Mail Archive and found 
> this article referring to almost the exact same problem I am having:

> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06314.ht
> ml. Basically,pieces of the subarachnoid space/pia 
> mater/arachnoid/dura mater/skull

> are being segmented as the cortex in certain slices and this occurs when it 
> is physically adjacent to the gray matter. Besides this point everything else 
> seems to be running smooth.

> In the related article I found that this may be caused by the MR parameters 
> so I will give you the acquisition information that I know.

> Theacquisitions are SPGRs, taken on either a GE 3T or 1.5T and the 
> resolution is 1mm isotropic. Any solutions besides going through each 
> series slice by

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

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

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


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Re: [Freesurfer] Edits to aparc+aseg.mgz

[Sarosh, Cyrus]

Doug,

Well we want to use the stats information for gray matter volume and thickness 
of certain vois and we want to use the aparc+aseg file to run PET image 
analysis to collect data from certain vois. Would performing the given actions 
correct any incorrect data in the stats files and create a new aparc+aseg.mgz 
file or will this require separate actions?

Thanks,

Cyrus

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Tuesday, August 14, 2012 11:28 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz


Depending upon how bad it is and what you are going to do with it, it may be a 
good idea to edit the brain.finalsurfs.mgz to remove the dura, then run 
recon-all -autorecon-pial ...
doug


On 08/14/2012 11:18 AM, Sarosh, Cyrus wrote:
> Doug,
>
> I looked at the surface files by using the command -tkmedit (subject ID) 
> brainmask.mgz -surfs -aseg. I also viewed the same surfs using the T1.mgz 
> file. The pial surface (red line) does identify the dura as part of the 
> cortex, but it doesn't look as bad as the aseg.mgz vois made it appear.
>
> Cyrus
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N 
> Greve
> Sent: Monday, August 13, 2012 4:13 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz
>
> Hi Cyrus, this may or may not be a problem. The cortical label in 
> aseg.mgz is not used for this reason. Usually, the surface-based 
> method will exclude the dura in these situations. Are the surfaces 
> accurate or are they including dura as well? BTW, you should not be 
> editing the
> aparc+aseg.mgz.
> doug
>
> On 08/13/2012 01:04 PM, Sarosh, Cyrus wrote:
>> Hello FreeSurfer Users,
>>
>> I looked for a possible solution to my problem in the Mail Archive and found 
>> this article referring to almost the exact same problem I am having:
>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06314.h
>> t ml. Basically,pieces of the subarachnoid space/pia 
>> mater/arachnoid/dura mater/skull are being segmented as the cortex in 
>> certain slices and this occurs when it is physically adjacent to the gray 
>> matter. Besides this point everything else seems to be running smooth.
>> In the related article I found that this may be caused by the MR parameters 
>> so I will give you the acquisition information that I know.
>> Theacquisitions are SPGRs, taken on either a GE 3T or 1.5T and the 
>> resolution is 1mm isotropic. Any solutions besides going through each 
>> series slice by
>>slice and making corrections would be greatly appreciated.
>>
>> Thanks,
>>
>> Cyrus
>>
>> **
>> Electronic Mail is not secure, may not be read every day, and should 
>> not be used for urgent or sensitive issues
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is 
> addressed. If you believe this e-mail was sent to you in error and the e-mail 
> contains patient information, please contact the Partners Compliance HelpLine 
> at http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error but does not contain patient information, please contact the sender and 
> properly dispose of the e-mail.
>
> **
> Electronic Mail is not secure, may not be read every day, and should 
> not be used for urgent or sensitive issues
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/

Re: [Freesurfer] Edits to aparc+aseg.mgz

[Sarosh, Cyrus]

Doug,

I edited the dura from the brain.finalsurfs.mgz file using the command tkmedit 
(subject ID) brain.finalsurfs.mgz -aux T1.mgz -surfs and going through the 
necessary slices that need fixing and erase the dura. I then ran this subject 
with the command recon-all -subjid (subject ID) -autorecon-pial. Looking at the 
date modified information it appears that new stat files were created, but no 
new aparc+aseg.mgz file was created. I loaded the brain.finalsurfs.mgz file, 
which contained a modify date of when I ran the new recon-all command and it 
looked identical to the original brain.finalsurfs.mgz file, so all of my edits 
were gone and all of the surfs were incorrect just like before. Also, loading 
the aparc+aseg.mgz file it looks identical to the previous aparc+aseg.mgz, so 
no changes were made. Looking at the log it appears my edits were useless 
because the first step that runs is the -maskbfs step which appears to generate 
the brain.finalsurfs.mgz file. So, do I need to edit a different file or was my 
command line incorrect? 

Thanks,

Cyrus

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Tuesday, August 14, 2012 1:43 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz


For GM volume and thickness, you will certainly want to fix it. Given how big 
the PET voxels are, it might not be such a big deal for that. To fix it, you 
would edit the dura from the brain.finalsurfs.mgz and run recon-all with 
-autorecon-pial. This will fix aparc+aseg and re-generate the stats files.
doug


On 08/14/2012 01:40 PM, Sarosh, Cyrus wrote:
> Doug,
>
> Well we want to use the stats information for gray matter volume and 
> thickness of certain vois and we want to use the aparc+aseg file to run PET 
> image analysis to collect data from certain vois. Would performing the given 
> actions correct any incorrect data in the stats files and create a new 
> aparc+aseg.mgz file or will this require separate actions?
>
> Thanks,
>
> Cyrus
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N 
> Greve
> Sent: Tuesday, August 14, 2012 11:28 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz
>
>
> Depending upon how bad it is and what you are going to do with it, it may be 
> a good idea to edit the brain.finalsurfs.mgz to remove the dura, then run 
> recon-all -autorecon-pial ...
> doug
>
>
> On 08/14/2012 11:18 AM, Sarosh, Cyrus wrote:
>> Doug,
>>
>> I looked at the surface files by using the command -tkmedit (subject ID) 
>> brainmask.mgz -surfs -aseg. I also viewed the same surfs using the T1.mgz 
>> file. The pial surface (red line) does identify the dura as part of the 
>> cortex, but it doesn't look as bad as the aseg.mgz vois made it appear.
>>
>> Cyrus
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas 
>> N Greve
>> Sent: Monday, August 13, 2012 4:13 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz
>>
>> Hi Cyrus, this may or may not be a problem. The cortical label in 
>> aseg.mgz is not used for this reason. Usually, the surface-based 
>> method will exclude the dura in these situations. Are the surfaces 
>> accurate or are they including dura as well? BTW, you should not be 
>> editing the
>> aparc+aseg.mgz.
>> doug
>>
>> On 08/13/2012 01:04 PM, Sarosh, Cyrus wrote:
>>> Hello FreeSurfer Users,
>>>
>>> I looked for a possible solution to my problem in the Mail Archive and 
>>> found this article referring to almost the exact same problem I am having:
>>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06314.
>>> h t ml. Basically,pieces of the subarachnoid space/pia 
>>> mater/arachnoid/dura mater/skull are being segmented as the cortex 
>>> in certain slices and this occurs when it is physically adjacent to the 
>>> gray matter. Besides this point everything else seems to be running smooth.
>>> In the related article I found that this may be caused by the MR parameters 
>>> so I will give you the acquisition information that I know.
>>> Theacquisitions are SPGRs, taken on either a GE 3T or 1.5T and the 
>>> resolution is 1mm isotropic. Any solutions besides going through 
>>> each series slice by
>>> slice and making corrections would be greatly appreciated.
>>>
>>> Tha

Re: [Freesurfer] Edits to aparc+aseg.mgz

[Sarosh, Cyrus]

Doug,

Thanks for the update and not much time was wasted so no worries. I edited the 
brainmask.mgz file and ran the new recon-all command with autorecon-pial, which 
created a new brain.finalsurfs.mgz with the dura edited out and correct surfs. 
New stat files were created, but no new aparc+aseg.mgz file. Loading this file 
still shows the segmentation including dura in the cortex and the modification 
date is the original recon-all date. Is there any way to create a new 
aparc+aseg.mgz file with this new surf data?

Thanks,

Cyrus

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Monday, August 20, 2012 2:18 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz

Hi Cyrus, my apologies, I told you to edit the wrong file. You should edit 
brainmask.mgz, not brainmask.finalsurfs.mgz. Sorry about, I hope you did not 
waste too much time.
doug

On 08/20/2012 09:31 AM, Sarosh, Cyrus wrote:
> Doug,
>
> I edited the dura from the brain.finalsurfs.mgz file using the command 
> tkmedit (subject ID) brain.finalsurfs.mgz -aux T1.mgz -surfs and going 
> through the necessary slices that need fixing and erase the dura. I then ran 
> this subject with the command recon-all -subjid (subject ID) -autorecon-pial. 
> Looking at the date modified information it appears that new stat files were 
> created, but no new aparc+aseg.mgz file was created. I loaded the 
> brain.finalsurfs.mgz file, which contained a modify date of when I ran the 
> new recon-all command and it looked identical to the original 
> brain.finalsurfs.mgz file, so all of my edits were gone and all of the surfs 
> were incorrect just like before. Also, loading the aparc+aseg.mgz file it 
> looks identical to the previous aparc+aseg.mgz, so no changes were made. 
> Looking at the log it appears my edits were useless because the first step 
> that runs is the -maskbfs step which appears to generate the 
> brain.finalsurfs.mgz file. So, do I need to edit a different file or was my 
> command line incorrect?
>
> Thanks,
>
> Cyrus
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N 
> Greve
> Sent: Tuesday, August 14, 2012 1:43 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz
>
>
> For GM volume and thickness, you will certainly want to fix it. Given how big 
> the PET voxels are, it might not be such a big deal for that. To fix it, you 
> would edit the dura from the brain.finalsurfs.mgz and run recon-all with 
> -autorecon-pial. This will fix aparc+aseg and re-generate the stats files.
> doug
>
>
> On 08/14/2012 01:40 PM, Sarosh, Cyrus wrote:
>> Doug,
>>
>> Well we want to use the stats information for gray matter volume and 
>> thickness of certain vois and we want to use the aparc+aseg file to run PET 
>> image analysis to collect data from certain vois. Would performing the given 
>> actions correct any incorrect data in the stats files and create a new 
>> aparc+aseg.mgz file or will this require separate actions?
>>
>> Thanks,
>>
>> Cyrus
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas 
>> N Greve
>> Sent: Tuesday, August 14, 2012 11:28 AM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz
>>
>>
>> Depending upon how bad it is and what you are going to do with it, it may be 
>> a good idea to edit the brain.finalsurfs.mgz to remove the dura, then run 
>> recon-all -autorecon-pial ...
>> doug
>>
>>
>> On 08/14/2012 11:18 AM, Sarosh, Cyrus wrote:
>>> Doug,
>>>
>>> I looked at the surface files by using the command -tkmedit (subject ID) 
>>> brainmask.mgz -surfs -aseg. I also viewed the same surfs using the T1.mgz 
>>> file. The pial surface (red line) does identify the dura as part of the 
>>> cortex, but it doesn't look as bad as the aseg.mgz vois made it appear.
>>>
>>> Cyrus
>>>
>>> -Original Message-
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas 
>>> N Greve
>>> Sent: Monday, August 13, 2012 4:13 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz
>>>
>>> Hi Cyrus, this may or may not be a problem. The cortical label in 
>>> aseg.mgz is not used for 

Re: [Freesurfer] Edits to aparc+aseg.mgz

[Sarosh, Cyrus]

Doug,

Sorry for so many questions, but can I run the autorecon3 command with my 
previous recon-all -subjid (subject ID) -autorecon-pial or will the autorecon3 
have to follow the previous command?

Thanks,

Cyrus

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Tuesday, August 21, 2012 3:52 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz

Run it with -autorecon3
doug

On 08/21/2012 10:44 AM, Sarosh, Cyrus wrote:
> Doug,
>
> Thanks for the update and not much time was wasted so no worries. I edited 
> the brainmask.mgz file and ran the new recon-all command with autorecon-pial, 
> which created a new brain.finalsurfs.mgz with the dura edited out and correct 
> surfs. New stat files were created, but no new aparc+aseg.mgz file. Loading 
> this file still shows the segmentation including dura in the cortex and the 
> modification date is the original recon-all date. Is there any way to create 
> a new aparc+aseg.mgz file with this new surf data?
>
> Thanks,
>
> Cyrus
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N 
> Greve
> Sent: Monday, August 20, 2012 2:18 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz
>
> Hi Cyrus, my apologies, I told you to edit the wrong file. You should edit 
> brainmask.mgz, not brainmask.finalsurfs.mgz. Sorry about, I hope you did not 
> waste too much time.
> doug
>
> On 08/20/2012 09:31 AM, Sarosh, Cyrus wrote:
>> Doug,
>>
>> I edited the dura from the brain.finalsurfs.mgz file using the command 
>> tkmedit (subject ID) brain.finalsurfs.mgz -aux T1.mgz -surfs and going 
>> through the necessary slices that need fixing and erase the dura. I then ran 
>> this subject with the command recon-all -subjid (subject ID) 
>> -autorecon-pial. Looking at the date modified information it appears that 
>> new stat files were created, but no new aparc+aseg.mgz file was created. I 
>> loaded the brain.finalsurfs.mgz file, which contained a modify date of when 
>> I ran the new recon-all command and it looked identical to the original 
>> brain.finalsurfs.mgz file, so all of my edits were gone and all of the surfs 
>> were incorrect just like before. Also, loading the aparc+aseg.mgz file it 
>> looks identical to the previous aparc+aseg.mgz, so no changes were made. 
>> Looking at the log it appears my edits were useless because the first step 
>> that runs is the -maskbfs step which appears to generate the 
>> brain.finalsurfs.mgz file. So, do I need to edit a different file or was my 
>> command line incorrect?
>>
>> Thanks,
>>
>> Cyrus
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas 
>> N Greve
>> Sent: Tuesday, August 14, 2012 1:43 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz
>>
>>
>> For GM volume and thickness, you will certainly want to fix it. Given how 
>> big the PET voxels are, it might not be such a big deal for that. To fix it, 
>> you would edit the dura from the brain.finalsurfs.mgz and run recon-all with 
>> -autorecon-pial. This will fix aparc+aseg and re-generate the stats files.
>> doug
>>
>>
>> On 08/14/2012 01:40 PM, Sarosh, Cyrus wrote:
>>> Doug,
>>>
>>> Well we want to use the stats information for gray matter volume and 
>>> thickness of certain vois and we want to use the aparc+aseg file to run PET 
>>> image analysis to collect data from certain vois. Would performing the 
>>> given actions correct any incorrect data in the stats files and create a 
>>> new aparc+aseg.mgz file or will this require separate actions?
>>>
>>> Thanks,
>>>
>>> Cyrus
>>>
>>> -Original Message-
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas 
>>> N Greve
>>> Sent: Tuesday, August 14, 2012 11:28 AM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz
>>>
>>>
>>> Depending upon how bad it is and what you are going to do with it, it may 
>>> be a good idea to edit the brain.finalsurfs.mgz to remove the dura, then 
>>> run recon-all -autorecon-pial ...
>>> doug
>>>
>>>
>>

Re: [Freesurfer] (no subject)

[Sarosh, Cyrus]

Doug,

I am also curious about this mri_label2vol upgrade. Will this work on the 
Windows virtual machine version of FreeSurfer? I downloaded and placed it in 
the FREESURFER/bin directory, but when trying to run it I receive an error that 
states: Exec format error. Binary file not executable. Thanks for your help.

Cyrus

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of José Ángel Pineda
Sent: Tuesday, December 04, 2012 9:07 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] (no subject)

Thanks Doug,

I already downloaded the new script for mri_label2vol, but it seems it is just 
compiled for linux, as I cannot execute it in my Mac. If it is so, could you 
please upload another compiled for mac, or source.
Thanks

Jose

For the missing insula problem, try using a newer version of mri_label2vol
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol

The 2nd problem is not so easy to fix. You might be better off using
aparc+aseg.mgz as input to mri_label2vol instead of the surface annotation.
doug


On 12/3/12 10:35 AM, Jos? ?ngel Pineda wrote:
> Dear experts,
>
> I am registering cortical labels from Talairach coordinates to my
> native T1. For doing this, I have run the next script lines:
>
>
> tkregister --targ brainmask.mgz --mov highres_brain.nii.gz --reg
> T1FS2Highres.dat --regheader --noedit
>
> mri_label2vol --annot rh.aparc.annot --temp highres_brain.nii.gz --reg
> T1FS2Highres.dat --o rh_aparc.nii.gz --hemi rh --subject FS --proj
> frac 0 1 .1 --fillthresh .3
>
> and the same for the left hemi.
>
> However I am finding two problems at the result. First Insula is
> missing for both hemispheres, and second the cortical ROIs have the
> shape of the figure attached, e.g. there are many voxels empty
>
> Im?genes integradas 1
>
> I found in previous topics, that the mri_label2vol, was updated as it
> left last volume from the list out of the conversion. I tried to
> download it, but it is just compiled for linux, and since Im working
> with mac I am not able to run it. Could you please give me any
> comments to solve the problem with the missing voxels.
> About the problem with the insula, the other option is to just extract
> it with mri_annotation2label, but if I could get the mri_label2vol
> working correctly it would be better.
>
> Thanks a lot
>
> Jose

--

José Angel Pineda Pardo

Center of Biomedical Technology (CTB)

Parque Científico y Tecnológico de la UPM

Campus de Montegancedo

28223 Pozuelo de Alarcón, Madrid, ES

**
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Re: [Freesurfer] (no subject)

[Sarosh, Cyrus]

Doug,

I am unsure if Jose did this in his attempts to get it to work, but I ran this 
command after downloading and receiving this error initially and even after 
running this command I still receive the same error in the Windows virtual 
machine version of FreeSurfer. Any other ideas?

Thanks,

Cyrus

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Tuesday, December 04, 2012 11:58 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] (no subject)

Hi Jose, did you set the permissions to be executable?
chmod a+x mri_label2vol
doug


On 12/04/2012 11:34 AM, Sarosh, Cyrus wrote:
>
> Doug,
>
> I am also curious about this mri_label2vol upgrade. Will this work on 
> the Windows virtual machine version of FreeSurfer? I downloaded and 
> placed it in the FREESURFER/bin directory, but when trying to run it I 
> receive an error that states: Exec format error. Binary file not 
> executable. Thanks for your help.
>
> Cyrus
>
> *From:*freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *José 
> Ángel Pineda
> *Sent:* Tuesday, December 04, 2012 9:07 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] (no subject)
>
> Thanks Doug,
>
> I already downloaded the new script for mri_label2vol, but it seems it 
> is just compiled for linux, as I cannot execute it in my Mac. If it is 
> so, could you please upload another compiled for mac, or source.
> Thanks
>
> Jose
>
> For the missing insula problem, try using a newer version of
> mri_label2vol
> 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_labe
> l2vol
>
> The 2nd problem is not so easy to fix. You might be better off using
> aparc+aseg.mgz as input to mri_label2vol instead of the surface
> annotation.
> doug
>
>
> On 12/3/12 10:35 AM, Jos? ?ngel Pineda wrote:
> > Dear experts,
> >
> > I am registering cortical labels from Talairach coordinates to my
> > native T1. For doing this, I have run the next script lines:
> >
> >
> > tkregister --targ brainmask.mgz --mov highres_brain.nii.gz --reg
> > T1FS2Highres.dat --regheader --noedit
> >
> > mri_label2vol --annot rh.aparc.annot --temp highres_brain.nii.gz
> --reg
> > T1FS2Highres.dat --o rh_aparc.nii.gz --hemi rh --subject FS --proj
> > frac 0 1 .1 --fillthresh .3
> >
> > and the same for the left hemi.
> >
> > However I am finding two problems at the result. First Insula is
> > missing for both hemispheres, and second the cortical ROIs have the
> > shape of the figure attached, e.g. there are many voxels empty
> >
> > Im?genes integradas 1
> >
> > I found in previous topics, that the mri_label2vol, was updated
> as it
> > left last volume from the list out of the conversion. I tried to
> > download it, but it is just compiled for linux, and since Im working
> > with mac I am not able to run it. Could you please give me any
> > comments to solve the problem with the missing voxels.
> > About the problem with the insula, the other option is to just
> extract
> > it with mri_annotation2label, but if I could get the mri_label2vol
> > working correctly it would be better.
> >
> > Thanks a lot
> >
> > Jose
>
>
> --
>
> José Angel Pineda Pardo
>
> Center of Biomedical Technology (CTB)
>
> Parque Científico y Tecnológico de la UPM
>
> Campus de Montegancedo
>
> 28223 Pozuelo de Alarcón, Madrid, ES
>
> **
> Electronic Mail is not secure, may not be read every day, and should 
> not be used for urgent or sensitive issues
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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Re: [Freesurfer] Mssing Insula and mri_label2vol script

[Sarosh, Cyrus]

Thanks Doug,

The mri_label2vol for linux32 works for the Windows virtual machine version of 
FreeSurfer.

Cyrus

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Wednesday, December 05, 2012 10:54 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Mssing Insula and mri_label2vol script


for mac use
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol.mac
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol.linux32>
doug

On 12/05/2012 05:11 AM, José Ángel Pineda wrote:
> Hi again,
>
> Sure I did set the permissions for execution, and also for this new 
> one I am still having the same error. "/Exec format error. Binary file 
> not executable/". I tried this on two macs (OSX Snow Leopard). I am 
> still thinking that this is a compilation issue of the script, that is 
> just compiled for linux.
>
> Thanks for your help
>
> Try this one
> 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_labe
> l2vol.linux32
>
> On 12/04/2012 12:13 PM, Sarosh, Cyrus wrote:
> > Doug,
> >
> > I am unsure if Jose did this in his attempts to get it to work,
> but I ran this command after downloading and receiving this error
> initially and even after running this command I still receive the
> same error in the Windows virtual machine version of FreeSurfer.
> Any other ideas?
> >
> > Thanks,
> >
> > Cyrus
> >
> > -Original Message-
> > From: freesurfer-boun...@nmr.mgh.harvard.edu
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] On Behalf Of
> Douglas N Greve
> > Sent: Tuesday, December 04, 2012 11:58 AM
> > To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > Subject: Re: [Freesurfer] (no subject)
> >
> > Hi Jose, did you set the permissions to be executable?
> > chmod a+x mri_label2vol
> > doug
> >
> >
> > On 12/04/2012 11:34 AM, Sarosh, Cyrus wrote:
> >> Doug,
> >>
> >> I am also curious about this mri_label2vol upgrade. Will this
> work on
> >> the Windows virtual machine version of FreeSurfer? I downloaded and
> >> placed it in the FREESURFER/bin directory, but when trying to
> run it I
> >> receive an error that states: Exec format error. Binary file not
> >> executable. Thanks for your help.
> >>
> >> Cyrus
> >>
> >> *From:*freesurfer-boun...@nmr.mgh.harvard.edu
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] *On Behalf Of *Jos?
> >> ?ngel Pineda
> >> *Sent:* Tuesday, December 04, 2012 9:07 AM
> >> *To:* freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> >> *Subject:* [Freesurfer] (no subject)
> >>
> >> Thanks Doug,
> >>
> >> I already downloaded the new script for mri_label2vol, but it
> seems it
> >> is just compiled for linux, as I cannot execute it in my Mac.
> If it is
> >> so, could you please upload another compiled for mac, or source.
> >> Thanks
> >>
> >> Jose
> >>
> >>  For the missing insula problem, try using a newer version of
> >>  mri_label2vol
> >>
> >>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_labe
> >> l2vol
> >>
> >>  The 2nd problem is not so easy to fix. You might be better
> off using
> >>  aparc+aseg.mgz as input to mri_label2vol instead of the
> surface
> >>  annotation.
> >>  doug
> >>
> >>
> >>  On 12/3/12 10:35 AM, Jos? ?ngel Pineda wrote:
> >>  > Dear experts,
> >>  >
> >>  > I am registering cortical labels from Talairach
> coordinates to my
> >>  > native T1. For doing this, I have run the next script lines:
> >>  >
> >>  >
> >>  > tkregister --targ brainmask.mgz --mov
> highres_brain.

Re: [Freesurfer] changes in tracula in the upcoming freesurfer release 5.2

[Sarosh, Cyrus]

Anastasia,

We have a set of MR data and all have the recon-all processing done in 
FreeSurfer version 5.1. Will we be able to use the results from the recon-all 
FreeSurfer version 5.1 for the new TRACULA version 5.2 or will we have to run 
recon-all in version 5.2 to use TRACULA version 5.2?

Thanks,
Cyrus

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Anastasia Yendiki
Sent: Tuesday, February 19, 2013 11:00 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] changes in tracula in the upcoming freesurfer release 5.2


Dear all - For those who have been using TRACULA or are considering using it in 
the future, it is strongly recommended to use the new (and hopefully
improved) version that will come out shortly with FreeSurfer 5.2.

For those who fear change and need some time to adjust, here's what to
expect:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

Best,
a.y
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contains patient information, please contact the Partners Compliance HelpLine 
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error but does not contain patient information, please contact the sender and 
properly dispose of the e-mail.

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[Freesurfer] Cerebellar Vermis

[Sarosh, Cyrus]

We are interested in using the Cerebellar vermis for an analysis with our PET 
data. Is the cerebellar vermis segmented during the FreeSurfer pipeline 
analysis? If it is, which file is it located in or how can I export a nifti 
file containing this segmentation?

Thanks,

Cyrus Sarosh
[Description: Description: Description: Description: Description: Description: 
Description: cid:image002.png@01CC3BB7.F8D9A990]
Research Technician Senior
Department of Radiology
Functional Neuroimaging, Cognitive and Mobility Laboratory


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The information in this e-mail is intended only for the person to whom it is
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Moving VOI to FreeSurfer Space

[Sarosh, Cyrus]

External Email - Use Caution

Hello FreeSurfer Experts,

I'm trying to find the best method and command to move a hand drawn VOI in 
original MRI space to FreeSurfer space. These scans have already been ran 
through the entire FreeSurfer process and the hand drawn VOIs have already been 
converted to .mgz files. Thanks for your help

Thanks,
Cyrus

Cyrus Sarosh
[Description: Description: Description: Description: Description: Description: 
Description: cid:image002.png@01CC3BB7.F8D9A990]
Research Area Specialist Associate
Department of Radiology
Functional Neuroimaging, Cognitive and Mobility Laboratory
Domino's Farms  Lobby B Suite 1200
24 Frank Lloyd Wright Dr  PO BOX 362
Ann Arbor, MI 48106
t: 734-998-4790
f: 734-998-8403

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[Freesurfer] Running recon-all fails during autorecon-2 -careg step

[Sarosh, Cyrus]

I have run recon-all on multiple subjects and have had it fail at the same step 
every time with the same error. I am using VirtualBox with the provided Disk 
Image and Windows 7.

0560: dt=0.001750, rms=0.358 (0.039%), neg=0, invalid=766
GCAMwrite(transforms/talairach.m3z): gzip encountered error.
writing output transformation to transforms/talairach.m3z...
GCAMwrite
GCAMwrite:: m3z loop
GCAMwrite:: the command is:  gzip -f -c > transforms/talairach.m3z
GCAMwrite:: the popen error code is:  12
mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed
ERROR: mri_ca_register with non-zero status 252
but continuing despite the error
#--
#@# CA Reg Inv Tue May  8 16:45:14 EDT 2012
/home/virtualuser/freesurfer/subjects/test/mri

mri_ca_register -invert-and-save transforms/talairach.m3z

Loading, Inverting, Saving, Exiting ...
Reading transforms/talairach.m3z
ERROR: cannot find or read transforms/talairach.m3z
ERROR: mri_ca_register with non-zero status 0
Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 
i686 GNU/Linux

recon-all -s test exited with ERRORS at Tue May  8 16:45:15 EDT 2012

Has anyone had this issue and resolved this problem? Thanks for your help.


-  Cyrus
**
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] VM ubuntu developer password

[Sarosh, Cyrus]

External Email - Use Caution

I have also just ran into this issue. Can someone send me the password as well?


Thansk,

Cyrus


Cyrus Sarosh
[1587656965587]
Research Area Specialist Intermediate
Department of Radiology
Functional Neuroimaging, Cognitive and Mobility Laboratory
Domino’s Farms  Lobby B Suite 1200
24 Frank Lloyd Wright Dr  PO BOX 362
Ann Arbor, MI 48106
t: 734-998-4790
f: 734-998-8403




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of FAIRS Amie 

Sent: Thursday, June 18, 2020 1:43 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] VM ubuntu developer password

External Email - Use Caution

External Email - Use Caution

Hello everyone,



I have been sent the VM ubuntu password. But in case this is useful for others 
– at least on my laptop the ubuntu distribution is using a US/international 
QWERTY keyboard. My laptop has an AZERTY keyboard (French) and so I had some 
problems with the password being rejected. In case future VM users encounter 
errors entering the password, you may need to switch keyboard layout.



Thank you to the people who sent me the password so speedily!



Best,



Amie



--

Dr. Amie Fairs

Post-doctorant

Aix-Marseille Université

Laboratoire Parole et Langage (LPL) | CNRS UMR 7309 | 5 Avenue Pasteur | 13100 
Aix-en-Provence

Email : amie.fa...@univ-amu.fr



While I may send this email outside of typical working hours, I have no 
expectation to receive an email outside of your typical hours.



From: fsbuild 
Sent: 18 June 2020 19:24
To: freesurfer@nmr.mgh.harvard.edu
Cc: FAIRS Amie 
Subject: Re: [Freesurfer] VM ubuntu developer password



Hello Amie,



I have just sent the password to your private email.



- R.



On Jun 18, 2020, at 08:57, FAIRS Amie 
mailto:amie.fa...@univ-amu.fr>> wrote:



External Email - Use Caution



Dear Freesurfer mailing list,



I have just downloaded the virtual machine + ubuntu package, as outlined on the 
website when running a VM in windows. However, ubuntu is asking for a developer 
password to open within the VM. I see on the help page (on the website) that 
the log in ID could be in the README doc, but I can’t actually get the VM open 
to get there.



Does anyone know the password so I can set up the VM and get started with 
freesurfer?



Thanks so much in advance!



Best,



Amie



--

Dr. Amie Fairs

Post-doctorant

Aix-Marseille Université

Laboratoire Parole et Langage (LPL) | CNRS UMR 7309 | 5 Avenue Pasteur | 13100 
Aix-en-Provence

Email : amie.fa...@univ-amu.fr



While I may send this email outside of typical working hours, I have no 
expectation to receive an email outside of your typical hours.



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