[Freesurfer] recon-all error

[Borzello, Mia]

Hi Freesurfers,

I'm wondering if you can help with the following error that occurred when 
trying to create a reconstruction:

FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0

Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514

RedHat release: CentOS release 6.5 (Final)

Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64

NMR Center info (/space/freesurfer exists):

  machine: huygens

  SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects

  PWD: /autofs/space/huygens_001/users/mia/subjects

  ssh huygens
  setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
  cd /autofs/space/huygens_001/users/mia/subjects


1)BI22
2)recon-all -autorecon1 -autorecon2 - autoreon3 -subject BI22_SurferOutput -i 
/autofs/space/huygens_001/users/mia/subjects/BI22_PreOp_MRI/DICOM_BI19/4571/4571157.dcm
3)recon-all -s  exited with ERRORS at Thu Jan  8 13:08:33 EST 2015


Thanks,
m
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Re: [Freesurfer] recon-all error

[Borzello, Mia]

I looked for that file and did not see a BI22_SurferOutput folder at all. 
 
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Thursday, January 08, 2015 2:34 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all error

Hi Mia

can you send us the recon-all.log? I don't think you included the error
message in your email so there isn't much for us to go on.

thanks
Bruce

On Thu, 8 Jan 2015, Borzello, Mia wrote:

>
> Hi Freesurfers,
>
> I'm wondering if you can help with the following error that occurred when
> trying to create a reconstruction:
>
> FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
>
> Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
>
> RedHat release: CentOS release 6.5 (Final)
>
> Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64
>
> NMR Center info (/space/freesurfer exists):
>
>   machine: huygens
>
>   SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects
>
>   PWD: /autofs/space/huygens_001/users/mia/subjects
>
>   ssh huygens
>   setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
>   cd /autofs/space/huygens_001/users/mia/subjects
>
>
> 1)BI22
> 2)recon-all -autorecon1 -autorecon2 - autoreon3 -subject BI22_SurferOutput
> -i/autofs/space/huygens_001/users/mia/subjects/BI22_PreOp_MRI/DICOM_BI19/4571
> /4571157.dcm
> 3)recon-all -s  exited with ERRORS at Thu Jan  8 13:08:33 EST 2015
>
>
> Thanks,
> m
>
>

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Re: [Freesurfer] recon-all error

[Borzello, Mia]

Yea I didn't see it in /autofs/space/huygens_001/users/mia/subjects. 
I attached the output error for recon-all. 

Thanks, 
m

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Thursday, January 08, 2015 4:27 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all error

did you look in

/autofs/space/huygens_001/users/mia/subjects

Can you send us the screen output of recon-all?

On Thu, 8 Jan 2015, Borzello,
Mia wrote:

> I looked for that file and did not see a BI22_SurferOutput folder at all.
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, January 08, 2015 2:34 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] recon-all error
>
> Hi Mia
>
> can you send us the recon-all.log? I don't think you included the error
> message in your email so there isn't much for us to go on.
>
> thanks
> Bruce
>
> On Thu, 8 Jan 2015, Borzello, Mia wrote:
>
>>
>> Hi Freesurfers,
>>
>> I'm wondering if you can help with the following error that occurred when
>> trying to create a reconstruction:
>>
>> FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
>>
>> Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
>>
>> RedHat release: CentOS release 6.5 (Final)
>>
>> Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64
>>
>> NMR Center info (/space/freesurfer exists):
>>
>>   machine: huygens
>>
>>   SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects
>>
>>   PWD: /autofs/space/huygens_001/users/mia/subjects
>>
>>   ssh huygens
>>   setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
>>   cd /autofs/space/huygens_001/users/mia/subjects
>>
>>
>> 1)BI22
>> 2)recon-all -autorecon1 -autorecon2 - autoreon3 -subject BI22_SurferOutput
>> -i/autofs/space/huygens_001/users/mia/subjects/BI22_PreOp_MRI/DICOM_BI19/4571
>> /4571157.dcm
>> 3)recon-all -s  exited with ERRORS at Thu Jan  8 13:08:33 EST 2015
>>
>>
>> Thanks,
>> m
>>
>>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] recon-all error

[Borzello, Mia]

I just fixed that but I'm still getting an error. I attached a screenshot. 

Thanks, 
Mia

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Krieger, Donald N. 
[krieg...@upmc.edu]
Sent: Friday, January 09, 2015 5:39 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all error

It looks like there's a typo in your recon-all command - there's a space 
between "-"  and autorecon3 .

Regards,

Don


Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text


> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Borzello, Mia
> Sent: Friday, January 09, 2015 5:30 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] recon-all error
>
> Yea I didn't see it in /autofs/space/huygens_001/users/mia/subjects.
> I attached the output error for recon-all.
>
> Thanks,
> m
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-
> boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, January 08, 2015 4:27 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] recon-all error
>
> did you look in
>
> /autofs/space/huygens_001/users/mia/subjects
>
> Can you send us the screen output of recon-all?
>
> On Thu, 8 Jan 2015, Borzello,
> Mia wrote:
>
> > I looked for that file and did not see a BI22_SurferOutput folder at all.
> > 
> > From: freesurfer-boun...@nmr.mgh.harvard.edu
> > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> > [fis...@nmr.mgh.harvard.edu]
> > Sent: Thursday, January 08, 2015 2:34 PM
> > To: Freesurfer support list
> > Subject: Re: [Freesurfer] recon-all error
> >
> > Hi Mia
> >
> > can you send us the recon-all.log? I don't think you included the
> > error message in your email so there isn't much for us to go on.
> >
> > thanks
> > Bruce
> >
> > On Thu, 8 Jan 2015, Borzello, Mia wrote:
> >
> >>
> >> Hi Freesurfers,
> >>
> >> I'm wondering if you can help with the following error that occurred
> >> when trying to create a reconstruction:
> >>
> >> FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
> >>
> >> Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
> >>
> >> RedHat release: CentOS release 6.5 (Final)
> >>
> >> Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64
> >>
> >> NMR Center info (/space/freesurfer exists):
> >>
> >>   machine: huygens
> >>
> >>   SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects
> >>
> >>   PWD: /autofs/space/huygens_001/users/mia/subjects
> >>
> >>   ssh huygens
> >>   setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
> >>   cd /autofs/space/huygens_001/users/mia/subjects
> >>
> >>
> >> 1)BI22
> >> 2)recon-all -autorecon1 -autorecon2 - autoreon3 -subject
> >> BI22_SurferOutput
> >> -
> i/autofs/space/huygens_001/users/mia/subjects/BI22_PreOp_MRI/DICOM_B
> >> I19/4571
> >> /4571157.dcm
> >> 3)recon-all -s  exited with ERRORS at Thu Jan  8 13:08:33 EST 2015
> >>
> >>
> >> Thanks,
> >> m
> >>
> >>
> >
> > ___
> > 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

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

Re: [Freesurfer] recon-all error

[Borzello, Mia]

Okay, just ran ls-l and don't see it- image attached.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Monday, January 12, 2015 8:39 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all error

does that dicom exist? Can you run ls -l on it?
On Sat, 10 Jan 2015,
Borzello, Mia wrote:

> I just fixed that but I'm still getting an error. I attached a screenshot.
>
> Thanks,
> Mia
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Krieger, Donald N. 
> [krieg...@upmc.edu]
> Sent: Friday, January 09, 2015 5:39 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] recon-all error
>
> It looks like there's a typo in your recon-all command - there's a space 
> between "-"  and autorecon3 .
>
> Regards,
>
> Don
>
>
> Don Krieger, Ph.D.
> Department of Neurological Surgery
> University of Pittsburgh
> (412)648-9654 Office
> (412)521-4431 Cell/Text
>
>
>> -Original Message-----
>> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
>> boun...@nmr.mgh.harvard.edu] On Behalf Of Borzello, Mia
>> Sent: Friday, January 09, 2015 5:30 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] recon-all error
>>
>> Yea I didn't see it in /autofs/space/huygens_001/users/mia/subjects.
>> I attached the output error for recon-all.
>>
>> Thanks,
>> m
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-
>> boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
>> [fis...@nmr.mgh.harvard.edu]
>> Sent: Thursday, January 08, 2015 4:27 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] recon-all error
>>
>> did you look in
>>
>> /autofs/space/huygens_001/users/mia/subjects
>>
>> Can you send us the screen output of recon-all?
>>
>> On Thu, 8 Jan 2015, Borzello,
>> Mia wrote:
>>
>>> I looked for that file and did not see a BI22_SurferOutput folder at all.
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
>>> [fis...@nmr.mgh.harvard.edu]
>>> Sent: Thursday, January 08, 2015 2:34 PM
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] recon-all error
>>>
>>> Hi Mia
>>>
>>> can you send us the recon-all.log? I don't think you included the
>>> error message in your email so there isn't much for us to go on.
>>>
>>> thanks
>>> Bruce
>>>
>>> On Thu, 8 Jan 2015, Borzello, Mia wrote:
>>>
>>>>
>>>> Hi Freesurfers,
>>>>
>>>> I'm wondering if you can help with the following error that occurred
>>>> when trying to create a reconstruction:
>>>>
>>>> FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
>>>>
>>>> Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
>>>>
>>>> RedHat release: CentOS release 6.5 (Final)
>>>>
>>>> Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64
>>>>
>>>> NMR Center info (/space/freesurfer exists):
>>>>
>>>>   machine: huygens
>>>>
>>>>   SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects
>>>>
>>>>   PWD: /autofs/space/huygens_001/users/mia/subjects
>>>>
>>>>   ssh huygens
>>>>   setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
>>>>   cd /autofs/space/huygens_001/users/mia/subjects
>>>>
>>>>
>>>> 1)BI22
>>>> 2)recon-all -autorecon1 -autorecon2 - autoreon3 -subject
>>>> BI22_SurferOutput
>>>> -
>> i/autofs/space/huygens_001/users/mia/subjects/BI22_PreOp_MRI/DICOM_B
>>>> I19/4571
>>>> /4571157.dcm
>>>> 3)recon-all -s  exited with ERRORS at Thu Jan  8 13:08:33 EST 2015
>>>>
>>>>
>>>> Thanks,
>>>> m
>>>>
>>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>

Re: [Freesurfer] recon-all error

[Borzello, Mia]

Hi Bruce, 

Thanks for e-mail. I did a search on the dicom file, and it said there was no 
file (top part of image). However, I can get myself in the folder and the 
dicome "4571157" is in there. I'm wondering if it's a file type issue. The 
files aren't listed as 4571157.dcm for example- could that be the problem? 

Thanks so much, 
m

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Monday, January 12, 2015 9:08 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all error

Hi Mia

you need to run it with the full path of the dicom you are trying to give
to recon-all

cheers
Bruce
On Tue, 13 Jan 2015,
Borzello, Mia wrote:

> Okay, just ran ls-l and don't see it- image attached.
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, January 12, 2015 8:39 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] recon-all error
>
> does that dicom exist? Can you run ls -l on it?
> On Sat, 10 Jan 2015,
> Borzello, Mia wrote:
>
>> I just fixed that but I'm still getting an error. I attached a screenshot.
>>
>> Thanks,
>> Mia
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Krieger, Donald N. 
>> [krieg...@upmc.edu]
>> Sent: Friday, January 09, 2015 5:39 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] recon-all error
>>
>> It looks like there's a typo in your recon-all command - there's a space 
>> between "-"  and autorecon3 .
>>
>> Regards,
>>
>> Don
>>
>>
>> Don Krieger, Ph.D.
>> Department of Neurological Surgery
>> University of Pittsburgh
>> (412)648-9654 Office
>> (412)521-4431 Cell/Text
>>
>>
>>> -Original Message-
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
>>> boun...@nmr.mgh.harvard.edu] On Behalf Of Borzello, Mia
>>> Sent: Friday, January 09, 2015 5:30 PM
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] recon-all error
>>>
>>> Yea I didn't see it in /autofs/space/huygens_001/users/mia/subjects.
>>> I attached the output error for recon-all.
>>>
>>> Thanks,
>>> m
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-
>>> boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
>>> [fis...@nmr.mgh.harvard.edu]
>>> Sent: Thursday, January 08, 2015 4:27 PM
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] recon-all error
>>>
>>> did you look in
>>>
>>> /autofs/space/huygens_001/users/mia/subjects
>>>
>>> Can you send us the screen output of recon-all?
>>>
>>> On Thu, 8 Jan 2015, Borzello,
>>> Mia wrote:
>>>
>>>> I looked for that file and did not see a BI22_SurferOutput folder at all.
>>>> ________
>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
>>>> [fis...@nmr.mgh.harvard.edu]
>>>> Sent: Thursday, January 08, 2015 2:34 PM
>>>> To: Freesurfer support list
>>>> Subject: Re: [Freesurfer] recon-all error
>>>>
>>>> Hi Mia
>>>>
>>>> can you send us the recon-all.log? I don't think you included the
>>>> error message in your email so there isn't much for us to go on.
>>>>
>>>> thanks
>>>> Bruce
>>>>
>>>> On Thu, 8 Jan 2015, Borzello, Mia wrote:
>>>>
>>>>>
>>>>> Hi Freesurfers,
>>>>>
>>>>> I'm wondering if you can help with the following error that occurred
>>>>> when trying to create a reconstruction:
>>>>>
>>>>> FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
>>>>>
>>>>> Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
>>>>>
>>>>> RedHat release: CentOS release 6.5 (Final)
>>>>>
>>>>> Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64
>>>>>
>>>>> NMR Center info (/spa

[Freesurfer] converting .nii to .mgz

[Borzello, Mia]

Hi Freesurfers, 

I'm looking at Freesurfer files from are from years ago trying to look at the 
ct.anat file. Unfortunately, i have the nifti file and not the mgz file, so I'm 
wondering if there is a way to create it. In trying to find an answer online, I 
found this: 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013493.html
I tried that but got an error. It may be a syntax error; this was my command 
line: recon-all -i 
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii 
MG17_SurferOutput 
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/


FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0

Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514

RedHat release: CentOS release 6.5 (Final)

Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64

NMR Center info (/space/freesurfer exists):

  machine: huygens

  SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects

  PWD: /autofs/space/huygens_001/users/mia/subjects

  ssh huygens
  setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
  cd /autofs/space/huygens_001/users/mia/subjects


1) MG17
2) recon-all -i 
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii 
MG17_SurferOutput 
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/
3) ERROR: Flag 
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii 
unrecognized.
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii 
MG17_SurferOutput 
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/
Linux huygens 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC 2014 
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s  exited with ERRORS at Mon Jan 19 22:27:18 EST 2015

For more details, see the log file 
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Thanks so much, 
Mia 
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Re: [Freesurfer] converting .nii to .mgz

[Borzello, Mia]

Hi Bruce, 

Thanks for getting back to me so quickly! 
I just tried that and got the following error: 
reading from ct.anat.nii...
niiRead(): error opening file 
/autofs/space/huygens_001/users/mia/subjects/ct.anat.nii

I'm wondering if the nifti file is possibly corrupted. Is there a way to check 
this?

Thanks so much, 
Mia 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Monday, January 19, 2015 10:38 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] converting .nii to .mgz

Hi Mia
If all you want to do is convert try

mri_convert ct.anat.nii ct.anat.mgz

Cheers
Bruce



> On Jan 19, 2015, at 10:33 PM, Borzello, Mia  wrote:
>
> Hi Freesurfers,
>
> I'm looking at Freesurfer files from are from years ago trying to look at the 
> ct.anat file. Unfortunately, i have the nifti file and not the mgz file, so 
> I'm wondering if there is a way to create it. In trying to find an answer 
> online, I found this: 
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013493.html
> I tried that but got an error. It may be a syntax error; this was my command 
> line: recon-all -i 
> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
>  MG17_SurferOutput 
> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/
>
>
> FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
>
> Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
>
> RedHat release: CentOS release 6.5 (Final)
>
> Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64
>
> NMR Center info (/space/freesurfer exists):
>
>  machine: huygens
>
>  SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects
>
>  PWD: /autofs/space/huygens_001/users/mia/subjects
>
>  ssh huygens
>  setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
>  cd /autofs/space/huygens_001/users/mia/subjects
>
>
> 1) MG17
> 2) recon-all -i 
> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
>  MG17_SurferOutput 
> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/
> 3) ERROR: Flag 
> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
>  unrecognized.
> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
>  MG17_SurferOutput 
> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/
> Linux huygens 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC 2014 
> x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s  exited with ERRORS at Mon Jan 19 22:27:18 EST 2015
>
> For more details, see the log file
> To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
> Thanks so much,
> Mia
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] converting .nii to .mgz

[Borzello, Mia]

Hi guys, 
full command line: mri_convert ct.anat.nii ct.anat.mgz

command line: ls -l 
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii 
-rw-rw-r-- 1 miaborz acqcash 32506208 Jan 19 22:12 
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii

I had to send the ct.anat.nii file separately because it was too large of a 
file for this email. 

Thanks, 
m

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Tuesday, January 20, 2015 7:43 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] converting .nii to .mgz

Hi Mia

can you please send us the full command line? And also do an ls -l of
that file and include it?

thanks
Bruce
On Tue, 20 Jan 2015, Borzello, Mia wrote:

> Hi Bruce,
>
> Thanks for getting back to me so quickly!
> I just tried that and got the following error:
> reading from ct.anat.nii...
> niiRead(): error opening file 
> /autofs/space/huygens_001/users/mia/subjects/ct.anat.nii
>
> I'm wondering if the nifti file is possibly corrupted. Is there a way to 
> check this?
>
> Thanks so much,
> Mia
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, January 19, 2015 10:38 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] converting .nii to .mgz
>
> Hi Mia
> If all you want to do is convert try
>
> mri_convert ct.anat.nii ct.anat.mgz
>
> Cheers
> Bruce
>
>
>
>> On Jan 19, 2015, at 10:33 PM, Borzello, Mia  wrote:
>>
>> Hi Freesurfers,
>>
>> I'm looking at Freesurfer files from are from years ago trying to look at 
>> the ct.anat file. Unfortunately, i have the nifti file and not the mgz file, 
>> so I'm wondering if there is a way to create it. In trying to find an answer 
>> online, I found this: 
>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013493.html
>> I tried that but got an error. It may be a syntax error; this was my command 
>> line: recon-all -i 
>> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
>>  MG17_SurferOutput 
>> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/
>>
>>
>> FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
>>
>> Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
>>
>> RedHat release: CentOS release 6.5 (Final)
>>
>> Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64
>>
>> NMR Center info (/space/freesurfer exists):
>>
>>  machine: huygens
>>
>>  SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects
>>
>>  PWD: /autofs/space/huygens_001/users/mia/subjects
>>
>>  ssh huygens
>>  setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
>>  cd /autofs/space/huygens_001/users/mia/subjects
>>
>>
>> 1) MG17
>> 2) recon-all -i 
>> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
>>  MG17_SurferOutput 
>> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/
>> 3) ERROR: Flag 
>> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
>>  unrecognized.
>> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
>>  MG17_SurferOutput 
>> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/
>> Linux huygens 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC 2014 
>> x86_64 x86_64 x86_64 GNU/Linux
>>
>> recon-all -s  exited with ERRORS at Mon Jan 19 22:27:18 EST 2015
>>
>> For more details, see the log file
>> To report a problem, see 
>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>
>>
>> Thanks so much,
>> Mia
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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Re: [Freesurfer] converting .nii to .mgz

[Borzello, Mia]

yes, definitely. I just tried to upload to this email: 
freesurfer@nmr.mgh.harvard.edu
and it says "Server Error! User 'freesurfer' is not a valid NMR Account holder"
I have a feeling this is a user error- sorry about that. 

Thanks, 
m

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, January 20, 2015 11:34 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] converting .nii to .mgz

Can you put this on our file drop?


On 01/20/2015 11:26 AM, mborze...@partners.org wrote:
> *
> You have received 1 secure file from mborze...@partners.org.
> *
> Use the secure link below to download.
> Here is the ct.anat.nii file
> Secure File Downloads:
> Available until: **30 January 2015**
> Click link to download:
> *ct.anat.nii*
> 
> 31,744.34 KB
> You have received attachment(s) within this email. To download the
> attachment(s), please click on the link(s) above. This service is
> provided by Partners Research Computing.
>
> http://rc.partners.org/
> mailto:r...@partners.org
>
> Secured by Accellion 
>
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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The information in this e-mail is intended only for the person to whom it is
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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
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Re: [Freesurfer] converting .nii to .mgz

[Borzello, Mia]

Okay, cool, I just tried with the full path to the .nii file and it worked. 
However, when I tried to load the ct.anat.mgz using tkmedit i get an error in 
loading the volume. 

FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0

Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514

RedHat release: CentOS release 6.5 (Final)

Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64

NMR Center info (/space/freesurfer exists):

  machine: huygens

  SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects

  PWD: /autofs/space/huygens_001/users/mia/subjects

  ssh huygens
  setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
  cd /autofs/space/huygens_001/users/mia/subjects

1) MG17
2) tkmedit MG17_SurferOutput norm.mgz lh.pial -aux ct.anat.mgz
3) this is the error: 
mghRead(/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.mgz,
 -1): could not open file
Converting main surface: 100% done.   
Converting main surface: 100% done.   
Converting original surface: 100% done.   
Converting pial surface: 100% done.   
Reading /usr/local/freesurfer/stable5_3_0/tktools/tkm_common.tcl
Reading /usr/local/freesurfer/stable5_3_0/tktools/tkm_wrappers.tcl
Reading /usr/local/freesurfer/stable5_3_0/lib/tcl/fsgdfPlot.tcl
Reading /usr/local/freesurfer/stable5_3_0/tktools/tkUtils.tcl

and the grey box pops up saying it couldn't load the volume. 

(not sure if I should start a new thread for this or not). Thanks again for all 
your help, 
m


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, January 20, 2015 2:57 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] converting .nii to .mgz

I was able to convert your file without problem. When you run mri_convert, you 
have to give a path to a file that exists. Below, the error says that it cannot 
find /autofs/space/huygens_001/users/mia/subjects/ct.anat.nii

Does this file exist? It is different than the one you have below, ie
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii




On 01/20/2015 11:26 AM, Borzello, Mia wrote:
> Hi guys,
> full command line: mri_convert ct.anat.nii ct.anat.mgz
>
> command line: ls -l 
> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
> -rw-rw-r-- 1 miaborz acqcash 32506208 Jan 19 22:12 
> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
>
> I had to send the ct.anat.nii file separately because it was too large of a 
> file for this email.
>
> Thanks,
> m
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Tuesday, January 20, 2015 7:43 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] converting .nii to .mgz
>
> Hi Mia
>
> can you please send us the full command line? And also do an ls -l of
> that file and include it?
>
> thanks
> Bruce
> On Tue, 20 Jan 2015, Borzello, Mia wrote:
>
>> Hi Bruce,
>>
>> Thanks for getting back to me so quickly!
>> I just tried that and got the following error:
>> reading from ct.anat.nii...
>> niiRead(): error opening file 
>> /autofs/space/huygens_001/users/mia/subjects/ct.anat.nii
>>
>> I'm wondering if the nifti file is possibly corrupted. Is there a way to 
>> check this?
>>
>> Thanks so much,
>> Mia
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>> [fis...@nmr.mgh.harvard.edu]
>> Sent: Monday, January 19, 2015 10:38 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] converting .nii to .mgz
>>
>> Hi Mia
>> If all you want to do is convert try
>>
>> mri_convert ct.anat.nii ct.anat.mgz
>>
>> Cheers
>> Bruce
>>
>>
>>
>>> On Jan 19, 2015, at 10:33 PM, Borzello, Mia  wrote:
>>>
>>> Hi Freesurfers,
>>>
>>> I'm looking at Freesurfer files from are from years ago trying to look at 
>>> the ct.anat file. Unfortunately, i have the nifti file and not the mgz 
>>> file, so I'm wondering if there is a way to create it. In trying to find an 
>>> answer online, I found this: 
>>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013493.html
>>> I tried that but got an error. It may be a syntax error; this was my 
>>> command line: recon-all -i 
>>> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/m

Re: [Freesurfer] converting .nii to .mgz

[Borzello, Mia]

It was initially in the wrong folder, but now it in the mri folder. 
ls -l 
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.mgz 
-rw-rw-r-- 1 miaborz acqcash 15954217 Jan 20 16:16 
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.mgz

Still unable to load with tkmedit though. 

Thanks, 
m

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, January 20, 2015 3:51 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] converting .nii to .mgz

does
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.mgz
exist?

On 01/20/2015 03:40 PM, Borzello, Mia wrote:
> Okay, cool, I just tried with the full path to the .nii file and it worked. 
> However, when I tried to load the ct.anat.mgz using tkmedit i get an error in 
> loading the volume.
>
> FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
>
> Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
>
> RedHat release: CentOS release 6.5 (Final)
>
> Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64
>
> NMR Center info (/space/freesurfer exists):
>
>machine: huygens
>
>SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects
>
>PWD: /autofs/space/huygens_001/users/mia/subjects
>
>ssh huygens
>setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
>cd /autofs/space/huygens_001/users/mia/subjects
>
> 1) MG17
> 2) tkmedit MG17_SurferOutput norm.mgz lh.pial -aux ct.anat.mgz
> 3) this is the error:
> mghRead(/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.mgz,
>  -1): could not open file
> Converting main surface: 100% done.
> Converting main surface: 100% done.
> Converting original surface: 100% done.
> Converting pial surface: 100% done.
> Reading /usr/local/freesurfer/stable5_3_0/tktools/tkm_common.tcl
> Reading /usr/local/freesurfer/stable5_3_0/tktools/tkm_wrappers.tcl
> Reading /usr/local/freesurfer/stable5_3_0/lib/tcl/fsgdfPlot.tcl
> Reading /usr/local/freesurfer/stable5_3_0/tktools/tkUtils.tcl
>
> and the grey box pops up saying it couldn't load the volume.
>
> (not sure if I should start a new thread for this or not). Thanks again for 
> all your help,
> m
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Tuesday, January 20, 2015 2:57 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] converting .nii to .mgz
>
> I was able to convert your file without problem. When you run mri_convert, 
> you have to give a path to a file that exists. Below, the error says that it 
> cannot find /autofs/space/huygens_001/users/mia/subjects/ct.anat.nii
>
> Does this file exist? It is different than the one you have below, ie
> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
>
>
>
>
> On 01/20/2015 11:26 AM, Borzello, Mia wrote:
>> Hi guys,
>> full command line: mri_convert ct.anat.nii ct.anat.mgz
>>
>> command line: ls -l 
>> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
>> -rw-rw-r-- 1 miaborz acqcash 32506208 Jan 19 22:12 
>> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
>>
>> I had to send the ct.anat.nii file separately because it was too large of a 
>> file for this email.
>>
>> Thanks,
>> m
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>> [fis...@nmr.mgh.harvard.edu]
>> Sent: Tuesday, January 20, 2015 7:43 AM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] converting .nii to .mgz
>>
>> Hi Mia
>>
>> can you please send us the full command line? And also do an ls -l of
>> that file and include it?
>>
>> thanks
>> Bruce
>> On Tue, 20 Jan 2015, Borzello, Mia wrote:
>>
>>> Hi Bruce,
>>>
>>> Thanks for getting back to me so quickly!
>>> I just tried that and got the following error:
>>> reading from ct.anat.nii...
>>> niiRead(): error opening file 
>>> /autofs/space/huygens_001/users/mia/subjects/ct.anat.nii
>>>
>>> I'm wondering if the nifti file is possibly corrupted. Is there a way to 
>>> check this?
>>>
>>> Thanks so much,
>>> Mia
>>> _______

Re: [Freesurfer] converting .nii to .mgz

[Borzello, Mia]

Also, i didn't attach the error I got- please see attached. 

Thanks!
m

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia
Sent: Tuesday, January 20, 2015 4:21 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] converting .nii to .mgz

It was initially in the wrong folder, but now it in the mri folder.
ls -l 
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.mgz
-rw-rw-r-- 1 miaborz acqcash 15954217 Jan 20 16:16 
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.mgz

Still unable to load with tkmedit though.

Thanks,
m

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, January 20, 2015 3:51 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] converting .nii to .mgz

does
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.mgz
exist?

On 01/20/2015 03:40 PM, Borzello, Mia wrote:
> Okay, cool, I just tried with the full path to the .nii file and it worked. 
> However, when I tried to load the ct.anat.mgz using tkmedit i get an error in 
> loading the volume.
>
> FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
>
> Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
>
> RedHat release: CentOS release 6.5 (Final)
>
> Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64
>
> NMR Center info (/space/freesurfer exists):
>
>machine: huygens
>
>SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects
>
>PWD: /autofs/space/huygens_001/users/mia/subjects
>
>ssh huygens
>setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
>cd /autofs/space/huygens_001/users/mia/subjects
>
> 1) MG17
> 2) tkmedit MG17_SurferOutput norm.mgz lh.pial -aux ct.anat.mgz
> 3) this is the error:
> mghRead(/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.mgz,
>  -1): could not open file
> Converting main surface: 100% done.
> Converting main surface: 100% done.
> Converting original surface: 100% done.
> Converting pial surface: 100% done.
> Reading /usr/local/freesurfer/stable5_3_0/tktools/tkm_common.tcl
> Reading /usr/local/freesurfer/stable5_3_0/tktools/tkm_wrappers.tcl
> Reading /usr/local/freesurfer/stable5_3_0/lib/tcl/fsgdfPlot.tcl
> Reading /usr/local/freesurfer/stable5_3_0/tktools/tkUtils.tcl
>
> and the grey box pops up saying it couldn't load the volume.
>
> (not sure if I should start a new thread for this or not). Thanks again for 
> all your help,
> m
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Tuesday, January 20, 2015 2:57 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] converting .nii to .mgz
>
> I was able to convert your file without problem. When you run mri_convert, 
> you have to give a path to a file that exists. Below, the error says that it 
> cannot find /autofs/space/huygens_001/users/mia/subjects/ct.anat.nii
>
> Does this file exist? It is different than the one you have below, ie
> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
>
>
>
>
> On 01/20/2015 11:26 AM, Borzello, Mia wrote:
>> Hi guys,
>> full command line: mri_convert ct.anat.nii ct.anat.mgz
>>
>> command line: ls -l 
>> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
>> -rw-rw-r-- 1 miaborz acqcash 32506208 Jan 19 22:12 
>> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
>>
>> I had to send the ct.anat.nii file separately because it was too large of a 
>> file for this email.
>>
>> Thanks,
>> m
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>> [fis...@nmr.mgh.harvard.edu]
>> Sent: Tuesday, January 20, 2015 7:43 AM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] converting .nii to .mgz
>>
>> Hi Mia
>>
>> can you please send us the full command line? And also do an ls -l of
>> that file and include it?
>>
>> thanks
>> Bruce
>> On Tue, 20 Jan 2015, Borzello, Mia wrote:
>>
>>> Hi Bruce,
>>>
>>> Thanks for getting back to me so quickly!
>>> I just tried that and got the following error:
>>> reading from ct.anat.nii...
>>&g

Re: [Freesurfer] Expediting the pial surface calculation

[Borzello, Mia]

I'm having the same issue- any updates on this problem that Jason Naftulin 
posted?

Thanks,
m

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Naftulin, Jason Scott
Sent: Friday, February 27, 2015 2:50 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Expediting the pial surface calculation

Hi,

We are wondering if there is a faster way to generate lh.pial and rh.pial than 
running the 24 hour long recon-all function. We took a look at 
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllFilesVsSteps  and it seems 
that the inputs for lh.pial and rh.pial are needed from the recon-all output. 
We were wondering how difficult it would be to generate a custom script to 
significantly decrease the amount of time needed to generate these two 
surfaces. Is there someone we can talk to who might be interested in doing this?

Also, we are wondering if there is an object in Freesurfer that handles the 
entire brain as one object instead of as two separate hemispheres. We would 
like to 3D print the entire brain at once with accurate inter-hemisphere 
relationship.

Any and all advice you can provide would be most helpful.


Thanks,
Jason
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Re: [Freesurfer] Expediting the pial surface calculation

[Borzello, Mia]

Great- thanks for the quick reply!

m

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Thursday, March 05, 2015 4:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Expediting the pial surface calculation

sorry, the answer is pretty much "no" to both questions. We have 3D-printed
surface models, but the steps for doing so aren't documented or supported.
I guess the easiest thing to do would be to combine the surfaces in matlab.
You'll have to add the # of vertices in one hemi to all the indices in the
other (so that the indices remain unique, then concatenate them into a
single surface tesselation and write it out

On Thu, 5 Mar 2015,
Borzello, Mia wrote:

> I'm having the same issue- any updates on this problem that Jason Naftulin
> posted?
> Thanks,
> m
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Naftulin, Jason Scott
> Sent: Friday, February 27, 2015 2:50 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] Expediting the pial surface calculation
>
> Hi,
>
> We are wondering if there is a faster way to generate lh.pial and rh.pial
> than running the 24 hour long recon-all function. We took a look
> at http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllFilesVsSteps  and it
> seems that the inputs for lh.pial and rh.pial are needed from the recon-all
> output. We were wondering how difficult it would be to generate a custom
> script to significantly decrease the amount of time needed to generate these
> two surfaces. Is there someone we can talk to who might be interested in
> doing this?
>
> Also, we are wondering if there is an object in Freesurfer that handles the
> entire brain as one object instead of as two separate hemispheres. We would
> like to 3D print the entire brain at once
> with accurate inter-hemisphere relationship.
>
> Any and all advice you can provide would be most helpful.
>
>
> Thanks,
> Jason
>
>

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[Freesurfer] Computing pial layers

[Borzello, Mia]

Hi Freesurfers,

I'm having some trouble computing the pial layers. Below are the details.

Thanks!

Here is the output from "bugr":
FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0

Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514

RedHat release: CentOS release 6.5 (Final)

Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64

NMR Center info (/space/freesurfer exists):

  machine: huygens

  SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects

  PWD: /autofs/space/huygens_001/users/mia/subjects/MG82_SurferOutput_CT3/surf

  ssh huygens
  setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
  cd /autofs/space/huygens_001/users/mia/subjects/MG82_SurferOutput_CT3/surf


1) MG82
2) mris_compute_lgi --i lh.pial --close_sphere_size 30 --smooth_iters 60
3) Error in dsearchn (line 79)
[d(i),t(i)] = min(sum((x-yi).^2,2));

Error in mesh_vertex_nearest (line 29)
nearestIndex = dsearchn(vertices,points);

Error in reorganize_verticeslist (line 28)

[nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:));

Error in make_roi_paths (line 93)
reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim,
verticeslist, step);

>>
ERROR:  make_roi_paths did not complete successfully!



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[Freesurfer] recon-all error

[Borzello, Mia]

Hi Freesurfers,

Hope you're doing well! I tried creating a reconstruction yesterday but got an 
error.

1)BI22
2)recon-all -autorecon1 -autorecon2 -autorecon3 -subject BI22_SurferOutput -i 
/autofs/space/huygens_001/users/mia/subjects/BI22_PreOp_MRI/8961/8968/896583
3)

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm 
***FAILED*** (p=0.0049, pval=0. < threshold=0.0050)
Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure the -notal-check flag follows -all
or -autorecon1 in the command string.
See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
Linux huygens 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC 2014 
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s BI22_SurferOutput exited with ERRORS at Sat May 16 19:44:42 EDT 
2015

Let me know if including the recon-all.log would be helpful.

Thanks so much,
Mia
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Re: [Freesurfer] recon-all error

[Borzello, Mia]

Thanks, Nick! I'll plan to try to series you suggested then. 

Fingers crossed, 
Mia 



> On May 17, 2015, at 3:03 PM, "Nick Schmansky, MGH" 
>  wrote:
> 
> Mia,
> 
> Hi, I took a quick look at your BI22_SurferOutput/mri/orig/001.mgz and
> the problem appears to be with this input.  The orientation is wrong,
> and it doesnt quite look like an mprage or equivalent.  Unfortunately,
> after looking through your dicom series, it doesnt look like any of them
> are ideal for freesurfer.  the best option though is 8964, although its
> 0.5x0.5x2mm.  its a T1 and the orientation is correct, so it might
> recon.
> 
> Nick
> 
> 
> 
> 
>> On Sun, 2015-05-17 at 16:33 +, Borzello, Mia wrote:
>> Hi Freesurfers,  
>> 
>> 
>> Hope you're doing well! I tried creating a reconstruction yesterday
>> but got an error. 
>> 
>> 
>> 1)BI22
>> 2)recon-all -autorecon1 -autorecon2 -autorecon3 -subject
>> BI22_SurferOutput
>> -i 
>> /autofs/space/huygens_001/users/mia/subjects/BI22_PreOp_MRI/8961/8968/896583
>> 3)
>> 
>> 
>> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
>> ***FAILED*** (p=0.0049, pval=0. < threshold=0.0050)
>> Manual Talairach alignment may be necessary, or
>> include the -notal-check flag to skip this test,
>> making sure the -notal-check flag follows -all
>> or -autorecon1 in the command string.
>> See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
>> Linux huygens 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45
>> UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
>> 
>> 
>> recon-all -s BI22_SurferOutput exited with ERRORS at Sat May 16
>> 19:44:42 EDT 2015
>> 
>> 
>> Let me know if including the recon-all.log would be helpful.
>> 
>> 
>> Thanks so much, 
>> Mia 
>> ___
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> 
> 
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[Freesurfer] frontal lobe problem on reconstruction

[Borzello, Mia]

Hi Freesurfers,

I ran recon-all and didn't initially get an error. I am not plotting the 
surface in matlab and am getting an error but am not sure why. Any help would 
be great! Thanks!

1) BW30
2) recon-all -autorecon1 -autorecon2 -autorecon3 -subject BW30_SurferOutput -i 
/autofs/space/huygens_001/users/mia/subjects/BW30_PreOp_MRI/1.3.12.2.1107.5.2.32.35311.2015032512254299614890687.0.0.0/1.3.12.2.1107.5.2.32.35311.2015032512330819010190759.dcm

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Re: [Freesurfer] frontal lobe problem on reconstruction

[Borzello, Mia]

Awesome thank you! Just found out this patient had a previous resection. 

Thanks again!


> On May 18, 2015, at 4:23 PM, "Nick Schmansky, MGH" 
>  wrote:
> 
> Mia,
> 
> Hi, what sort of error?  I looked at the image in freeview, and it looks
> like the patient is missing their left frontal lobe.  The surfaces look
> ok in that region given that.
> 
> btw, to make viewing in freeview easy, add this to your .cshrc, all one
> line:
> 
> alias fv "freeview -v mri/T1.mgz mri/brainmask.mgz
> mri/aseg.mgz:colormap=lut -f surf/lh.pial:edgecolor=red
> surf/rh.pial:edgecolor=red surf/lh.white:edgecolor=blue
> surf/rh.white:edgecolor=blue"
> 
> then, to use:
> 
> cd BW30_PreOp_MRI
> fv
> 
> it will bring-up the major volumes and surfaces.
> 
> N.
> 
> 
> 
>> On Mon, 2015-05-18 at 20:02 +, Borzello, Mia wrote:
>> Hi Freesurfers,  
>> 
>> 
>> I ran recon-all and didn't initially get an error. I am not plotting
>> the surface in matlab and am getting an error but am not sure why. Any
>> help would be great! Thanks!
>> 
>> 
>> 1) BW30
>> 2) recon-all -autorecon1 -autorecon2 -autorecon3
>> -subjectBW30_SurferOutput -i 
>> /autofs/space/huygens_001/users/mia/subjects/BW30_PreOp_MRI/1.3.12.2.1107.5.2.32.35311.2015032512254299614890687.0.0.0/1.3.12.2.1107.5.2.32.35311.2015032512330819010190759.dcm
>> 
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
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[Freesurfer] trouble computing outer pial surfaces

[Borzello, Mia]

Hi Freesurfers,

I was just running the right and left outer pial layers for a subject and came 
up with an error.

1) MG84
2)  mris_compute_lgi --i rh.pial --close_sphere_size 30 --smooth_iters 60
3) Error in dsearchn (line 79)
[d(i),t(i)] = min(sum((x-yi).^2,2));

Error in mesh_vertex_nearest (line 29)
nearestIndex = dsearchn(vertices,points);

Error in reorganize_verticeslist (line 28)

[nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:));

Error in make_roi_paths (line 93)
reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim,
verticeslist, step);

>>
ERROR:  make_roi_paths did not complete successfully!



Thank you!
Mia
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Re: [Freesurfer] frontal lobe problem on reconstruction

[Borzello, Mia]

what is a .cshr? 

do i just type the long command at the command line? sorry if this is a dumb 
question

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Nick Schmansky, MGH 
[ni...@nmr.mgh.harvard.edu]
Sent: Monday, May 18, 2015 4:23 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] frontal lobe problem on reconstruction

Mia,

Hi, what sort of error?  I looked at the image in freeview, and it looks
like the patient is missing their left frontal lobe.  The surfaces look
ok in that region given that.

btw, to make viewing in freeview easy, add this to your .cshrc, all one
line:

alias fv "freeview -v mri/T1.mgz mri/brainmask.mgz
mri/aseg.mgz:colormap=lut -f surf/lh.pial:edgecolor=red
surf/rh.pial:edgecolor=red surf/lh.white:edgecolor=blue
surf/rh.white:edgecolor=blue"

then, to use:

cd BW30_PreOp_MRI
fv

it will bring-up the major volumes and surfaces.

N.



On Mon, 2015-05-18 at 20:02 +, Borzello, Mia wrote:
> Hi Freesurfers,
>
>
> I ran recon-all and didn't initially get an error. I am not plotting
> the surface in matlab and am getting an error but am not sure why. Any
> help would be great! Thanks!
>
>
> 1) BW30
> 2) recon-all -autorecon1 -autorecon2 -autorecon3
> -subjectBW30_SurferOutput -i 
> /autofs/space/huygens_001/users/mia/subjects/BW30_PreOp_MRI/1.3.12.2.1107.5.2.32.35311.2015032512254299614890687.0.0.0/1.3.12.2.1107.5.2.32.35311.2015032512330819010190759.dcm
>
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[Freesurfer] registering NHP data

[Borzello, Mia]

Hi Freesurfer experts,

Does Freesurfer have a separate pipeline for registering NHP data? I am trying 
to register macaque data and localize the implanted electrodes, but the normal 
protocol errored. I did a google search and found this- is this what I should 
be using?: https://surfer.nmr.mgh.harvard.edu/fswiki/MonkeyData

I downloaded the scripts but I'm not sure what commands I'm supposed to be 
running, etc.
Any guidance you can give would be must appreciated!

Thanks,
m
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Re: [Freesurfer] registering NHP data

[Borzello, Mia]

Awesome that you guys are working a parcellation! In the meantime, if I wanted 
to try to use the atlases you suggested, how would I go about processing the 
data? Is there documentation I can follow?

Thanks so much,
Mia





From: MCLAREN, Donald [mclaren.don...@gmail.com]
Sent: Tuesday, August 04, 2015 9:36 AM
To: Borzello, Mia
Subject: Re: [Freesurfer] registering NHP data

Mia,

You could use the 112RM-SL atlas for normalization and then use the 
Saleem-Logothetis Atlas for localization. Hopefully, by August, we'll have a 
parcellation on the the MR image so that localization can be done automatically.

Best Regards,
Donald McLaren, PhD


On Mon, Aug 3, 2015 at 2:01 PM, Borzello, Mia 
mailto:mborze...@partners.org>> wrote:
Hi Freesurfer experts,

Does Freesurfer have a separate pipeline for registering NHP data? I am trying 
to register macaque data and localize the implanted electrodes, but the normal 
protocol errored. I did a google search and found this- is this what I should 
be using?: https://surfer.nmr.mgh.harvard.edu/fswiki/MonkeyData

I downloaded the scripts but I'm not sure what commands I'm supposed to be 
running, etc.
Any guidance you can give would be must appreciated!

Thanks,
m

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[Freesurfer] mri_convert IMA to MGZ

[Borzello, Mia]

Hi freesurfers,

I want to localize electrode locations from a NHP CT scan, am i able to do that 
with tkmedit without coregistering first? I don't need all the parcellations of 
a specific atlas, just the RAS coordinates.

Also, the CT images are IMA files. Is there a way to convert from IMA to MGZ, 
something like:
mri_convert -i first_ct_dicom.dcm -o ct.mgz

I tried this and it created a file but i want to make sure i didn't need to 
make any specifications in the command.

Thanks,
m
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[Freesurfer] dicom loading difficulty

[Borzello, Mia]

Hi Freesurfers,

I'm trying to convert CT dicoms to the MGZ format, but am getting an error 
saying "the pixel data cannot be loaded as it is JPEG compressed." I originally 
got dicoms without the extension .dcm, but then resaved them with the 
extension. Using either version didn't work. If you can shed some light on 
this, that would be great!

Thanks,
m
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Re: [Freesurfer] dicom loading difficulty

[Borzello, Mia]

Hmm this didn't seem to work. I converted all 78 files. Is it okay to leave 
both versions of the dicoms (the ones with the .dcm extension and the original 
in the same folder)? 

Thanks, 
m

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, February 04, 2014 11:21 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] dicom loading difficulty

FS does not natively uncompress jpeg compressed dicoms, however, you can
get and use the dcmdjpeg to do the decompression like this

 dcmdjpeg +te dicomfile dicomfile

this will overwrite the dicom file, so make a backup. You will have to
run this for all of your dicoms

doug


On 02/04/2014 10:31 AM, Borzello, Mia wrote:
> Hi Freesurfers,
>
> I'm trying to convert CT dicoms to the MGZ format, but am getting an
> error saying "the pixel data cannot be loaded as it is JPEG
> compressed." I originally got dicoms without the extension .dcm, but
> then resaved them with the extension. Using either version didn't
> work. If you can shed some light on this, that would be great!
>
> Thanks,
> m
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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Re: [Freesurfer] dicom loading difficulty

[Borzello, Mia]

Okay, I separated and moved everything into its own folder. I just ran 
spmregister and then tkregister and the CT is really skewed. I'm wondering if I 
accidentally fussed with something or if there is another way I can fix this. 
Can someone look at the data? I chose the CT with the most slices, and the 
second highest scan has 35 slices. 

Thanks so much, 
m

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, February 04, 2014 3:01 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] dicom loading difficulty

I would put the new ones into a different folder
doug

On 02/04/2014 02:35 PM, Borzello, Mia wrote:
> Hmm this didn't seem to work. I converted all 78 files. Is it okay to leave 
> both versions of the dicoms (the ones with the .dcm extension and the 
> original in the same folder)?
>
> Thanks,
> m
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Tuesday, February 04, 2014 11:21 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] dicom loading difficulty
>
> FS does not natively uncompress jpeg compressed dicoms, however, you can
> get and use the dcmdjpeg to do the decompression like this
>
>   dcmdjpeg +te dicomfile dicomfile
>
> this will overwrite the dicom file, so make a backup. You will have to
> run this for all of your dicoms
>
> doug
>
>
> On 02/04/2014 10:31 AM, Borzello, Mia wrote:
>> Hi Freesurfers,
>>
>> I'm trying to convert CT dicoms to the MGZ format, but am getting an
>> error saying "the pixel data cannot be loaded as it is JPEG
>> compressed." I originally got dicoms without the extension .dcm, but
>> then resaved them with the extension. Using either version didn't
>> work. If you can shed some light on this, that would be great!
>>
>> Thanks,
>> m
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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

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

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[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

[Borzello, Mia]

Is this okay to do even if I've done a coregistration, nothing will be deleted? 
Also, are the pial surfaces necessary for plotting? I'm wondering if I can just 
use the files that I have to create a plot without having to rerun anything. 

Thanks, 
Mia 





> On Feb 10, 2014, at 4:31 PM, "Bruce Fischl"  
> wrote:
> 
> 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] creating specific files

[Borzello, Mia]

Okay and is there a way to check if the files I currently have are sufficient 
to plot with? 

Thanks, 
m



> On Feb 11, 2014, at 9:58 AM, "Bruce Fischl"  
> wrote:
> 
> if they are zero length there is nothing there now
>> On Tue, 11 Feb 2014, Borzello, Mia wrote:
>> 
>> Is this okay to do even if I've done a coregistration, nothing will be 
>> deleted? Also, are the pial surfaces necessary for plotting? I'm wondering 
>> if I can just use the files that I have to create a plot without having to 
>> rerun anything.
>> 
>> Thanks,
>> Mia
>> 
>> 
>> 
>> 
>> 
>>> On Feb 10, 2014, at 4:31 PM, "Bruce Fischl"  
>>> wrote:
>>> 
>>> 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
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>> 
>> 

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Re: [Freesurfer] creating specific files

[Borzello, Mia]

woops- sorry meant to include everyone. The name of the file I use to plot is 
"lh.pial-outer-smoothed." So I either want to create this file or figure out 
another way to plot. Do i need lh.pial to make lh.pial-outer-smoothed? 

From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Tuesday, February 11, 2014 10:51 AM
To: Borzello, Mia
Subject: Re: [Freesurfer] creating specific files

Hi Mia

can you keep ccing the list? I don't know what the "outer smoothed pial
surface" is. Is this something we create? I don't think so
Bruce


On Tue,
11 Feb 2014, Borzello, Mia wrote:

> Plotting the electrodes on the surface using matlab. I usually use the
outer smoothed pial surface- do I first need the normal pial surface to
create this?   >
>
>
>> On Feb 11, 2014, at 10:42 AM, "Bruce Fischl"  
>> wrote:
>>
>> what kind of plotting do you mean?
>>> On Tue, 11 Feb 2014, Borzello, Mia wrote:
>>>
>>> Okay and is there a way to check if the files I currently have are 
>>> sufficient to plot with?
>>>
>>> Thanks,
>>> m
>>>
>>>
>>>
>>>> On Feb 11, 2014, at 9:58 AM, "Bruce Fischl"  
>>>> wrote:
>>>>
>>>> if they are zero length there is nothing there now
>>>>> On Tue, 11 Feb 2014, Borzello, Mia wrote:
>>>>>
>>>>> Is this okay to do even if I've done a coregistration, nothing will be 
>>>>> deleted? Also, are the pial surfaces necessary for plotting? I'm 
>>>>> wondering if I can just use the files that I have to create a plot 
>>>>> without having to rerun anything.
>>>>>
>>>>> Thanks,
>>>>> Mia
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> On Feb 10, 2014, at 4:31 PM, "Bruce Fischl"  
>>>>>> wrote:
>>>>>>
>>>>>> 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
>>>>>
>>>>> ___
>>>>> 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
>>>
>>>
>>>
>
>
>

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Re: [Freesurfer] creating specific files

[Borzello, Mia]

Another question- will I need to re-coregister if I rerun a reconstruction?

Thanks, 
m

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia
Sent: Tuesday, February 11, 2014 11:05 AM
To: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] creating specific files

woops- sorry meant to include everyone. The name of the file I use to plot is 
"lh.pial-outer-smoothed." So I either want to create this file or figure out 
another way to plot. Do i need lh.pial to make lh.pial-outer-smoothed?

From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Tuesday, February 11, 2014 10:51 AM
To: Borzello, Mia
Subject: Re: [Freesurfer] creating specific files

Hi Mia

can you keep ccing the list? I don't know what the "outer smoothed pial
surface" is. Is this something we create? I don't think so
Bruce


On Tue,
11 Feb 2014, Borzello, Mia wrote:

> Plotting the electrodes on the surface using matlab. I usually use the
outer smoothed pial surface- do I first need the normal pial surface to
create this?   >
>
>
>> On Feb 11, 2014, at 10:42 AM, "Bruce Fischl"  
>> wrote:
>>
>> what kind of plotting do you mean?
>>> On Tue, 11 Feb 2014, Borzello, Mia wrote:
>>>
>>> Okay and is there a way to check if the files I currently have are 
>>> sufficient to plot with?
>>>
>>> Thanks,
>>> m
>>>
>>>
>>>
>>>> On Feb 11, 2014, at 9:58 AM, "Bruce Fischl"  
>>>> wrote:
>>>>
>>>> if they are zero length there is nothing there now
>>>>> On Tue, 11 Feb 2014, Borzello, Mia wrote:
>>>>>
>>>>> Is this okay to do even if I've done a coregistration, nothing will be 
>>>>> deleted? Also, are the pial surfaces necessary for plotting? I'm 
>>>>> wondering if I can just use the files that I have to create a plot 
>>>>> without having to rerun anything.
>>>>>
>>>>> Thanks,
>>>>> Mia
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> On Feb 10, 2014, at 4:31 PM, "Bruce Fischl"  
>>>>>> wrote:
>>>>>>
>>>>>> 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
>>>>>
>>>>> ___
>>>>> 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
>>>
>>>
>>>
>
>
>

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[Freesurfer] error at spmregister

[Borzello, Mia]

Hi Freesurfers,

I get an error when using spmregister saying "Maximum variable size allowed by 
the program is exceeded"- is that a problem with the number of dicoms?
I can attach a screenshot of the error if that helps.

Thanks,
Mia
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Re: [Freesurfer] error at spmregister

[Borzello, Mia]

the last line of "error_spm" is the command line, and the errors for that 
command are above. 

Thanks,
m

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, February 28, 2014 11:58 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] error at spmregister

never seen that. can you send your command line and the log file?
On 02/28/2014 11:43 AM, Borzello, Mia wrote:
> Hi Freesurfers,
>
> I get an error when using spmregister saying "Maximum variable size
> allowed by the program is exceeded"- is that a problem with the number
> of dicoms?
> I can attach a screenshot of the error if that helps.
>
> Thanks,
> Mia
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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spmregister.log
Description: spmregister.log
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[Freesurfer] aligning/quality of CT

[Borzello, Mia]

Hi Freesurfers,

In general when aligning an MR and a CT, is a 32 slices CT sufficient? I've 
done a coregistration and am looking at it in tkmedit and the quality of the 
image isn't so good.

Thanks,
Mia
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Re: [Freesurfer] error at spmregister

[Borzello, Mia]

I haven't actually changed anything in the setup though- how do I figure out 
what to change?

Thanks, 
Mia

Sent from my iPhone

> On Feb 28, 2014, at 7:31 PM, "Douglas N Greve"  
> wrote:
> 
> looks like there is something going wrong in your matlab setup
> 
> Warning: Executing startup failed in matlabrc.
> This indicates a potentially serious problem in your MATLAB setup,
> which should be resolved as soon as possible.  Error detected was:
> MATLAB:UndefinedFunction
> Undefined function or variable 'mne_setup_toolbox'.
> 
> 
> 
>> On 02/28/2014 12:01 PM, Borzello, Mia wrote:
>> the last line of "error_spm" is the command line, and the errors for that 
>> command are above.
>> 
>> Thanks,
>> m
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Friday, February 28, 2014 11:58 AM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] error at spmregister
>> 
>> never seen that. can you send your command line and the log file?
>>> On 02/28/2014 11:43 AM, Borzello, Mia wrote:
>>> Hi Freesurfers,
>>> 
>>> I get an error when using spmregister saying "Maximum variable size
>>> allowed by the program is exceeded"- is that a problem with the number
>>> of dicoms?
>>> I can attach a screenshot of the error if that helps.
>>> 
>>> Thanks,
>>> Mia
>>> 
>>> 
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>> 
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] error at spmregister

[Borzello, Mia]

So I'm running spmregister from a new computer now, and I'm still not getting a 
successful output. I am not longer getting a matlab error, but after I run 
spmregister, I then run tkregister2 but get an error that it couldn't open 
spm.reg.dat. It wasn't created in the spmregister I guess. What would be the 
problem when I ran spmregister

Thanks, 
m

From: Douglas Greve [gr...@nmr.mgh.harvard.edu]
Sent: Saturday, March 01, 2014 10:31 AM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] error at spmregister

this is a matlab problem, not a FreeSurfer problem, so I'm not sure. It
might be the MNE toolbox. I would try commenting out all the non-FS
stuff in your ~/matlab/startup.m file and see if the problem goes away.

On 3/1/14 8:50 AM, Borzello, Mia wrote:
> I haven't actually changed anything in the setup though- how do I figure out 
> what to change?
>
> Thanks,
> Mia
>
> Sent from my iPhone
>
>> On Feb 28, 2014, at 7:31 PM, "Douglas N Greve"  
>> wrote:
>>
>> looks like there is something going wrong in your matlab setup
>>
>> Warning: Executing startup failed in matlabrc.
>> This indicates a potentially serious problem in your MATLAB setup,
>> which should be resolved as soon as possible.  Error detected was:
>> MATLAB:UndefinedFunction
>> Undefined function or variable 'mne_setup_toolbox'.
>>
>>
>>
>>> On 02/28/2014 12:01 PM, Borzello, Mia wrote:
>>> the last line of "error_spm" is the command line, and the errors for that 
>>> command are above.
>>>
>>> Thanks,
>>> m
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Friday, February 28, 2014 11:58 AM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] error at spmregister
>>>
>>> never seen that. can you send your command line and the log file?
>>>> On 02/28/2014 11:43 AM, Borzello, Mia wrote:
>>>> Hi Freesurfers,
>>>>
>>>> I get an error when using spmregister saying "Maximum variable size
>>>> allowed by the program is exceeded"- is that a problem with the number
>>>> of dicoms?
>>>> I can attach a screenshot of the error if that helps.
>>>>
>>>> Thanks,
>>>> Mia
>>>>
>>>>
>>>> ___
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu
>>> Phone Number: 617-724-2358
>>> Fax: 617-726-7422
>>>
>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>


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Re: [Freesurfer] tkmedit contrast

[Borzello, Mia]

no it doesn't help at all.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, March 14, 2014 1:11 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] tkmedit contrast

does the brightness/contrast window you display not work?
On 03/14/2014 12:59 PM, Borzello, Mia wrote:
> Hi Freesurfers,
>
> I recently coregisered a patient and am trying to visualize the
> electrodes in tkmedit now, but I'm unable to see them very clearly.
> The CT has 1mm slices, so I don't think there should be anything wrong
> with the CT. Is there an option on the gui that deals with the
> contrast? I attached a picture of the max intensity projection that
> shows wires but no electrodes.
>
> Thanks!
> Mia B.
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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Re: [Freesurfer] tkmedit contrast

[Borzello, Mia]

Was there any solution for this?

Thanks, 
Mia

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia
Sent: Friday, March 14, 2014 1:17 PM
To: Douglas N Greve; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] tkmedit contrast

no it doesn't help at all.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, March 14, 2014 1:11 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] tkmedit contrast

does the brightness/contrast window you display not work?
On 03/14/2014 12:59 PM, Borzello, Mia wrote:
> Hi Freesurfers,
>
> I recently coregisered a patient and am trying to visualize the
> electrodes in tkmedit now, but I'm unable to see them very clearly.
> The CT has 1mm slices, so I don't think there should be anything wrong
> with the CT. Is there an option on the gui that deals with the
> contrast? I attached a picture of the max intensity projection that
> shows wires but no electrodes.
>
> Thanks!
> Mia B.
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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Re: [Freesurfer] tkmedit contrast

[Borzello, Mia]

I haven't checked that yet- would i still be able to pick points in freeview?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Wednesday, March 19, 2014 7:16 PM
To: Freesurfer support list
Cc: Douglas N Greve
Subject: Re: [Freesurfer] tkmedit contrast

does it work in freeview?
On Wed, 19 Mar 2014, Borzello, Mia wrote:

> Was there any solution for this?
>
> Thanks,
> Mia
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia
> Sent: Friday, March 14, 2014 1:17 PM
> To: Douglas N Greve; freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] tkmedit contrast
>
> no it doesn't help at all.
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, March 14, 2014 1:11 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] tkmedit contrast
>
> does the brightness/contrast window you display not work?
> On 03/14/2014 12:59 PM, Borzello, Mia wrote:
>> Hi Freesurfers,
>>
>> I recently coregisered a patient and am trying to visualize the
>> electrodes in tkmedit now, but I'm unable to see them very clearly.
>> The CT has 1mm slices, so I don't think there should be anything wrong
>> with the CT. Is there an option on the gui that deals with the
>> contrast? I attached a picture of the max intensity projection that
>> shows wires but no electrodes.
>>
>> Thanks!
>> Mia B.
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
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> 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
>
>
>
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Re: [Freesurfer] tkmedit contrast

[Borzello, Mia]

picking the electrode points for an intracranial patient. I can usually do it 
pretty easily in tkmedit, but I'm just getting an odd contrast with this CT. 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Thursday, March 20, 2014 12:39 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] tkmedit contrast

what kind of points? Almost certainly yes, but it will also be
interesting debugging information for us to see whether it works or not
On
Thu, 20 Mar 2014, Borzello, Mia wrote:

> I haven't checked that yet- would i still be able to pick points in freeview?
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Wednesday, March 19, 2014 7:16 PM
> To: Freesurfer support list
> Cc: Douglas N Greve
> Subject: Re: [Freesurfer] tkmedit contrast
>
> does it work in freeview?
> On Wed, 19 Mar 2014, Borzello, Mia wrote:
>
>> Was there any solution for this?
>>
>> Thanks,
>> Mia
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia
>> Sent: Friday, March 14, 2014 1:17 PM
>> To: Douglas N Greve; freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] tkmedit contrast
>>
>> no it doesn't help at all.
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Friday, March 14, 2014 1:11 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] tkmedit contrast
>>
>> does the brightness/contrast window you display not work?
>> On 03/14/2014 12:59 PM, Borzello, Mia wrote:
>>> Hi Freesurfers,
>>>
>>> I recently coregisered a patient and am trying to visualize the
>>> electrodes in tkmedit now, but I'm unable to see them very clearly.
>>> The CT has 1mm slices, so I don't think there should be anything wrong
>>> with the CT. Is there an option on the gui that deals with the
>>> contrast? I attached a picture of the max intensity projection that
>>> shows wires but no electrodes.
>>>
>>> Thanks!
>>> Mia B.
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
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[Freesurfer] sheered CT in tkregister2

[Borzello, Mia]

Hi Freesurfers,

I am trying to coregister with a high-res CT, but for some reason am getting a 
very sheered image when I am in tkregister. Should I use another CT?
Thank you!


1) MG93
2)tkregister2 --s MG93_SurferOutput --mov ct.mgz --reg spm.reg.dat --surf orig
3) no error message, just a sheered image


FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0

'build-stamp.txt file does not exist!
This appears to be a very old version of FreeSurfer!

RedHat release: CentOS release 6.7 (Final)

Kernel info: Linux 2.6.32-573.3.1.el6.x86_64 x86_64

NMR Center info (/space/freesurfer exists):

  machine: huygens

  SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects

  PWD: /autofs/space/huygens_001/users/mia/subjects/MG93_SurferOutput/mri

  ssh huygens
  setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
  cd /autofs/space/huygens_001/users/mia/subjects/MG93_SurferOutput/mri

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Re: [Freesurfer] sheered CT in tkregister2

[Borzello, Mia]

Are any of the CT scans for this patient okay? How can I check? The one I 
picked is 1 mm so I thought it was fine. Also, what does 9 dof refer to?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, November 20, 2015 12:52 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] sheered CT in tkregister2

The CT itself has incorrect parameters for the pixel size. You can try
using 9 dof instead of 6, but in the end you'll want to fix your CT probably

On 11/20/2015 12:47 PM, Borzello, Mia wrote:
> Hi Freesurfers,
>
> I am trying to coregister with a high-res CT, but for some reason am
> getting a very sheered image when I am in tkregister. Should I use
> another CT?
> Thank you!
>
>
> 1) MG93
> 2)tkregister2 --s MG93_SurferOutput --mov ct.mgz --reg spm.reg.dat
> --surf orig
> 3) no error message, just a sheered image
>
>
> FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
>
> 'build-stamp.txt file does not exist!
> This appears to be a very old version of FreeSurfer!
>
> RedHat release: CentOS release 6.7 (Final)
>
> Kernel info: Linux 2.6.32-573.3.1.el6.x86_64 x86_64
>
> NMR Center info (/space/freesurfer exists):
>
>   machine: huygens
>
>   SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects
>
>   PWD: /autofs/space/huygens_001/users/mia/subjects/MG93_SurferOutput/mri
>
>   ssh huygens
>   setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
>   cd /autofs/space/huygens_001/users/mia/subjects/MG93_SurferOutput/mri
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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Re: [Freesurfer] sheered CT in tkregister2

[Borzello, Mia]

Is there a way to change the scale in freeview?

Thanks,
Mia

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, November 20, 2015 1:38 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] sheered CT in tkregister2

look at them in freeview
9 dof means 9 degrees of freedom in the registration, 3 translation, 3
rotation, and 3 scale. The 3 scale may account for errors in the voxels
size of the ct

On 11/20/2015 12:54 PM, Borzello, Mia wrote:
> Are any of the CT scans for this patient okay? How can I check? The one I 
> picked is 1 mm so I thought it was fine. Also, what does 9 dof refer to?
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, November 20, 2015 12:52 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] sheered CT in tkregister2
>
> The CT itself has incorrect parameters for the pixel size. You can try
> using 9 dof instead of 6, but in the end you'll want to fix your CT probably
>
> On 11/20/2015 12:47 PM, Borzello, Mia wrote:
>> Hi Freesurfers,
>>
>> I am trying to coregister with a high-res CT, but for some reason am
>> getting a very sheered image when I am in tkregister. Should I use
>> another CT?
>> Thank you!
>>
>>
>> 1) MG93
>> 2)tkregister2 --s MG93_SurferOutput --mov ct.mgz --reg spm.reg.dat
>> --surf orig
>> 3) no error message, just a sheered image
>>
>>
>> FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
>>
>> 'build-stamp.txt file does not exist!
>> This appears to be a very old version of FreeSurfer!
>>
>> RedHat release: CentOS release 6.7 (Final)
>>
>> Kernel info: Linux 2.6.32-573.3.1.el6.x86_64 x86_64
>>
>> NMR Center info (/space/freesurfer exists):
>>
>>machine: huygens
>>
>>SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects
>>
>>PWD: /autofs/space/huygens_001/users/mia/subjects/MG93_SurferOutput/mri
>>
>>ssh huygens
>>setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
>>cd /autofs/space/huygens_001/users/mia/subjects/MG93_SurferOutput/mri
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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

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

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[Freesurfer] spmregister error

[Borzello, Mia]

Hi Freesurfers,

I'm in the middle of coregistering  a CT and MRI, and after running
spmregister --s MGXX_SurferOutput --mov ct.mgz --reg spm.reg.dat --fsvol orig

I get the error that orig.mgz is not found in COR or MGZ formats, but I have an 
orig.mgz file in my folder. Any help on this would be awesome!

Thanks,
Mia

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[Freesurfer] coregistering- ideal CT type

[Borzello, Mia]

Hi freesurfers,

I working on a coregistration right now with a few different CT scans. None of 
them have looked that good with tkregister (for example when I used one CT 
scan, the electrodes didn't even show up). Is there an certain CT I need to be 
using?

Thanks,
m

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[Freesurfer] odd tkregister

[Borzello, Mia]

Hi freesurfers,

In using tkregister, I generated an odd (see attached): the image not only 
looks sheered but there is an old white box showing up. I'm not sure how to 
resolve this.

Thanks a lot,
Mia
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[Freesurfer] Exiting with errors but not sure why

[Borzello, Mia]

Hi freesurfers!

Great tutorial this week!

I've recently run a recon, and it's exited with errors, but I'm not completely 
sure why. I've attached the error.log, but le tme know if I should attach 
another file.

Thanks so much,
Mia


error.log
Description: error.log
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Re: [Freesurfer] Exiting with errors but not sure why

[Borzello, Mia]

Great! I've attached it. 

Thanks,
m


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Thursday, May 02, 2013 11:45 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Exiting with errors but not sure why

Hi Mia, I'm glad your enjoyed the course. Can you send the recon-all.log
file from the subject/scripts folder?
doug

On 05/02/2013 11:36 AM, Borzello, Mia wrote:
> Hi freesurfers!
>
> Great tutorial this week!
>
> I've recently run a recon, and it's exited with errors, but I'm not
> completely sure why. I've attached the error.log, but le tme know if I
> should attach another file.
>
> Thanks so much,
> Mia
>
>
> ___
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--
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
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recon-all.log
Description: recon-all.log
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[Freesurfer] Recon-all error

[Borzello, Mia]

Hi freesurfers,



I recently ran a reconstruction, but it's errored. I'm not sure why thought, 
but I've attached the recon log.



Thanks,

Mia
--
SUBJECT MGH009_SurferOutput
DATE Mon May 13 11:25:37 EDT 2013
USER miaborz
HOST huygens
PROCESSOR x86_64
OS Linux
Linux huygens 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
$Id: recon-all,v 1.379.2.65 2013/02/19 22:34:56 nicks Exp $
/usr/local/freesurfer/stable5_2_0/bin/recon-all
PWD /autofs/space/huygens_001/users/mia/subjects/MGH009_SurferOutput/mri
CMD talairach_afd -T 0.005 -xfm transforms/talairach.xfm
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Re: [Freesurfer] Recon-all error

[Borzello, Mia]

sorry, recon-all.log attached!

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia
Sent: Tuesday, May 14, 2013 4:23 PM
To: freesurfer
Subject: [Freesurfer] Recon-all error


Hi freesurfers,



I recently ran a reconstruction, but it's errored. I'm not sure why thought, 
but I've attached the recon log.



Thanks,

Mia


recon-all.log
Description: recon-all.log
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Re: [Freesurfer] Recon-all error

[Borzello, Mia]

I actually didn't change any of the parameters for this patient- not the dicoms 
or headers, just put the dicoms as they were through the freesurfer stream. I 
can send you all the possible sequences I could have used from the MR? I think 
that this was an mprage, so I thought it would work. 

Thanks so much, 
Mia 

From: Nick Schmansky [ni...@nmr.mgh.harvard.edu]
Sent: Tuesday, May 14, 2013 4:57 PM
To: Borzello, Mia
Cc: freesurfer
Subject: Re: [Freesurfer] Recon-all error

Mia,

Hi, in looking at the mri/orig/001.mgz, the image in the sagital and
coronal planes look inverted. also, i noticed this mri_info:

dimensions: 566 x 256 x 992
   voxel sizes: 1., 1., 1.

which seems like unusual input.  how was this converted from the dicom?
did it necessitate altering the header?

Nick



On Tue, 2013-05-14 at 20:23 +0000, Borzello, Mia wrote:
> Hi freesurfers,
>
>
>
> I recently ran a reconstruction, but it's errored. I'm not sure why
> thought, but I've attached the recon log.
>
>
>
> Thanks,
>
> Mia
>
>
> ___
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[Freesurfer] ct.anat.nii file

[Borzello, Mia]

Hi Freesurfers,

I'm wondering if there is a way to figure out if a ct.anat.nii file is corrupt 
or not. I'm using MRICro as a viewer, and the file doesn't look right.

Thanks,
Mia
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[Freesurfer] recon error- too many arguments?

[Borzello, Mia]

Hi,

I'm trying to run a recon, but I keep getting the error: too many arguments for 
the following command:
econ-all -autorecon1 -autorecon2 -autorecon3 -subject _SurferOutput -i 
[path to dicom]

Any help on this would be excellent!

Thanks,
M

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Re: [Freesurfer] recon error- too many arguments?

[Borzello, Mia]

Yes! I attached a screen shot. Thanks!


From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Friday, June 15, 2012 11:33 AM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon error- too many arguments?

Hi Mia

can you send us the actual command and screen output?

thanks
Bruce
On Fri, 15 Jun 2012,
Borzello, Mia wrote:

> Hi,
>
> I'm trying to run a recon, but I keep getting the error: too many arguments 
> for the following command:
> econ-all -autorecon1 -autorecon2 -autorecon3 -subject _SurferOutput -i 
> [path to dicom]
>
> Any help on this would be excellent!
>
> Thanks,
> M
>
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>
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] recon error- too many arguments?

[Borzello, Mia]

bingo! 
thanks a lot!
m

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, June 15, 2012 1:31 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon error- too many arguments?

Hi Mia, I think the problem is that you have a space in the path to the
dicom. Even though you put a backslash there, I think it is still
causing the problem
doug

On 06/15/2012 01:13 PM, Borzello, Mia wrote:
> Yes! I attached a screen shot. Thanks!
>
> 
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: Friday, June 15, 2012 11:33 AM
> To: Borzello, Mia
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] recon error- too many arguments?
>
> Hi Mia
>
> can you send us the actual command and screen output?
>
> thanks
> Bruce
> On Fri, 15 Jun 2012,
> Borzello, Mia wrote:
>
>> Hi,
>>
>> I'm trying to run a recon, but I keep getting the error: too many arguments 
>> for the following command:
>> econ-all -autorecon1 -autorecon2 -autorecon3 -subject _SurferOutput -i 
>> [path to dicom]
>>
>> Any help on this would be excellent!
>>
>> Thanks,
>> M
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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[Freesurfer] lh.pial question

[Borzello, Mia]

Hi all,

Is there a way to edit the pial files (e.g. lh.pial)? I want to delete a few 
vertices we think are causing errors for a 3D printing we are trying to do.

Thanks,
m

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Re: [Freesurfer] axial sheer

[Borzello, Mia]

sure!
at the command line: tkregister2 --s BWXX_SurferOutput --mov ct.mgz --reg 
spm.reg.dat --surf orig
this it's a CT of 124 slices from bwh

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Sunday, July 01, 2012 11:28 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] axial sheer

Can you give more info? Command line, description of data, where you got it 
from etc
doug


On 7/1/12 9:58 PM, Borzello, Mia wrote:

Hi freesurfers,

Is there a way to fix sheering. The views are good on both coronal and sagittal 
slices, but the horizonal view is pretty skewed. I've attached a screen shot.

Thanks for the help,
Mia B.




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Re: [Freesurfer] axial sheer

[Borzello, Mia]

i can fix this if I work with the identity matrix (emacs spm.reg.dat) after 
automatically coregistering (using spmregister), right?

thanks, 
m

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia
Sent: Monday, July 02, 2012 10:05 AM
To: Douglas Greve; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] axial sheer

sure!
at the command line: tkregister2 --s BWXX_SurferOutput --mov ct.mgz --reg 
spm.reg.dat --surf orig
this it's a CT of 124 slices from bwh

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Sunday, July 01, 2012 11:28 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] axial sheer

Can you give more info? Command line, description of data, where you got it 
from etc
doug


On 7/1/12 9:58 PM, Borzello, Mia wrote:

Hi freesurfers,

Is there a way to fix sheering. The views are good on both coronal and sagittal 
slices, but the horizonal view is pretty skewed. I've attached a screen shot.

Thanks for the help,
Mia B.




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Re: [Freesurfer] slanted

[Borzello, Mia]

Will he be back today? Upload it in an e-mail?

Thanks, 
m

From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Wednesday, July 11, 2012 12:21 PM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] slanted

Hi Mia,

you'll probably have to wait until Doug is back to get an answer. In the
meantime, feel free to upload your data so we can take a look

cheers
Bruce
On Wed, 11 Jul
2012, Borzello, Mia wrote:

> Hi,
>
> I'm not exactly sure what the problem is, but for some reason, this brain is 
> kind of sheered. I'm not sure if it's because of the CT, but on the right 
> side of the picture i attached, it kind of wider on one side. It's alignment 
> isn't right, and using "rotate" does help. How should I correct this?
>
> Thanks,
> Mia
>

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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] slanted

[Borzello, Mia]

i saw the instructions, but it doesn't give an e-mail specifically for that and 
ftp surfer.nmr.mgh.harvard.edu doesn't work.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Wednesday, July 11, 2012 1:24 PM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] slanted

Hi Mia,

no, there are instructions on the wiki for uploading your data using
either ftp or the filedrop. And no, I think it will be another couple of
days
Bruce
On Wed, 11 Jul 2012, Borzello, Mia wrote:

> Will he be back today? Upload it in an e-mail?
>
> Thanks,
> m
> 
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: Wednesday, July 11, 2012 12:21 PM
> To: Borzello, Mia
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] slanted
>
> Hi Mia,
>
> you'll probably have to wait until Doug is back to get an answer. In the
> meantime, feel free to upload your data so we can take a look
>
> cheers
> Bruce
> On Wed, 11 Jul
> 2012, Borzello, Mia wrote:
>
>> Hi,
>>
>> I'm not exactly sure what the problem is, but for some reason, this brain is 
>> kind of sheered. I'm not sure if it's because of the CT, but on the right 
>> side of the picture i attached, it kind of wider on one side. It's alignment 
>> isn't right, and using "rotate" does help. How should I correct this?
>>
>> Thanks,
>> Mia
>>
>
>
>
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Re: [Freesurfer] slanted

[Borzello, Mia]

oh i'm trying to do the e-mail file drop though, that's fine too right? i'm 
just not sure what e-mail to use for the recipient e-mail.

From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Wednesday, July 11, 2012 1:58 PM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] slanted

when you say ftp doesn't work, what do you mean? It works for me:

ftp surfer.nmr.mgh.harvard.edu
Connected to surfer.nmr.mgh.harvard.edu (132.183.202.158).
220-This is the Martinos Center Anonymous FTP service. Use of this site
220-shows implicit consent to our Acceptable Use Policy outlined at
220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php
220-
220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
220-
220-229 Entering Extended Passive Mode
220-
220-   and nothing happens OR
220-
220-229 Entering Extended Passive Mode
220-500 Bad EPRT protocol.
220-
220-  try issuing the EPSV command prior to GET or PUT.
220-
220
Name (surfer.nmr.mgh.harvard.edu:fischl): anonymous
331 Please specify the password.
Password:
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd /space/incoming
250 Directory successfully changed.
ftp> ls
227 Entering Passive Mode (132,183,202,158,147,239)
150 Here comes the directory listing.
226 Transfer done (but failed to open directory).
ftp> put test.mgz
local: test.mgz remote: test.mgz
227 Entering Passive Mode (132,183,202,158,147,226)
150 Ok to send data.
226 File receive OK.
1696595 bytes sent in 0.209 secs (7.9e+03 Kbytes/sec)


On Wed, 11 Jul 2012, Borzello, Mia wrote:

> i saw the instructions, but it doesn't give an e-mail specifically for that 
> and ftp surfer.nmr.mgh.harvard.edu doesn't work.
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Wednesday, July 11, 2012 1:24 PM
> To: Borzello, Mia
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] slanted
>
> Hi Mia,
>
> no, there are instructions on the wiki for uploading your data using
> either ftp or the filedrop. And no, I think it will be another couple of
> days
> Bruce
> On Wed, 11 Jul 2012, Borzello, Mia wrote:
>
>> Will he be back today? Upload it in an e-mail?
>>
>> Thanks,
>> m
>> ________
>> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
>> Sent: Wednesday, July 11, 2012 12:21 PM
>> To: Borzello, Mia
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] slanted
>>
>> Hi Mia,
>>
>> you'll probably have to wait until Doug is back to get an answer. In the
>> meantime, feel free to upload your data so we can take a look
>>
>> cheers
>> Bruce
>> On Wed, 11 Jul
>> 2012, Borzello, Mia wrote:
>>
>>> Hi,
>>>
>>> I'm not exactly sure what the problem is, but for some reason, this brain 
>>> is kind of sheered. I'm not sure if it's because of the CT, but on the 
>>> right side of the picture i attached, it kind of wider on one side. It's 
>>> alignment isn't right, and using "rotate" does help. How should I correct 
>>> this?
>>>
>>> Thanks,
>>> Mia
>>>
>>
>>
>>
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>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] slanted

[Borzello, Mia]

can i just send it to freesurfer@nmr.mgh.harvard.edu?

thanks

From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Wednesday, July 11, 2012 1:58 PM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] slanted

when you say ftp doesn't work, what do you mean? It works for me:

ftp surfer.nmr.mgh.harvard.edu
Connected to surfer.nmr.mgh.harvard.edu (132.183.202.158).
220-This is the Martinos Center Anonymous FTP service. Use of this site
220-shows implicit consent to our Acceptable Use Policy outlined at
220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php
220-
220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
220-
220-229 Entering Extended Passive Mode
220-
220-   and nothing happens OR
220-
220-229 Entering Extended Passive Mode
220-500 Bad EPRT protocol.
220-
220-  try issuing the EPSV command prior to GET or PUT.
220-
220
Name (surfer.nmr.mgh.harvard.edu:fischl): anonymous
331 Please specify the password.
Password:
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd /space/incoming
250 Directory successfully changed.
ftp> ls
227 Entering Passive Mode (132,183,202,158,147,239)
150 Here comes the directory listing.
226 Transfer done (but failed to open directory).
ftp> put test.mgz
local: test.mgz remote: test.mgz
227 Entering Passive Mode (132,183,202,158,147,226)
150 Ok to send data.
226 File receive OK.
1696595 bytes sent in 0.209 secs (7.9e+03 Kbytes/sec)


On Wed, 11 Jul 2012, Borzello, Mia wrote:

> i saw the instructions, but it doesn't give an e-mail specifically for that 
> and ftp surfer.nmr.mgh.harvard.edu doesn't work.
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Wednesday, July 11, 2012 1:24 PM
> To: Borzello, Mia
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] slanted
>
> Hi Mia,
>
> no, there are instructions on the wiki for uploading your data using
> either ftp or the filedrop. And no, I think it will be another couple of
> days
> Bruce
> On Wed, 11 Jul 2012, Borzello, Mia wrote:
>
>> Will he be back today? Upload it in an e-mail?
>>
>> Thanks,
>> m
>> ____
>> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
>> Sent: Wednesday, July 11, 2012 12:21 PM
>> To: Borzello, Mia
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] slanted
>>
>> Hi Mia,
>>
>> you'll probably have to wait until Doug is back to get an answer. In the
>> meantime, feel free to upload your data so we can take a look
>>
>> cheers
>> Bruce
>> On Wed, 11 Jul
>> 2012, Borzello, Mia wrote:
>>
>>> Hi,
>>>
>>> I'm not exactly sure what the problem is, but for some reason, this brain 
>>> is kind of sheered. I'm not sure if it's because of the CT, but on the 
>>> right side of the picture i attached, it kind of wider on one side. It's 
>>> alignment isn't right, and using "rotate" does help. How should I correct 
>>> this?
>>>
>>> Thanks,
>>> Mia
>>>
>>
>>
>>
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>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

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[Freesurfer] creating a skull

[Borzello, Mia]

Hi freesurfer family,

I am trying to create the inner skull boundary and ran: mri_watershed -atlas - 
surf -useSRAS mri.nii brain

However, after it finished running it said it was saving "brain", but "brain" 
was an unknown file type. Am i supposed to specify that somewhere?

Thanks in advance,
m

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Re: [Freesurfer] creating a skull

[Borzello, Mia]

Hi, 

I make it an mgz. When trying to load (tried using a load and read command) to 
make sure it looks okay, but it's not working. How can I view this mgz file or 
ascertain that it has an error?

Thanks, 
m

From: Louis Nicholas Vinke [vi...@nmr.mgh.harvard.edu]
Sent: Friday, August 31, 2012 10:29 AM
To: Borzello, Mia
Cc: freesurfer
Subject: Re: [Freesurfer] creating a skull

Hi,
You need to add an extension onto the file name, something like brain.mgz
or brain.nii.  The extension will tell it what format to save the output
in.
-Louis

On Fri, 31 Aug 2012, Borzello, Mia wrote:

> Hi freesurfer family,
>
> I am trying to create the inner skull boundary and ran: mri_watershed -atlas 
> - surf -useSRAS mri.nii brain
>
> However, after it finished running it said it was saving "brain", but "brain" 
> was an unknown file type. Am i supposed to specify that somewhere?
>
> Thanks in advance,
> m
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

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

Re: [Freesurfer] creating a skull

[Borzello, Mia]

I've been referred to the following link on the freesurfer site to handle this, 
but is this still current (i.e. is linux still needed to do this?): 
http://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004679.html

thanks, 
m

From: Louis Nicholas Vinke [vi...@nmr.mgh.harvard.edu]
Sent: Friday, August 31, 2012 10:29 AM
To: Borzello, Mia
Cc: freesurfer
Subject: Re: [Freesurfer] creating a skull

Hi,
You need to add an extension onto the file name, something like brain.mgz
or brain.nii.  The extension will tell it what format to save the output
in.
-Louis

On Fri, 31 Aug 2012, Borzello, Mia wrote:

> Hi freesurfer family,
>
> I am trying to create the inner skull boundary and ran: mri_watershed -atlas 
> - surf -useSRAS mri.nii brain
>
> However, after it finished running it said it was saving "brain", but "brain" 
> was an unknown file type. Am i supposed to specify that somewhere?
>
> Thanks in advance,
> m
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

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Re: [Freesurfer] creating a skull

[Borzello, Mia]

Also, is there a way to create a skull from a CT scan?

From: Borzello, Mia
Sent: Friday, August 31, 2012 12:17 PM
To: freesurfer
Subject: RE: [Freesurfer] creating a skull

I've been referred to the following link on the freesurfer site to handle this, 
but is this still current (i.e. is linux still needed to do this?): 
http://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004679.html

thanks,
m

From: Louis Nicholas Vinke [vi...@nmr.mgh.harvard.edu]
Sent: Friday, August 31, 2012 10:29 AM
To: Borzello, Mia
Cc: freesurfer
Subject: Re: [Freesurfer] creating a skull

Hi,
You need to add an extension onto the file name, something like brain.mgz
or brain.nii.  The extension will tell it what format to save the output
in.
-Louis

On Fri, 31 Aug 2012, Borzello, Mia wrote:

> Hi freesurfer family,
>
> I am trying to create the inner skull boundary and ran: mri_watershed -atlas 
> - surf -useSRAS mri.nii brain
>
> However, after it finished running it said it was saving "brain", but "brain" 
> was an unknown file type. Am i supposed to specify that somewhere?
>
> Thanks in advance,
> m
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

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Re: [Freesurfer] creating a skull

[Borzello, Mia]

I'm using Unix. Should I try something else?

Thanks, 
m

From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Monday, September 03, 2012 2:45 PM
To: Borzello, Mia
Cc: freesurfer
Subject: Re: [Freesurfer] creating a skull

Hi Mia

what platform are you running on?

Bruce
On Fri, 31 Aug 2012, Borzello, Mia wrote:

> I've been referred to the following link on the freesurfer site to handle 
> this, but is this still current (i.e. is linux still needed to do this?): 
> http://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004679.html
>
> thanks,
> m
> 
> From: Louis Nicholas Vinke [vi...@nmr.mgh.harvard.edu]
> Sent: Friday, August 31, 2012 10:29 AM
> To: Borzello, Mia
> Cc: freesurfer
> Subject: Re: [Freesurfer] creating a skull
>
> Hi,
> You need to add an extension onto the file name, something like brain.mgz
> or brain.nii.  The extension will tell it what format to save the output
> in.
> -Louis
>
> On Fri, 31 Aug 2012, Borzello, Mia wrote:
>
>> Hi freesurfer family,
>>
>> I am trying to create the inner skull boundary and ran: mri_watershed -atlas 
>> - surf -useSRAS mri.nii brain
>>
>> However, after it finished running it said it was saving "brain", but 
>> "brain" was an unknown file type. Am i supposed to specify that somewhere?
>>
>> Thanks in advance,
>> m
>>
>> ___
>> 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
>
>
>

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[Freesurfer] picking peculiar points

[Borzello, Mia]

Hi,
I'm picking points for a coregistration using tkmedit, but oddly all of the R 
coordinates have been 0. For example, one point is [0 -14 73.5]. Does this seem 
right?

Thanks in advance,
Mia

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Re: [Freesurfer] picking peculiar points

[Borzello, Mia]

Okay, so what could be the cause of this error? My choice of CT sequence?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Wednesday, September 12, 2012 12:59 PM
To: Borzello, Mia
Cc: freesurfer
Subject: Re: [Freesurfer] picking peculiar points

definitely not.
On Wed, 12 Sep 2012, Borzello, Mia wrote:

> Hi,
> I'm picking points for a coregistration using tkmedit, but oddly all of the R 
> coordinates have been 0. For example, one point is [0 -14 73.5]. Does this 
> seem right?
>
> Thanks in advance,
> Mia
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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[Freesurfer] pial not computing

[Borzello, Mia]

Hi Freesurfers,

I just ran a recon, and it seems that only  the lh.pial computed, but not the 
rh.pial. What would be the cause of this?
Thanks,
m

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Re: [Freesurfer] pial not computing

[Borzello, Mia]

great. is there a freesurfer page on mris_topo_fixer? I'm not sure how/where to 
run this and I don't see a page on the freesurfer site. 

Thanks so much,
m

From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Thursday, January 17, 2013 1:30 PM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] pial not computing

Hi Mia

this is fixed in the newest version. You can grab a new mris_topo_fixer
and you rerun and it should be all set. You probably should take a look
at the ?h.orig.nofix to make sure it's reasonable (meaning no cerebellum
or skull attached, and the hemispherees successfully separated)

cheers
Bruce
On Thu, 17
Jan 2013, Borzello, Mia wrote:

> Okay, so it didn't complete without error. I've attached the recon-all.log. 
> Also, I was using another post op patient's MRI scans.
>
> thanks so much,
> m
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, January 17, 2013 11:22 AM
> To: Borzello, Mia
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] pial not computing
>
> Hi Mia
>
> we need to see the recon-all.log. Did it end with an error?
> Bruce
> On Thu, 17 Jan
> 2013, Borzello, Mia wrote:
>
>> Hi Freesurfers,
>>
>> I just ran a recon, and it seems that only  the lh.pial computed, but not 
>> the rh.pial. What would be the cause of this?
>> Thanks,
>> m
>>
>> ___
>> 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

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Re: [Freesurfer] pial not computing

[Borzello, Mia]

Cool, it's running. Hopefully I did that right. 
Thanks for your help!

From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Friday, January 18, 2013 11:28 AM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] pial not computing

it's run as part of recon-all. If you grab a new one and run

recon-all -make all ...

you should be all set
Bruce


On Fri, 18 Jan 2013, Borzello, Mia wrote:

> great. is there a freesurfer page on mris_topo_fixer? I'm not sure how/where 
> to run this and I don't see a page on the freesurfer site.
>
> Thanks so much,
> m
> 
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, January 17, 2013 1:30 PM
> To: Borzello, Mia
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] pial not computing
>
> Hi Mia
>
> this is fixed in the newest version. You can grab a new mris_topo_fixer
> and you rerun and it should be all set. You probably should take a look
> at the ?h.orig.nofix to make sure it's reasonable (meaning no cerebellum
> or skull attached, and the hemispherees successfully separated)
>
> cheers
> Bruce
> On Thu, 17
> Jan 2013, Borzello, Mia wrote:
>
>> Okay, so it didn't complete without error. I've attached the recon-all.log. 
>> Also, I was using another post op patient's MRI scans.
>>
>> thanks so much,
>> m
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>> [fis...@nmr.mgh.harvard.edu]
>> Sent: Thursday, January 17, 2013 11:22 AM
>> To: Borzello, Mia
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] pial not computing
>>
>> Hi Mia
>>
>> we need to see the recon-all.log. Did it end with an error?
>> Bruce
>> On Thu, 17 Jan
>> 2013, Borzello, Mia wrote:
>>
>>> Hi Freesurfers,
>>>
>>> I just ran a recon, and it seems that only  the lh.pial computed, but not 
>>> the rh.pial. What would be the cause of this?
>>> Thanks,
>>> m
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

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[Freesurfer] "average" brain files

[Borzello, Mia]

Hi Freesurfers,

I was wondering if the SurferOutput files for the average subject's brain were 
somewhere tobe downloaded on the wiki or within the toolbox?

Thanks,
m
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[Freesurfer] creating norm.mgz

[Borzello, Mia]

Hi all,

I'm trying to use tkmedit to pick electrode points for a patient. For the mri, 
I'm using the average brain provided by freesurfer. I realized that I have no 
norm.mgz file which tkmedit calls. How do I create this?

Thanks,
Mia
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Re: [Freesurfer] creating norm.mgz

[Borzello, Mia]

Right that will work. I will try that. Also in using the average brain am I 
able to compute the pial layers(lh.pial-outer-smoothed, 
rh.pial-outer-smoothed)? I tried and it errored- i attached a screenshot of the 
error. 

Thanks a lot, 
m

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, May 30, 2014 3:34 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] creating norm.mgz

why not just use the orig.mgz that is there?

On 05/30/2014 02:40 PM, Borzello, Mia wrote:
> Hi all,
>
> I'm trying to use tkmedit to pick electrode points for a patient. For
> the mri, I'm using the average brain provided by freesurfer. I
> realized that I have no norm.mgz file which tkmedit calls. How do I
> create this?
>
> Thanks,
> Mia
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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Re: [Freesurfer] creating norm.mgz

[Borzello, Mia]

Or is there a file that corresponds to the outer-smoothed pials? like 
lh.pial_avg or lh.pial.avg.area.mgh that I can use?

Thanks, 
m

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, May 30, 2014 3:34 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] creating norm.mgz

why not just use the orig.mgz that is there?

On 05/30/2014 02:40 PM, Borzello, Mia wrote:
> Hi all,
>
> I'm trying to use tkmedit to pick electrode points for a patient. For
> the mri, I'm using the average brain provided by freesurfer. I
> realized that I have no norm.mgz file which tkmedit calls. How do I
> create this?
>
> Thanks,
> Mia
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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[Freesurfer] pial layers

[Borzello, Mia]

Hi Freesurfers,

I ran mris_compute_lgi to make the pial layers but they've error- I've included 
a screenshot. It says it can't find that directory, but I'm pretty sure that 
directly exists.

Thanks so much for your help,
Mia
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[Freesurfer] problem with format of CT dicoms

[Borzello, Mia]

Hi Freesurfers,

I'm in the process of creating the ct.mgz file, but it is erroring and saying 
there is a "segmentation fault (core dumped)."

What can I do to remedy this?

Thanks,
m
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Re: [Freesurfer] problem with format of CT dicoms

[Borzello, Mia]

Right, sorry. I was running a command with mri_convert in order to convert the 
ct dicoms to mgz format. The error I ran into was:
UseSliceScaleFactor 0 (slice 0: 1)
Segmentation fault (core dumped)

Thanks, 
m

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, August 22, 2014 12:31 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] problem with format of CT dicoms

Hi Mia, do you realize that your description of the problem is too vague
for us to help you? If you want help in a timely fashion, please include
more detail like the problem you ran, the command-line arguments, the
terminal output, etc. Please see the following web page for the types
information we are looking for:

surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

The easier you make it for us, the more likely you are to get help.

thanks
doug


On 08/22/2014 12:17 PM, Borzello, Mia wrote:
> Hi Freesurfers,
>
> I'm in the process of creating the ct.mgz file, but it is erroring and
> saying there is a "segmentation fault (core dumped)."
>
> What can I do to remedy this?
>
> Thanks,
> m
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
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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] problem with format of CT dicoms

[Borzello, Mia]

Hi Freesurfers, 

Apologies, I've never used this format before.
Here's the error:

FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0

Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514

RedHat release: CentOS release 6.5 (Final)

Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64

NMR Center info (/space/freesurfer exists):

  machine: huygens

  SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects

  PWD: 
/autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri

  ssh huygens
  setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
  cd /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri

For additional information: 
1. Neuropace2JB
2. mri_convert -i 
/autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_PostOp_CT/BENNETT^JACOB^F/1.2.124.113532.80.22200.7094.20140812.155724.232143365/1.3.12.2.1107.5.1.4.11060.3014081213381840600011010/IMG84.dcm
 -o ct.mgz
3. UseSliceScaleFactor 0 (slice 0: 1)
Segmentation fault (core dumped)

Thanks so much, 
m
____
From: Borzello, Mia
Sent: Friday, August 22, 2014 1:14 PM
To: Freesurfer support list
Subject: RE: [Freesurfer] problem with format of CT dicoms

Hi Freesurfers,

Apologies, I've never used this format before.
Here's the error:

FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0

Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514

RedHat release: CentOS release 6.5 (Final)

Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64

NMR Center info (/space/freesurfer exists):

  machine: huygens

  SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects

  PWD: 
/autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri

  ssh huygens
  setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
  cd /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri

For additional information:
1. Neuropace2JB
2. mri_convert -i 
/autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_PostOp_CT/BENNETT^JACOB^F/1.2.124.113532.80.22200.7094.20140812.155724.232143365/1.3.12.2.1107.5.1.4.11060.3014081213381840600011010/IMG84.dcm
 -o ct.mgz
3. UseSliceScaleFactor 0 (slice 0: 1)
Segmentation fault (core dumped)

Thanks so much,
m

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, August 22, 2014 12:43 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] problem with format of CT dicoms

Hi Mia, please follow the instructions on the web site below for
submitting bug reports.
thanks
doug

On 08/22/2014 12:37 PM, Borzello, Mia wrote:
> Right, sorry. I was running a command with mri_convert in order to convert 
> the ct dicoms to mgz format. The error I ran into was:
> UseSliceScaleFactor 0 (slice 0: 1)
> Segmentation fault (core dumped)
>
> Thanks,
> m
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, August 22, 2014 12:31 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] problem with format of CT dicoms
>
> Hi Mia, do you realize that your description of the problem is too vague
> for us to help you? If you want help in a timely fashion, please include
> more detail like the problem you ran, the command-line arguments, the
> terminal output, etc. Please see the following web page for the types
> information we are looking for:
>
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
> The easier you make it for us, the more likely you are to get help.
>
> thanks
> doug
>
>
> On 08/22/2014 12:17 PM, Borzello, Mia wrote:
>> Hi Freesurfers,
>>
>> I'm in the process of creating the ct.mgz file, but it is erroring and
>> saying there is a "segmentation fault (core dumped)."
>>
>> What can I do to remedy this?
>>
>> Thanks,
>> m
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/lis

Re: [Freesurfer] problem with format of CT dicoms

[Borzello, Mia]

Awesome! Thanks a lot for your help!

m

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, August 22, 2014 2:28 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] problem with format of CT dicoms

These dicoms are run-length encoded, which FS does not read. What you
can do is the following

cd /place/where/dicoms/are

foreach dcm (*.dcm)
dcmdrle $dcm $dcm
end

then run mri_convert, like

mri_convert -it dicom IMG10.dcm ct.mgz

I did this and it converts, but the slice thickness looks wrong. I don't
know how to fix it because we always trust the slice thickness in the dicom

doug



On 08/22/2014 01:51 PM, Borzello, Mia wrote:
> Hi Freesurfers,
>
> Apologies, I've never used this format before.
> Here's the error:
>
> FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
>
> Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
>
> RedHat release: CentOS release 6.5 (Final)
>
> Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64
>
> NMR Center info (/space/freesurfer exists):
>
>machine: huygens
>
>SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects
>
>PWD: 
> /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri
>
>ssh huygens
>setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
>cd 
> /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri
>
> For additional information:
> 1. Neuropace2JB
> 2. mri_convert -i 
> /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_PostOp_CT/XXX/1.2.124.113532.80.22200.7094.20140812.155724.232143365/1.3.12.2.1107.5.1.4.11060.3014081213381840600011010/IMG84.dcm
>  -o ct.mgz
> 3. UseSliceScaleFactor 0 (slice 0: 1)
> Segmentation fault (core dumped)
>
> Thanks so much,
> m
> 
> From: Borzello, Mia
> Sent: Friday, August 22, 2014 1:14 PM
> To: Freesurfer support list
> Subject: RE: [Freesurfer] problem with format of CT dicoms
>
> Hi Freesurfers,
>
> Apologies, I've never used this format before.
> Here's the error:
>
> FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
>
> Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
>
> RedHat release: CentOS release 6.5 (Final)
>
> Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64
>
> NMR Center info (/space/freesurfer exists):
>
>machine: huygens
>
>SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects
>
>PWD: 
> /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri
>
>ssh huygens
>setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
>cd 
> /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri
>
> For additional information:
> 1. Neuropace2JB
> 2. mri_convert -i 
> /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_PostOp_CT//1.2.124.113532.80.22200.7094.20140812.155724.232143365/1.3.12.2.1107.5.1.4.11060.3014081213381840600011010/IMG84.dcm
>  -o ct.mgz
> 3. UseSliceScaleFactor 0 (slice 0: 1)
> Segmentation fault (core dumped)
>
> Thanks so much,
> m
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, August 22, 2014 12:43 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] problem with format of CT dicoms
>
> Hi Mia, please follow the instructions on the web site below for
> submitting bug reports.
> thanks
> doug
>
> On 08/22/2014 12:37 PM, Borzello, Mia wrote:
>> Right, sorry. I was running a command with mri_convert in order to convert 
>> the ct dicoms to mgz format. The error I ran into was:
>> UseSliceScaleFactor 0 (slice 0: 1)
>> Segmentation fault (core dumped)
>>
>> Thanks,
>> m
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Friday, August 22, 2014 12:31 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] problem with format of CT dicoms
>>
>> Hi Mia, do you realize that your description of the problem is too vague
>> for us to help you? If you want help in a timely fashion, please include
>> more detail like the problem you ran, the command-line arguments, the
>> terminal output, etc. Please see the following web page for the 

Re: [Freesurfer] skewed CT viewed in tkregister2

[Borzello, Mia]

Hi, 

Any insight on this problem I'm having with tkregister2? I haven't been able to 
resolve this yet. My original posting is below with the output from bugr. 

Thanks! 
Mia

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia
Sent: Monday, October 06, 2014 11:08 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] skewed CT viewed in tkregister2

Hi Freesurfers

I'm having trouble viewing a CT in tkregister2. Here is the output from bugr:

FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0

Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514

RedHat release: CentOS release 6.5 (Final)

Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64

NMR Center info (/space/freesurfer exists):

  machine: huygens

  SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects

  PWD: /autofs/space/huygens_001/users/mia/subjects/BI20v2_SurferOutput/mri

  ssh huygens
  setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
  cd /autofs/space/huygens_001/users/mia/subjects/BI20v2_SurferOutput/mri


1. BI20
2. tkregister2 --s BI20v2_SurferOutput --mov ct.mgz --reg spm.reg.dat --surf 
orig
3. the coronal/saggital/horizontal views were skewed
4.attached.

Thanks a lot,
Mia

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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.

Re: [Freesurfer] skewed CT viewed in tkregister2

[Borzello, Mia]

Hi, no problem. I used the command "mri_convert" but I just checked the slice 
thickness on it, and it's has a thickness of 2. So that's probably the problem 
then? Sorry for all the issues, I thought this CT would work.

Thanks, 
m

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, October 20, 2014 6:43 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] skewed CT viewed in tkregister2

Hi Mia, sorry for the delay. I think the problem is that the geometry
info in the CT header is incorrect. The directions are not orgthogonal,
and, when made orthogonal, the pixel sizes look wrong. How did you
create ct.mgz?

doug

On 10/12/2014 08:52 PM, Borzello, Mia wrote:
> Hi,
>
> Any insight on this problem I'm having with tkregister2? I haven't been able 
> to resolve this yet. My original posting is below with the output from bugr.
>
> Thanks!
> Mia
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia
> Sent: Monday, October 06, 2014 11:08 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] skewed CT viewed in tkregister2
>
> Hi Freesurfers
>
> I'm having trouble viewing a CT in tkregister2. Here is the output from bugr:
>
> FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
>
> Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
>
> RedHat release: CentOS release 6.5 (Final)
>
> Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64
>
> NMR Center info (/space/freesurfer exists):
>
>machine: huygens
>
>SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects
>
>PWD: /autofs/space/huygens_001/users/mia/subjects/BI20v2_SurferOutput/mri
>
>ssh huygens
>setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
>cd /autofs/space/huygens_001/users/mia/subjects/BI20v2_SurferOutput/mri
>
>
> 1. BI20
> 2. tkregister2 --s BI20v2_SurferOutput --mov ct.mgz --reg spm.reg.dat --surf 
> orig
> 3. the coronal/saggital/horizontal views were skewed
> 4.attached.
>
> Thanks a lot,
> Mia
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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

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

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

___
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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.

[Freesurfer] coreg error

[Borzello, Mia]

Hey guys,

When i run mri_convert to get ct.mgz, everything runs, and i get a ct.mgz
file. but when i use spmregister, it says that spm.reg.dat is
unrecognizable. How can i remedy this?

Thanks so much!
Mia

___
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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] coreg error

[Borzello, Mia]

is PE Dir = UNKNOWN okay?

when i run this command "spmregister --s RIH_E1_SurferOutput --mov ct.mgz--reg 
spm.reg.dat --fsvol orig", i get the following error:
ERROR: Flag spm.reg.dat unrecognized.
--s RIH_E1_SurferOutput --mov ct.mgz--reg spm.reg.dat --fsvol orig

From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Monday, April 02, 2012 1:39 PM
To: Borzello, Mia; Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] coreg error

There does not appear to be an error at the end.
doug

On 04/02/2012 12:58 PM, Borzello, Mia wrote:
> mri_convert -i ~/subjects/RIH-E1_PostOp_CT/S/SE0003/I -o ct.mgz
> mri_convert -i /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S/SE0003/I 
> -o ct.mgz
> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
> reading from /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S/SE0003/I...
> Starting DICOMRead2()
> dcmfile = /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S/SE0003/I
> dcmdir = /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S/SE0003
> Ref Series No = 6
> Found 138 files, checking for dicoms
> Found 136 dicom files in series.
> First Sorting
> Computing Slice Direction
> Vs: 0 0 1.25
> Vs: 0 0 1
> Second Sorting
> Counting frames
> nframes = 1
> nslices = 136
> ndcmfiles = 136
> PE Dir = UNKNOWN (dicom read)
> TransferSyntaxUID: --1.2.840.10008.1.2.1--
> jpegUID:   --1.2.840.10008.1.2.4--
> Loading pixel data
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, -0, 0)
> j_ras = (-0, -1, 0)
> k_ras = (-0, -0, 1)
> writing to ct.mgz...
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, April 02, 2012 10:00 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] coreg error
>
> Can you paste the terminal output into the email instead of sending a pic?
>
> On 4/2/12 9:54 AM, Borzello, Mia wrote:
>
> Morning guys,
>
>
> I ran the MRI recon Saturday and today was trying to convert the CT dicoms to 
> mgz format using the command "mri_convert -i first ct.dicom -o ct.mgz", but 
> got an error. I'm sure there's a better way to do this, but i attached a 
> screenshot of the error (I don't know how to copy and paste since ctrl + c 
> doesn't work.)
>
>
>
> Thanks!
> Mia
> 
> From: 
> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>   
> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
>  on behalf of Borzello, Mia
> Sent: Sunday, April 01, 2012 10:59 PM
> To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
> Subject: [Freesurfer] coreg error
>
> Hey guys,
>
> When i run mri_convert to get ct.mgz, everything runs, and i get a ct.mgz
> file. but when i use spmregister, it says that spm.reg.dat is
> unrecognizable. How can i remedy this?
>
> Thanks so much!
> Mia
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu<mailto: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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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] coreg error

[Borzello, Mia]

K I corrected that. I reran, and this was the error (below)..is there a way to 
change the double forward slashes? I'm not sure how that happened.

thanks!



spmregister --s RIH_E1_SurferOutput --mov ct.mgz --reg spm.reg.dat --fsvol orig
Log file is ./spmregister.log
Mon Apr  2 13:47:24 EDT 2012
--s RIH_E1_SurferOutput --mov ct.mgz --reg spm.reg.dat --fsvol orig
$Id: spmregister,v 1.39 2011/03/02 20:16:40 nicks Exp $
matlab matlab
fmt img
UseSPMGetSpace 1
ERROR: /autofs/homes/009/miaborz/subjects//RIH_E1_SurferOutput/mri/orig.mgz not 
found in either COR or MGZ formats

From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Monday, April 02, 2012 1:45 PM
To: Borzello, Mia
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] coreg error

You need a space between ct.mgz and --reg. PE Dir unknown is ok.

On 04/02/2012 01:43 PM, Borzello, Mia wrote:
> is PE Dir = UNKNOWN okay?
>
> when i run this command "spmregister --s RIH_E1_SurferOutput --mov 
> ct.mgz--reg spm.reg.dat --fsvol orig", i get the following error:
> ERROR: Flag spm.reg.dat unrecognized.
> --s RIH_E1_SurferOutput --mov ct.mgz--reg spm.reg.dat --fsvol orig
> 
> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, April 02, 2012 1:39 PM
> To: Borzello, Mia; Freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] coreg error
>
> There does not appear to be an error at the end.
> doug
>
> On 04/02/2012 12:58 PM, Borzello, Mia wrote:
>> mri_convert -i ~/subjects/RIH-E1_PostOp_CT/S/SE0003/I -o ct.mgz
>> mri_convert -i /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S/SE0003/I 
>> -o ct.mgz
>> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
>> reading from /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S/SE0003/I...
>> Starting DICOMRead2()
>> dcmfile = /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S/SE0003/I
>> dcmdir = /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S/SE0003
>> Ref Series No = 6
>> Found 138 files, checking for dicoms
>> Found 136 dicom files in series.
>> First Sorting
>> Computing Slice Direction
>> Vs: 0 0 1.25
>> Vs: 0 0 1
>> Second Sorting
>> Counting frames
>> nframes = 1
>> nslices = 136
>> ndcmfiles = 136
>> PE Dir = UNKNOWN (dicom read)
>> TransferSyntaxUID: --1.2.840.10008.1.2.1--
>> jpegUID:   --1.2.840.10008.1.2.4--
>> Loading pixel data
>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-1, -0, 0)
>> j_ras = (-0, -1, 0)
>> k_ras = (-0, -0, 1)
>> writing to ct.mgz...
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Monday, April 02, 2012 10:00 AM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] coreg error
>>
>> Can you paste the terminal output into the email instead of sending a pic?
>>
>> On 4/2/12 9:54 AM, Borzello, Mia wrote:
>>
>> Morning guys,
>>
>>
>> I ran the MRI recon Saturday and today was trying to convert the CT dicoms 
>> to mgz format using the command "mri_convert -i first ct.dicom -o ct.mgz", 
>> but got an error. I'm sure there's a better way to do this, but i attached a 
>> screenshot of the error (I don't know how to copy and paste since ctrl + c 
>> doesn't work.)
>>
>>
>>
>> Thanks!
>> Mia
>> 
>> From: 
>> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>>
>> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
>>  on behalf of Borzello, Mia
>> Sent: Sunday, April 01, 2012 10:59 PM
>> To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
>> Subject: [Freesurfer] coreg error
>>
>> Hey guys,
>>
>> When i run mri_convert to get ct.mgz, everything runs, and i get a ct.mgz
>> file. but when i use spmregister, it says that spm.reg.dat is
>> unrecognizable. How can i remedy this?
>>
>> Thanks so much!
>> Mia
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Fr

Re: [Freesurfer] coreg error

[Borzello, Mia]

Yes it's in RIH_E1_SurferOutput/mri. Would the double forward slashes before 
RIH_E1_SurferOutput have effect?

From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Monday, April 02, 2012 1:51 PM
To: Borzello, Mia
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] coreg error

It says that it cannot find a file. Does that file exist?

On 04/02/2012 01:50 PM, Borzello, Mia wrote:
> K I corrected that. I reran, and this was the error (below)..is there a way 
> to change the double forward slashes? I'm not sure how that happened.
>
> thanks!
>
>
>
> spmregister --s RIH_E1_SurferOutput --mov ct.mgz --reg spm.reg.dat --fsvol 
> orig
> Log file is ./spmregister.log
> Mon Apr  2 13:47:24 EDT 2012
> --s RIH_E1_SurferOutput --mov ct.mgz --reg spm.reg.dat --fsvol orig
> $Id: spmregister,v 1.39 2011/03/02 20:16:40 nicks Exp $
> matlab matlab
> fmt img
> UseSPMGetSpace 1
> ERROR: /autofs/homes/009/miaborz/subjects//RIH_E1_SurferOutput/mri/orig.mgz 
> not found in either COR or MGZ formats
> 
> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, April 02, 2012 1:45 PM
> To: Borzello, Mia
> Cc: Freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] coreg error
>
> You need a space between ct.mgz and --reg. PE Dir unknown is ok.
>
> On 04/02/2012 01:43 PM, Borzello, Mia wrote:
>> is PE Dir = UNKNOWN okay?
>>
>> when i run this command "spmregister --s RIH_E1_SurferOutput --mov 
>> ct.mgz--reg spm.reg.dat --fsvol orig", i get the following error:
>> ERROR: Flag spm.reg.dat unrecognized.
>> --s RIH_E1_SurferOutput --mov ct.mgz--reg spm.reg.dat --fsvol orig
>> ________
>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>> Sent: Monday, April 02, 2012 1:39 PM
>> To: Borzello, Mia; Freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] coreg error
>>
>> There does not appear to be an error at the end.
>> doug
>>
>> On 04/02/2012 12:58 PM, Borzello, Mia wrote:
>>> mri_convert -i ~/subjects/RIH-E1_PostOp_CT/S/SE0003/I -o ct.mgz
>>> mri_convert -i 
>>> /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S/SE0003/I -o ct.mgz
>>> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
>>> reading from 
>>> /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S/SE0003/I...
>>> Starting DICOMRead2()
>>> dcmfile = /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S/SE0003/I
>>> dcmdir = /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S/SE0003
>>> Ref Series No = 6
>>> Found 138 files, checking for dicoms
>>> Found 136 dicom files in series.
>>> First Sorting
>>> Computing Slice Direction
>>> Vs: 0 0 1.25
>>> Vs: 0 0 1
>>> Second Sorting
>>> Counting frames
>>> nframes = 1
>>> nslices = 136
>>> ndcmfiles = 136
>>> PE Dir = UNKNOWN (dicom read)
>>> TransferSyntaxUID: --1.2.840.10008.1.2.1--
>>> jpegUID:   --1.2.840.10008.1.2.4--
>>> Loading pixel data
>>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
>>> i_ras = (-1, -0, 0)
>>> j_ras = (-0, -1, 0)
>>> k_ras = (-0, -0, 1)
>>> writing to ct.mgz...
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Monday, April 02, 2012 10:00 AM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] coreg error
>>>
>>> Can you paste the terminal output into the email instead of sending a pic?
>>>
>>> On 4/2/12 9:54 AM, Borzello, Mia wrote:
>>>
>>> Morning guys,
>>>
>>>
>>> I ran the MRI recon Saturday and today was trying to convert the CT dicoms 
>>> to mgz format using the command "mri_convert -i first ct.dicom -o ct.mgz", 
>>> but got an error. I'm sure there's a better way to do this, but i attached 
>>> a screenshot of the error (I don't know how to copy and paste since ctrl + 
>>> c doesn't work.)
>>>
>>>
>>>
>>> Thanks!
>>> Mia
>>> 
>>> From: 
>>> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>>> 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
>>>  on beh

[Freesurfer] inability to pick points

[Borzello, Mia]

Hi,

I'm just wondering if there is something that needs to be selected using 
tkmedit to get electrode coordinates. I usually don't have this issue, but 
right now i'm unable to move my cursor to a new location.

Thanks so much,
Mia

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Re: [Freesurfer] inability to pick points

[Borzello, Mia]

"Select voxels" is actually highlighted already (and "Navigation" isn't), but 
it's still not working.
Thanks, 
m

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, May 07, 2012 2:43 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] inability to pick points

Make sure that the "Select Voxel Tool" is activated in the tool bar (or
drop down tool menu). Sounds like you have the navigation button selected.
doug

On 05/07/2012 02:05 PM, Borzello, Mia wrote:
> Hi,
>
> I'm just wondering if there is something that needs to be selected using 
> tkmedit to get electrode coordinates. I usually don't have this issue, but 
> right now i'm unable to move my cursor to a new location.
>
> Thanks so much,
> Mia
>
> ___
> 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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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] inability to pick points

[Borzello, Mia]

I'm not sure what you mean by "conformed"? My input volume is that one that I 
coregistered if that's what you mean?

From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Monday, May 07, 2012 2:57 PM
To: Borzello, Mia
Cc: Douglas N Greve; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] inability to pick points

is your input volume "conformed"? I think tkmedit disables some features
if it is not
On Mon, 7 May 2012, Borzello, Mia wrote:

> "Select voxels" is actually highlighted already (and "Navigation" isn't), but 
> it's still not working.
> Thanks,
> m
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, May 07, 2012 2:43 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] inability to pick points
>
> Make sure that the "Select Voxel Tool" is activated in the tool bar (or
> drop down tool menu). Sounds like you have the navigation button selected.
> doug
>
> On 05/07/2012 02:05 PM, Borzello, Mia wrote:
>> Hi,
>>
>> I'm just wondering if there is something that needs to be selected using 
>> tkmedit to get electrode coordinates. I usually don't have this issue, but 
>> right now i'm unable to move my cursor to a new location.
>>
>> Thanks so much,
>> Mia
>>
>> ___
>> 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
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

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Re: [Freesurfer] inability to pick points

[Borzello, Mia]

tkmedit MGXX_SuferOutput_original norm.mgz lh.pial -aux ct.anat.mgz

I named the folder with the extra "_original" because this person already had a 
SurferOuput folder. Could that be the problem?

thanks.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, May 07, 2012 3:04 PM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] inability to pick points

conformed means 1mm isotropic. What is your tkmedit cmd line?

On 05/07/2012 03:04 PM, Borzello, Mia wrote:
> I'm not sure what you mean by "conformed"? My input volume is that one that I 
> coregistered if that's what you mean?
> 
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, May 07, 2012 2:57 PM
> To: Borzello, Mia
> Cc: Douglas N Greve; freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] inability to pick points
>
> is your input volume "conformed"? I think tkmedit disables some features
> if it is not
> On Mon, 7 May 2012, Borzello, Mia wrote:
>
>> "Select voxels" is actually highlighted already (and "Navigation" isn't), 
>> but it's still not working.
>> Thanks,
>> m
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Monday, May 07, 2012 2:43 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] inability to pick points
>>
>> Make sure that the "Select Voxel Tool" is activated in the tool bar (or
>> drop down tool menu). Sounds like you have the navigation button selected.
>> doug
>>
>> On 05/07/2012 02:05 PM, Borzello, Mia wrote:
>>> Hi,
>>>
>>> I'm just wondering if there is something that needs to be selected using 
>>> tkmedit to get electrode coordinates. I usually don't have this issue, but 
>>> right now i'm unable to move my cursor to a new location.
>>>
>>> Thanks so much,
>>> Mia
>>>
>>> ___
>>> 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
>>
>> ___
>> 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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Re: [Freesurfer] "cannot allocate memory" issue

[Borzello, Mia]

How do I check this? (Apologies for my ignorance.) So I might need to just use 
a different set of dicoms then?

thanks, 
Mia

From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
Sent: Monday, May 14, 2012 1:02 PM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] "cannot allocate memory" issue

It looks like there is too huge a topology error for it to continue:

CORRECTING DEFECT 23 (vertices=143258, convex hull=19937)
Excessive topologic defect encountered: could not allocate -729782272
edges for retessellation
Cannot allocate memory

I would suggested looking at the filled.mgz to make sure skull and/or
cerebellum are not included.
Allison

On Mon, 14 May 2012, Borzello, Mia wrote:

> Hi all,
>
> I was wondering if you could help me figure out why the recon isn't running 
> to completion. I've attached the log file (recon-all.log), but it's unclear 
> to me what I should do to fix this problem. I tried to compute the lh.pial, 
> but I guess it was never made in the recon.
>
> Thanks so much,
> Mia
>

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Re: [Freesurfer] "cannot allocate memory" issue

[Borzello, Mia]

It says that it couldn't open rh.orig.nofix and  lh.orig.nofix. On the popup 
image, it doesn't look like the skull is present, but it does look like the 
cerebellum is.

From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
Sent: Monday, May 14, 2012 1:28 PM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] "cannot allocate memory" issue

You can do:
tkmedit subjid filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix

When you downloaded FreeSurfer, you would have also received the subject
"bert" who is a good example to compare to. He will likely be located in:
$FREESURFER_HOME/subjects/bert

If you do the same command above for bert:
tkmedit bert filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix

You'll see what the filled.mgz should look like.
Allison

On Mon, 14 May 2012, Borzello, Mia wrote:

> How do I check this? (Apologies for my ignorance.) So I might need to just 
> use a different set of dicoms then?
>
> thanks,
> Mia
> 
> From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
> Sent: Monday, May 14, 2012 1:02 PM
> To: Borzello, Mia
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] "cannot allocate memory" issue
>
> It looks like there is too huge a topology error for it to continue:
>
> CORRECTING DEFECT 23 (vertices=143258, convex hull=19937)
> Excessive topologic defect encountered: could not allocate -729782272
> edges for retessellation
> Cannot allocate memory
>
> I would suggested looking at the filled.mgz to make sure skull and/or
> cerebellum are not included.
> Allison
>
> On Mon, 14 May 2012, Borzello, Mia wrote:
>
>> Hi all,
>>
>> I was wondering if you could help me figure out why the recon isn't running 
>> to completion. I've attached the log file (recon-all.log), but it's unclear 
>> to me what I should do to fix this problem. I tried to compute the lh.pial, 
>> but I guess it was never made in the recon.
>>
>> Thanks so much,
>> Mia
>>
>
>
>

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

Re: [Freesurfer] "cannot allocate memory" issue

[Borzello, Mia]

would it be worth it at this point, to use another set of dicoms?
thanks, 
m

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia
Sent: Monday, May 14, 2012 1:37 PM
To: Allison Stevens Player
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] "cannot allocate memory" issue

It says that it couldn't open rh.orig.nofix and  lh.orig.nofix. On the popup 
image, it doesn't look like the skull is present, but it does look like the 
cerebellum is.

From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
Sent: Monday, May 14, 2012 1:28 PM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] "cannot allocate memory" issue

You can do:
tkmedit subjid filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix

When you downloaded FreeSurfer, you would have also received the subject
"bert" who is a good example to compare to. He will likely be located in:
$FREESURFER_HOME/subjects/bert

If you do the same command above for bert:
tkmedit bert filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix

You'll see what the filled.mgz should look like.
Allison

On Mon, 14 May 2012, Borzello, Mia wrote:

> How do I check this? (Apologies for my ignorance.) So I might need to just 
> use a different set of dicoms then?
>
> thanks,
> Mia
> 
> From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
> Sent: Monday, May 14, 2012 1:02 PM
> To: Borzello, Mia
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] "cannot allocate memory" issue
>
> It looks like there is too huge a topology error for it to continue:
>
> CORRECTING DEFECT 23 (vertices=143258, convex hull=19937)
> Excessive topologic defect encountered: could not allocate -729782272
> edges for retessellation
> Cannot allocate memory
>
> I would suggested looking at the filled.mgz to make sure skull and/or
> cerebellum are not included.
> Allison
>
> On Mon, 14 May 2012, Borzello, Mia wrote:
>
>> Hi all,
>>
>> I was wondering if you could help me figure out why the recon isn't running 
>> to completion. I've attached the log file (recon-all.log), but it's unclear 
>> to me what I should do to fix this problem. I tried to compute the lh.pial, 
>> but I guess it was never made in the recon.
>>
>> Thanks so much,
>> Mia
>>
>
>
>

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___
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Re: [Freesurfer] "cannot allocate memory" issue

[Borzello, Mia]

Hey Allison, 

Thanks for you help. What do you mean by check your talairach? I'll hold off on 
using a different set of dicoms, and make that my last resort since it takes a 
day to complete. 
Thanks, 
m

From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
Sent: Monday, May 14, 2012 3:16 PM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] "cannot allocate memory" issue

Hi Mia,
You may want to check your talairach to make sure that looks okay. If
that's not causing the problem, you can edit the wm.mgz to remove the
cerebellum and then rerun and this should fix the problem.
Allison

On Mon, 14 May 2012, Borzello, Mia wrote:

> It says that it couldn't open rh.orig.nofix and  lh.orig.nofix. On the popup 
> image, it doesn't look like the skull is present, but it does look like the 
> cerebellum is.
> 
> From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
> Sent: Monday, May 14, 2012 1:28 PM
> To: Borzello, Mia
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] "cannot allocate memory" issue
>
> You can do:
> tkmedit subjid filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix
>
> When you downloaded FreeSurfer, you would have also received the subject
> "bert" who is a good example to compare to. He will likely be located in:
> $FREESURFER_HOME/subjects/bert
>
> If you do the same command above for bert:
> tkmedit bert filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix
>
> You'll see what the filled.mgz should look like.
> Allison
>
> On Mon, 14 May 2012, Borzello, Mia wrote:
>
>> How do I check this? (Apologies for my ignorance.) So I might need to just 
>> use a different set of dicoms then?
>>
>> thanks,
>> Mia
>> 
>> From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
>> Sent: Monday, May 14, 2012 1:02 PM
>> To: Borzello, Mia
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] "cannot allocate memory" issue
>>
>> It looks like there is too huge a topology error for it to continue:
>>
>> CORRECTING DEFECT 23 (vertices=143258, convex hull=19937)
>> Excessive topologic defect encountered: could not allocate -729782272
>> edges for retessellation
>> Cannot allocate memory
>>
>> I would suggested looking at the filled.mgz to make sure skull and/or
>> cerebellum are not included.
>> Allison
>>
>> On Mon, 14 May 2012, Borzello, Mia wrote:
>>
>>> Hi all,
>>>
>>> I was wondering if you could help me figure out why the recon isn't running 
>>> to completion. I've attached the log file (recon-all.log), but it's unclear 
>>> to me what I should do to fix this problem. I tried to compute the lh.pial, 
>>> but I guess it was never made in the recon.
>>>
>>> Thanks so much,
>>> Mia
>>>
>>
>>
>>
>
>
>

___
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] "cannot allocate memory" issue

[Borzello, Mia]

so that's most likely the problem?

From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Monday, May 14, 2012 3:46 PM
To: Borzello, Mia
Cc: Allison Stevens Player; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] "cannot allocate memory" issue

actually I wanted one from tkmedit. Can you tell us something about the
acquisition? What kind of scan is it? What resolution? And if you can
send us images from tkmedit in coronal and sagittal view that would help
too (say of the orig.mgz)

Bruce
On Mon, 14 May 2012, Borzello, Mia wrote:

> I have two sets of dicoms: one is an axial view, while the other is coronal 
> (this is the one i was using). I attached a screenshot. I'm not sure if 
> that's what you wanted?
>
> thanks
> mia
> 
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, May 14, 2012 3:32 PM
> To: Borzello, Mia
> Cc: Allison Stevens Player; freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] "cannot allocate memory" issue
>
> Hi Mia
>
> can you clarify what you mean by "a different set of dicoms"? Did you
> acquire more than 1 T1-weighted structural on this subject? And can you
> send us an image of the acquisition, say in coronal view?
>
> thanks
> Bruce
>
>
> On Mon, 14 May
> 2012, Borzello, Mia wrote:
>
>> Hey Allison,
>>
>> Thanks for you help. What do you mean by check your talairach? I'll hold off 
>> on using a different set of dicoms, and make that my last resort since it 
>> takes a day to complete.
>> Thanks,
>> m
>> 
>> From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
>> Sent: Monday, May 14, 2012 3:16 PM
>> To: Borzello, Mia
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: RE: [Freesurfer] "cannot allocate memory" issue
>>
>> Hi Mia,
>> You may want to check your talairach to make sure that looks okay. If
>> that's not causing the problem, you can edit the wm.mgz to remove the
>> cerebellum and then rerun and this should fix the problem.
>> Allison
>>
>> On Mon, 14 May 2012, Borzello, Mia wrote:
>>
>>> It says that it couldn't open rh.orig.nofix and  lh.orig.nofix. On the 
>>> popup image, it doesn't look like the skull is present, but it does look 
>>> like the cerebellum is.
>>> 
>>> From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
>>> Sent: Monday, May 14, 2012 1:28 PM
>>> To: Borzello, Mia
>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>> Subject: RE: [Freesurfer] "cannot allocate memory" issue
>>>
>>> You can do:
>>> tkmedit subjid filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix
>>>
>>> When you downloaded FreeSurfer, you would have also received the subject
>>> "bert" who is a good example to compare to. He will likely be located in:
>>> $FREESURFER_HOME/subjects/bert
>>>
>>> If you do the same command above for bert:
>>> tkmedit bert filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix
>>>
>>> You'll see what the filled.mgz should look like.
>>> Allison
>>>
>>> On Mon, 14 May 2012, Borzello, Mia wrote:
>>>
>>>> How do I check this? (Apologies for my ignorance.) So I might need to just 
>>>> use a different set of dicoms then?
>>>>
>>>> thanks,
>>>> Mia
>>>> 
>>>> From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
>>>> Sent: Monday, May 14, 2012 1:02 PM
>>>> To: Borzello, Mia
>>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>>> Subject: Re: [Freesurfer] "cannot allocate memory" issue
>>>>
>>>> It looks like there is too huge a topology error for it to continue:
>>>>
>>>> CORRECTING DEFECT 23 (vertices=143258, convex hull=19937)
>>>> Excessive topologic defect encountered: could not allocate -729782272
>>>> edges for retessellation
>>>> Cannot allocate memory
>>>>
>>>> I would suggested looking at the filled.mgz to make sure skull and/or
>>>> cerebellum are not included.
>>>> Allison
>>>>
>>>> On Mon, 14 May 2012, Borzello, Mia wrote:
>>>>
>>>>> Hi all,
>>>>>
>>>>> I was wondering if you could help me figure out why the recon isn't 
>>>&g

Re: [Freesurfer] "cannot allocate memory" issue

[Borzello, Mia]

oh woops. sorry. 
so both of these sets of dicoms are T2

From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Monday, May 14, 2012 3:46 PM
To: Borzello, Mia
Cc: Allison Stevens Player; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] "cannot allocate memory" issue

actually I wanted one from tkmedit. Can you tell us something about the
acquisition? What kind of scan is it? What resolution? And if you can
send us images from tkmedit in coronal and sagittal view that would help
too (say of the orig.mgz)

Bruce
On Mon, 14 May 2012, Borzello, Mia wrote:

> I have two sets of dicoms: one is an axial view, while the other is coronal 
> (this is the one i was using). I attached a screenshot. I'm not sure if 
> that's what you wanted?
>
> thanks
> mia
> 
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, May 14, 2012 3:32 PM
> To: Borzello, Mia
> Cc: Allison Stevens Player; freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] "cannot allocate memory" issue
>
> Hi Mia
>
> can you clarify what you mean by "a different set of dicoms"? Did you
> acquire more than 1 T1-weighted structural on this subject? And can you
> send us an image of the acquisition, say in coronal view?
>
> thanks
> Bruce
>
>
> On Mon, 14 May
> 2012, Borzello, Mia wrote:
>
>> Hey Allison,
>>
>> Thanks for you help. What do you mean by check your talairach? I'll hold off 
>> on using a different set of dicoms, and make that my last resort since it 
>> takes a day to complete.
>> Thanks,
>> m
>> 
>> From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
>> Sent: Monday, May 14, 2012 3:16 PM
>> To: Borzello, Mia
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: RE: [Freesurfer] "cannot allocate memory" issue
>>
>> Hi Mia,
>> You may want to check your talairach to make sure that looks okay. If
>> that's not causing the problem, you can edit the wm.mgz to remove the
>> cerebellum and then rerun and this should fix the problem.
>> Allison
>>
>> On Mon, 14 May 2012, Borzello, Mia wrote:
>>
>>> It says that it couldn't open rh.orig.nofix and  lh.orig.nofix. On the 
>>> popup image, it doesn't look like the skull is present, but it does look 
>>> like the cerebellum is.
>>> 
>>> From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
>>> Sent: Monday, May 14, 2012 1:28 PM
>>> To: Borzello, Mia
>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>> Subject: RE: [Freesurfer] "cannot allocate memory" issue
>>>
>>> You can do:
>>> tkmedit subjid filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix
>>>
>>> When you downloaded FreeSurfer, you would have also received the subject
>>> "bert" who is a good example to compare to. He will likely be located in:
>>> $FREESURFER_HOME/subjects/bert
>>>
>>> If you do the same command above for bert:
>>> tkmedit bert filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix
>>>
>>> You'll see what the filled.mgz should look like.
>>> Allison
>>>
>>> On Mon, 14 May 2012, Borzello, Mia wrote:
>>>
>>>> How do I check this? (Apologies for my ignorance.) So I might need to just 
>>>> use a different set of dicoms then?
>>>>
>>>> thanks,
>>>> Mia
>>>> 
>>>> From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
>>>> Sent: Monday, May 14, 2012 1:02 PM
>>>> To: Borzello, Mia
>>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>>> Subject: Re: [Freesurfer] "cannot allocate memory" issue
>>>>
>>>> It looks like there is too huge a topology error for it to continue:
>>>>
>>>> CORRECTING DEFECT 23 (vertices=143258, convex hull=19937)
>>>> Excessive topologic defect encountered: could not allocate -729782272
>>>> edges for retessellation
>>>> Cannot allocate memory
>>>>
>>>> I would suggested looking at the filled.mgz to make sure skull and/or
>>>> cerebellum are not included.
>>>> Allison
>>>>
>>>> On Mon, 14 May 2012, Borzello, Mia wrote:
>>>>
>>>>> Hi all,
>>>>>
>>>>> I was wondering if you could help me figure out why the recon isn't 

Re: [Freesurfer] "cannot allocate memory" issue

[Borzello, Mia]

okay, well i'll give it a try with a set of T1s. Thanks guys!

From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Monday, May 14, 2012 3:57 PM
To: Borzello, Mia
Cc: Allison Stevens Player; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] "cannot allocate memory" issue

yes, that's the kind of thing I was worried about. You need a relatively
high resolution set of T1s (mprage, FLASH/SPGR, close to 1mm isotropic).

On Mon, 14 May 2012,
Borzello, Mia wrote:

> oh woops. sorry.
> so both of these sets of dicoms are T2
> 
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, May 14, 2012 3:46 PM
> To: Borzello, Mia
> Cc: Allison Stevens Player; freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] "cannot allocate memory" issue
>
> actually I wanted one from tkmedit. Can you tell us something about the
> acquisition? What kind of scan is it? What resolution? And if you can
> send us images from tkmedit in coronal and sagittal view that would help
> too (say of the orig.mgz)
>
> Bruce
> On Mon, 14 May 2012, Borzello, Mia wrote:
>
>> I have two sets of dicoms: one is an axial view, while the other is coronal 
>> (this is the one i was using). I attached a screenshot. I'm not sure if 
>> that's what you wanted?
>>
>> thanks
>> mia
>> ________
>> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
>> Sent: Monday, May 14, 2012 3:32 PM
>> To: Borzello, Mia
>> Cc: Allison Stevens Player; freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] "cannot allocate memory" issue
>>
>> Hi Mia
>>
>> can you clarify what you mean by "a different set of dicoms"? Did you
>> acquire more than 1 T1-weighted structural on this subject? And can you
>> send us an image of the acquisition, say in coronal view?
>>
>> thanks
>> Bruce
>>
>>
>> On Mon, 14 May
>> 2012, Borzello, Mia wrote:
>>
>>> Hey Allison,
>>>
>>> Thanks for you help. What do you mean by check your talairach? I'll hold 
>>> off on using a different set of dicoms, and make that my last resort since 
>>> it takes a day to complete.
>>> Thanks,
>>> m
>>> 
>>> From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
>>> Sent: Monday, May 14, 2012 3:16 PM
>>> To: Borzello, Mia
>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>> Subject: RE: [Freesurfer] "cannot allocate memory" issue
>>>
>>> Hi Mia,
>>> You may want to check your talairach to make sure that looks okay. If
>>> that's not causing the problem, you can edit the wm.mgz to remove the
>>> cerebellum and then rerun and this should fix the problem.
>>> Allison
>>>
>>> On Mon, 14 May 2012, Borzello, Mia wrote:
>>>
>>>> It says that it couldn't open rh.orig.nofix and  lh.orig.nofix. On the 
>>>> popup image, it doesn't look like the skull is present, but it does look 
>>>> like the cerebellum is.
>>>> 
>>>> From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
>>>> Sent: Monday, May 14, 2012 1:28 PM
>>>> To: Borzello, Mia
>>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>>> Subject: RE: [Freesurfer] "cannot allocate memory" issue
>>>>
>>>> You can do:
>>>> tkmedit subjid filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix
>>>>
>>>> When you downloaded FreeSurfer, you would have also received the subject
>>>> "bert" who is a good example to compare to. He will likely be located in:
>>>> $FREESURFER_HOME/subjects/bert
>>>>
>>>> If you do the same command above for bert:
>>>> tkmedit bert filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix
>>>>
>>>> You'll see what the filled.mgz should look like.
>>>> Allison
>>>>
>>>> On Mon, 14 May 2012, Borzello, Mia wrote:
>>>>
>>>>> How do I check this? (Apologies for my ignorance.) So I might need to 
>>>>> just use a different set of dicoms then?
>>>>>
>>>>> thanks,
>>>>> Mia
>>>>> 
>>>>> From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
>>>>> Sent: Monday, May 14, 2012 1:02 PM
>>>>>