Re: [Freesurfer] Re: Re: Re: Re: Re: Time Series to Surface

[Crawford, Anna]

What do I put for the email to send to? freesurfer@nmr.mgh.harvard.edu and 
freesurfer-boun...@nmr.mgh.harvard.edu said it was not a valid account


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas Greve 

Sent: Friday, April 6, 2018 12:44 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [EXT] Re: [Freesurfer] Re: Re: Re: Re: Time Series to Surface


Can you upload the volume (img and hdr) here: 
https://gate.nmr.mgh.harvard.edu/filedrop2

On 4/6/18 12:24 PM, Crawford, Anna wrote:

1227 frames

Thanks,
Anna

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas Greve 

Sent: Friday, April 6, 2018 12:14 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [EXT] Re: [Freesurfer]  Re: Re: Re: Time Series to Surface

How many frames are in your input file? Eg, if you run mri_info on it?


On 4/6/18 12:05 PM, Crawford, Anna wrote:


I just opened freeview and loaded everything in the GUI. I did not use the 
command line to open it. I do not see a slider bar.

Thanks,
Anna

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas Greve 

Sent: Friday, April 6, 2018 11:54 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [EXT] Re: [Freesurfer]  Re: Re: Time Series to Surface

what is your freeview command line? Do you see a "frame" slider bar?


On 4/6/18 10:46 AM, Crawford, Anna wrote:


I tried without --init-fsl and adding in the --projfrac 0.5 for mri_vol2surf, 
but I am still not able to view the time course.

Thanks,
Anna

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas Greve 

Sent: Friday, April 6, 2018 10:21 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [EXT] Re: [Freesurfer]  Re: Time Series to Surface

No need to use --init-fsl (if using version 6). For mri_vol2surf add
--projfrac 0.5 to sample in the middle of the ribbon  (unless you
specifically want to sample on the gray/white border)


On 4/6/18 10:11 AM, Crawford, Anna wrote:


Hello,

I used the following commands and then opened the surface as an overlay on the 
inflated volume, but I am not about to look at the time series. The view time 
course is grayed out so that I can not click on it. Did I miss a step or lose 
the actual time series somewhere?

bbregister --s S2sdt/subject/ --mov 
/mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr 
 --reg S41vol.mocoafni.reg.dat --init-fsl --bold --gm-proj-frac 0.5

mri_vol2surf --src 
/mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr 
 --out 
/mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S2sdt/subject/surf/S41mocoafni.vol2surf.mgz
 --srcreg 
/mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.reg.dat
 --hemi lh


Thank you,
Anna


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas N. Greve 

Sent: Thursday, April 5, 2018 5:29 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [EXT] Re: [Freesurfer] Time Series to Surface

Use bbregister. Run with --help to get docs (make sure to use --projfrac
0.5). Once you have it on the surface, you can step through each frame
in freeview


On 04/05/2018 01:49 PM, Crawford, Anna wrote:


Hello,

I have a time series (.hdr/.img) that I want to overlay onto a
surface, specifically the inflated surface from the anatomy. I suspect
I have to use mri_vol2surf, which requires a source registration
file. How do I get this file? Then once I have this file, will I be
able to view step by step through the time series on the inflated volume?

Thanks for your help,
Anna


===

Please consider the environment before printing this e-mail

Cleveland Clinic is currently ranked as the No. 2 hospital in the
country by U.S. News & World Report (2017-2018). Visit us online at

Re: [Freesurfer] Re: Re: Re: Re: Time Series to Surface

[Douglas Greve]

Can you upload the volume (img and hdr) here: 
https://gate.nmr.mgh.harvard.edu/filedrop2



On 4/6/18 12:24 PM, Crawford, Anna wrote:

1227 frames

Thanks,
Anna

From: freesurfer-boun...@nmr.mgh.harvard.edu  
on behalf of Douglas Greve 
Sent: Friday, April 6, 2018 12:14 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [EXT] Re: [Freesurfer]  Re: Re: Re: Time Series to Surface

How many frames are in your input file? Eg, if you run mri_info on it?


On 4/6/18 12:05 PM, Crawford, Anna wrote:

I just opened freeview and loaded everything in the GUI. I did not use the 
command line to open it. I do not see a slider bar.

Thanks,
Anna

From: freesurfer-boun...@nmr.mgh.harvard.edu  
on behalf of Douglas Greve 
Sent: Friday, April 6, 2018 11:54 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [EXT] Re: [Freesurfer]  Re: Re: Time Series to Surface

what is your freeview command line? Do you see a "frame" slider bar?


On 4/6/18 10:46 AM, Crawford, Anna wrote:

I tried without --init-fsl and adding in the --projfrac 0.5 for mri_vol2surf, 
but I am still not able to view the time course.

Thanks,
Anna

From: freesurfer-boun...@nmr.mgh.harvard.edu  
on behalf of Douglas Greve 
Sent: Friday, April 6, 2018 10:21 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [EXT] Re: [Freesurfer]  Re: Time Series to Surface

No need to use --init-fsl (if using version 6). For mri_vol2surf add
--projfrac 0.5 to sample in the middle of the ribbon  (unless you
specifically want to sample on the gray/white border)


On 4/6/18 10:11 AM, Crawford, Anna wrote:

Hello,

I used the following commands and then opened the surface as an overlay on the 
inflated volume, but I am not about to look at the time series. The view time 
course is grayed out so that I can not click on it. Did I miss a step or lose 
the actual time series somewhere?

bbregister --s S2sdt/subject/ --mov 
/mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr 
 --reg S41vol.mocoafni.reg.dat --init-fsl --bold --gm-proj-frac 0.5

mri_vol2surf --src 
/mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr 
 --out 
/mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S2sdt/subject/surf/S41mocoafni.vol2surf.mgz
 --srcreg 
/mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.reg.dat
 --hemi lh


Thank you,
Anna


From: freesurfer-boun...@nmr.mgh.harvard.edu  
on behalf of Douglas N. Greve 
Sent: Thursday, April 5, 2018 5:29 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [EXT] Re: [Freesurfer] Time Series to Surface

Use bbregister. Run with --help to get docs (make sure to use --projfrac
0.5). Once you have it on the surface, you can step through each frame
in freeview


On 04/05/2018 01:49 PM, Crawford, Anna wrote:

Hello,

I have a time series (.hdr/.img) that I want to overlay onto a
surface, specifically the inflated surface from the anatomy. I suspect
I have to use mri_vol2surf, which requires a source registration
file. How do I get this file? Then once I have this file, will I be
able to view step by step through the time series on the inflated volume?

Thanks for your help,
Anna


===

Please consider the environment before printing this e-mail

Cleveland Clinic is currently ranked as the No. 2 hospital in the
country by U.S. News & World Report (2017-2018). Visit us online at
http://www.clevelandclinic.org for a complete listing of our services,
staff and locations. Confidentiality Note: This message is intended
for use only by the individual or entity to which it is addressed and
may contain information that is privileged, confidential, and exempt
from disclosure under applicable law. If the reader of this message is
not the intended recipient or the employee or agent responsible for
delivering the message to the intended recipient, you are hereby
notified that any dissemination, distribution or copying of this
communication is strictly prohibited. If you have received this
communication in error, please contact the sender immediately and
destroy the material in its entirety, whether electronic or hard copy.
Thank you.


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

___
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 

Re: [Freesurfer] Re: Re: Re: Re: Time Series to Surface

[Crawford, Anna]

1227 frames

Thanks,
Anna

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas Greve 

Sent: Friday, April 6, 2018 12:14 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [EXT] Re: [Freesurfer]  Re: Re: Re: Time Series to Surface

How many frames are in your input file? Eg, if you run mri_info on it?


On 4/6/18 12:05 PM, Crawford, Anna wrote:
> I just opened freeview and loaded everything in the GUI. I did not use the 
> command line to open it. I do not see a slider bar.
>
> Thanks,
> Anna
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas Greve 
> 
> Sent: Friday, April 6, 2018 11:54 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [EXT] Re: [Freesurfer]  Re: Re: Time Series to Surface
>
> what is your freeview command line? Do you see a "frame" slider bar?
>
>
> On 4/6/18 10:46 AM, Crawford, Anna wrote:
>> I tried without --init-fsl and adding in the --projfrac 0.5 for 
>> mri_vol2surf, but I am still not able to view the time course.
>>
>> Thanks,
>> Anna
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Douglas Greve 
>> 
>> Sent: Friday, April 6, 2018 10:21 AM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: [EXT] Re: [Freesurfer]  Re: Time Series to Surface
>>
>> No need to use --init-fsl (if using version 6). For mri_vol2surf add
>> --projfrac 0.5 to sample in the middle of the ribbon  (unless you
>> specifically want to sample on the gray/white border)
>>
>>
>> On 4/6/18 10:11 AM, Crawford, Anna wrote:
>>> Hello,
>>>
>>> I used the following commands and then opened the surface as an overlay on 
>>> the inflated volume, but I am not about to look at the time series. The 
>>> view time course is grayed out so that I can not click on it. Did I miss a 
>>> step or lose the actual time series somewhere?
>>>
>>> bbregister --s S2sdt/subject/ --mov 
>>> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr
>>>   --reg S41vol.mocoafni.reg.dat --init-fsl --bold --gm-proj-frac 0.5
>>>
>>> mri_vol2surf --src 
>>> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr
>>>   --out 
>>> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S2sdt/subject/surf/S41mocoafni.vol2surf.mgz
>>>  --srcreg 
>>> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.reg.dat
>>>  --hemi lh
>>>
>>>
>>> Thank you,
>>> Anna
>>>
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>  on behalf of Douglas N. Greve 
>>> 
>>> Sent: Thursday, April 5, 2018 5:29 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: [EXT] Re: [Freesurfer] Time Series to Surface
>>>
>>> Use bbregister. Run with --help to get docs (make sure to use --projfrac
>>> 0.5). Once you have it on the surface, you can step through each frame
>>> in freeview
>>>
>>>
>>> On 04/05/2018 01:49 PM, Crawford, Anna wrote:
 Hello,

 I have a time series (.hdr/.img) that I want to overlay onto a
 surface, specifically the inflated surface from the anatomy. I suspect
 I have to use mri_vol2surf, which requires a source registration
 file. How do I get this file? Then once I have this file, will I be
 able to view step by step through the time series on the inflated volume?

 Thanks for your help,
 Anna


 ===

 Please consider the environment before printing this e-mail

 Cleveland Clinic is currently ranked as the No. 2 hospital in the
 country by U.S. News & World Report (2017-2018). Visit us online at
 http://www.clevelandclinic.org for a complete listing of our services,
 staff and locations. Confidentiality Note: This message is intended
 for use only by the individual or entity to which it is addressed and
 may contain information that is privileged, confidential, and exempt
 from disclosure under applicable law. If the reader of this message is
 not the intended recipient or the employee or agent responsible for
 delivering the message to the intended recipient, you are hereby
 notified that any dissemination, distribution or copying of this
 communication is strictly prohibited. If you have received this
 communication in error, please contact the sender immediately and
 destroy the material in its entirety, whether electronic or hard copy.
 Thank you.


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

Re: [Freesurfer] Re: Re: Re: Time Series to Surface

[Douglas Greve]

How many frames are in your input file? Eg, if you run mri_info on it?


On 4/6/18 12:05 PM, Crawford, Anna wrote:
> I just opened freeview and loaded everything in the GUI. I did not use the 
> command line to open it. I do not see a slider bar.
>
> Thanks,
> Anna
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas Greve 
> 
> Sent: Friday, April 6, 2018 11:54 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [EXT] Re: [Freesurfer]  Re: Re: Time Series to Surface
>
> what is your freeview command line? Do you see a "frame" slider bar?
>
>
> On 4/6/18 10:46 AM, Crawford, Anna wrote:
>> I tried without --init-fsl and adding in the --projfrac 0.5 for 
>> mri_vol2surf, but I am still not able to view the time course.
>>
>> Thanks,
>> Anna
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Douglas Greve 
>> 
>> Sent: Friday, April 6, 2018 10:21 AM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: [EXT] Re: [Freesurfer]  Re: Time Series to Surface
>>
>> No need to use --init-fsl (if using version 6). For mri_vol2surf add
>> --projfrac 0.5 to sample in the middle of the ribbon  (unless you
>> specifically want to sample on the gray/white border)
>>
>>
>> On 4/6/18 10:11 AM, Crawford, Anna wrote:
>>> Hello,
>>>
>>> I used the following commands and then opened the surface as an overlay on 
>>> the inflated volume, but I am not about to look at the time series. The 
>>> view time course is grayed out so that I can not click on it. Did I miss a 
>>> step or lose the actual time series somewhere?
>>>
>>> bbregister --s S2sdt/subject/ --mov 
>>> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr
>>>   --reg S41vol.mocoafni.reg.dat --init-fsl --bold --gm-proj-frac 0.5
>>>
>>> mri_vol2surf --src 
>>> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr
>>>   --out 
>>> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S2sdt/subject/surf/S41mocoafni.vol2surf.mgz
>>>  --srcreg 
>>> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.reg.dat
>>>  --hemi lh
>>>
>>>
>>> Thank you,
>>> Anna
>>>
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>  on behalf of Douglas N. Greve 
>>> 
>>> Sent: Thursday, April 5, 2018 5:29 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: [EXT] Re: [Freesurfer] Time Series to Surface
>>>
>>> Use bbregister. Run with --help to get docs (make sure to use --projfrac
>>> 0.5). Once you have it on the surface, you can step through each frame
>>> in freeview
>>>
>>>
>>> On 04/05/2018 01:49 PM, Crawford, Anna wrote:
 Hello,

 I have a time series (.hdr/.img) that I want to overlay onto a
 surface, specifically the inflated surface from the anatomy. I suspect
 I have to use mri_vol2surf, which requires a source registration
 file. How do I get this file? Then once I have this file, will I be
 able to view step by step through the time series on the inflated volume?

 Thanks for your help,
 Anna


 ===

 Please consider the environment before printing this e-mail

 Cleveland Clinic is currently ranked as the No. 2 hospital in the
 country by U.S. News & World Report (2017-2018). Visit us online at
 http://www.clevelandclinic.org for a complete listing of our services,
 staff and locations. Confidentiality Note: This message is intended
 for use only by the individual or entity to which it is addressed and
 may contain information that is privileged, confidential, and exempt
 from disclosure under applicable law. If the reader of this message is
 not the intended recipient or the employee or agent responsible for
 delivering the message to the intended recipient, you are hereby
 notified that any dissemination, distribution or copying of this
 communication is strictly prohibited. If you have received this
 communication in error, please contact the sender immediately and
 destroy the material in its entirety, whether electronic or hard copy.
 Thank you.


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

Re: [Freesurfer] Re: Re: Re: Time Series to Surface

[Crawford, Anna]

I just opened freeview and loaded everything in the GUI. I did not use the 
command line to open it. I do not see a slider bar.

Thanks,
Anna

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas Greve 

Sent: Friday, April 6, 2018 11:54 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [EXT] Re: [Freesurfer]  Re: Re: Time Series to Surface

what is your freeview command line? Do you see a "frame" slider bar?


On 4/6/18 10:46 AM, Crawford, Anna wrote:
> I tried without --init-fsl and adding in the --projfrac 0.5 for mri_vol2surf, 
> but I am still not able to view the time course.
>
> Thanks,
> Anna
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas Greve 
> 
> Sent: Friday, April 6, 2018 10:21 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [EXT] Re: [Freesurfer]  Re: Time Series to Surface
>
> No need to use --init-fsl (if using version 6). For mri_vol2surf add
> --projfrac 0.5 to sample in the middle of the ribbon  (unless you
> specifically want to sample on the gray/white border)
>
>
> On 4/6/18 10:11 AM, Crawford, Anna wrote:
>> Hello,
>>
>> I used the following commands and then opened the surface as an overlay on 
>> the inflated volume, but I am not about to look at the time series. The view 
>> time course is grayed out so that I can not click on it. Did I miss a step 
>> or lose the actual time series somewhere?
>>
>> bbregister --s S2sdt/subject/ --mov 
>> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr
>>   --reg S41vol.mocoafni.reg.dat --init-fsl --bold --gm-proj-frac 0.5
>>
>> mri_vol2surf --src 
>> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr
>>   --out 
>> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S2sdt/subject/surf/S41mocoafni.vol2surf.mgz
>>  --srcreg 
>> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.reg.dat
>>  --hemi lh
>>
>>
>> Thank you,
>> Anna
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Douglas N. Greve 
>> 
>> Sent: Thursday, April 5, 2018 5:29 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: [EXT] Re: [Freesurfer] Time Series to Surface
>>
>> Use bbregister. Run with --help to get docs (make sure to use --projfrac
>> 0.5). Once you have it on the surface, you can step through each frame
>> in freeview
>>
>>
>> On 04/05/2018 01:49 PM, Crawford, Anna wrote:
>>> Hello,
>>>
>>> I have a time series (.hdr/.img) that I want to overlay onto a
>>> surface, specifically the inflated surface from the anatomy. I suspect
>>> I have to use mri_vol2surf, which requires a source registration
>>> file. How do I get this file? Then once I have this file, will I be
>>> able to view step by step through the time series on the inflated volume?
>>>
>>> Thanks for your help,
>>> Anna
>>>
>>>
>>> ===
>>>
>>> Please consider the environment before printing this e-mail
>>>
>>> Cleveland Clinic is currently ranked as the No. 2 hospital in the
>>> country by U.S. News & World Report (2017-2018). Visit us online at
>>> http://www.clevelandclinic.org for a complete listing of our services,
>>> staff and locations. Confidentiality Note: This message is intended
>>> for use only by the individual or entity to which it is addressed and
>>> may contain information that is privileged, confidential, and exempt
>>> from disclosure under applicable law. If the reader of this message is
>>> not the intended recipient or the employee or agent responsible for
>>> delivering the message to the intended recipient, you are hereby
>>> notified that any dissemination, distribution or copying of this
>>> communication is strictly prohibited. If you have received this
>>> communication in error, please contact the sender immediately and
>>> destroy the material in its entirety, whether electronic or hard copy.
>>> Thank you.
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> ___
>> 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
>> 

Re: [Freesurfer] Re: Re: Time Series to Surface

[Douglas Greve]

what is your freeview command line? Do you see a "frame" slider bar?


On 4/6/18 10:46 AM, Crawford, Anna wrote:
> I tried without --init-fsl and adding in the --projfrac 0.5 for mri_vol2surf, 
> but I am still not able to view the time course.
>
> Thanks,
> Anna
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas Greve 
> 
> Sent: Friday, April 6, 2018 10:21 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [EXT] Re: [Freesurfer]  Re: Time Series to Surface
>
> No need to use --init-fsl (if using version 6). For mri_vol2surf add
> --projfrac 0.5 to sample in the middle of the ribbon  (unless you
> specifically want to sample on the gray/white border)
>
>
> On 4/6/18 10:11 AM, Crawford, Anna wrote:
>> Hello,
>>
>> I used the following commands and then opened the surface as an overlay on 
>> the inflated volume, but I am not about to look at the time series. The view 
>> time course is grayed out so that I can not click on it. Did I miss a step 
>> or lose the actual time series somewhere?
>>
>> bbregister --s S2sdt/subject/ --mov 
>> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr
>>   --reg S41vol.mocoafni.reg.dat --init-fsl --bold --gm-proj-frac 0.5
>>
>> mri_vol2surf --src 
>> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr
>>   --out 
>> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S2sdt/subject/surf/S41mocoafni.vol2surf.mgz
>>  --srcreg 
>> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.reg.dat
>>  --hemi lh
>>
>>
>> Thank you,
>> Anna
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Douglas N. Greve 
>> 
>> Sent: Thursday, April 5, 2018 5:29 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: [EXT] Re: [Freesurfer] Time Series to Surface
>>
>> Use bbregister. Run with --help to get docs (make sure to use --projfrac
>> 0.5). Once you have it on the surface, you can step through each frame
>> in freeview
>>
>>
>> On 04/05/2018 01:49 PM, Crawford, Anna wrote:
>>> Hello,
>>>
>>> I have a time series (.hdr/.img) that I want to overlay onto a
>>> surface, specifically the inflated surface from the anatomy. I suspect
>>> I have to use mri_vol2surf, which requires a source registration
>>> file. How do I get this file? Then once I have this file, will I be
>>> able to view step by step through the time series on the inflated volume?
>>>
>>> Thanks for your help,
>>> Anna
>>>
>>>
>>> ===
>>>
>>> Please consider the environment before printing this e-mail
>>>
>>> Cleveland Clinic is currently ranked as the No. 2 hospital in the
>>> country by U.S. News & World Report (2017-2018). Visit us online at
>>> http://www.clevelandclinic.org for a complete listing of our services,
>>> staff and locations. Confidentiality Note: This message is intended
>>> for use only by the individual or entity to which it is addressed and
>>> may contain information that is privileged, confidential, and exempt
>>> from disclosure under applicable law. If the reader of this message is
>>> not the intended recipient or the employee or agent responsible for
>>> delivering the message to the intended recipient, you are hereby
>>> notified that any dissemination, distribution or copying of this
>>> communication is strictly prohibited. If you have received this
>>> communication in error, please contact the sender immediately and
>>> destroy the material in its entirety, whether electronic or hard copy.
>>> Thank you.
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>> error
>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
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>>
>> ===
>>
>>
>>Please consider the environment before printing this e-mail
>>
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>> U.S. News & World Report (2017-2018). Visit us online at 
>> http://www.clevelandclinic.org for a complete listing of our services, staff 
>> and locations. Confidentiality Note: This message is intended for use only 
>> by the 

Re: [Freesurfer] Re: Re: Time Series to Surface

[Crawford, Anna]

I tried without --init-fsl and adding in the --projfrac 0.5 for mri_vol2surf, 
but I am still not able to view the time course.

Thanks,
Anna

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas Greve 

Sent: Friday, April 6, 2018 10:21 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [EXT] Re: [Freesurfer]  Re: Time Series to Surface

No need to use --init-fsl (if using version 6). For mri_vol2surf add
--projfrac 0.5 to sample in the middle of the ribbon  (unless you
specifically want to sample on the gray/white border)


On 4/6/18 10:11 AM, Crawford, Anna wrote:
> Hello,
>
> I used the following commands and then opened the surface as an overlay on 
> the inflated volume, but I am not about to look at the time series. The view 
> time course is grayed out so that I can not click on it. Did I miss a step or 
> lose the actual time series somewhere?
>
> bbregister --s S2sdt/subject/ --mov 
> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr
>   --reg S41vol.mocoafni.reg.dat --init-fsl --bold --gm-proj-frac 0.5
>
> mri_vol2surf --src 
> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr
>   --out 
> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S2sdt/subject/surf/S41mocoafni.vol2surf.mgz
>  --srcreg 
> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.reg.dat
>  --hemi lh
>
>
> Thank you,
> Anna
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N. Greve 
> 
> Sent: Thursday, April 5, 2018 5:29 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [EXT] Re: [Freesurfer] Time Series to Surface
>
> Use bbregister. Run with --help to get docs (make sure to use --projfrac
> 0.5). Once you have it on the surface, you can step through each frame
> in freeview
>
>
> On 04/05/2018 01:49 PM, Crawford, Anna wrote:
>> Hello,
>>
>> I have a time series (.hdr/.img) that I want to overlay onto a
>> surface, specifically the inflated surface from the anatomy. I suspect
>> I have to use mri_vol2surf, which requires a source registration
>> file. How do I get this file? Then once I have this file, will I be
>> able to view step by step through the time series on the inflated volume?
>>
>> Thanks for your help,
>> Anna
>>
>>
>> ===
>>
>> Please consider the environment before printing this e-mail
>>
>> Cleveland Clinic is currently ranked as the No. 2 hospital in the
>> country by U.S. News & World Report (2017-2018). Visit us online at
>> http://www.clevelandclinic.org for a complete listing of our services,
>> staff and locations. Confidentiality Note: This message is intended
>> for use only by the individual or entity to which it is addressed and
>> may contain information that is privileged, confidential, and exempt
>> from disclosure under applicable law. If the reader of this message is
>> not the intended recipient or the employee or agent responsible for
>> delivering the message to the intended recipient, you are hereby
>> notified that any dissemination, distribution or copying of this
>> communication is strictly prohibited. If you have received this
>> communication in error, please contact the sender immediately and
>> destroy the material in its entirety, whether electronic or hard copy.
>> Thank you.
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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.
>
>
> ===
>
>
>   Please consider the environment before printing this e-mail
>
> Cleveland Clinic is currently ranked as the No. 2 hospital in the country by 
> U.S. News & World Report (2017-2018). Visit us online at 
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> and locations. Confidentiality Note: This message is intended for use only by 
> the individual or entity to which it is addressed and may contain information 
> that is privileged, confidential, and exempt from disclosure under applicable 
> law. If the reader of this message is not the intended recipient or the 
> employee or agent 

Re: [Freesurfer] FSGD design for multi-centre study

[Douglas Greve]

Create a separate class for each combination of diagnosis, sex, and 
center, then create contrasts that average over center.

On 4/6/18 7:11 AM, C.P.E. Rollins wrote:
> Dear Freesurfer Developers,
>
> I'd like to do a standard CT analysis (patients vs. controls, covaried
> for age and sex) on data from a multi-centre study and I'm wondering how
> I should construct my FSGD file to code centre as a dummy variable.
> Currently, my FSGD looks something like this:
> GroupDescriptorFile 1
> Group Control_Male
> Group Control_Female
> Group Patient_Male
> Group Patient_Female
> Variables Age
> Input subj001-002 Patient_Male32
> Input subj001-003 Patient_Male19
> Input subj001-040 Patient_Female  28
> ...
> To include centre as dummy variable, would I add an additional column
> for each centre and enter either a 1 or a 0 depending on whether that
> scan is from that centre? For instance, there were 6 centres (scans for
> patients and controls collected at each) in the study, so centre as a
> dummy variable might look something like this (columns added on after
> age)?
> 0 0 1 0 0 0
> 0 0 0 1 0 0
> 1 0 0 0 0 0
> Moreover, would this be the best way to control for centre?
>
> Many thanks,
> Colleen
>
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Re: [Freesurfer] Quality of fMRI registration

[Douglas Greve]

There is no way to give a hard-and-fast threshold on the quality. 
0.5-0.6 is not considered bad. If the registrations look good to you 
visually then it is fine



On 4/5/18 5:43 PM, Arsenije Subotic wrote:


Dear experts,


When it comes to assessing the quality of fMRI integration in 
Freesurfer, is a value of > 0.5 considered a good registration? I was 
led to believe that from the multimodal tutorial website, and after 
checking the quality of my output I was satisfied with the result for 
each of my participants. However, I came back to the multimodal 
tutorial later after two weeks, and noticed that the page had been 
edited and now it says that any value <0.5 is considered a good 
registration. How would I go about resolving this issue, seeing as I 
visually inspected my output after each automatic registration and 
everything seemed fine? Most of my registration values were about 
0.5-0.6.



Please let me know.


Thanks!

Arsenije



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Re: [Freesurfer] Re: Time Series to Surface

[Douglas Greve]

No need to use --init-fsl (if using version 6). For mri_vol2surf add 
--projfrac 0.5 to sample in the middle of the ribbon  (unless you 
specifically want to sample on the gray/white border)


On 4/6/18 10:11 AM, Crawford, Anna wrote:
> Hello,
>
> I used the following commands and then opened the surface as an overlay on 
> the inflated volume, but I am not about to look at the time series. The view 
> time course is grayed out so that I can not click on it. Did I miss a step or 
> lose the actual time series somewhere?
>
> bbregister --s S2sdt/subject/ --mov 
> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr
>   --reg S41vol.mocoafni.reg.dat --init-fsl --bold --gm-proj-frac 0.5
>
> mri_vol2surf --src 
> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr
>   --out 
> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S2sdt/subject/surf/S41mocoafni.vol2surf.mgz
>  --srcreg 
> /mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.reg.dat
>  --hemi lh
>
>
> Thank you,
> Anna
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N. Greve 
> 
> Sent: Thursday, April 5, 2018 5:29 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [EXT] Re: [Freesurfer] Time Series to Surface
>
> Use bbregister. Run with --help to get docs (make sure to use --projfrac
> 0.5). Once you have it on the surface, you can step through each frame
> in freeview
>
>
> On 04/05/2018 01:49 PM, Crawford, Anna wrote:
>> Hello,
>>
>> I have a time series (.hdr/.img) that I want to overlay onto a
>> surface, specifically the inflated surface from the anatomy. I suspect
>> I have to use mri_vol2surf, which requires a source registration
>> file. How do I get this file? Then once I have this file, will I be
>> able to view step by step through the time series on the inflated volume?
>>
>> Thanks for your help,
>> Anna
>>
>>
>> ===
>>
>> Please consider the environment before printing this e-mail
>>
>> Cleveland Clinic is currently ranked as the No. 2 hospital in the
>> country by U.S. News & World Report (2017-2018). Visit us online at
>> http://www.clevelandclinic.org for a complete listing of our services,
>> staff and locations. Confidentiality Note: This message is intended
>> for use only by the individual or entity to which it is addressed and
>> may contain information that is privileged, confidential, and exempt
>> from disclosure under applicable law. If the reader of this message is
>> not the intended recipient or the employee or agent responsible for
>> delivering the message to the intended recipient, you are hereby
>> notified that any dissemination, distribution or copying of this
>> communication is strictly prohibited. If you have received this
>> communication in error, please contact the sender immediately and
>> destroy the material in its entirety, whether electronic or hard copy.
>> Thank you.
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> ___
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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.
>
>
> ===
>
>
>   Please consider the environment before printing this e-mail
>
> Cleveland Clinic is currently ranked as the No. 2 hospital in the country by 
> U.S. News & World Report (2017-2018). Visit us online at 
> http://www.clevelandclinic.org for a complete listing of our services, staff 
> and locations. Confidentiality Note: This message is intended for use only by 
> the individual or entity to which it is addressed and may contain information 
> that is privileged, confidential, and exempt from disclosure under applicable 
> law. If the reader of this message is not the intended recipient or the 
> employee or agent responsible for delivering the message to the intended 
> recipient, you are hereby notified that any dissemination, distribution or 
> copying of this communication is strictly prohibited. If you have received 
> this communication in error, please contact the sender immediately and 
> destroy the material in its entirety, whether electronic or hard copy. Thank 
> you.
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> 

Re: [Freesurfer] Re: Time Series to Surface

[Crawford, Anna]

Hello,

I used the following commands and then opened the surface as an overlay on the 
inflated volume, but I am not about to look at the time series. The view time 
course is grayed out so that I can not click on it. Did I miss a step or lose 
the actual time series somewhere?

bbregister --s S2sdt/subject/ --mov 
/mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr 
 --reg S41vol.mocoafni.reg.dat --init-fsl --bold --gm-proj-frac 0.5

mri_vol2surf --src 
/mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.hdr 
 --out 
/mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S2sdt/subject/surf/S41mocoafni.vol2surf.mgz
 --srcreg 
/mnt/netScratch/crawforda/Epilepsy/EEG-fMRI/study488/S41sdt/S41vol.mocoafni.reg.dat
 --hemi lh


Thank you,
Anna


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Thursday, April 5, 2018 5:29 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [EXT] Re: [Freesurfer] Time Series to Surface

Use bbregister. Run with --help to get docs (make sure to use --projfrac
0.5). Once you have it on the surface, you can step through each frame
in freeview


On 04/05/2018 01:49 PM, Crawford, Anna wrote:
> Hello,
>
> I have a time series (.hdr/.img) that I want to overlay onto a
> surface, specifically the inflated surface from the anatomy. I suspect
> I have to use mri_vol2surf, which requires a source registration
> file. How do I get this file? Then once I have this file, will I be
> able to view step by step through the time series on the inflated volume?
>
> Thanks for your help,
> Anna
>
>
> ===
>
> Please consider the environment before printing this e-mail
>
> Cleveland Clinic is currently ranked as the No. 2 hospital in the
> country by U.S. News & World Report (2017-2018). Visit us online at
> http://www.clevelandclinic.org for a complete listing of our services,
> staff and locations. Confidentiality Note: This message is intended
> for use only by the individual or entity to which it is addressed and
> may contain information that is privileged, confidential, and exempt
> from disclosure under applicable law. If the reader of this message is
> not the intended recipient or the employee or agent responsible for
> delivering the message to the intended recipient, you are hereby
> notified that any dissemination, distribution or copying of this
> communication is strictly prohibited. If you have received this
> communication in error, please contact the sender immediately and
> destroy the material in its entirety, whether electronic or hard copy.
> Thank you.
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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dispose of the e-mail.


===


 Please consider the environment before printing this e-mail

Cleveland Clinic is currently ranked as the No. 2 hospital in the country by 
U.S. News & World Report (2017-2018). Visit us online at 
http://www.clevelandclinic.org for a complete listing of our services, staff 
and locations. Confidentiality Note: This message is intended for use only by 
the individual or entity to which it is addressed and may contain information 
that is privileged, confidential, and exempt from disclosure under applicable 
law. If the reader of this message is not the intended recipient or the 
employee or agent responsible for delivering the message to the intended 
recipient, you are hereby notified that any dissemination, distribution or 
copying of this communication is strictly prohibited. If you have received this 
communication in error, please contact the sender immediately and destroy the 
material in its entirety, whether electronic or hard copy. Thank you.

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Re: [Freesurfer] Tracula - Could not find satisfactory control point fit

[Yendiki, Anastasia]

Hi Desiree - It looks like this is happening for the corticospinal tract. Is 
there anything going on with that scan in the area of that tract, let's say 
slices cut off from the top of the motor cortex or from the brainstem?


Best,

a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Lussier,Desiree 

Sent: Thursday, April 5, 2018 3:21:18 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Tracula - Could not find satisfactory control point fit

Dear Freesurfer experts,


I have been trying run trac-all -prep on two subjects but it seems to be stuck 
on the priors pathway estimation. The following (with updated number of tries) 
keeps appearing in the terminal:


  WARN: Could not find satisfactory control point fit - try 288
  Finding center streamline
  INFO: Step is 5 voxels
  WARN: Turning off deviation check for center streamline
  INFO: Step is 5 voxels
  WARN: Turning off FA check for center streamline
  INFO: Step is 5 voxels


I've attached the log here. Previous communications I've seen regarding this 
are years old and were solved by upgrading to 5.3. However, I'm already using 
the 64 bit 6.0.


Advice regarding this situation would be greatly appreciated.


Thank you,

Desiree Lussier


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Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

[Anna Daniels]

Hi Bruce, hi Srishti,

I have exactly the same problem with several subjects rerunning recon-all
and there was sufficient memory available. I also tried out the last
command directly which resulted in the same error log.

 mri_normalize -f /home/anna/FREESURFER/00_DATA_MABT1T2/02a_MABT1T2_cross_
edits_transfer/rreruncrosstest_cp17/22275_T1_fs_edit/tmp/control.dat
-mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz

Attached you can find the input file.

Thank you and best,
Anna​
 22275_T1_fs_edit.zip

​



> can you email us the input file and the full command line you ran?
> On Thu, 5
> Apr 2018, srishti goel wrote:
>
> > So it gave this error:
> >
> > 3d normalization pass 1 of 2
> >
> > white matter peak found at 110
> >
> > HISTOalloc(-2147483648): could not allocate histogram
> >
> > Cannot allocate memory
> >
> >
> > Best,
> > Srishti
> > Social/Clinical Research Specialist
> > Child Imaging Research and Life Experiences Lab
> > University of North Carolina at Chapel Hill
> > email (W): srish...@email.unc.edu
> > skype: srishti.goel12
> >
> >
> > On Thu, Apr 5, 2018 at 12:43 PM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
> >   let's see if it works. If it does, you should be able to run
> >
> >   recon-all -s SUBJID -make all
> >
> >   cheers
> >   Bruce
> >
> >
> >   On Thu, 5 Apr 2018, srishti goel wrote:
> >
> > Should I re-run the recon-all after running the last command
> from recon-all.cmd?
> >
> > Best,
> > Srishti
> > Social/Clinical Research Specialist
> > Child Imaging Research and Life Experiences Lab
> > University of North Carolina at Chapel Hill
> > email (W): srish...@email.unc.edu
> > skype: srishti.goel12
> >
> >
> > On Thu, Apr 5, 2018 at 12:31 PM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
> > ? ? ? Hi Srishti
> >
> > ? ? ? if you look in the subject's scripts dir there should
> be a file named "recon-all.cmd". Try
> > rerunning the last
> > ? ? ? command in it (probably from the mri dir)
> >
> > ? ? ? cheers
> > ? ? ? Bruce
> > ? ? ? On Thu, 5 Apr 2018, srishti goel wrote:
> >
> > ? ? ? ? ? ? I am sorry, I am not sure what do you mean by
> running the command line directly?
> > ? ? ? ? ? ? I use the following command:
> >
> > ? ? ? ? ? ? sbatch --mem 2200 -t 6-00:00 --mail-type END
> --mail-user srish...@email.unc.edu --wrap
> > "export
> > ? ? ? ? ? ? SUBJECTS_DIR=/proj/hng/sherida
> nlab/freeSurfer/DukeYAS/Freesurfer_out/; recon-all -s 13166
> > ? ? ? ? ? ? -autorecon2-cp -autorecon3 -nowmsa"
> >
> >
> > ? ? ? ? ? ? where sbatch. until export is our local
> server submission command and I run this
> > command from the
> > ? ? ? ? ? ? command line itself, not
> > ? ? ? ? ? ? using any script.
> >
> >
> > ? ? ? ? ? ? Best,
> > ? ? ? ? ? ? Srishti
> > ? ? ? ? ? ? Social/Clinical Research Specialist
> > ? ? ? ? ? ? Child Imaging Research and Life Experiences Lab
> > ? ? ? ? ? ? University of North Carolina at Chapel Hill
> > ? ? ? ? ? ? email (W): srish...@email.unc.edu
> > ? ? ? ? ? ? skype: srishti.goel12
> >
> >
> > ? ? ? ? ? ? On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
> > ? ? ? ? ? ? ? ? ? if you run the command that failed again
> on the command line directly (that is, not
> > in
> > ? ? ? ? ? ? recon-all) does it fail
> > ? ? ? ? ? ? ? ? ? again?
> >
> > ? ? ? ? ? ? ? ? ? On Thu, 5 Apr 2018, srishti goel wrote:
> >
> > ? ? ? ? ? ? ? ? ? ? ? ? Hi Bruce,
> >
> > ? ? ? ? ? ? ? ? ? ? ? ? The machine definitely hasn't run
> out of memory. Here is the memory usage
> > ? ? ? ? ? ? ? ? ? ? ? ? from recon-all.log ?
> >
> > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?total ? ? ? ? ?
> ? ?used ? ? ? ?free ? ? ? ? ? ? ? ? ?
> > ? ? ? ? ? ? ? ? ? ? ? ? shared ?buff/cache ? available
> > ? ? ? ? ? ? ? ? ? ? ? ? Mem: ? ? ?263726968 ? ?34330048 ?
> 152102696 ? ? ? 12944 ? ?77294224 ?
> > ? ? ? ? ? ? ? ? ? ? ? ? 191963372
> > ? ? ? ? ? ? ? ? ? ? ? ? Swap: ? ? ? 2097148 ? ? ? ? ? 0 ? ?
> ? ? ? ? 2097148
> >
> >
> >
> >
> > ? ? ? ? ? ? ? ? ? ? ? ? Best,
> > ? ? ? ? ? ? ? ? ? ? ? ? Srishti
> > ? ? ? ? ? ? ? ? ? ? ? ? Social/Clinical Research Specialist
> > ? ? ? ? ? ? ? ? ? ? ? ? Child Imaging Research and Life
> Experiences Lab
> > ? ? ? ? ? ? ? ? ? ? ? ? University of North Carolina at
> Chapel 

[Freesurfer] FSGD design for multi-centre study

[C.P.E. Rollins]

Dear Freesurfer Developers,

I'd like to do a standard CT analysis (patients vs. controls, covaried 
for age and sex) on data from a multi-centre study and I'm wondering how 
I should construct my FSGD file to code centre as a dummy variable. 
Currently, my FSGD looks something like this:
GroupDescriptorFile 1
Group Control_Male
Group Control_Female
Group Patient_Male
Group Patient_Female
Variables   Age
Input   subj001-002 Patient_Male32
Input   subj001-003 Patient_Male19
Input   subj001-040 Patient_Female  28
...
To include centre as dummy variable, would I add an additional column 
for each centre and enter either a 1 or a 0 depending on whether that 
scan is from that centre? For instance, there were 6 centres (scans for 
patients and controls collected at each) in the study, so centre as a 
dummy variable might look something like this (columns added on after 
age)?
0 0 1 0 0 0
0 0 0 1 0 0
1 0 0 0 0 0
Moreover, would this be the best way to control for centre?

Many thanks,
Colleen

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