If I don't use --sd it uses the default subject directory (SUBJECTS_DIR    
/tools/freesurfer/subjects) which is not where my data is located.

Thanks,
Anna
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, September 27, 2016 10:50 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Co-registering different source data

Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that
is already set properly, then do not use the --sd.


On 9/27/16 9:38 AM, Crawford, Anna wrote:
> Hi,
>
> I keep getting an error when I use mri_label2label. Below is my input and 
> output. I have tried various paths all the way down to the label and above 
> the subject level, but still always get the same error. I have also verified 
> it is the path with the label. Why is it not recognizing it?
>
> Thank you,
> Anna
>
>
> mri_label2label --sd 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label  
> --srcsubject segfs --srclabel Testing.label --trgsubject segfs --trglabel 
> Testing1N.label --regmethod volume
>
> srclabel = Testing.label
> srcsubject = segfs
> trgsubject = segfs
> trglabel = Testing1N.label
> regmethod = volume
>
> usehash = 1
> Use ProjAbs  = 0, 0
> Use ProjFrac = 0, 0
> DoPaint 0
>
> SUBJECTS_DIR    
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label
> FREESURFER_HOME /tools/freesurfer
> Loading source label.
> No such file or directory
> mri_label2label: could not open label file Testing.label
> No such file or directory
> ERROR reading Testing.label
>
> ________________________________________
> 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, September 26, 2016 6:20 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Co-registering different source data
>
> Hi Anna
>
> freeview now checks (in the dev version I believe) if the label has been
> sampled onto the surface and won't crash, but you need to use
> mri_label2label to sample it onto the surface before loading it onto the
> inflated surface in freeview
>
> cheers
> Bruce
>
>
> On Mon, 26 Sep 2016, Crawford, Anna wrote:
>
>> Hi,
>>
>> i created a test ROI which saves as a label. Every time I try to load it as 
>> a label on the surface (inflated), it crashed FreeView. I'm not sure why it 
>> won't load there. I noticed this happens with some other ore-made labels as 
>> well. What could be the cause of this?
>>
>> I also tried doing mri_label2vol (to then do vol2surf), but I am getting an 
>> errorL option unknown. I did the following:
>>
>> mri_label2vol \  --label Testing.label \ --temp ../mri/brainmask.mgz
>>
>> among other similar variations. Am I just inputting it wrong or am I just 
>> missing information?
>>
>> Thank you,
>> Anna
>> ________________________________________
>> 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, September 26, 2016 4:23 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] Co-registering different source data
>>
>> Hi Anna
>>
>> scuba is very old and deprecated. Try using freeview instead
>>
>> cheers
>> Bruce
>> On Mon, 26 Sep
>> 2016, Crawford, Anna wrote:
>>
>>> To create the volume ROI, I found something that said to use:
>>>
>>> scuba -v $filename
>>>
>>> to then make a new ROI.
>>>
>>> I got en error that I could not open scuba. Is this the correct way to go 
>>> about this, or is there some other means that I should be doing not 'scuba'?
>>>
>>> Thank you,
>>> Anna
>>> ________________________________________
>>> 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, September 26, 2016 1:52 PM
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] Co-registering different source data
>>>
>>> yes, create a volume ROI and you can map it onto the surface using
>>> mri_vol2surf
>>>
>>> cheers
>>> Bruce
>>> On Mon, 26 Sep 2016, Crawford, Anna wrote:
>>>
>>>> For now, I am just trying to get any arbitrary ROI that I define. (I'm new 
>>>> to this and am just trying to figure out how to get the basic process 
>>>> first.) Eventually, I will want it related to another signal such as the 
>>>> EEG from an epilepsy subject for example. In that case, it would be the 
>>>> active region that I want to capture and then map it to the surface. 
>>>> First, I want to be sure that I can get an ROI that I can then project to 
>>>> the surface (which I assume would be something like mri_vol2surf) if that 
>>>> makes sense. So i first need to be able to create the volume or label.
>>>>
>>>> Thank you,
>>>> Anna
>>>> ________________________________________
>>>>
>>>> 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, September 26, 2016 1:16 PM
>>>> To: Freesurfer support list
>>>> Subject: Re: [Freesurfer] Co-registering different source data
>>>>
>>>> can you explain what the ROI is supposed to represent? If you can create
>>>> it in the volume, you can use mri_vol2surf to map it onto the surface.
>>>>
>>>> cheers
>>>> Bruce
>>>>
>>>>
>>>> On Mon, 26 Sep 2016, Crawford, Anna wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I am having trouble figuring out how to create my own ROI. I can 
>>>>> visualize the anatomical ROI created automatically. How do I create a new 
>>>>> ROI?
>>>>>
>>>>> Thanks,
>>>>> Anna
>>>>> ________________________________________
>>>>> 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, September 26, 2016 10:44 AM
>>>>> To: Freesurfer support list
>>>>> Subject: Re: [Freesurfer] Co-registering different source data
>>>>>
>>>>> Hi Anna
>>>>>
>>>>> I'm not exactly sure what you mean, but if you register EEG electrodes to
>>>>> the white or pial surface, then you can visualize them on the inflated
>>>>> surface trivially. That is, you can create your ROI on any surface of the
>>>>> same hemisphere/subject and visualize it on any other
>>>>>
>>>>> cheers
>>>>> Bruce
>>>>>
>>>>>
>>>>> On Mon, 26 Sep 2016, Crawford, Anna
>>>>> wrote:
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> I am trying to create a new surface area on the inflated brain given by 
>>>>>> freesurfer
>>>>>> using recon-all. I make to create my own ROI that is co-registered onto 
>>>>>> this surfer.
>>>>>> Ultimately, I want to be able to take information from a different data 
>>>>>> source such as
>>>>>> EEG and have it co-registered onto the inflated surface. How do I go 
>>>>>> about creating
>>>>>> this new ROI surface?
>>>>>>
>>>>>> Thanks,
>>>>>> Anna
>>>>>>
>>>>>> ===================================
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>>>> Please consider the environment before printing this e-mail
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>>>> Cleveland Clinic is ranked as one of the top hospitals in America by 
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>>>> Confidentiality Note:  This message is intended for use only by the 
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>>> Cleveland Clinic is ranked as one of the top hospitals in America by 
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>> _______________________________________________
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>>
>> Please consider the environment before printing this e-mail
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>> Cleveland Clinic is ranked as one of the top hospitals in America by 
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>> Visit us online at http://www.clevelandclinic.org for a complete listing of 
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> _______________________________________________
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ===================================
>
>
>   Please consider the environment before printing this e-mail
>
> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News 
> & World Report (2015).
> 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 
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 Please consider the environment before printing this e-mail

Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & 
World Report (2015).  
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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