Re: [Freesurfer] Getting Waveform from Label - dim mismatch

[Douglas N Greve]

you need to transfer the label into the space of subject 401 using 
mri_label2label. Currently, the label is in fsaverage space which is why 
you get the mismatch


On 09/12/2016 12:53 PM, ERIK JAHNER wrote:
> (sorry if you got this multiple times this morning I had some server 
> issues)
>
> I had not seen a post based on this email, so I am resending it. It is 
> my understanding that I can use freesurfer and FSfast to get 
> activation levels after data has been smoothed across the surface 
> instead of 3D volume. Is the mir_segstats only able to use the 3D 
> volume and not the surface data stored within vertices? Sorry if this 
> questions is obvious to everyone. I want to basically get the average 
> activation for a set of vertices at each time point included in a 
> label from the surface mapped functional data. See below for 
> additional details of the parameters I entered.
>
> Thanks
> Erik Jahner
>
>> On Sep 9, 2016, at 8:20 AM, ERIK JAHNER > > wrote:
>>
>>
>>> Dear Freesurfer experts,
>>>
>>> I am attempting to get the waveform from a subject (401)using the 
>>> preprocessed data (fmcpr.siemens.sm5.fsaverage.lh.nii.gz) by means 
>>> of a label I created from the icosahedron 3 (lh.ic3.tri_vertex_638). 
>>>  This label was created from the subjects “sphere.reg" file.
>>>
>>> I am using the following command:
>>>
>>> mri_segstats
>>> --slabel 401 lh 
>>> /Applications/freesurfer/subjects/fsaverage/label/ic3/lh.ic3.tri_vertex_638.label
>>>  
>>>
>>> --avgwf out.dat
>>> --id 1
>>> --i 
>>> /Applications/freesurfer/LagStructure/401/rest/007/fmcpr.siemens.sm5.fsaverage.lh.nii.gz
>>>  
>>>
>>>
>>> However I am getting the following error:
>>>
>>> ERROR: dimension mismatch between input volume and seg
>>>   input 163842 1 1
>>>   seg   140104 1 1
>>>
>>> Obviously there is something wrong with my file dimensions. But, I 
>>> am unsure of how to fix this. I checked some of the files in my 
>>> subject anatomical folder like the thickness file and they also have 
>>> 140104 1 1 as the dimensions. But, as would be predicted the 
>>> "fmcpr.siemens.sm5.fsaverage.lh.nii.gz” file has the dimensions 
>>> 163842 1 1 210. Is there an easy way to fix this problem? I am 
>>> unsure what I did to create this discrepancy.
>>>
>>> Thanks for your continued support,
>>> Erik Jahner
>
>
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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
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] Getting Waveform from Label - dim mismatch

[ERIK JAHNER]

(sorry if you got this multiple times this morning I had some server issues)

I had not seen a post based on this email, so I am resending it. It is my 
understanding that I can use freesurfer and FSfast to get activation levels 
after data has been smoothed across the surface instead of 3D volume. Is the 
mir_segstats only able to use the 3D volume and not the surface data stored 
within vertices? Sorry if this questions is obvious to everyone. I want to 
basically get the average activation for a set of vertices at each time point 
included in a label from the surface mapped functional data. See below for 
additional details of the parameters I entered. 

Thanks 
Erik Jahner

> On Sep 9, 2016, at 8:20 AM, ERIK JAHNER  > wrote:
> 
> 
>> Dear Freesurfer experts,
>> 
>> I am attempting to get the waveform from a subject (401)using the 
>> preprocessed data (fmcpr.siemens.sm5.fsaverage.lh.nii.gz) by means of a 
>> label I created from the icosahedron 3 (lh.ic3.tri_vertex_638).  This label 
>> was created from the subjects “sphere.reg" file. 
>> 
>> I am using the following command: 
>> 
>> mri_segstats 
>> --slabel 401 lh 
>> /Applications/freesurfer/subjects/fsaverage/label/ic3/lh.ic3.tri_vertex_638.label
>>  
>> --avgwf out.dat 
>> --id 1 
>> --i 
>> /Applications/freesurfer/LagStructure/401/rest/007/fmcpr.siemens.sm5.fsaverage.lh.nii.gz
>>   
>> 
>> However I am getting the following error:
>> 
>> ERROR: dimension mismatch between input volume and seg
>>   input 163842 1 1
>>   seg   140104 1 1
>> 
>> Obviously there is something wrong with my file dimensions. But, I am unsure 
>> of how to fix this. I checked some of the files in my subject anatomical 
>> folder like the thickness file and they also have 140104 1 1 as the 
>> dimensions. But, as would be predicted the 
>> "fmcpr.siemens.sm5.fsaverage.lh.nii.gz” file has the dimensions 163842 1 1 
>> 210. Is there an easy way to fix this problem? I am unsure what I did to 
>> create this discrepancy.
>> 
>> Thanks for your continued support,
>> Erik Jahner
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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.