Hi Doug,
Thanks for your response.
I have another question related to functional ROIs. The method below produces
ROIs based on individual subjects' activation for a contrast. I would also
like to make ROIs based on averaged group activation for a contrast and extract
individuals' percent signal change from that ROI. In the past I have done this
by creating a label in tkmedit out of the activation and using the
mri_label2label command to fit it to the individual subjects' spaces:
mri_label2label --srclabel ${SUBJECTS_DIR}/fsaverage/label/${label}
--srcsubject fsaverage --trglabel ${SUBJECTS_DIR}/${subject}/label/${label}
--trgsubject ${subject} --regmethod volume
Then I would run func2roi, which is no longer used in current versions of
freesurfer.
When I was running this label2label command in previous analyses, I did not
have the -mni305 2 flag in my mkanalysis command. In my current analysis, I do
have the -mni305 2 flag. Does this change how I have to run mri_label2label?
Since the individual level analysis is in mni305 space, do I not even need to
run mri_label2label at all? Could I just run funcroi-config with -label and
then the name of the label file instead of seg?
Thanks!
Emily
On Dec 12, 2013, at 11:36 AM, Douglas N Greve wrote:
>
> On 12/12/2013 10:08 AM, Emily Boeke wrote:
>> Hi Freesurfers,
>>
>> I would like to make sure I am using the funcroi commands correctly for
>> anatomical and functional ROI analyses (using the aseg to anatomically
>> constrain), and I have some questions about the commands.
>>
>> If I want to extract the average percent signal change in the whole left
>> amygdala for a particular contrast, is this the correct version of the
>> commands to run?
>>
>> 1. funcroi-config -seg aseg.mgz 18 -roi <name>.cfg -analysis <analysisname>
>> 2. funcroi-sess -roi <name>.cfg -sf sf.txt -df sesspar
>> 3. funcroi-table-sess -roi <name>.cfg -sf sf.txt -df sesspar -o <name>.txt
>> -c <contrast> -m cespct
>>
>> If I want to extract the average percent signal change from an anatomically
>> constrained functional ROI (e.g. an ROI representing activation in a certain
>> contrast within the lh amygdala), is this the correct version of the
>> commands to run:
>>
>> 4. funcroi-config -seg aseg.mgz 18 -roi <name>.cfg -analysis <analysisname>
>> -contrast <contrast> -sign pos -thresh 1.3
>> 5. funcroi-sess -roi <name>.cfg -sf sf.txt -df sesspar
>> 6. funcroi-table-sess -roi <name>.cfg -sf sf.txt -df sesspar -o <name>.txt
>> -a <analysisname> -c <contrast> -m cespct
>>
>> My questions are (regarding the second set of commands):
>>
>> -in the right hippocampus example under funcroi-config --help, the
>> anatomical constraint is specified with --annot aseg.mgz 53, but it should
>> be --seg aseg.mgz 53 like in my examples, correct? Otherwise you get an
>> error.
> Oops, you're right. I've made the change in our tree.
>> -Is it ok to use one analysis name in the funcroi-config file and another
>> in funcroi-table-sess? Would that allow me to make an ROI from one analysis
>> and use it to extract signal from another analysis?
> Yes
>> -If I get a message saying some subjects had "empty ROIs" and the value in
>> the table for them is 0, does this mean that subjects had no activation
>> (meeting the threshold specified) in the first contrast I specified (in
>> funcroi-config) so no ROI could be created from their activation?
> Correct
>> -If I want to look at activation in more than one anatomical region (for
>> example, bilateral amygdala), is there any way to do that with the -seg
>> option?
> The way to do this is to create a new segmentation for each subject that
> contains only the amyg, eg,
> mri_binarize --i aseg.mgz --match 18 54 --o amyg.mgz
> This creates a mask of the amygdalae in which the amygdala voxels = 1 and
> everything else is 0
> Then specify --seg amyg.mgz 1 Use 1 here because the amygdala voxels = 1
>
> doug
>
>>
>> Pardon the long message. Thanks for the help!
>>
>> Emily
>>
>>
>
> --
> 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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