sorry, the command I gave you is not quite right. Use
--regheader $SUBJECTS_DIR/fsaverage/mri/orig.mgz
instead
doug
On 12/13/2013 09:17 AM, Emily Boeke wrote:
> Hi Doug,
>
> I tried the mri_label2vol command but the mask created does not match the
> label. The mask is shifted so that it's posterior to the label (by ~15
> slices), and the shape of the blob is a little different. Any idea why this
> may be?
>
> Emily
>
> On Dec 12, 2013, at 2:11 PM, Douglas N Greve wrote:
>
>> Hi Emily, there may be a simpler way to get at what you want. You can use
>> mri_label2vol to create a mask of the label in mni305 2mm space, something
>> like
>>
>> mri_label2vol --label yourlabel --temp
>> $SUBJECTS_DIR/fsaverage/mri.2mm/orig.mgz --regheader
>> $SUBJECTS_DIR/fsaverage/mri.2mm/orig.mgz --o labelmask.mgz --labelvoxvol 8
>>
>> Make sure the mask looks ok
>> tkmedit fsaverage orig.mgz -overlay labelmask.mgz -fminmax .5 1
>>
>> Then run
>> mri_segstats --i ces.nii.gz --seg labelmask.mgz --segid 1 --avgwf
>> ces.label.dat
>>
>> where ces.nii.gz is the output of isxconcat-sess for the analysis/contrast
>> you want to extract the data from
>>
>> doug
>>
>> On 12/12/2013 02:04 PM, Emily Boeke wrote:
>>> 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/
>>>>
>>>>
>>>
>> --
>> 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/
>>
>>
>
>
--
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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