Yes, the edges might not be right on because it is being sampled into a
2mm space. If you play with the --fillthresh you might be able to make
it line up better.
On 12/13/2013 12:55 PM, Emily Boeke wrote:
> Ok, it doesn't seem shifted anymore, but it is still not exactly the same as
> the label. Is this to be expected?
>
> Emily
>
> On Dec 13, 2013, at 11:46 AM, Douglas N Greve wrote:
>
>> 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/
>>
>>
>
>
--
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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