So now that I am using --no-prune, I'm getting this error: group wrfx error: MRInormWeights: value less than or eq to 0. ?I found another thread in the mailing list about this error saying that there may be values in cesvar.nii that are =0, and that pruning normally masks out these values. But here, I am trying to use my own masks to do so. Is it possible now that my masks and my --y input have different sizes? If so, how can I solve this? ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu Sent: Friday, July 7, 2017 11:57 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Subject with missing fMRI data {Disarmed}
Add --no-prune
On 7/7/17 11:38 AM, Sadie Marvel wrote:
?When I use a script like this,
mri_glmfit --y ces.nii --wls cesvar.nii --osgm --frame-mask masks.nii --surface fsaverage rh --glmdir my-glm2.wls --nii.gz?
using the individual binary masks for all the subjects, the command seems to revert to using mask.nii, the single mask that was averaged over subjects. The output then just looks like it was using the single mask instead of being subject specific. Any idea why?
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Sent: Thursday, July 6, 2017 12:58 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Subject with missing fMRI data {Disarmed}
yes
On 7/6/17 12:50 PM, Sadie Marvel wrote:
From using isxconcat-sess to concatenate all of my subjects together, the command creates binary masks called masks.nii and mask.nii, masks.nii being all of the binary masks for each subject. Is this what I would use with --frame-mask?
Thanks,
Sadie
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Sent: Wednesday, July 5, 2017 7:28 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Subject with missing fMRI data
We don't have any tools to do imputation. It is possible to have a subject specific mask with the --frame-mask option to mri_glmfit. The frame mask must be the same size as the input (--y) with 1s and 0s to indicate whether a given voxel for a given subject should be included in the model. I've not been happy with this method as it can create some strange results as different voxels will now have different DOFs.
On 6/29/17 8:49 AM, Sadie Marvel wrote:
Hi List,
I am currently doing a group analysis of 26 subjects, one of which has missing fMRI data where the signal cuts off through parts of the occipital and temporal lobes. I was wondering if freesurfer has any way of dealing with this, such as multiple imputation, or other methods of filling the missing data. Alternatively, is there a way to only use the portions of the brain that have data when doing mri_glmfit? Does freesurfer do this automatically?
Thanks.
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