Re: [Freesurfer] ROI labeling?
Sorry, I meant that I would somehow want to merge all of these masks together into one. Not changing the values in the masks, but somehow combining them. Also, with the mri_glmfit --label flag, is it possible to have multiple labels listed (like one label per subject)? Sort of like a frame mask where we we want to take into account every subject's individual ROI label. From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve <gr...@nmr.mgh.harvard.edu> Sent: Thursday, August 3, 2017 4:55 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ROI labeling? what do you mean by an average of the mask? Such an average would not be binary. On 08/03/2017 04:30 PM, Sadie Marvel wrote: > And what if I wanted to compute just one ROI mask (for each region) that is > an average of all the subjects individual ROI masks? > > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve > <gr...@nmr.mgh.harvard.edu> > Sent: Thursday, August 3, 2017 4:15 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] ROI labeling? > > If you are just going to use them as a mask for mri_glmfit, then you can > just pass it as --mask or --label, no need to map it back to the > individual (which you could do with mri_surf2surf) > > > On 08/03/2017 04:08 PM, Sadie Marvel wrote: >> Hi again Freesurfers, >> >> I am doing a surface based ROI analysis where for each subject, >> isomorphic ROIs of 300 vertices (centered around peak functional >> activations) were found on the fsaverage surface space. I was >> wondering if I should register these masks that I have created back to >> each subject's individual surface before creating labels for these >> ROIs, and if so, what would the registration file be to register the >> fsaverage space back to each subject's space? The goal of this is to >> be able to run mri_glmfit on just the spaces within these labels. Is >> there a better method? Also, each subject will have a different number >> of labels considering that not every ROI was present on every subject. >> will this be a problem when running glmfit? >> >> Thanks >> >> >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=bOaERSxG_JqDNQmM_8K52LCjnCr_2F55jAz7ZN-9dqg=PH0Vk-WgDboZq0KcG9suX371edaDZRvf4IyyOXZWHVQ=F2PgY5a-UpmIys4GjIY91-18ok4YKa7QNdxfaZWaA0M= > -- > 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://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=bOaERSxG_JqDNQmM_8K52LCjnCr_2F55jAz7ZN-9dqg=PH0Vk-WgDboZq0KcG9suX371edaDZRvf4IyyOXZWHVQ=dNTiTZM2k4H_ZFSLvXIpaHUFlf2j9OsxSfiZbdVVy1Y= > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: > https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_transfer_outgoing_flat_greve_=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=bOaERSxG_JqDNQmM_8K52LCjnCr_2F55jAz7ZN-9dqg=PH0Vk-WgDboZq0KcG9suX371edaDZRvf4IyyOXZWHVQ=-MNH1l23vgFGiXhqvaJyfT33Qag5-ddnxlYIHUU99W0= > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=bOaERSxG_JqDNQmM_8K52LCjnCr_2F55jAz7ZN-9dqg=PH0Vk-WgDboZq0KcG9suX371edaDZRvf4IyyOXZWHVQ=F2PgY5a-UpmIys4GjIY91-18ok4YKa7QNdxfaZWaA0M= > > > The information in this e-mail is intended only for the person to whom it is > 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 > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=bOaERSxG_JqDNQmM_8K52LCjnCr_2F55jAz7ZN-9dqg=PH0Vk-WgDboZq0KcG9suX371edaDZRvf4IyyOXZWHVQ=C3lAhbV3ZwBBXlYZT58CMcDnypDoDoJZxiTFeHyxq-0= > . 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. > >
Re: [Freesurfer] ROI labeling?
And what if I wanted to compute just one ROI mask (for each region) that is an average of all the subjects individual ROI masks? From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve <gr...@nmr.mgh.harvard.edu> Sent: Thursday, August 3, 2017 4:15 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ROI labeling? If you are just going to use them as a mask for mri_glmfit, then you can just pass it as --mask or --label, no need to map it back to the individual (which you could do with mri_surf2surf) On 08/03/2017 04:08 PM, Sadie Marvel wrote: > Hi again Freesurfers, > > I am doing a surface based ROI analysis where for each subject, > isomorphic ROIs of 300 vertices (centered around peak functional > activations) were found on the fsaverage surface space. I was > wondering if I should register these masks that I have created back to > each subject's individual surface before creating labels for these > ROIs, and if so, what would the registration file be to register the > fsaverage space back to each subject's space? The goal of this is to > be able to run mri_glmfit on just the spaces within these labels. Is > there a better method? Also, each subject will have a different number > of labels considering that not every ROI was present on every subject. > will this be a problem when running glmfit? > > Thanks > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=bOaERSxG_JqDNQmM_8K52LCjnCr_2F55jAz7ZN-9dqg=PH0Vk-WgDboZq0KcG9suX371edaDZRvf4IyyOXZWHVQ=F2PgY5a-UpmIys4GjIY91-18ok4YKa7QNdxfaZWaA0M= -- 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://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=bOaERSxG_JqDNQmM_8K52LCjnCr_2F55jAz7ZN-9dqg=PH0Vk-WgDboZq0KcG9suX371edaDZRvf4IyyOXZWHVQ=dNTiTZM2k4H_ZFSLvXIpaHUFlf2j9OsxSfiZbdVVy1Y= www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_transfer_outgoing_flat_greve_=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=bOaERSxG_JqDNQmM_8K52LCjnCr_2F55jAz7ZN-9dqg=PH0Vk-WgDboZq0KcG9suX371edaDZRvf4IyyOXZWHVQ=-MNH1l23vgFGiXhqvaJyfT33Qag5-ddnxlYIHUU99W0= ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=bOaERSxG_JqDNQmM_8K52LCjnCr_2F55jAz7ZN-9dqg=PH0Vk-WgDboZq0KcG9suX371edaDZRvf4IyyOXZWHVQ=F2PgY5a-UpmIys4GjIY91-18ok4YKa7QNdxfaZWaA0M= The information in this e-mail is intended only for the person to whom it is 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=bOaERSxG_JqDNQmM_8K52LCjnCr_2F55jAz7ZN-9dqg=PH0Vk-WgDboZq0KcG9suX371edaDZRvf4IyyOXZWHVQ=C3lAhbV3ZwBBXlYZT58CMcDnypDoDoJZxiTFeHyxq-0= . 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is 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.
[Freesurfer] ROI labeling?
Hi again Freesurfers, I am doing a surface based ROI analysis where for each subject, isomorphic ROIs of 300 vertices (centered around peak functional activations) were found on the fsaverage surface space. I was wondering if I should register these masks that I have created back to each subject's individual surface before creating labels for these ROIs, and if so, what would the registration file be to register the fsaverage space back to each subject's space? The goal of this is to be able to run mri_glmfit on just the spaces within these labels. Is there a better method? Also, each subject will have a different number of labels considering that not every ROI was present on every subject. will this be a problem when running glmfit? ?Thanks ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is 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.
[Freesurfer] Volume based ROI projected to surface
Hi Freesurfers, I am doing a surfaced based ROI analysis on each of my subjects functional data. Using information from other papers, the size of the ROI really matters when doing the analysis, and I want to take this information from these papers and apply them to my own data. However, these papers use volume based ROI analysis, by making spheres that have 6 mm radiuses around the location of peak activity. To translate what they did to a surface based approach, I thought I would try to approximate how large this sphere would be if it were projected onto the surface of the brain by creating cubes around a certain location in the volume and projecting them to the surface using mri_vol2surf. That way, I would have approximately the same amount of information in my surface ROI. This is more of a general question, but I was wondering how this command actually works and whether it takes just one face or slice of the volume I created and projects that to the surface, or if it would project all 6 faces of the cube to the surface. And how is this volume actually translated into vertices? And how does the location of the cube in the volume space of the brain determine how large it will be on the surface? Do you have any suggestions as to how I can approach this problem better? Thanks?! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is 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.
Re: [Freesurfer] Subject with missing fMRI data {Disarmed}
yes, I figured it out! Thanks for your help!
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve
<gr...@nmr.mgh.harvard.edu>
Sent: Wednesday, July 12, 2017 6:16 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Subject with missing fMRI data {Disarmed}
the command and terminal output look ok. You should compare it to the
results without the frame mask (just use the regular mask). They should
be the same in areas where the frame mask and regular mask completely
agree.
On 07/12/2017 01:54 PM, Sadie Marvel wrote:
> The command will run now without --wls, but I'm still not sure the output is
> correct.
> Here is my entire output:
> cwd /Freiwald/smarvel/cooked/mygroup4/a_FOB.sm05.lh
> cmdline mri_glmfit.bin --y c1_2/ces.nii --osgm --no-prune --frame-mask
> masks.nii --surface fsaverage lh --glmdir c1_2/my-glm2.wls --nii.gz
> sysname Linux
> hostname turing.rockefeller.edu
> machine x86_64
> user smarvel
> FixVertexAreaFlag = 1
> UseMaskWithSmoothing 1
> OneSampleGroupMean 1
> y/Freiwald/smarvel/cooked/mygroup4/a_FOB.sm05.lh/c1_2/ces.nii
> logyflag 0
> usedti 0
> labelmask
> /Freiwald/lab_files/opt/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0/subjects/fsaverage/label/lh.cortex.label
> maskinv 0
> glmdir c1_2/my-glm2.wls
> IllCondOK 0
> ReScaleX 1
> DoFFx 0
> Creating output directory c1_2/my-glm2.wls
> Loading y from /Freiwald/smarvel/cooked/mygroup4/a_FOB.sm05.lh/c1_2/ces.nii
> ... done reading.
> Saving design matrix to c1_2/my-glm2.wls/Xg.dat
> Computing normalized matrix
> Normalized matrix condition is 1
> Matrix condition is 1
> Found 149955 points in label.
> Found 149955 voxels in mask
> Saving mask to c1_2/my-glm2.wls/mask.nii.gz
> Reshaping mriglm->mask...
> search space = 74612.583051
> DOF = 25
> Starting fit and test
> Fit completed in 0.0106667 minutes
> Computing spatial AR1 on surface
> Residual: ar1mn=0.987809, ar1std=0.026903, gstd=3.653971, fwhm=8.60
> Writing results
>osgm
> maxvox sig=-6.33498 F=47.9826 at index 135220 0 0seed=1499971484
> mri_glmfit done
>
> My question now is the part "Saving mask to c1_2/my-glm2.wls/mask.nii.gz
> Reshaping mriglm->mask..."
> Is it taking the mask I input and saving it to the new location? If so, the
> mask.nii.gz doesn't look like the mask I specified in the command, and it
> doesn't even have 26 subjects concatenated together. So instead of a
> 163842x1x1x26 mask it is a 163842x1x1 mask. When I look at my outputs, it
> seems as though it still isn't using the masks I specified.
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve
> <gr...@nmr.mgh.harvard.edu>
> Sent: Wednesday, July 12, 2017 12:19 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Subject with missing fMRI data {Disarmed}
>
> it might not be possible to use the frame mask with wls. Does it work
> without it?
>
>
> On 07/09/2017 04:46 PM, Sadie Marvel wrote:
>> 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-boun...@nmr.mgh.harvard.edu
>> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve
>> <gr...@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?
>>>
>>>
>>>
>>>
Re: [Freesurfer] Subject with missing fMRI data {Disarmed}
The command will run now without --wls, but I'm still not sure the output is
correct.
Here is my entire output:
cwd /Freiwald/smarvel/cooked/mygroup4/a_FOB.sm05.lh
cmdline mri_glmfit.bin --y c1_2/ces.nii --osgm --no-prune --frame-mask
masks.nii --surface fsaverage lh --glmdir c1_2/my-glm2.wls --nii.gz
sysname Linux
hostname turing.rockefeller.edu
machine x86_64
user smarvel
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 1
y/Freiwald/smarvel/cooked/mygroup4/a_FOB.sm05.lh/c1_2/ces.nii
logyflag 0
usedti 0
labelmask
/Freiwald/lab_files/opt/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0/subjects/fsaverage/label/lh.cortex.label
maskinv 0
glmdir c1_2/my-glm2.wls
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory c1_2/my-glm2.wls
Loading y from /Freiwald/smarvel/cooked/mygroup4/a_FOB.sm05.lh/c1_2/ces.nii
... done reading.
Saving design matrix to c1_2/my-glm2.wls/Xg.dat
Computing normalized matrix
Normalized matrix condition is 1
Matrix condition is 1
Found 149955 points in label.
Found 149955 voxels in mask
Saving mask to c1_2/my-glm2.wls/mask.nii.gz
Reshaping mriglm->mask...
search space = 74612.583051
DOF = 25
Starting fit and test
Fit completed in 0.0106667 minutes
Computing spatial AR1 on surface
Residual: ar1mn=0.987809, ar1std=0.026903, gstd=3.653971, fwhm=8.60
Writing results
osgm
maxvox sig=-6.33498 F=47.9826 at index 135220 0 0seed=1499971484
mri_glmfit done
My question now is the part "Saving mask to c1_2/my-glm2.wls/mask.nii.gz
Reshaping mriglm->mask..."
Is it taking the mask I input and saving it to the new location? If so, the
mask.nii.gz doesn't look like the mask I specified in the command, and it
doesn't even have 26 subjects concatenated together. So instead of a
163842x1x1x26 mask it is a 163842x1x1 mask. When I look at my outputs, it seems
as though it still isn't using the masks I specified.
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve
<gr...@nmr.mgh.harvard.edu>
Sent: Wednesday, July 12, 2017 12:19 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Subject with missing fMRI data {Disarmed}
it might not be possible to use the frame mask with wls. Does it work
without it?
On 07/09/2017 04:46 PM, Sadie Marvel wrote:
> 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-boun...@nmr.mgh.harvard.edu
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve
> <gr...@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-boun...@nmr.mgh.harvard.edu
>> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve
>> <gr...@nmr.mgh.harvard.edu>
>> *Sent:* Thursday, July 6, 2017 12:58 PM
>> *To:* 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-boun...@nmr.mgh.harvard.edu
>>> <freesurfer-boun..
[Freesurfer] error with mri_glmfit --frame-mask
?Hi list, I am trying to run mri_glmfit on a group of subjects using the --frame-mask flag because I want the design to be changed based on which subjects have a value at a single voxel. This is because I have one subject in my group whose signal was cut off through parts of their occipital and temporal lobes. This is the command I am using: mri_glmfit --y ces.nii --wls cesvar.nii --osgm --no-prune --frame-mask masks.nii --surface fsaverage rh --glmdir my-glm2.wls --nii.gz? where masks.nii is a file that contains each individual's binary mask. However, when I use this command, I get this error: ERROR: MRInormWeights: value less than or eq to 0.? which I assumed may have something to do with my ces/cesvar files being a different size than my masks file; however, all three of the files have the same dimensions (163842x1x1x26 where 26 is the number of subjects in my group) Any idea why I am getting this error? I also tried creating a file of binary masks by first concatenating ces.nii and cesvar.nii and binarizing it, but I am getting the same error. Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is 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.
Re: [Freesurfer] Subject with missing fMRI data {Disarmed}
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve
<gr...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Douglas Greve
<gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu>
Sent: Thursday, July 6, 2017 12:58 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto: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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Douglas Greve
<gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu>
Sent: Wednesday, July 5, 2017 7:28 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto: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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Re: [Freesurfer] Subject with missing fMRI data {Disarmed}
?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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve
<gr...@nmr.mgh.harvard.edu>
Sent: Thursday, July 6, 2017 12:58 PM
To: 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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Douglas Greve
<gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu>
Sent: Wednesday, July 5, 2017 7:28 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto: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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Re: [Freesurfer] Subject with missing fMRI data {Disarmed}
>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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve <gr...@nmr.mgh.harvard.edu> Sent: Wednesday, July 5, 2017 7:28 PM To: 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwMC-g=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=bOaERSxG_JqDNQmM_8K52LCjnCr_2F55jAz7ZN-9dqg=DhD2aaHH4v0l556v1tTQWGefdhjxGef9QZtInzhlGAw=bQIJi6_pIGgShFkxwNFbAaJNwv2UyXNY15PnOqVX3Jk=> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is 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.
[Freesurfer] Subject with missing fMRI data
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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is 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.
