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Message: 1
Date: Fri, 7 Jul 2017 10:42:23 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] WM surface ignoring wm.mgz edits
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <alpine.LRH.2.20.1707071041590.9265@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-15"

Hi Kaley

are you using the "recon edit" tool in freeview?

cheers
Bruce

On Fri, 7 Jul 2017, KALEY E
ELLIS wrote:

>
> Dear?FreeSurfer?Developers,
>
>
> We are attempting to make manual white matter edits to our subjects. The
> edits are saving; however, after running with recon-all, the WM surface does
> not appear to be taking into account our edits made to wm.mgz. Below is
> additional information, and I have attached our recon-all.log. We are only
> editing the cross because our dataset is comprised of single timepoints.
>
>
> We are using?FreeSurfer?v5.3 and our operating system is OS X El?Capitan
> version 10.11.6.
>
> Command to open and edit WM:?
>
> freeview -v mri/T1.mgz mri/brainmask.mgz mri/wm.mgz:opacity=0.5 -f
> surf/lh.white:edgecolor=yellow surf/lh.pial:edgecolor=red
> surf/rh.white:edgecolor=yellow surf/rh.pial:edgecolor=red
>
>
> Command to submit edits:
>
> recon-all -autorecon2-wm -autorecon3 -subjid?
>
>
> Recon-all log (see attached)
>
>
> Thank you,
>
> Kaley?Ellis
>
>
>
> Associate Research Specialist
> Center for?Healthy Minds
> Waisman Center for Brain Imaging and Behavior
> University of Wisconsin-Madison
>
>

------------------------------

Message: 2
Date: Fri, 7 Jul 2017 14:51:53 +0000
From: "Boyd, Emma" <EBOYD2@mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all on newborn
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <MWHPR04MB0558426F0D765C043BEDCABAD1AA0@MWHPR04MB0558.namprd04.prod.outlook.com>
       
Content-Type: text/plain; charset="us-ascii"

Hi Sarbani,
Please see this paper for more information:
https://www.ncbi.nlm.nih.gov/pubmed/25741260


Emma

________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Das S. <Sarbani.Das@soton.ac.uk>
Sent: Friday, July 7, 2017 4:58:39 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all on newborn

Is there any paper that you can share that can explain why recon-all is not suitable for neonates brain apart from atlas.
Sarbani

-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Lilla Zollei
Sent: 06 July 2017 21:43
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all on newborn


It is not only the atlas but the tools that are different.

Lilla

On Wed, 5 Jul 2017, Das S. wrote:

> Dear Lilla,
> In that case you mean if I have my own atlas specific to neonates then I can follow these steps of auto recon.
> If you give me little more details will be easy for me to understand the gap.
> many thanks
> Sarbani
> ________________________________________
> From: freesurfer-bounces@nmr.mgh.harvard.edu
> [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Lilla Zollei
> [lzollei@nmr.mgh.harvard.edu]
> Sent: 05 July 2017 22:32
> To: Freesurfer support list
> Subject: Re: [Freesurfer] recon-all on newborn
>
> We use a similar pipeline but with different atlases and processing
> steps for the newborns.
> Lilla
>
> On Wed, 5 Jul 2017, Das S. wrote:
>
>>
>> Thanks for the reply. If you let me know, among the below list of steps of current recon-all, currently which is not suitable to perform on neonates MRI image, will really appreciate.
>>
>> Autorecon Processing Stages:
>>    Motion Correction and Conform
>>    NU (Non-Uniform intensity normalization)
>>    Talairach transform computation
>>    Intensity Normalization 1
>>    Skull Strip
>>    EM Register (linear volumetric registration)
>>    CA Intensity Normalization
>>    CA Non-linear Volumetric Registration
>>    Remove Neck
>>    LTA with Skull
>>    CA Label (Volumetric Labeling, ie Aseg) and Statistics
>>    Intensity Normalization 2 (start here for control points)
>>    White matter segmentation
>>    Edit WM With ASeg
>>    Fill (start here for wm edits)
>>    Tessellation (begins per-hemisphere operations)
>>    Smooth1
>>    Inflate1
>>    QSphere
>>    Automatic Topology Fixer
>>    Final Surfs (start here for brain edits for pial surf)
>>    Smooth2
>>    Inflate2
>>    Spherical Mapping
>>    Spherical Registration
>>    Spherical Registration, Contralateral hemisphere
>>    Map average curvature to subject
>>    Cortical Parcellation - Desikan_Killiany and Christophe (Labeling)
>>    Cortical Parcellation Statistics
>>    Cortical Ribbon Mask
>>    Cortical Parcellation mapping to Aseg
>>
>> BW
>> S Das
>> ________________________________________
>> From: freesurfer-bounces@nmr.mgh.harvard.edu
>> [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Lilla Zollei
>> [lzollei@nmr.mgh.harvard.edu]
>> Sent: 04 July 2017 22:04
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] recon-all on newborn
>>
>> Hi S Das,
>>
>> We are trying to release the infant pipeline by the end of the summer.
>>
>> Lilla
>>
>> On Tue, 4 Jul 2017, Das S. wrote:
>>
>>> Dear Freesurfer expert,
>>> I want to perform recon-all pipeline on neonates data.Can I do so?
>>> I was going through some mail archives and there it is said that on T1 image of neonates data we can't perform recon-all.
>>> But again there is another paper where it says Freesurfer can perform segmentation of neonates image.
>>> Any input will be appreciated.
>>> Thanks
>>> S Das
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>> _______________________________________________
>> 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.
>>
>>
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>> Freesurfer mailing list
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> _______________________________________________
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Message: 3
Date: Fri, 7 Jul 2017 11:05:14 -0400
From: Karla Rivera Figueroa <karla.rivera_figueroa@uconn.edu>
Subject: Re: [Freesurfer] wm.mgz in the internal structures
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CAN27gbjw0BLtcOzVk9vCCLr3f_0STp0nWB=ojUf-1F+1F=rdVQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Thank you for the clarification.
Have a nice weekend,
Karla

On Jul 7, 2017 10:16 AM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote:

Hi Karla

you shouldn't have to worry about the wm.mgz in those regions if the aseg
is accurate.

cheers
Bruce



On Fri, 7 Jul 2017, Karla Rivera Figueroa wrote:

Hi all, Do you need to edit the wm mask where the internal structures shown
> in the aseg are? are the structures supposed to be covered entirely with
> the
> wm mask?
>
> Karla
>
>
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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
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Message: 4
Date: Fri, 7 Jul 2017 15:38:26 +0000
From: Sadie Marvel <smarvel@mail.rockefeller.edu>
Subject: Re: [Freesurfer] Subject with missing fMRI data {Disarmed}
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <1499441907778.47672@rockefeller.edu>
Content-Type: text/plain; charset="iso-8859-1"

?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.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas Greve <greve@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-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas Greve <greve@nmr.mgh.harvard.edu><mailto:greve@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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Message: 5
Date: Fri, 7 Jul 2017 11:57:01 -0400
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Subject with missing fMRI data {Disarmed}
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <d70be06e-d0ff-dfd1-af20-bb9601d26392@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

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.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas Greve
> <greve@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-bounces@nmr.mgh.harvard.edu
>> <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas Greve
>> <greve@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
>>> *MailScanner has detected a possible fraud attempt from
>>> "urldefense.proofpoint.com" claiming to be*
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> *MailScanner has detected a possible fraud attempt from
>> "urldefense.proofpoint.com" claiming to be*
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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