[Freesurfer] ?????? Hippocampal Subfields Atlas

[ZZY]

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Dear Doug??
I know the fsfast but have never used it 
before, and I just preprocessed my resting-state fMRI data by using SPM 
toolbox. Next, we want to analyze the functional connecitvity between
the hippocampal subregions.


Best,


Zhiyong


----
??:"Greve, Douglas N.,Ph.D."https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] Corpus Callosum area

[Greve, Douglas N.,Ph.D.]

We don't output or have tools to compute it. I can tell you how you can get a 
number for it, but it would not be with a validated method. Let me know.

On 9/24/2019 5:37 AM, Fernanda Hansen P. de Moraes wrote:

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Dear Freesurfer experts,

how can I extract the corpus callosum cross sectional area for each hemisphere?

Thank you very much in advance,
Fernanda Hansen P. de Moraes

fernandahmor...@gmail.com
Física Médica | Rede D'Or São Luiz
Doutoranda em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino



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[Freesurfer] Color scale in TkSurfer and Freeview

[Zhi Li]

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Dear Freesurfer experts,

May I ask how could I customize the color scale in TkSufer? The default
heat scale is blue-red. Could I change it to other colors, such as
green-yellow or blue-white-red (like gradient)?

Now I know how to customize the color scale in Freeview. The problem is in
the 'custom' of Freeview I can not ignore zeros. Actually I'd like to
display deactivation/negative value in 'light bule-white',
activation/positive value in 'white-light red'. Any suggestions would be
much appreciated.

Best,

lizhi
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Re: [Freesurfer] Freesurfer vs. CAT12

[Greve, Douglas N.,Ph.D.]

Hi Omar, we have played around with CAT12 a little bit and are finding 
systematic differences (eg, CAT thickness is thicker than FS). In the 
one study we tried, the group analysis was quite different. We have not 
had time to really dig into it yet.
best
doug

On 9/20/19 3:14 PM, Maximo, Jose Omar wrote:
>
> External Email - Use Caution
>
> Hi,
>
> Recently, I ran an analysis on Freesurfer and found increased cortical 
> thickness on the patients compared to controls.
>
> Then, I heard about CAT12 and wanted to see if my results would be 
> robust enough and be replicated using this other software. When I ran 
> the analysis on CAT12, the results look completely different (both 
> increased and decreases). I was not able to see the same clusters on 
> the CAT12 results. I used the same subjects and covariates.
>
> I ran recon-all using both T1 and T2 images, whereas in CAT12 you can 
> only use T1 images.
>
> Has anyone experimented with both software before?
>
> Best,
>
> Omar
>
>
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Re: [Freesurfer] Hippocampal Subfields Atlas

[Greve, Douglas N.,Ph.D.]

Are you using fsfast?

On 9/25/19 7:00 AM, ZZY wrote:
>
> ?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External Email - Use Caution
>
> Dear ?0?2Doug??
>
> ?0?2 ?0?2 ?0?2I have a group of multimode MRI data, including functional MRI, 
> T1WI and diffusion MRI. We want to analyze the functional and 
> structual connectivity between the hippocampal subregions.?0?2 Now, we 
> have obtained individual-level atlas of hippocampal subfields for each 
> subject by using FREESURFER 6.0 on the T1 image. What should we do 
> next step? How do get a group-level atlas of hippocampal subfields and 
> apply it to functuional and diffusion data?
>
> Best,
>
> Zhiyong
>
>
>
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Re: [Freesurfer] issue with lesions

[Greve, Douglas N.,Ph.D.]

If they are aligned in tkregisterfv, then you can use use --regheader 
instead of --reg something.lta

On 9/24/19 7:10 PM, Sam W wrote:
>
> External Email - Use Caution
>
> Hi Doug,
> anat is a T1w image and is well aligned with orig when I run the 
> tkregisterfv command.
> But I suspect I know what the problem might be. When I run
>
> mri_vol2vol --mov /data/sub01/anat.nii --fstarg --reg 
> /data/sub01/reg.lta --o anat-in-fs.mgz --s sub01
>
> (the lta file was generated with mri_coreg), the orientation of 
> anat-in-fs.mgz turns out incorrect. In freeview the superior label is 
> at the back of the brain and the inferior label at the front of the 
> brain (ie, the face is facing down). I don't understand this as the 
> anat is in RAS, and the anat and orig appeared well aligned when I ran 
> the tkregisterfv command above.
> Do you have an idea what I might be doing wrong?
>
> Best regards,
> Sam
>
> On Mon, Sep 23, 2019 at 8:18 PM Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> mri_coreg should have printed out tkregisterfv command. Try
> running that to see if the registration is accurate. What is the
> nature of anat.nii?
>
> On 9/20/2019 4:41 PM, Sam W wrote:
>>
>> External Email - Use Caution
>>
>> Thanks Doug, I'll try that. How would you register the lesion
>> image (which is anatomical space) to orig.mgz? I thought this
>> would work:
>> mri_coreg --mov /data/sub01/anat.nii.gz --targ orig.mgz --reg
>> /data/sub01/reg.lta
>> mri_vol2vol --mov /data/sub01/lesion.nii --fstarg --reg
>> /data/sub01/reg.lta --o lesion-in-fs.mgz --s sub01
>>
>> but the resulting lesion-in-fs.mgz does not align well with
>> orig.mgz...
>> Best regards,
>> Sam
>>
>>
>>
>> On Thu, Sep 19, 2019 at 4:54 PM Greve, Douglas N.,Ph.D.
>> mailto:dgr...@mgh.harvard.edu>> wrote:
>>
>> There is  not an easy way to do this. FS expects an intact
>> whole brain,
>> and it tries to fit such into every brain, ie, it is trying
>> to force a
>> whole cerebellum where there is none. What some people do is
>> to fill the
>> lesion with "reasonable" intensities, eg, from the
>> contralateral side.
>> Eg, you could left-right reverse the subject:
>> mri_convert orig.mgz --left-right-reverse-pix orig.lrrev.mgz
>> mri_coreg --mov orig.lrrev.mgz --targ orig.mgz --reg lrrev.lta
>> mri_vol2vol --mov orig.lrrev.mgz --targ orig.mgz --reg
>> lrrev.lta --o
>> orig.lrrev-in-orig.mgz
>> Then replace the voxels in the lesion in orig.mgz with voxels
>> from
>> orig.lrrev-in-orig.mgz and re-run
>> Let me know how it goes
>>
>> On 9/18/19 6:52 PM, Sam W wrote:
>> >
>> > External Email - Use Caution
>> >
>> > Thanks Doug. The problem is that for some patients the
>> lesion affects
>> > the segmentation dramatically. For example I have one
>> patient with a
>> > large lesion in the right cerebellum which is partly in GM
>> and partly
>> > in WM. If I load the aseg file I see that a portion of the
>> right
>> > cerebellar hemisphere is assigned to the left cerebellar
>> hemisphere
>> > (the right white matter is also being assigned to the left
>> hemisphere)
>> > and the whole cerebellum looks distorted. I suppose there
>> is no way to
>> > inform freesurfer about the lesion during recon-all?
>> > I followed the steps in the FsTutorials for the cerebral
>> cortex, but
>> > how can I do the same for the cerebellum patient? What is the
>> > recommended way to fix a bad segmentation due to cerebellum
>> lesions?
>> > Control points, white matter edits, or something else?
>> > Sam
>> >
>> > On Fri, Sep 6, 2019 at 4:28 PM Greve, Douglas N.,Ph.D.
>> > mailto:dgr...@mgh.harvard.edu>
>> > >> wrote:
>> >
>> >     You can get the volume from the aseg.stats file.
>> Unfortunately, we
>> >     do not separate the lesions into left and right. You
>> could do
>> >     something like
>> >     mri_binarize --i aseg.mgz --match 77 --o wmlesions.mgz
>> >     mri_volcluster --i wmlesions.mgz --sum lesions.sum.dat
>> --thmin 0.5
>> >     --regheader subject
>> >     This will output a list of lesions clusters in
>> lesions.sum.dat and
>> >     their coordinates. you can see which ones are left and
>> with ones
>> >     are right.
>> >
>> >
>> >
>> >     On 9/3/2019 5:17 PM, Sam W wrote:
>> >>
>> >>     External Email - Use Caution
>> >>

Re: [Freesurfer] Unable to access previous email archives

[Greve, Douglas N.,Ph.D.]

I did not have any problems. Were you on this link?
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/

On 9/25/19 10:10 AM, Mageshwar Selvakumar wrote:
>
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>
> Dear Freesurfer community,
>
> I have not been able to access the mail archives this week. It 
> redirects to Martinos Center and asks me for a NMR Login and password. 
> Is this the same login details we used to subscribe to the mailing 
> list? I tried but my details didn't work. Looking forward for your 
> replies.
>
> Thank you,
>
> Kind regards
>
> Mageshwar Selvakumar, M.Sc
>
> Department of Pharmakologische Bildgebung und Bildanalyse
>
> Friedrich Alexander Universität Erlangen Nürnberg
>
>
> Office:Fahrstr. 17, 91054 Erlangen
>
> Phone:+ 49-9131-8522898
>
>
>
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[Freesurfer] Unable to access previous email archives

[Mageshwar Selvakumar]

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Dear Freesurfer community,

I have not been able to access the mail archives this week. It redirects to 
Martinos Center and asks me for a NMR Login and password. Is this the same 
login details we used to subscribe to the mailing list?  I tried but my details 
didn't work. Looking forward for your replies.

Thank you,


Kind regards

Mageshwar Selvakumar, M.Sc

Department of Pharmakologische Bildgebung und Bildanalyse

Friedrich Alexander Universität Erlangen Nürnberg


Office: Fahrstr. 17, 91054 Erlangen

Phone: + 49-9131-8522898

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[Freesurfer] Hippocampal Subfields Atlas

[ZZY]

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Dear Doug??

  I have a group of multimode MRI data, including functional 
MRI, T1WI and diffusion MRI. We want to analyze the functional and structual 
connectivity between the hippocampal subregions. Now, we have obtained 
individual-level atlas of hippocampal subfields for each subject by using 
FREESURFER 6.0 on the T1 image. What should we do next step? How do get a 
group-level atlas of hippocampal subfields and apply it to functuional and 
diffusion data?







Best,


Zhiyong___
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