Re: [Freesurfer] How to edit GM when WM is ok

2021-03-26 Thread Caroline Chwiesko 
External Email - Use Caution

Thank you for your response! I followed the instructions for FTP file
exchange. And did then:

ftp> cd transfer/incoming
ftp> put filename.txt

Are the images not there?
Cheers
Carolin

On Fri, Mar 26, 2021 at 3:20 PM Fischl, Bruce 
wrote:

> Hi Carolin
>
>
>
> Where did you upload the images?
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Caroline Chwiesko
> *Sent:* Friday, March 26, 2021 6:08 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] How to edit GM when WM is ok
>
>
>
> *External Email - Use Caution*
>
> Hello Bruce,
>
> I wrote a week ago to this mailing list to ask for advice about how to
> edit an issue where an entire Gyrus will not be captured by the pial
> surface. I uploaded some images to show what that looks like. I just wanted
> to send a friendly reminder to make sure it won't be forgotten ;)
>
> Thank you very much for any help!
>
>
>
> Cheers
>
> Carolin
>
>
>
> On Fri, Mar 19, 2021 at 4:54 PM Caroline Chwiesko 
> wrote:
>
> Hi Bruce,
>
> thank you very much for taking a look at that. I uploaded 3 images in
> different orientations. I can not see any white matter.
>
>
>
> Cheers
>
> Carolin
>
>
>
>
>
> On Fri, Mar 19, 2021 at 7:26 AM Fischl, Bruce 
> wrote:
>
> Hi Carolin
>
>
>
> Yes, I guess send along images using all 3 orientations. There has to be
> some white matter there somewhere….
>
> Cheers
>
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Caroline Chwiesko
> *Sent:* Friday, March 19, 2021 12:28 AM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] How to edit GM when WM is ok
>
>
>
> *External Email - Use Caution*
>
> Hello Freesurfer experts,
>
>
>
> i am doing some editing after recon-all. I have the issue that one gyrus
> is not captured by the pial  surface. There is no wm that is wrong and that
> i could correct. It looks like this gyrus has a weird angle so there is
> actually no WM visible. How can such an error be corrected? I am happy to
> send a couple images if needed.
>
>
>
> Thank you very much in advance for any help!
>
> Cheers
>
> Carolin
>
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Re: [Freesurfer] How to edit GM when WM is ok

2021-03-26 Thread Fischl, Bruce 
Hi Carolin

Where did you upload the images?
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Caroline Chwiesko
Sent: Friday, March 26, 2021 6:08 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] How to edit GM when WM is ok


External Email - Use Caution
Hello Bruce,
I wrote a week ago to this mailing list to ask for advice about how to edit an 
issue where an entire Gyrus will not be captured by the pial surface. I 
uploaded some images to show what that looks like. I just wanted to send a 
friendly reminder to make sure it won't be forgotten ;)
Thank you very much for any help!

Cheers
Carolin

On Fri, Mar 19, 2021 at 4:54 PM Caroline Chwiesko 
mailto:cchwi...@uci.edu>> wrote:
Hi Bruce,
thank you very much for taking a look at that. I uploaded 3 images in different 
orientations. I can not see any white matter.

Cheers
Carolin


On Fri, Mar 19, 2021 at 7:26 AM Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Carolin

Yes, I guess send along images using all 3 orientations. There has to be some 
white matter there somewhere….
Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Caroline Chwiesko
Sent: Friday, March 19, 2021 12:28 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] How to edit GM when WM is ok


External Email - Use Caution
Hello Freesurfer experts,

i am doing some editing after recon-all. I have the issue that one gyrus is not 
captured by the pial  surface. There is no wm that is wrong and that i could 
correct. It looks like this gyrus has a weird angle so there is actually no WM 
visible. How can such an error be corrected? I am happy to send a couple images 
if needed.

Thank you very much in advance for any help!
Cheers
Carolin
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Re: [Freesurfer] How to edit GM when WM is ok

2021-03-26 Thread Caroline Chwiesko 
External Email - Use Caution

Hello Bruce,
I wrote a week ago to this mailing list to ask for advice about how to edit
an issue where an entire Gyrus will not be captured by the pial surface. I
uploaded some images to show what that looks like. I just wanted to send a
friendly reminder to make sure it won't be forgotten ;)
Thank you very much for any help!

Cheers
Carolin

On Fri, Mar 19, 2021 at 4:54 PM Caroline Chwiesko  wrote:

> Hi Bruce,
> thank you very much for taking a look at that. I uploaded 3 images in
> different orientations. I can not see any white matter.
>
> Cheers
> Carolin
>
>
> On Fri, Mar 19, 2021 at 7:26 AM Fischl, Bruce 
> wrote:
>
>> Hi Carolin
>>
>>
>>
>> Yes, I guess send along images using all 3 orientations. There has to be
>> some white matter there somewhere….
>>
>> Cheers
>>
>> Bruce
>>
>>
>>
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Caroline Chwiesko
>> *Sent:* Friday, March 19, 2021 12:28 AM
>> *To:* Freesurfer support list 
>> *Subject:* [Freesurfer] How to edit GM when WM is ok
>>
>>
>>
>> *External Email - Use Caution*
>>
>> Hello Freesurfer experts,
>>
>>
>>
>> i am doing some editing after recon-all. I have the issue that one gyrus
>> is not captured by the pial  surface. There is no wm that is wrong and that
>> i could correct. It looks like this gyrus has a weird angle so there is
>> actually no WM visible. How can such an error be corrected? I am happy to
>> send a couple images if needed.
>>
>>
>>
>> Thank you very much in advance for any help!
>>
>> Cheers
>>
>> Carolin
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
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>
>
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Re: [Freesurfer] Can FS use the recon all command to automatically divide it into DKT32 areas?

2021-03-26 Thread Fischl, Bruce 
Hi

I'm not entirely sure what the question is, but if you run recon-all on 
appropriate input data you will get a DKT parcellation as one of the outputs

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of 1248742467
Sent: Thursday, March 25, 2021 10:59 PM
To: freesurfer 
Subject: [Freesurfer] Can FS use the recon all command to automatically divide 
it into DKT32 areas?


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Hello, Fs
I saw an article that gave the Dice coefficient and ACC of Freesurfer's 
automatic segmentation, so I am curious, can Fs automatically divide it into 32 
regions?


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Re: [Freesurfer] Problem with freesurfer measures

2021-03-26 Thread Alberto Del Cerro Leon 
External Email - Use Caution

Hello Douglas, i tried but when i look at the wmparc.mgz created by the
code >>mri_aparc2aseg --s 215 --labelwm --hypo-as-wm --rip-unknown
--volmask --o mri/wmparc.mgz --annot myAAL it takes the index and the names
from FreeSurferColorLUT instead of the names in the colorLUT
associated with myAAL.annot then the ROIs are disorganized. Could you help
me with this problem?

El jue, 25 mar 2021 a las 14:59, Douglas N. Greve ()
escribió:

> Look in recon-all.log to find the command that creates the wmparc.mgz. Run
> that command changing the aparc annot to your annot and the output to a new
> file name. Look in wmparc.stats; at the top will be an mri_segstats command
> line. Copy that command line changing the file names as needed.
>
> On 3/22/2021 9:06 AM, Alberto Del Cerro Leon wrote:
>
> External Email - Use Caution
> Thanks!, how can I obtain the white matter volume stats using my
> annotation file?
>
> El mar, 16 mar 2021 a las 16:59, Douglas N. Greve ()
> escribió:
>
>> I think they will give very similar results, but my guess is that #1 is a
>> little better
>>
>> On 3/8/2021 11:40 AM, Alberto Del Cerro Leon wrote:
>>
>> External Email - Use Caution
>> I want to use the annotation file created by myself in fsaverage to
>> calculate the anatomical stats, but i dont know what is the best workflow.
>>
>> 1. Convert the annotation file to each subject space using mri_sur2surf
>> and using mri_anatomical_stats in each subject
>> 2. Convert the surface of each subject to fsaverage space and use
>> mri_segstats to obtain the data, in this case i dont know what surface i
>> have to convert to fsaverage space to do it (i can see thickness
>> (lh/rh.thickness) and volume (lh/rh.volume) but not folding index and white
>> matter volume)
>>
>> Any idea?
>>
>> El lun, 8 mar 2021 a las 16:04, Fischl, Bruce ()
>> escribió:
>>
>>> Hi Alberto
>>>
>>>
>>>
>>>1. And 4. Are not properties of single surfaces – they are computed
>>>from the white and the pial. For 2 and 3 that is really up to you
>>>
>>> Cheers
>>> Bruce
>>>
>>>
>>>
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Alberto Del
>>> Cerro Leon
>>> *Sent:* Monday, March 8, 2021 7:02 AM
>>> *To:* Freesurfer support list 
>>> *Subject:* [Freesurfer] Problem with freesurfer measures
>>>
>>>
>>>
>>> *External Email - Use Caution*
>>>
>>> Hello Freesurfer team, I am using an annotation file that i've created
>>> previously to obtain the measures of some ROIs. To do that i am using de
>>> commands mri_surf2surf and mri_segstats. I want to obtain the following
>>> measures:
>>>
>>> 1. Gray and White Matter Volume
>>>
>>> 2. Folding Index
>>>
>>> 3. Curvature measures
>>>
>>> 4. Thickness
>>>
>>> However I don't know what surface in the surf folder of each subject I
>>> have to use. Could u help me?
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>>
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