Re: [Freesurfer] FreeSurfer atlases

2024-06-28 Thread Fischl, Bruce R.,PHD 
In freeview I believe you can right click on a given label in the list in the 
left-hand pane and “go to centroid” or something is an option

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Friday, June 28, 2024 9:22 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FreeSurfer atlases

Try looking at it in freeview first. Some of the regions may be small, so you 
may have to hunt to get them. FYI you can specify nii as the output of 
mri_binarize
On 6/28/2024 5:30 AM, Savoia, Alice (Stud. FPN) wrote:

External Email - Use Caution
Thank you for the reply,
I need to create a mask of each segmented subfield (segmented with freesufer) 
and then I need to use the obtained mask in FSL to do a DTI. However, I am not 
sure about the pipeline I have to follow to do so. So far I have been following 
this one:

  *   mri_label2vol --seg <> --temp rawavg.mgz --regheader <> --o "".mgz
  *   mri_binarize --i --o --match "17"


  *   mri_convert --in_type mgz --out_type nii


  *   flirt -in -out -init  -applyxfm


  *   fslmaths -bin

But when I try to open the mask in FSL I cannot visualize them. Does anyone 
have suggestions?
Thanks,
Alice

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
Sent: Thursday, June 27, 2024 12:36 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FreeSurfer atlases

I'm not sure what you mean. We don't have an image of the subfields in, eg, mni 
space. Usually, you just run the subfield seg on the data that you want 
subfields for
On 6/26/2024 7:58 AM, Savoia, Alice (Stud. FPN) wrote:

External Email - Use Caution
Hello,
I am looking for a freesufer standard atlas for hippocampal subfields (to be 
used for a DTI pipeline in FSL) but I cannot find it in fsaversage/label.
Does anyone have any suggestion?
Thank for the help,
Alice



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Re: [Freesurfer] FreeSurfer atlases

2024-06-28 Thread Douglas N. Greve 
Try looking at it in freeview first. Some of the regions may be small, 
so you may have to hunt to get them. FYI you can specify nii as the 
output of mri_binarize


On 6/28/2024 5:30 AM, Savoia, Alice (Stud. FPN) wrote:


External Email - Use Caution

Thank you for the reply,
I need to create a mask of each segmented subfield (segmented with 
freesufer) and then I need to use the obtained mask in FSL to do a 
DTI. However, I am not sure about the pipeline I have to follow to do 
so. So far I have been following this one:


  * mri_label2vol --seg <> --temp rawavg.mgz --regheader <> --o "".mgz
  * mri_binarize --i --o --match "17"


  * mri_convert --in_type mgz --out_type nii


  * flirt -in -out -init  -applyxfm


  * fslmaths -bin


But when I try to open the mask in FSL I cannot visualize them. Does 
anyone have suggestions?

Thanks,
Alice

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Sent:* Thursday, June 27, 2024 12:36 AM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] FreeSurfer atlases
I'm not sure what you mean. We don't have an image of the subfields 
in, eg, mni space. Usually, you just run the subfield seg on the data 
that you want subfields for


On 6/26/2024 7:58 AM, Savoia, Alice (Stud. FPN) wrote:


External Email - Use Caution

Hello,
I am looking for a freesufer standard atlas for hippocampal subfields 
(to be used for a DTI pipeline in FSL) but I cannot find it in 
fsaversage/label.

Does anyone have any suggestion?
Thank for the help,
Alice

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<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>



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Re: [Freesurfer] FreeSurfer atlases

2024-06-28 Thread Savoia, Alice (Stud. FPN) 
External Email - Use Caution

Thank you for the reply,
I need to create a mask of each segmented subfield (segmented with freesufer) 
and then I need to use the obtained mask in FSL to do a DTI. However, I am not 
sure about the pipeline I have to follow to do so. So far I have been following 
this one:

  *   mri_label2vol --seg <> --temp rawavg.mgz --regheader <> --o "".mgz
  *   mri_binarize --i --o --match "17"


  *   mri_convert --in_type mgz --out_type nii


  *   flirt -in -out -init  -applyxfm


  *   fslmaths -bin

But when I try to open the mask in FSL I cannot visualize them. Does anyone 
have suggestions?
Thanks,
Alice

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Thursday, June 27, 2024 12:36 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] FreeSurfer atlases

I'm not sure what you mean. We don't have an image of the subfields in, eg, mni 
space. Usually, you just run the subfield seg on the data that you want 
subfields for

On 6/26/2024 7:58 AM, Savoia, Alice (Stud. FPN) wrote:

External Email - Use Caution

Hello,
I am looking for a freesufer standard atlas for hippocampal subfields (to be 
used for a DTI pipeline in FSL) but I cannot find it in fsaversage/label.
Does anyone have any suggestion?
Thank for the help,
Alice



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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
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Re: [Freesurfer] FreeSurfer atlases

2024-06-26 Thread Douglas N. Greve 
I'm not sure what you mean. We don't have an image of the subfields in, 
eg, mni space. Usually, you just run the subfield seg on the data that 
you want subfields for


On 6/26/2024 7:58 AM, Savoia, Alice (Stud. FPN) wrote:


External Email - Use Caution

Hello,
I am looking for a freesufer standard atlas for hippocampal subfields 
(to be used for a DTI pipeline in FSL) but I cannot find it in 
fsaversage/label.

Does anyone have any suggestion?
Thank for the help,
Alice

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 .
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Re: [Freesurfer] freesurfer atlases/versions

2012-12-28 Thread Christophe Destrieux 
Hi Narly

You are right: The anatomical parcellation is the same (aparc.a2009s) as the 
one included in the 4.5 FS version (see also 
http://surfer.nmr.mgh.harvard.edu/fswiki/DestrieuxAtlasChanges).

Cheers

-- 
Christophe 


- Mail original -
 De: Narly Golestani narly.golest...@unige.ch
 À: freesurfer@nmr.mgh.harvard.edu
 Envoyé: Vendredi 28 Décembre 2012 21:13:05
 Objet: [Freesurfer] freesurfer atlases/versions
 
 
 
 Dear all,
 
 I have a quick question re- the different atlases used by the
 different versions of freesurfer. I'd like to know if there will be
 any differences in the auditory cortex labelization process if we
 use freesurfer version 4.5 and upwards. From the below post I have
 the impression that version 4.5 and upwards (until 5.2?) all apply
 similar rules for parcellating the 3 auditory cortex ROIs that we're
 interested in (the transverse temporal gyrus and sulcus, and the
 planum temporale).
 http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20932.html
 
 Thanks in advance for your input,
 with best wishes,
 Narly Golestani.
 
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 dispose of the e-mail.
 
 

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