Re: [Freesurfer] FreeSurfer atlases

2024-06-28 Thread Savoia, Alice (Stud. FPN) 
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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:

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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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[Freesurfer] Can find "mri_WMHsynthseg" command in freesurfer 7.4.1

2024-06-28 Thread Byripudi Naveen Kumar ed20d402 
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Dear freesurfer experts,

I was trying to use synthseg for segmenting and parcellating a
heterogeneous brain with lesions. It is advised in the freesurfer synthseg
webpage to use mri_WMHsynthseg command for these cases. How ever when I
tried to run the command, it shows that command not found. I checked
mri_synsthseg command works. What shall I do to resolve this? Is there a
way to install the mri_WMHsynthseg or is it part of some existing commands?

Regards,
Naveen Kumar
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Re: [Freesurfer] 回复: The file absence problem of the recon-all -all output

2024-06-28 Thread Douglas N. Greve 

Use orig.mgz

On 6/27/2024 9:47 PM, Quanjiang Liu wrote:


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  Sorry to bother you again. I want to know that the standard input to 
get the standard lh.seghead and rh.seghead. Is it the T1.mgz or the 
brain.mgz in the mri folder which is one of the output files of 
recon-all -all command.

Best,


*发件人:* freesurfer-boun...@nmr.mgh.harvard.edu 
 代表 Douglas N. Greve 


*发送时间:* 2024年6月27日 6:35
*收件人:* freesurfer@nmr.mgh.harvard.edu 
*主题:* Re: [Freesurfer] The file absence problem of the recon-all -all 
output



你通常不会收到来自 dgr...@mgh.harvard.edu 
的电子邮件。了解这一点为什么很重要 




that has to be created with a separate process (mri_seghead)

On 6/26/2024 2:11 PM, Quanjiang Liu wrote:


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  Hi, I ran the recon-all -all command successfully. But the 
lh.seghead and rh.seghead didn't appear in my output folder. The 
attachment is the process record. Can you help to solve it?

  Sorry to bother.
Best

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Re: [Freesurfer] Error saying cannot find my file for recon-all

2024-06-28 Thread Douglas N. Greve 
It can't find the file struct.nii. You have to give it the full path to 
the file. It looks like $Users is not set to anything (blank)


On 6/28/2024 12:03 AM, Lydia Luck wrote:


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Hello-

I am trying to do recon-all on my brain MRI and I’ve rewritten it so 
many times I have absolutely no clue what is going wrong. Ultimately, 
the main error message I’m getting is that my file is not found. I’ve 
tried typing out the complete path, made multiple different folders, 
renamed the file and the folders, changed the file type, changed the 
location of the folder, exited terminal and tried again, switched to 
the other user on the computer (got the same error) even restarted my 
computer, etc. Kind of at a loss at this point. I am using a Mac with 
an M1 chip and the 7.4.1 version


This is my current line of commands:

export FREESURFER_HOME=/Applications/freesurfer/7.4.1

source $FREESURFER_HOME/SetUpFreeSurfer.sh

export FS_LICENSE=/opt/freesurfer/license.txt

export SUBJECTS_DIR=$Users/lydialuck/3DBRAIN

recon-all -s lydiasbrain -i $Users/lydialuck/3DBRAIN/struct.nii.gz 
-parallel -all



And then getting this back:

ERROR: cannot find /lydialuck/3DBRAIN/struct.nii.gz

Darwin Blazes-MBP.lan 23.4.0 Darwin Kernel Version 23.4.0: Wed Feb 21 
21:44:06 PST 2024; root:xnu-10063.101.15~2/RELEASE_ARM64_T8103 arm64



recon-all -s lydiasbrain exited with ERRORS at Thu Jun 27 01:13:56 EDT 
2024



If you could help me figure this out that would be great; I’ve 
probably spent well over 6 hours now trying different things.



Thanks so much,

Lydia


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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:


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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 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
 

 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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[Freesurfer] Inquiry about alpha inflation in multiple comparison

2024-06-28 Thread Emma Harper 
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Dear Freesufer teams,

Does anyone have any recommendations to correct for alpha inflation when
doing the multiple comparisons in freesurfer? We are trying to avoid using
the Bonferroni Correction so any recommendations for ways beside that would
be greatly appreciated.

Thanks,
Emma Harper
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Re: [Freesurfer] Inquiry about alpha inflation in multiple comparison

2024-06-28 Thread Douglas N. Greve 

Have you seen this page?
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm

On 6/28/2024 9:48 AM, Emma Harper wrote:


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Dear Freesufer teams,

Does anyone have any recommendations to correct for alpha inflation 
when doing the multiple comparisons in freesurfer? We are trying to 
avoid using the Bonferroni Correction so any recommendations for ways 
beside that would be greatly appreciated.


Thanks,
Emma Harper

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Re: [Freesurfer] Can find "mri_WMHsynthseg" command in freesurfer 7.4.1

2024-06-28 Thread Iglesias Gonzalez, Juan E. 
Dear Naveen,
WMH-SynthSeg is currently only available in the development version of 
FreeSurfer.
I have updated the wiki with this information.
Apologies for the inconvenience.
/E
--
Juan Eugenio Iglesias
http://www.jeiglesias.com

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Byripudi Naveen Kumar 
ed20d402 
Date: Friday, June 28, 2024 at 5:40 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Can find "mri_WMHsynthseg" command in freesurfer 7.4.1

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Dear freesurfer experts,

I was trying to use synthseg for segmenting and parcellating a heterogeneous 
brain with lesions. It is advised in the freesurfer synthseg webpage to use 
mri_WMHsynthseg command for these cases. How ever when I tried to run the 
command, it shows that command not found. I checked mri_synsthseg command 
works. What shall I do to resolve this? Is there a way to install the 
mri_WMHsynthseg or is it part of some existing commands?

Regards,
Naveen Kumar
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