date:20221220

Re: [Freesurfer] mri_sclimbic_seg patch issue?

2022-12-20 Thread Kumar, Avnish

Hi Randy and Yann,

For this fix you will have to update the surfa package that ships with 
Freesurfer. You can do this by:
fspython -m pip install --upgrade surfa

Best,
Avnish

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yann Quidé 

Sent: Tuesday, December 20, 2022 3:25 PM
To: Freesurfer support list 
Cc: daedalu...@aol.com 
Subject: Re: [Freesurfer] mri_sclimbic_seg patch issue?


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Hi all,

I have the same issue on Ubuntu 22.04, patch is installed.
Many thanks,

Yann

On 20 Dec 2022, at 04:29, daedalu...@aol.com wrote:


External Email - Use Caution

Dear FreeSurfer Developers,

We are interested in implementing " mri_sclimbic_seg " from FreeSurfer 7.3.2 
and are having trouble getting it to finish processing.

When I tried to run mri_sclimbic_seg. I keep getting a python error and the 
process never finishes. I searched through the forum and it said that this was 
a known error and that there was a patch. When I installed the patch I got the 
exact same error.

The error message is: “ValueError: operands could not be broadcast together 
with shapes (4,) (3,)”
The link to the forum post is:
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg73652.html

We tried running it on the test subject “bert” just to make sure the issue is 
not with our test scan and I got the same error.

We are getting the error even after installing the patch.  Here are the details 
of the command line I used to run it and the error message:

Command line:
mri_sclimbic_seg --s bert --o 
/usr/local/freesurfer/7.3.2-1/subjects/bert/mri/mri_sclimbic_seg.mgz 
--write_volumes --write_qa_stat

Error:
Traceback (most recent call last):
  File "/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg", line 
1049, in 
main()
  File "/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg", line 
232, in main
segmenter.process_files(**params)
  File "/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg", line 
578, in process_files
post, seg, vox_counts, volumes, mean_probs = self.segment(image)
  File "/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg", line 
498, in segment
conformed = self.preprocess(image)
  File "/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg", line 
490, in preprocess
processed = image.conform(shape=(*self.inshape, self.nchannels), 
voxsize=1.0, orientation='RAS', dtype='float32', copy=False)
  File 
"/usr/local/freesurfer/7.3.2-1/python/lib/python3.8/site-packages/surfa/image/framed.py",
 line 574, in conform
conformed = conformed.reshape(shape, copy=False)
  File 
"/usr/local/freesurfer/7.3.2-1/python/lib/python3.8/site-packages/surfa/image/framed.py",
 line 515, in reshape
delta = (np.array(shape) - np.array(self.baseshape)) / 2
ValueError: operands could not be broadcast together with shapes (4,) (3,)


We are beginning to study professional and amateur fighters, and we suspect 
that shearing/disruptions to the septum pellucidum may have downstream 
consequences to the connectivity/DTI measures in the septal nuclei, mammilary 
bodies, etc.

Thanks in advance for any help or comments you can provide.

Sincerely

-Randy

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Re: [Freesurfer] Tetrahedral mesh

2022-12-20 Thread Douglas N. Greve


Why not samseg?

On 12/20/2022 12:50 PM, Donatas Sederevičius wrote:


External Email - Use Caution

Hi, is there a tool to make a tetrahedral mesh of the brain from the 
MRI T1w image and/or its whole-brain segmentation? I need it for the 
finite elements method.


-Don

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Re: [Freesurfer] questions about mri_glmfit

2022-12-20 Thread Douglas N. Greve




On 12/20/2022 12:22 PM, James Brown wrote:


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Dear Freesurfer experts,
I have 2 questions about the command mri_glmfit and I appreciate your 
help.
1- Are there any settings or flags that can be used in mri_glmfit to 
restrict statistical comparison of surface based analysis to specific 
ROIs rather than whole brain analysis. I would like to show the 
difference on the brain surface in lobes rather than in sub lobar labels.
You can create a mask or label and feed it into mri_glmfit with --mask 
or --label
2- I understand that the flag "--table" in command mri_glmfit allows 
for feeding spreadsheets instead of images. Can we restrict the number 
of columns in this spreadsheet to 8 columns for lobs (frontal, 
temporal, occipital and parietal) left and right? Also, is there any 
way to generate a statistical map from the spreadsheet statistics?

Remove the columns you don't want?


Thank you and happy holidays :)
James

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Re: [Freesurfer] mri_sclimbic_seg patch issue?

2022-12-20 Thread Yann Quidé

External Email - Use Caution

Hi all,

I have the same issue on Ubuntu 22.04, patch is installed.
Many thanks,

Yann 

> On 20 Dec 2022, at 04:29, daedalu...@aol.com wrote:
> 
> External Email - Use Caution
> 
> 
> Dear FreeSurfer Developers,
> 
> We are interested in implementing " mri_sclimbic_seg " from FreeSurfer 7.3.2 
> and are having trouble getting it to finish processing.
> 
> When I tried to run mri_sclimbic_seg. I keep getting a python error and the 
> process never finishes. I searched through the forum and it said that this 
> was a known error and that there was a patch. When I installed the patch I 
> got the exact same error.
> 
> The error message is: “ValueError: operands could not be broadcast together 
> with shapes (4,) (3,)”
> The link to the forum post is:
> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
> claiming to be 
> https://secure-web.cisco.com/1AOO2G3Y9tIa3C9R7SheXdTmfFlIb7ZE6S7sOyW05Pn5KgUixvaLbdD9R1S6_Zi3KZjHAxNtpCZE3cPPjsACbaj0MP4zQqxSVGDRjTV8yfBtix-5EBxDDM_u2DGLzEPfKHNrV4jtEvpXA7sKFoxeMQ8XnpvNXlnaNbUityY1bkGrb7RK49FccouDavh7x8l2DNWz-w00BObPqu2ZP7CSfM5W5DffZk5ZiDpMH8GCh_WApOI6SwGuqz90fE2YtOFT2hjq3BMCI6Uyut8rMbXgLh38CxtmF5PXbBQREWN6aF5kqZFfB05KyviFvQALJWJ-Tl_T1E6eUQAgjiJv1_Ws3eg/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg73652.html
>  
> 
>  
> We tried running it on the test subject “bert” just to make sure the issue is 
> not with our test scan and I got the same error.
> 
> We are getting the error even after installing the patch.  Here are the 
> details of the command line I used to run it and the error message:
>  
> Command line:
> mri_sclimbic_seg --s bert --o 
> /usr/local/freesurfer/7.3.2-1/subjects/bert/mri/mri_sclimbic_seg.mgz 
> --write_volumes --write_qa_stat
>  
> Error:
> Traceback (most recent call last):
>   File "/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg", line 
> 1049, in 
> main()
>   File "/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg", line 
> 232, in main
> segmenter.process_files(**params)
>   File "/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg", line 
> 578, in process_files
> post, seg, vox_counts, volumes, mean_probs = self.segment(image)
>   File "/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg", line 
> 498, in segment
> conformed = self.preprocess(image)
>   File "/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg", line 
> 490, in preprocess
> processed = image.conform(shape=(*self.inshape, self.nchannels), 
> voxsize=1.0, orientation='RAS', dtype='float32', copy=False)
>   File 
> "/usr/local/freesurfer/7.3.2-1/python/lib/python3.8/site-packages/surfa/image/framed.py",
>  line 574, in conform
> conformed = conformed.reshape(shape, copy=False)
>   File 
> "/usr/local/freesurfer/7.3.2-1/python/lib/python3.8/site-packages/surfa/image/framed.py",
>  line 515, in reshape
> delta = (np.array(shape) - np.array(self.baseshape)) / 2
> ValueError: operands could not be broadcast together with shapes (4,) (3,)
>  
> 
> We are beginning to study professional and amateur fighters, and we suspect 
> that shearing/disruptions to the septum pellucidum may have downstream 
> consequences to the connectivity/DTI measures in the septal nuclei, mammilary 
> bodies, etc.
> 
> Thanks in advance for any help or comments you can provide.
> 
> Sincerely
> 
> -Randy
> 
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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 
> Compliance HelpLine at 
>

[Freesurfer] Tetrahedral mesh

2022-12-20 Thread Donatas Sederevičius

External Email - Use Caution

Hi, is there a tool to make a tetrahedral mesh of the brain from the MRI
T1w image and/or its whole-brain segmentation? I need it for the finite
elements method.

-Don
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 .
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Re: [Freesurfer] Freeview quit unexpectedly

2022-12-20 Thread Wang, Ruopeng

After you load the image from the command-line, can you then load more images 
from the GUI?

Ruopeng

On Dec 20, 2022, at 3:23 AM, Addison, Reuben 
mailto:raddi...@mghihp.edu>> wrote:

The answer to this is question ‘ opening an image from the gui ‘ is yes. The 
image only opens when I open from the command line

Reuben A.

Get Outlook for iOS

From: fsbuild mailto:fsbu...@contbay.com>>
Sent: Tuesday, December 20, 2022 7:56:12 AM
To: freesurfer@nmr.mgh.harvard.edu 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: Addison, Reuben mailto:raddi...@mghihp.edu>>
Subject: Re: [Freesurfer] Freeview quit unexpectedly


External Email - Use Caution


By crashing from the GUI do you mean that you when you try to navigate to open 
a file, e.g.,   $SUBJECTS_DIR/bert/mri/brain.mgz,  using the freeview GUI 
Open-> pull down menu that you get the core dump listed below, but it works 
when your run “freeview  $SUBJECTS_DIR/bert/mri/brain.mgz” from the command 
line in the terminal window?

The core dump shows a memory allocation error on MacOSX.  Some postings 
indicate setting MallocNanoZone to zero before running your program/command can 
remedy this,

$ bash
$ export MallocNanoZone=0 && freeview

- but this may not work.   I don’t see any other workarounds for this right 
now.  I have not seen this error before with freeview on older versions of 
MacOS, so it may be related to running on MacOS 10.13.

- R.

On Dec 19, 2022, at 14:03, Addison, Reuben 
mailto:raddi...@mghihp.edu>> wrote:

I updated the Xquartz yet still same issue. Freeview only works with the 
command line but the gui is till crashing.

Gkxgears seems to work fine

I have attached images of both the crash report and the graphics information 
about my mac.

Reuben A



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[Freesurfer] questions about mri_glmfit

2022-12-20 Thread James Brown

External Email - Use Caution

Dear Freesurfer experts,
I have 2 questions about the command mri_glmfit and I appreciate your help.
1- Are there any settings or flags that can be used in mri_glmfit to
restrict statistical comparison of surface based analysis to specific ROIs
rather than whole brain analysis. I would like to show the difference on
the brain surface in lobes rather than in sub lobar labels.
2- I understand that the flag "--table" in command mri_glmfit allows for
feeding spreadsheets instead of images. Can we restrict the number of
columns in this spreadsheet to 8 columns for lobs (frontal, temporal,
occipital and parietal) left and right? Also, is there any way to generate
a statistical map from the spreadsheet statistics?

Thank you and happy holidays :)
James
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[Freesurfer] Password to decrypt 7zip Virtualbox Image

2022-12-20 Thread Jaron Shelow

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When I try to extract the 7zip containing the virtualbox image with
freesurfer, it prompts me for a decryption password. I can't find it
anywhere. Could you help?
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Re: [Freesurfer] lh.pial lh.pialT1n same file?

2022-12-20 Thread Huang, Yujing

Hi Rene,

Can you send your recon-all.log? It is in the ‘scripts’ directory.

‘lh.pial’ should be created as a link to ‘lh.pial.T1’ if you are not processing 
T2/FLAIR.  If you go ‘surf’ directory, do ‘ls -l lh.pial*’, what does it shows?

Best,

Yujing

From: Renew Andrade 
Sent: Tuesday, December 20, 2022 1:23 AM
To: Huang, Yujing ; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] lh.pial lh.pialT1n same file?


External Email - Use Caution
Dear Yujing:
I wasn’t aware that there was an answer to my email that’s the reason it took 
me a while to write back. But I answer here.
Yes I mean lh.pial.T1. I don’t have any other lh.pial. The recon-all command is 
properly correct like recon-all -all -i -s -openmp 8. Yes the freesurfer 
version is 7.1.1.

Best,
Rene Andrade.







Hi Rene,



Do you mean lh.pial.T1? Do you have any other lh.pial* files in the directory?

What is your recon-all command line? And can you also provide the Freesurfer

version you are running?



Best,



Yujing



-Original Message-

From: 
freesurfer-boun...@nmr.mgh.harvard.edu

mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Renew Andrade

Sent: Tuesday, December 13, 2022 7:24 AM

To: freesurfer@nmr.mgh.harvard.edu

Subject: [Freesurfer] lh.pial lh.pialT1n same file?



External Email - Use Caution



Dear experts:



I am wondering if lh.pial and lh.pialT1 are the same files. I don’t have

lh.pial is that an error from recon-all? Should I rerun recon-all. Or just

autorecon-pial? Would that change anything?



Best,

Rene Andrade.



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>
 .

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Re: [Freesurfer] Freeview quit unexpectedly

2022-12-20 Thread Addison, Reuben

The answer to this is question ‘ opening an image from the gui ‘ is yes. The 
image only opens when I open from the command line

Reuben A.

Get Outlook for iOS

From: fsbuild 
Sent: Tuesday, December 20, 2022 7:56:12 AM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Addison, Reuben 
Subject: Re: [Freesurfer] Freeview quit unexpectedly

External Email - Use Caution

By crashing from the GUI do you mean that you when you try to navigate to open 
a file, e.g.,   $SUBJECTS_DIR/bert/mri/brain.mgz,  using the freeview GUI 
Open-> pull down menu that you get the core dump listed below, but it works 
when your run “freeview  $SUBJECTS_DIR/bert/mri/brain.mgz” from the command 
line in the terminal window?

The core dump shows a memory allocation error on MacOSX.  Some postings 
indicate setting MallocNanoZone to zero before running your program/command can 
remedy this,

$ bash
$ export MallocNanoZone=0 && freeview

- but this may not work.   I don’t see any other workarounds for this right 
now.  I have not seen this error before with freeview on older versions of 
MacOS, so it may be related to running on MacOS 10.13.

- R.

On Dec 19, 2022, at 14:03, Addison, Reuben  wrote:

I updated the Xquartz yet still same issue. Freeview only works with the 
command line but the gui is till crashing.

Gkxgears seems to work fine

I have attached images of both the crash report and the graphics information 
about my mac.

Reuben A

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Re: [Freesurfer] mri_sclimbic_seg patch issue?

Re: [Freesurfer] Tetrahedral mesh

Re: [Freesurfer] questions about mri_glmfit

Re: [Freesurfer] mri_sclimbic_seg patch issue?

[Freesurfer] Tetrahedral mesh

Re: [Freesurfer] Freeview quit unexpectedly

[Freesurfer] questions about mri_glmfit

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