Re: [Freesurfer] freeview (visualize pial and white surface)

[DS]

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Hi experts,
I sent several images to troubleshot the problem by e-mail. But, I received an 
email saying that these files need approval from moderator. However, so far, I 
still did not get any reply from the moderator. I am not sure how to send you 
these files and how long it usually takes. Do I need to send a reminder to the 
moderator?
Thank you so much for help.
















At 2023-08-04 04:10:42, "Wang, Ruopeng"  wrote:

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Would it be possible to send us the two surface files?
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of DS 
Sent: Thursday, August 3, 2023 3:30:12 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] freeview (visualize pial and white surface)
 

External Email - Use Caution

Hi experts,

I have a question about freeview. Recently, when I loaded lh.pial and lh.white 
at the same time, the freeview was suddenly aborted and reported the following 
error.




../mesa-22.0.3/src/mesa/vbo/vbo_attrib_tmp.h:234:_save_Vertex3fv: Assertion 
`used_next <= save->vertex_store->buffer_in_ram_size' failed.




But, if I only load lh.pial or lh.white separately, I found it’s working. I 
guess there might be inconsistent parameters between the two files, because 
when I check another subject, both files can be visualized. 




Do you have any thoughts about this issue? Thank you so much for any 
suggestions.


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Re: [Freesurfer] error in my software

[fsbuild]

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Hello Mikel,
Can you send us more details like terminal output or perhaps screenshot from 
the terminal that shows the error ?
- R.

On Aug 4, 2023, at 15:54, MIKEL GARCÍA AGUIRRE mikel.gar...@alu.uclm.es 
wrote:External Email - Use 
CautionHello,I am working with 
a MacBook M1 from 2020 and I downloaded two versions of Freesurfer. The first 
one was the 7.4.1 version, but I have also tried the 7.2.0 version. The problem 
that I have is that whenever I tried to upload one file, the program directly 
produces a force quit and I can not work with it.Do you have any 
recommendations for fixing this problem?Looking forward to hearing from 
you,Best regards,Mikel___Freesurfer 
mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesurfer] error in my software

[MIKEL GARCÍA AGUIRRE]

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Hello,

I am working with a MacBook M1 from 2020 and I downloaded two versions of 
Freesurfer. The first one was the 7.4.1 version, but I have also tried the 
7.2.0 version. The problem that I have is that whenever I tried to upload one 
file, the program directly produces a force quit and I can not work with it.

Do you have any recommendations for fixing this problem?

Looking forward to hearing from you,

Best regards,

Mikel
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[Freesurfer] Errors Running tkmedit

[Edwards, Vincent]

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Hello,

Our lab has been using Freesurfer 5.3 for it's ongoing longitudinal study. I 
attempted to quality check one of our brains using tkmedit - I usually don't 
have any issues following our pipeline or running the tool. This time I 
received this message:

ERROR: A segfault has occurred. This is not your fault,
  : but is most likely an unrecoverable error and has
  : made the program unstable.
  :
  : Please send the contents of the file .xdebug_tkmedit
  : that should be in this directory to freesurfer@nmr.mgh.harvard.edu
  :
  : Now exiting...
  :

I'm not sure where the xdebug file is located - it isn't anywhere in our 
Freesurfer directory in the server. Where can I find this file, and how can I 
fix this error? I've tried trouble shooting with some solutions I've seen in 
the archive. We have checked permissions, I use a PC - not a mac, and I have 
checked the main freesurfer directories as well as the directories associated 
with the brain I want to check. I have also tried to open other brains in the 
viewer resulting in the same error message. Is there a fix for this - ideally, 
one that doesn't require switching Freesurfer versions?

Thanks for any help you can provide!

Vincent Edwards
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Re: [Freesurfer] Is there an inverse function to mris_flatten?

[Fischl, Bruce R.,PHD]

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Hi Phillip

The flattening preserves vertex correspondence between the flat maps and all 
our surfaces (for that hemisphere). So if you can map data onto the flattened 
patches,  you should be able to look up the vertex index and use that to go 
from flat patch to white or pial or inflated  (which all have the same number 
of vertices)

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Phillip Tran
Sent: Friday, August 4, 2023 11:37 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Is there an inverse function to mris_flatten?


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Hello FreeSurfer team,

I'm new to FreeSurfer and would greatly appreciate your help. My objective is 
to reverse the flattening process of mris_flatten.

I successfully got flatmaps by using mris_flatten on "bert" inflated 
hemispheres with manual relaxation cuts (in Freeview/tksurferfv as opposed to 
deprecated tksurfer) as directed by these instructions:

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/1M2Tb4cjkT8PLRafbZM7DJf5cOcQWQ2kDHJ2GDqzD7yfQhO_Ws8Ng0xqAyA3g3Wxn8_m_tdd9Xa1F36SqjR1VG6n8B0KIiMfn_was3p8JX7vBEmDfda7twOwLv4gyqgpXHde0gckOAc6bbbBarvZ1ND72rggqVz4ic_Xdv7u5ZZG7hNWG6vcfZw-zzQPZHN9aaXtEhM__bVikUf2dyZd8NXocABYmXxcllqZjHYcD49lwT3pcOW4g733bLQVrHBFG/https%3A%2F%2Ffreesurfer.net%2Ffswiki%2FFreeSurferOccipitalFlattenedPatch

I also have a small 2-D patch of non-MRI image data that's been registered to 
and fused with the hemisphere flatmap. Is there an inverse function or 
procedure for mris_flatten?

E.g.: I would input a .dcm/.jpg/etc. containing the patch-fused flatmap, then 
get in response the original inflated hemisphere with the fused patch 
appropriately deformed to fit the 3d shape.

Then, is there potentially a way to return the patch-fused inflated hemisphere 
back into the pial surface from which it was inflated?

FreeSurfer version:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460
Ubuntu version:
22.04.2 Jammy Jellyfish

Thank you for your time,
Phillip
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[Freesurfer] Issue with mri_vol2surf nearest interpolation

[Sun, Wendy]

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Good afternoon,
We are encountering an issue with getting non-integer values (input file has 
all integers) when using the “nearest” interpolation method in mri_vol2surf. 
Here is the command we ran:

mri_vol2surf --mov ${anatIn} --regheader ${REG} --hemi lh --projfrac 0.5 
--trgsubject fsaverage6 --o $Limg --reshape --interp nearest

The input file ${anatIn} has values ranging from 0 to 255 and are all integers. 
The ${REG} folder is created during recon-All.

We expected the output to be all integers, given the interpolation method, but 
we see non-integer values.

Do you know why this is the case and how to fix it?

Thank you,
Wendy

—
Wendy Sun
Graduate Student, Buckner Lab
PD Soros Fellow, 2020
Cambridge Integrated Clerkship 18
MD/PhD Candidate, HMS

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[Freesurfer] Is there an inverse function to mris_flatten?

[Phillip Tran]

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Hello FreeSurfer team,

I'm new to FreeSurfer and would greatly appreciate your help. My objective is 
to reverse the flattening process of mris_flatten.

I successfully got flatmaps by using mris_flatten on "bert" inflated 
hemispheres with manual relaxation cuts (in Freeview/tksurferfv as opposed to 
deprecated tksurfer) as directed by these instructions:

https://secure-web.cisco.com/1A7xoXmR8WDKrZnRfFGHzLvRwUtKyRcCICrInChTpRemfCwgtieF1HtkrlGtDfCNp_T5VDTNvtZMA0sCRos-SSz6ZJUvptek2VLWVouP23sbPJEjYY7q0wE5lo1iMhHcwYBtUJ2k2GxvQy6n01yaOWy9YXevRpfhdWZJBPeViVgD0RtjJlCegeQNcCw61PszMxyQags3-jpftGeQ1PVoOuF0C-dP1Ajo9KjFfNJZPAwrN7Dwec-5ig3WZLhvZfZcqLhLolNkCNXCrqVJq9XdWcHO54zSo5cJYRy1KSMAWm5ejMPkEnDz0UV61dSpgEokg463D1jkqX2dS__ZHeMEQoA/https%3A%2F%2Ffreesurfer.net%2Ffswiki%2FFreeSurferOccipitalFlattenedPatch

I also have a small 2-D patch of non-MRI image data that's been registered to 
and fused with the hemisphere flatmap. Is there an inverse function or 
procedure for mris_flatten?

E.g.: I would input a .dcm/.jpg/etc. containing the patch-fused flatmap, then 
get in response the original inflated hemisphere with the fused patch 
appropriately deformed to fit the 3d shape.

Then, is there potentially a way to return the patch-fused inflated hemisphere 
back into the pial surface from which it was inflated?

FreeSurfer version:
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460
Ubuntu version:
22.04.2 Jammy Jellyfish

Thank you for your time,
Phillip
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Re: [Freesurfer] freeview (visualize pial and white surface)

[DS]

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Hi expert,
Yes, sure. I sent both lh.pial and lh.white files, but the automatic reply 
email showed "two files are being held until the list moderator can review it 
for approval". Hopefully, you will get both files soon. Please let me know if 
you did not receive these files. Thank you so much.













At 2023-08-04 04:10:42, "Wang, Ruopeng"  wrote:

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Would it be possible to send us the two surface files?
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of DS 
Sent: Thursday, August 3, 2023 3:30:12 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] freeview (visualize pial and white surface)
 

External Email - Use Caution

Hi experts,

I have a question about freeview. Recently, when I loaded lh.pial and lh.white 
at the same time, the freeview was suddenly aborted and reported the following 
error.




../mesa-22.0.3/src/mesa/vbo/vbo_attrib_tmp.h:234:_save_Vertex3fv: Assertion 
`used_next <= save->vertex_store->buffer_in_ram_size' failed.




But, if I only load lh.pial or lh.white separately, I found it’s working. I 
guess there might be inconsistent parameters between the two files, because 
when I check another subject, both files can be visualized. 




Do you have any thoughts about this issue? Thank you so much for any 
suggestions.


___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
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continue to communicate over unencrypted e-mail.