[Freesurfer] 7.4.1 release archive has extra directory prepended

2024-02-25 Thread fsbuild 
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The leading ./ in the path looks like a by-product of needing to use 
various/different options now in creating the tar archives and also the tar 
command running may be from a different system. Not sure that can be 
reverted.
- R.Hi Freesurfer,Wasn’t sure where to post this as the github is more 
for source code issues.The 7.4.1 archives all have ‘./’ prepended to them 
(i.e., ‘./freesurfer/’ vs ‘freesurfer/’). This is causing an issue with 
neurodocker as the definition file it creates strips the first directory 
when building images. Thus, containers built on the 7.4.1 archives need to have 
their paths changed compared to prior versions or they need to strip the first 
2 levels of the path.It’s not a big deal and easy to fix in the def files 
once it's figured out, but given that it’s a departure from prior releases and 
is breaking some of the downstream tools, perhaps the next releases can go back 
to just 1 level deep (i.e. ‘freesurfer’)?Cheers,Dylan 
WagnerAttached Message Part.txt
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Re: [Freesurfer] recon-all-clinical synthseg error

2024-02-25 Thread fsbuild 
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It could help to know what OS version and what Freesurfer version you are 
running. From your path /usr/local/freesurfer it looks like you are 
running a Freesurfer release, e.g., 7.4.1.
- R.

On Feb 25, 2024, at 21:45, Agata Wolna awo...@mit.edu 
wrote:External Email - Use 
CautionHi!I'm trying to run 
recon-all-clinical but I'm running into an error with the SynthSeg at the very 
beginning. Do you have any hints what the problem might be here? Here's the 
full error message:the following problem occured with 
image[mypath]/mri/native.mgz :Traceback (most recent call last): 
File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 303, in 
predict  image, aff, h, im_res, shape, pad_idx, crop_idx = 
preprocess(path_image=path_images[i], File 
"/usr/local/freesurfer/python/scripts/mri_synthseg", line 554, in 
preprocess  im, _, aff, n_dims, n_channels, h, im_res = 
get_volume_info(path_image, True) File 
"/usr/local/freesurfer/python/scripts/mri_synthseg", line 1456, in 
get_volume_info  im, aff, header = load_volume(path_volume, 
im_only=False) File "/usr/local/freesurfer/python/scripts/mri_synthseg", 
line 1377, in load_volume  x = nib.load(path_volume) File 
"/usr/local/freesurfer/python/lib/python3..8/site-packages/nibabel/loadsave.py",
 line 110, in load  img = image_klass.from_filename(filename, 
**kwargs) File 
"/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/dataobj_images.py",
 line 503, in from_filename  return klass.from_file_map(file_map, 
mmap=mmap, keep_file_open=keep_file_open) File 
"/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/freesurfer/mghformat.py",
 line 526, in from_file_map  header = 
klass.header_class.from_fileobj(mghf) File 
"/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/freesurfer/mghformat.py",
 line 171, in from_fileobj  + 
int(klass._data_type_codes.bytespervox[tp]) * 
np.prod(hdr_str_to_np['dims'])KeyError: 10resuming program executionERROR: some 
problems occured for the following inputs (see corresponding errors 
above):[mypath]/mri/native.mgzError in 
SynthSegBest,Agata___Freesurfer 
mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesurfer] recon-all-clinical synthseg error

2024-02-25 Thread Agata Wolna 
External Email - Use Caution

Hi!

I'm trying to run recon-all-clinical but I'm running into an error with the
SynthSeg at the very beginning. Do you have any hints what the problem
might be here? Here's the full error message:

the following problem occured with image [mypath]/mri/native.mgz :
Traceback (most recent call last):
  File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 303, in
predict
image, aff, h, im_res, shape, pad_idx, crop_idx =
preprocess(path_image=path_images[i],
  File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 554, in
preprocess
im, _, aff, n_dims, n_channels, h, im_res = get_volume_info(path_image,
True)
  File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 1456, in
get_volume_info
im, aff, header = load_volume(path_volume, im_only=False)
  File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 1377, in
load_volume
x = nib.load(path_volume)
  File
"/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/loadsave.py",
line 110, in load
img = image_klass.from_filename(filename, **kwargs)
  File
"/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/dataobj_images.py",
line 503, in from_filename
return klass.from_file_map(file_map, mmap=mmap,
keep_file_open=keep_file_open)
  File
"/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/freesurfer/mghformat.py",
line 526, in from_file_map
header = klass.header_class.from_fileobj(mghf)
  File
"/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/freesurfer/mghformat.py",
line 171, in from_fileobj
+ int(klass._data_type_codes.bytespervox[tp]) *
np.prod(hdr_str_to_np['dims'])
KeyError: 10

resuming program execution


ERROR: some problems occured for the following inputs (see corresponding
errors above):
[mypath]/mri/native.mgz
Error in SynthSeg

Best,
Agata
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Re: [Freesurfer] Fwd: Vertex / voxel lesion symptom mapping

2024-02-25 Thread Martin Juneja 
External Email - Use Caution

Hi Doug,

Sorry for not elaborating in my previous email.

Voxel lesion symptom mapping (VLSM) is a method to calculate symptom
localization by estimating statistical relationships between damage to
specific brain regions (it could be stroke lesion, tumor lesion or TBI
lesion etc.) and resulting deficits (e.g.,
https://secure-web.cisco.com/1UiWVbssc136ehHR7fbKC3mJg7kJQVmdWhaRoU7E29vpu5yNgNVpd0lZiq4aR019jbUXsgd9ifhWAi0IlkNaX6x9xio5om5mkSpOTNvua1cW-cEEjvzxDi3L2sB29VZVsnhEZ8Tb3UH9P0xee7U6UR5dzGEOh8QJNPNhtL65F1jvipA-Phq6I6tlLdM_es5V3bNy-Uc2GG6yXw2BY9-tSYOxCFzZ8xvUgiqlPE8H6y5TPAXxx9g0S5ELQ2MYBhZc4scdk6uSlw8_4_qsmFzE3pHqfDGZ0Q_Jv3szY1k1AqHkxkI9t7LPh8R6dSgTpNeL4WUyRopXxirT8r-0IxK7nYA/https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC4724038%2F
 and
https://secure-web.cisco.com/1Sv3DQt7ECt7yYskA3qSYiurVnqwYgQMrW8bVWoluBQmsM_yLtTYU5rsNedrt7kfxvXWRFNBdsUI4A1g3RXw72SMBIG6ZQrrv9cyiZQGDsnk8bidCzCK_lFen7x0alY7ZhJs5O1HBwG06GFvTNxoPfkbR1hD87w8QzlmPBxoAV_migSoy78DKyb73PilyF7D9vRCcWNAx4UOdo0SSrO_Shf1_py0ygzhtUB2FOJo-0Z-5e1wnn3cKO0-MJMcDUhRdVzUXTYWyey2rVOBEqbKBye_yDzoaxLIKzESNFAVFJGY8t8AlAjZS0kE9aqzZKXXtHqmihL1X2aNJDuA_eQsRZA/https%3A%2F%2Facademic.oup.com%2Fbrain%2Farticle%2F137%2F9%2F2532%2F2848278).
 This method can
guide the development of targeted interventions and rehabilitation
strategies aimed at improving symptoms by targeting specific brain regions
(or networks, if we use network lesion symptom mapping:
https://secure-web.cisco.com/10LgUitf4Y4lehNjHOInoyAOPPrjXpKyw8QudhBNFrI-HEs531siCcOCZApchqgDvWDYKy7cM6QODz-i1dQPhiBuCX-00bXDcm2EF8XZrhB_Rknetjx1FVS8u1BBOZ16mMYnGswaNPzNgbt15-7OR0ZajBrz3jJMaAXx2tGeFbJuIT_cwpTPX2u7uVcKu40byzK3CksUD9sBXUODMzo1dWFYJ7dqv9jzjPyhXiM51d49k7iGamx_SlWvcrdjka0R328JXdXbqwiXqt2FEwAVsz1ioBdFbSPNdth73sqgmm1hDt5vQsBMMp8Txr8bGJeZxE6q-ZHf8yqwxiFsXOOVtBw/https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC9724189%2F).

On Fri, Feb 23, 2024 at 10:27 AM Douglas N. Greve 
wrote:

> Sorry, don't know what VLSM is. Can you elaborate?
>
> On 2/6/2024 3:19 PM, Martin Juneja wrote:
>
> External Email - Use Caution
> Dear FreeSurfer community and experts,
>
> I would greatly appreciate any help/response with the following.
>
> Thanks.
>
> -- Forwarded message -
> From: Martin Juneja 
> Date: Wed, Jan 31, 2024 at 7:51 PM
> Subject: Vertex / voxel lesion symptom mapping
> To: Freesurfer support list 
>
>
> Greetings FreeSurfer community,
>
> I was just wondering if it's possible to perform vertex/voxel lesion
> symptom mapping (VLSM) using FreeSurfer? In other words, I would like to
> assess the impact of lesion topography (of course, heterogenous locations
> across patients) on neurocognitive function in brain tumor patients.
>
> I would greatly appreciate any help/response.
>
> Thanks!
>
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