[Freesurfer] editing segmentations from recon-all-clinical

[Agata Wolna]

External Email - Use Caution

Hi!

I have a question regarding the recon-all-clinical pipeline: is it possible
to edit the outputs of the synthseg segmentation run as a part of the
pipeline (synthseg.mgz) similarly to editing recons from the standard
freesurfer pipeline, and getting updated segmentation estimates (the
synthseg.vol.csv files) for these manually updated segmentation?

Thanks for your help!
Agata
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Re: [Freesurfer] recon-all-clinical synthseg error

[Agata Wolna]

External Email - Use Caution

Hi!

I've managed to debug the problem and it turns out that it was generated by
the mri_convert function - it produced a corrupted native.mgz image that
synthseg couldn't correctly read. I encounter this problem when pulling the
freesurfer:7.4.1 from dockerhub and when I was using a version downloaded
from the freesurfer website. Replacing the mri_convert script with a one
from a previous release (7.1.1) solved the problem, but I'm just letting
you know, in case that's a more general issue (and in all cases I was
running the script in a singularity containers).

Best wishes,
Agata

pon., 26 lut 2024 o 11:02 Agata Wolna  napisał(a):

> Hi!
>
> Thanks for getting back to me. I'm running it on CentOS Linux 7 in a
> singularity container. What I did is to pull the freesurfer container from
> the DockerHub 
> (https://secure-web.cisco.com/171ahSlRX4vDMQD6prCFbKOWLRaTb3TeYqaUPEw1RHNCsVe3tGhp2kLFzWK3DJBLSx-UgUbpykn2uadM_p35sDDmGGUu-97iv7xWk1uOF7fCA5zzinTnVGh-ThVdtMXCb9wrWbtVUluLHZqPDir9P61Y41lyQx6J8ExkHyMN3nDhsdJG3NKQ0YCbHpN6OXcbMXy6k6AGFamQP8CZo_1lxhCV5WCZD26w_wkehvkhvpWl7Dd8-79VHNEEopR-cjICmGSqmg7GHDHiBc1SkoGDf-Hrij5PrwTlD6yLqb5U83FrN3wzFoW9dq-kjChSC2PKLUxnb8MKiKmHqCpn6WhL36g/https%3A%2F%2Fhub.docker.com%2Fr%2Ffreesurfer%2Ffreesurfer%3A7.1.1)
>  and
> I replaced the /usr/local/freesurfer with this version:
> https://secure-web.cisco.com/1kTRkrixWgWU1iw8Qqe5X9q-Fz5Cs0dBxd03uelbVyK3aahbt-NDyUMFDpzSxsqPZKM2WUqoyOMnywfNkFMZP_5uzLcnYmhRlPJwt6eoOMbmo_-bFRvK9YV6H-tS6FGTlH7lZCDQw4Tr2_WlN4a-2ByEqPmRw_RHrKq8SU2Sk4aNDWHoS5lPwMqIs5td3Mpd2KWBbQCJ7f20xoIDdqxcxnMQ5K3m5nC2y5sS1QzfGMOTXHSLiC-7D-Dr218ggnoS6u3Eg-UqVFYGtZZm_ACvQ6OSAYJ7z7VdTRgX6PRuMv1mQLduPWJ1CXUv1RmUDCBI4mZKBJZd0GkBTpL_9yzF30w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2F
>  (build-stamp
> is freesurfer-linux-centos7_x86_64-dev-20240209-8d5b885).
>
> Do you think that this might be an issue related to the differences in
> dependencies for the 7.1.1 and the dev version that I replaced the 7.1.1
> with? Also, if you happen to have a containerized version of the newest dev
> version (or any version higher than 7.4, as I assume they would all support
> the recon-all-clinical function, right?) maybe I could just pull the entire
> container from somewhere and see if it solves the problem?
>
> Best wishes,
> Agata
>
> niedz., 25 lut 2024 o 21:56 fsbuild  napisał(a):
>
>>
>> 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  wrote:
>>
>> 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['

Re: [Freesurfer] recon-all-clinical synthseg error

[Agata Wolna]

External Email - Use Caution

Hi!

Thanks for getting back to me. I'm running it on CentOS Linux 7 in a
singularity container. What I did is to pull the freesurfer container from
the DockerHub 
(https://secure-web.cisco.com/1mn_DXGJRkbRZaR60gIIXGTJuR-LMjZIaTJCeez5OyFU1R7CR20ybjGOUz4tzd1AxyLGwPEti0x8dbFUB84ln0O_02-s6U0uTIK8MKNSC2PQi8YfCoEy1p0wItYQUPIb5iUXIN6xmG1NisixJAmoRH2aeiF1Hp2ua8Vwv7N3sV2qz3yq-FulWe5CIozSDdVtKxL-8HDqKu5m6Qmq6GfHUwkb68AW0vPu6pVuINPmzlucZN1FMBI-oVzetjru-RxRd8CEUnQYS0kfVzJqg3J8RkaraRyC-2GgBwrxi-VPObQTTobQn8Ty4Vssycv8t2gGm0EGMq-eSNszHNtFSMXl9qw/https%3A%2F%2Fhub.docker.com%2Fr%2Ffreesurfer%2Ffreesurfer%3A7.1.1)
 and I
replaced the /usr/local/freesurfer with this version:
https://secure-web.cisco.com/1VhsOWK6YuynPJZSTzGZep_xoqWFKijIbzVFTJkUW7wK3Iy1o63M730diiMYWK024Swr3mw9BBOIoTghZHgsLX-zhfP6VJWPQXHIZMmwb38t5iynLb8UTlDh2ES7braGKK28KbwDzrtuKHr6KKC__ikcHay2_nyeyuJS4IwgMAiqy9kk1c_jRMvKIvmNtHZnGGZHc2CGMi8aPtk5G4xQDteY56lAA64yYnRe_Lps-504c6Cz_3e4Nn8HCIblzADgs-Wd5j6sMe98DjAVApWr795qdo3M4CC3109D_5-l10o8bPlPWv6GeKT8TnmDAKUfThVbrpLKOB8jq9QJ6Pm1jmQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2F
 (build-stamp
is freesurfer-linux-centos7_x86_64-dev-20240209-8d5b885).

Do you think that this might be an issue related to the differences in
dependencies for the 7.1.1 and the dev version that I replaced the 7.1.1
with? Also, if you happen to have a containerized version of the newest dev
version (or any version higher than 7.4, as I assume they would all support
the recon-all-clinical function, right?) maybe I could just pull the entire
container from somewhere and see if it solves the problem?

Best wishes,
Agata

niedz., 25 lut 2024 o 21:56 fsbuild  napisał(a):

>
> 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  wrote:
>
> 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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>
>
>
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[Freesurfer] recon-all-clinical synthseg error

[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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The information in this e-mail is intended only for the person to whom it is 
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 https://www.massgeneralbrigham.org/complianceline 
 .
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 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.