Re: [Freesurfer] [External] Re: 7.3.2-patch issues - thalamic segmentation

2023-02-24 Thread Kumar, Avnish 
Hi Aaron,

This patch fixes a bug in the core.py file on FS-v7.3.2. In the file, one of 
the arguments for the image.resize() function call was accidentally named 
'interp<https://github.com/freesurfer/freesurfer/blob/fs-7.3.2-test2/python/freesurfer/subregions/core.py#L240>'.
 The correct argument name is 
'method<https://github.com/freesurfer/surfa/blob/v0.0.8/surfa/image/framed.py#L241>'.

This fix shouldn't affect the standard recon-all results.

Best,
Avnish


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Aaron Tanenbaum 

Sent: Thursday, February 23, 2023 9:12 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] [External] Re: 7.3.2-patch issues - thalamic 
segmentation


External Email - Use Caution

Hi,
I saw this thread and was wondering about the details of this patch. Does this 
patch affect the standard recon-all call or is this meant for a special flag. 
Also I was also wondering what issue did it solve?
Thank you.

On Wed, Feb 22, 2023 at 11:52 PM Kumar, Avnish 
mailto:avnish.ku...@mgh.harvard.edu>> wrote:
Hi Katie,

The core.py file has been updated now. Please try downloading it again and 
applying the same 
fix<https://secure-web.cisco.com/1jL26L7yFavOUgcWfxYm-k3h15hb0c5gOBHa9Fed4BCYLubpwr-niyJ-R1e6v30g6M7KnS_6WZxqflmAWLgjRPfEPSuoq0dklfegUn03H-r36juVobk3F3SYqLW5gq23xrLQiPF5G2vENSKbNdvxNLPIgVwOC0_84R3mVkvdBCElZhtZ5UDlXd0WzMLSjf7gJDbB651AHUCT9wh-91j-A0iUNu79mTXPZtmayJ77YNgMlH9qiSwRzhRT0H2iC6FCqMgCLC7PinAV99aNZo4EAzLIQZNZ4fOtEjm51OZZ4T_077e6kprzhNwFhcMaW-CIBATU8VSigXdH9B-i_aPvXxQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.3.2-patch%2Fsegment_subregions%2F>
 as before.

Best,
Avnish

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Katie Rose Jobson 
mailto:katie.job...@temple.edu>>
Sent: Monday, February 6, 2023 3:17 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] [External] Re: 7.3.2-patch issues - thalamic 
segmentation


External Email - Use Caution

Hi FS experts,

Apologies for my late follow up.

In reference to the previous conversation, I added the core.py file to the 
correct subdirectory to complete the thalamic nuclei segmentation. I received 
an error still, albeit a different error:


Traceback (most recent call last):

  File "/usr/local/freesurfer-7.3.2/python/scripts/segment_subregions", line 6, 
in 

from freesurfer import subregions

  File 
"/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/__init__.py",
 line 1, in 

from freesurfer.subregions.process import structure_names

  File 
"/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/process.py", 
line 8, in 

from freesurfer.subregions.thalamus import ThalamicNuclei

  File 
"/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/thalamus.py",
 line 9, in 

from freesurfer.subregions.core import MeshModel

  File 
"/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/core.py", 
line 9, in 

from gems.subregions import utils

ImportError: cannot import name 'utils' from 'gems.subregions' (unknown 
location)

I am assuming this is because the core.py script was previously housed in the 
'/gems/subregions' subdirectory, and is attempting to import 'utils' from 
there. Is there any way to edit this file (core.py) to call on this 'utils' 
function?

Please let me know if I can clarify my question in any way and thank you in 
advance for your help!

Best Wishes,
Katie
--
Katie Jobson, M.S. | Personal 
Website<https://secure-web.cisco.com/1ho9yNMxPXcFe1keXWE6wU20yOWqSzwoLYY9yARkmRCu9A8_XhOXs1813M6_RxM-r3s-D_p5KtP47zZHAwIEOLNo2SWUEMb8izbw-aoPMo5VaQrkfHwPEQR-A_1Ndy0swiCQkRPIUc3N5YrjPIPddJbD0uuvB9ahtxvje-xF2ONHK4BV8UxSW4KsdBelaJeRTLEi6OmnEK9n9LxWCfulEB20fM8BR8uo6J-I1HfMdGt94a5FStVqF_XoAkXTpu7BHr_u_tNTaFPaAzGv-YMiazbNylkbOsNOUtl1x9J8dy3t1wyH3YuvujxkpFJyq3Boq/https%3A%2F%2Fkjobson-neuro.github.io%2F>
Ph.D. Student | Cognitive Neuroscience 
Lab<https://secure-web.cisco.com/1uRVKqr-OerGkjpg37lgmTfI8G88BkyD_v1y97KKQvh5AZ4-HIw6jDi1X-egyGybN70R_3IK7JfG6NBpr7vyUJs6WmRkCn0xt_y_-KnhH46kTj-7Xn600oPlnbidSm5PAMKsicH6XpINAZ0uytQwlGJO10m-1Wubg_6xkcOK3296_lntwqYHR_qBE8jCt_VavyEQlx9OOKNnyIvRNXgfYS1GthgtdQ3D4XNDSGtEHB-GO7JnX5Megar67weLsVe37-oqGC5wOwyl6Uq7To5l5z51YzmCl9D-NB0kzfykkgB-RTA_RD5aGb3uH5vCO16LW/https%3A%2F%2Fsites.temple.edu%2Fcnltu%2F>
Department of Psychology and Neuroscience | Temple University


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Ku

Re: [Freesurfer] [External] Re: 7.3.2-patch issues - thalamic segmentation

2023-02-23 Thread Aaron Tanenbaum 
External Email - Use Caution

Hi,
I saw this thread and was wondering about the details of this patch. Does
this patch affect the standard recon-all call or is this meant for a
special flag. Also I was also wondering what issue did it solve?
Thank you.

On Wed, Feb 22, 2023 at 11:52 PM Kumar, Avnish 
wrote:

> Hi Katie,
>
> The core.py file has been updated now. Please try downloading it again and
> applying the same fix
> <https://secure-web.cisco.com/1jL26L7yFavOUgcWfxYm-k3h15hb0c5gOBHa9Fed4BCYLubpwr-niyJ-R1e6v30g6M7KnS_6WZxqflmAWLgjRPfEPSuoq0dklfegUn03H-r36juVobk3F3SYqLW5gq23xrLQiPF5G2vENSKbNdvxNLPIgVwOC0_84R3mVkvdBCElZhtZ5UDlXd0WzMLSjf7gJDbB651AHUCT9wh-91j-A0iUNu79mTXPZtmayJ77YNgMlH9qiSwRzhRT0H2iC6FCqMgCLC7PinAV99aNZo4EAzLIQZNZ4fOtEjm51OZZ4T_077e6kprzhNwFhcMaW-CIBATU8VSigXdH9B-i_aPvXxQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.3.2-patch%2Fsegment_subregions%2F>
> as before.
>
> Best,
> Avnish
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Katie Rose Jobson <
> katie.job...@temple.edu>
> *Sent:* Monday, February 6, 2023 3:17 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] [External] Re: 7.3.2-patch issues - thalamic
> segmentation
>
>
> External Email - Use Caution
>
> Hi FS experts,
>
> Apologies for my late follow up.
>
> In reference to the previous conversation, I added the core.py file to the
> correct subdirectory to complete the thalamic nuclei segmentation. I
> received an error still, albeit a different error:
>
> Traceback (most recent call last):
>
>   File "/usr/local/freesurfer-7.3.2/python/scripts/segment_subregions",
> line 6, in 
>
> from freesurfer import subregions
>
>   File
> "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/__init__.py",
> line 1, in 
>
> from freesurfer.subregions.process import structure_names
>
>   File
> "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/process.py",
> line 8, in 
>
> from freesurfer.subregions.thalamus import ThalamicNuclei
>
>   File
> "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/thalamus.py",
> line 9, in 
>
> from freesurfer.subregions.core import MeshModel
>
>   File
> "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/core.py",
> line 9, in 
>
> from gems.subregions import utils
>
> ImportError: cannot import name 'utils' from 'gems.subregions' (unknown
> location)
>
> I am assuming this is because the core.py script was previously housed in
> the '/gems/subregions' subdirectory, and is attempting to import 'utils'
> from there. Is there any way to edit this file (core.py) to call on this
> 'utils' function?
>
> Please let me know if I can clarify my question in any way and thank you
> in advance for your help!
>
> Best Wishes,
> Katie
> --
> Katie Jobson, M.S. | Personal Website
> <https://secure-web.cisco.com/1ho9yNMxPXcFe1keXWE6wU20yOWqSzwoLYY9yARkmRCu9A8_XhOXs1813M6_RxM-r3s-D_p5KtP47zZHAwIEOLNo2SWUEMb8izbw-aoPMo5VaQrkfHwPEQR-A_1Ndy0swiCQkRPIUc3N5YrjPIPddJbD0uuvB9ahtxvje-xF2ONHK4BV8UxSW4KsdBelaJeRTLEi6OmnEK9n9LxWCfulEB20fM8BR8uo6J-I1HfMdGt94a5FStVqF_XoAkXTpu7BHr_u_tNTaFPaAzGv-YMiazbNylkbOsNOUtl1x9J8dy3t1wyH3YuvujxkpFJyq3Boq/https%3A%2F%2Fkjobson-neuro.github.io%2F>
> Ph.D. Student | Cognitive Neuroscience Lab
> <https://secure-web.cisco.com/1uRVKqr-OerGkjpg37lgmTfI8G88BkyD_v1y97KKQvh5AZ4-HIw6jDi1X-egyGybN70R_3IK7JfG6NBpr7vyUJs6WmRkCn0xt_y_-KnhH46kTj-7Xn600oPlnbidSm5PAMKsicH6XpINAZ0uytQwlGJO10m-1Wubg_6xkcOK3296_lntwqYHR_qBE8jCt_VavyEQlx9OOKNnyIvRNXgfYS1GthgtdQ3D4XNDSGtEHB-GO7JnX5Megar67weLsVe37-oqGC5wOwyl6Uq7To5l5z51YzmCl9D-NB0kzfykkgB-RTA_RD5aGb3uH5vCO16LW/https%3A%2F%2Fsites.temple.edu%2Fcnltu%2F>
> Department of Psychology and Neuroscience | Temple University
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Kumar, Avnish <
> avnish.ku...@mgh.harvard.edu>
> *Sent:* Thursday, December 8, 2022 10:19 AM
> *To:* Freesurfer support list 
> *Subject:* [External] Re: [Freesurfer] 7.3.2-patch issues - thalamic
> segmentation
>
> Hi Katie,
>
> Thank you for pointing this out! Yes, please make changes to the core.py
> script in your '$FREESURFER/python/packages/freesurfer/subregions/'
> folder. I will update the patch instructions to reflect this as well.
>
> Best,
> Avnish
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
&

Re: [Freesurfer] [External] Re: 7.3.2-patch issues - thalamic segmentation

2023-02-22 Thread Kumar, Avnish 
Hi Katie,

The core.py file has been updated now. Please try downloading it again and 
applying the same 
fix<https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.2-patch/segment_subregions/>
 as before.

Best,
Avnish

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Katie Rose Jobson 

Sent: Monday, February 6, 2023 3:17 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] [External] Re: 7.3.2-patch issues - thalamic 
segmentation


External Email - Use Caution

Hi FS experts,

Apologies for my late follow up.

In reference to the previous conversation, I added the core.py file to the 
correct subdirectory to complete the thalamic nuclei segmentation. I received 
an error still, albeit a different error:


Traceback (most recent call last):

  File "/usr/local/freesurfer-7.3.2/python/scripts/segment_subregions", line 6, 
in 

from freesurfer import subregions

  File 
"/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/__init__.py",
 line 1, in 

from freesurfer.subregions.process import structure_names

  File 
"/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/process.py", 
line 8, in 

from freesurfer.subregions.thalamus import ThalamicNuclei

  File 
"/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/thalamus.py",
 line 9, in 

from freesurfer.subregions.core import MeshModel

  File 
"/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/core.py", 
line 9, in 

from gems.subregions import utils

ImportError: cannot import name 'utils' from 'gems.subregions' (unknown 
location)

I am assuming this is because the core.py script was previously housed in the 
'/gems/subregions' subdirectory, and is attempting to import 'utils' from 
there. Is there any way to edit this file (core.py) to call on this 'utils' 
function?

Please let me know if I can clarify my question in any way and thank you in 
advance for your help!

Best Wishes,
Katie
--
Katie Jobson, M.S. | Personal 
Website<https://secure-web.cisco.com/1ho9yNMxPXcFe1keXWE6wU20yOWqSzwoLYY9yARkmRCu9A8_XhOXs1813M6_RxM-r3s-D_p5KtP47zZHAwIEOLNo2SWUEMb8izbw-aoPMo5VaQrkfHwPEQR-A_1Ndy0swiCQkRPIUc3N5YrjPIPddJbD0uuvB9ahtxvje-xF2ONHK4BV8UxSW4KsdBelaJeRTLEi6OmnEK9n9LxWCfulEB20fM8BR8uo6J-I1HfMdGt94a5FStVqF_XoAkXTpu7BHr_u_tNTaFPaAzGv-YMiazbNylkbOsNOUtl1x9J8dy3t1wyH3YuvujxkpFJyq3Boq/https%3A%2F%2Fkjobson-neuro.github.io%2F>
Ph.D. Student | Cognitive Neuroscience 
Lab<https://secure-web.cisco.com/1uRVKqr-OerGkjpg37lgmTfI8G88BkyD_v1y97KKQvh5AZ4-HIw6jDi1X-egyGybN70R_3IK7JfG6NBpr7vyUJs6WmRkCn0xt_y_-KnhH46kTj-7Xn600oPlnbidSm5PAMKsicH6XpINAZ0uytQwlGJO10m-1Wubg_6xkcOK3296_lntwqYHR_qBE8jCt_VavyEQlx9OOKNnyIvRNXgfYS1GthgtdQ3D4XNDSGtEHB-GO7JnX5Megar67weLsVe37-oqGC5wOwyl6Uq7To5l5z51YzmCl9D-NB0kzfykkgB-RTA_RD5aGb3uH5vCO16LW/https%3A%2F%2Fsites.temple.edu%2Fcnltu%2F>
Department of Psychology and Neuroscience | Temple University


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Kumar, Avnish 

Sent: Thursday, December 8, 2022 10:19 AM
To: Freesurfer support list 
Subject: [External] Re: [Freesurfer] 7.3.2-patch issues - thalamic segmentation

Hi Katie,

Thank you for pointing this out! Yes, please make changes to the core.py script 
in your '$FREESURFER/python/packages/freesurfer/subregions/' folder. I will 
update the patch instructions to reflect this as well.

Best,
Avnish

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Katie Rose Jobson 

Sent: Wednesday, December 7, 2022 3:35 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] 7.3.2-patch issues - thalamic segmentation


External Email - Use Caution

Hi FS experts,

I am attempting to implement the patch on version 7.3.2 for issues with 
thalamic segmentation. I followed the instructions found here: MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.2-patch/readme.txt<https://secure-web.cisco.com/1t1MSwicSbVaKTZz26QQcqNH4nacgccE3ISyro01uNnj95812z_YeG8e-DFrygCnFv6ktzMUExhmiUbDqFCf0KpNXHr5RRUcxC1AVcCaSsWWiaxtTasb5Nv7Ri_-7l4aFJc-3z8v4jMcuMuarQHkVMdfQFpDlwx_JPNCkzIF5bYbOAbLpgF5bFi1S7RGHvbfQJzCvT-GHwedW82ZkC0XRXlRJuOk5tvcxrjxhnlP_J0o1XiFpmUB27GQrmlDo4RruZFSRCORXtarTTjw4Ev2G9p7K_-aX2-nkBsHZuSRRYBIEgbqijea_xNPhBMogTCeJ/https%3A%2F%2Fnam10.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1JULaWPox6hiL5oNotdoE4us3D1hhs0HqpeHRUYFRvLuHPjNtpIrfTSk2Oor44j2FBUk_pFk20EpHFiM3R1FVkDnc65JJPCI2jaG74UkvfjSzqwjWygwvquVzF3AUampB5BRXbiKSY7Eq72Qbr3mY5H5t3RtHvfghMkNSXw1ggCZ3hzozbWLX2XVfU6Y5rB9JzogJtWSki-SikTk1LjM-Zp5AqdAc4RDMLOPK5MST93Dqz207lgJp4Isj6YZIOqM1Fms1_LkZdkfuWRZVT-8jSSycyBTF13XHfqQC3TqOL541UgCoyh-f4b9wH1

Re: [Freesurfer] [External] Re: 7.3.2-patch issues - thalamic segmentation

2023-02-06 Thread Katie Rose Jobson 
External Email - Use Caution

Hi FS experts,

Apologies for my late follow up.

In reference to the previous conversation, I added the core.py file to the 
correct subdirectory to complete the thalamic nuclei segmentation. I received 
an error still, albeit a different error:


Traceback (most recent call last):

  File "/usr/local/freesurfer-7.3.2/python/scripts/segment_subregions", line 6, 
in 

from freesurfer import subregions

  File 
"/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/__init__.py",
 line 1, in 

from freesurfer.subregions.process import structure_names

  File 
"/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/process.py", 
line 8, in 

from freesurfer.subregions.thalamus import ThalamicNuclei

  File 
"/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/thalamus.py",
 line 9, in 

from freesurfer.subregions.core import MeshModel

  File 
"/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/core.py", 
line 9, in 

from gems.subregions import utils

ImportError: cannot import name 'utils' from 'gems.subregions' (unknown 
location)

I am assuming this is because the core.py script was previously housed in the 
'/gems/subregions' subdirectory, and is attempting to import 'utils' from 
there. Is there any way to edit this file (core.py) to call on this 'utils' 
function?

Please let me know if I can clarify my question in any way and thank you in 
advance for your help!

Best Wishes,
Katie
--
Katie Jobson, M.S. | Personal 
Website
Ph.D. Student | Cognitive Neuroscience 
Lab
Department of Psychology and Neuroscience | Temple University


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Kumar, Avnish 

Sent: Thursday, December 8, 2022 10:19 AM
To: Freesurfer support list 
Subject: [External] Re: [Freesurfer] 7.3.2-patch issues - thalamic segmentation

Hi Katie,

Thank you for pointing this out! Yes, please make changes to the core.py script 
in your '$FREESURFER/python/packages/freesurfer/subregions/' folder. I will 
update the patch instructions to reflect this as well.

Best,
Avnish

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Katie Rose Jobson 

Sent: Wednesday, December 7, 2022 3:35 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] 7.3.2-patch issues - thalamic segmentation


External Email - Use Caution

Hi FS experts,

I am attempting to implement the patch on version 7.3.2 for issues with 
thalamic segmentation. I followed the instructions found here: MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1ybbkYd44XfCbWYGDHnTnGesawx-z2R5rxCzSMgW9lGZ60Fb_tMxVfba4lp50-fTv1FbGBwZ3q2oFEY2eUJzdaJJQWfhhyfBI_a4f9KMk_dA1f8sKfq04FxCQskibmq0q8hKvnoOehKhSfW3gekr4Yw2vEAR4LKjvBXSbnifygwslP99gu-Cc0QK3G68SmZsT8t8lcrQh5yu6-QkgZVmRxeHIcDwkFB-IF5iKBYwqd_0v7ljLi5MwyALPYc2bNUlL5Ve5TyF191T2Tppx9XD66crq8DJ3mtBgqTPHOTX0NA9U6CsZw822drfsMN0KUxtN/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.3.2-patch%2Freadme.txt