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Welcome to the ASHS Users' Group.

ASHS is open-source software for segmentation of hippocampal subfields in MRI scans. Please visit the new ASHS website for information about the software!

Paul

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gran...@uci.edu

2/7/23

Unable to Download Securely

Hi ASHS group, I am having some trouble downloading the necessary .tar files. I am getting an error

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Unable to Download Securely

Hi ASHS group, I am having some trouble downloading the necessary .tar files. I am getting an error

2/7/23

Pau Packard Blasco, … joue.ni...@gmail.com5

2/5/23

Trying to run the script --> line 189: ASHS_WORK: parameter null or not set

I figured out the source of the message/my error -- my script basically wasn't calling ashs_main.

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Trying to run the script --> line 189: ASHS_WORK: parameter null or not set

I figured out the source of the message/my error -- my script basically wasn't calling ashs_main.

2/5/23

Catherine Tallman, Paul Yushkevich2

1/23/23

Issue with registration within ASHS

hi Catherine, Eyeballing the screenshot you sent, I don't see any major registration issues

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Issue with registration within ASHS

hi Catherine, Eyeballing the screenshot you sent, I don't see any major registration issues

1/23/23

11/8/22

Odd segmentations

Hello all, I ran a batch of hippocampal segmentations recently and most turned out fine, but a few

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Odd segmentations

Hello all, I ran a batch of hippocampal segmentations recently and most turned out fine, but a few

11/8/22

pierreyv...@gmail.com2

11/3/22

qa subfolder: how to get the qc screenshots?

Dear users, I would like to ask this question again, in case one of you could help me. Many thanks in

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qa subfolder: how to get the qc screenshots?

Dear users, I would like to ask this question again, in case one of you could help me. Many thanks in

11/3/22

helena.g...@googlemail.com

8/24/22

Problems with the greedy command in ASHS

Dear ASHS users, lately I have been having problems running ASHS. The processing would stop either at

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Problems with the greedy command in ASHS

Dear ASHS users, lately I have been having problems running ASHS. The processing would stop either at

8/24/22

nimzod...@gmail.com

7/12/22

HS3 link on ASHS site leads to spam site

HS3 link on ASHS site leads to spam site https://sites.google.com/view/ashs-dox/resources/related-

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HS3 link on ASHS site leads to spam site

HS3 link on ASHS site leads to spam site https://sites.google.com/view/ashs-dox/resources/related-

7/12/22

3/4/22

Issue installing ashsfast atlases

Hello, I am trying to run ASHS on some 3T older adult data. I have installed ashs-fastashs_2.0.0

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Issue installing ashsfast atlases

Hello, I am trying to run ASHS on some 3T older adult data. I have installed ashs-fastashs_2.0.0

3/4/22

Francesco Pupillo

2/10/22

Validity check at end of stage 4 detected missing files.

Hi, I have been running into an issue while trying to run segmentation with ASHS. The error "

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Validity check at end of stage 4 detected missing files.

Hi, I have been running into an issue while trying to run segmentation with ASHS. The error "

2/10/22

joue.ni...@gmail.com

1/3/22

registration advice

Hi, I have high-res T2w structural slabs and T1w whole brain structural images to run ASHS with the

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registration advice

Hi, I have high-res T2w structural slabs and T1w whole brain structural images to run ASHS with the

1/3/22

Lorenz, G Joue (NIN)4

10/14/21

Registration problems when viewing segmentation results in MRIcron or SPM

Update: I found out that the solution which I previously posted above is flawed. Luckily, I found out

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Registration problems when viewing segmentation results in MRIcron or SPM

Update: I found out that the solution which I previously posted above is flawed. Luckily, I found out

10/14/21

Helena Gellersen, … lok.ki...@gmail.com3

10/12/21

Problems with data manifest file during atlas building

I was wondering what the solution here was. I'm running into exactly the same error, and I can

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Problems with data manifest file during atlas building

I was wondering what the solution here was. I'm running into exactly the same error, and I can

10/12/21

10/12/21

Cloud-based ASHS service restored

Dear ASHS users, If you tried running the ASHS distributed segmentation service in ITK-SNAP over the

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Cloud-based ASHS service restored

Dear ASHS users, If you tried running the ASHS distributed segmentation service in ITK-SNAP over the

10/12/21

Virag Anna Varga

9/15/21

No output in 'final' folder & error

Dear all, I'm trying to run fast-ashs (ashs-fastashs-20170223.zip) with GNU parallel on a

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No output in 'final' folder & error

Dear all, I'm trying to run fast-ashs (ashs-fastashs-20170223.zip) with GNU parallel on a

9/15/21

Virag Anna Varga

9/3/21

No files in 'final' folder

Hi everyone! I have just started to learn using ASHS. a have tried running the ashs with several

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No files in 'final' folder

Hi everyone! I have just started to learn using ASHS. a have tried running the ashs with several

9/3/21

8/6/21

Different dimensions T1 and ASHS output

Hi all, I'm trying to run ASHS-T1 on T1 scans- they're isotropic 1mm- and have an issue with

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Different dimensions T1 and ASHS output

Hi all, I'm trying to run ASHS-T1 on T1 scans- they're isotropic 1mm- and have an issue with

8/6/21

Catherine Tallman

7/29/21

c3d_affine_tool error

Hello, I am running ASHS locally and am receiving the following error: + c3d_affine_tool /mnt/

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c3d_affine_tool error

Hello, I am running ASHS locally and am receiving the following error: + c3d_affine_tool /mnt/

7/29/21

7/1/21

Cloud ASHS failing on partial T2 slab

Good Afternoon! I am learning ASHS. Eventually I want to run ASHS locally. I have been trying to use

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Cloud ASHS failing on partial T2 slab

Good Afternoon! I am learning ASHS. Eventually I want to run ASHS locally. I have been trying to use

7/1/21

Hwee Ling Lee, … Yi-En Quek13

6/2/21

Validity check at end of stage 1 detected missing files

Hi Long and Paul, I did suspect a compatibility issue. I tried running ASHS-T1 on a Linux machine and

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Validity check at end of stage 1 detected missing files

Hi Long and Paul, I did suspect a compatibility issue. I tried running ASHS-T1 on a Linux machine and

6/2/21

Marianna Pope, Paul Yushkevich2

6/1/21

ASHS Cortical Thickness scripts

Hi Marianna, I am copying Dr. Long Xie, who I believe has Docker containers that can be used for

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ASHS Cortical Thickness scripts

Hi Marianna, I am copying Dr. Long Xie, who I believe has Docker containers that can be used for

6/1/21

lo...@hrz.tu-chemnitz.de

3/19/21

ASHS for young adults with T1 scans?

Dear ASHS developers, I'm doing a secondary analysis of an fMRI study with young and old subjects

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ASHS for young adults with T1 scans?

Dear ASHS developers, I'm doing a secondary analysis of an fMRI study with young and old subjects

3/19/21

helena.g...@googlemail.com, Paul Yushkevich4

2/9/21

Using GNU or Slurm for atlas building

Hi Helena, It might be that the command bl needs more memory and is crashing because it is not

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Using GNU or Slurm for atlas building

Hi Helena, It might be that the command bl needs more memory and is crashing because it is not

2/9/21

helena.g...@googlemail.com

1/28/21

Issue with atlas building

Hi Paul, I am trying to run atlas building on a cluster that uses Slurm (without GNU) using the 2017

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Issue with atlas building

Hi Paul, I am trying to run atlas building on a cluster that uses Slurm (without GNU) using the 2017

1/28/21

1/12/21

ASHS preprocessing and config

Hi Paul and other ASHS users, I have a couple of generic ASHS usage questions that I can't find

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ASHS preprocessing and config

Hi Paul and other ASHS users, I have a couple of generic ASHS usage questions that I can't find

1/12/21

Coco Newton, Paul Yushkevich3

1/6/21

ASHS cloud issue

Thanks, all good now! On Wednesday, January 6, 2021 at 3:52:41 PM UTC PaulY wrote: Hi Coco, Please

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ASHS cloud issue

Thanks, all good now! On Wednesday, January 6, 2021 at 3:52:41 PM UTC PaulY wrote: Hi Coco, Please

1/6/21

James K. Park, Paul Yushkevich3

12/18/20

Errors using Penn Memory Center 3T ASHS Atlas for T1 weighted MRI

Dear Paul and Long, Thank you so much for your quick response! Any help would be greatly appreciated.

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Errors using Penn Memory Center 3T ASHS Atlas for T1 weighted MRI

Dear Paul and Long, Thank you so much for your quick response! Any help would be greatly appreciated.

12/18/20

svinci...@gmail.com

12/15/20

MTL segmentation nifti example?

Dear ASHS team, I am trying to create an ASHS atlas from 29 subjects using ashs_train.sh. I am

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MTL segmentation nifti example?

Dear ASHS team, I am trying to create an ASHS atlas from 29 subjects using ashs_train.sh. I am

12/15/20

Nicholas Christopher-Hayes

12/3/20

ICV Calculation

Hello, I've been processing subfield data through both FreeSurfer and ASHS. While I understand

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ICV Calculation

Hello, I've been processing subfield data through both FreeSurfer and ASHS. While I understand

12/3/20

Frederik Bergmann, Paul Yushkevich3

11/9/20

Thank you! I will give it a try once I have data. Good to know that it will probably work for the

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Thank you! I will give it a try once I have data. Good to know that it will probably work for the

11/9/20

9/22/20

the results of right hippocampus is worse than the left one

The atlas package is downloaded here: https://osf.io/hrv9n 在2020年9月22日星期二 UTC+8 下午7:45:48<debin

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the results of right hippocampus is worse than the left one

The atlas package is downloaded here: https://osf.io/hrv9n 在2020年9月22日星期二 UTC+8 下午7:45:48<debin

9/22/20

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