Missing {subject}

[LZhangCWRU]

I am using Docker version halfpipe on my Mac (M1 chip) as below, and it shows warning message:

docker run --interactive --tty --volume /:/ext halfpipe/halfpipe
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested

Then: It shows missing {subject} as attached with BIDS format NO. My data file name as attached 2.

If I chose BIDS format Yes, it shows below under my sub01 folder:
Found 0 T1-weighted image files
Found 0 BOLD image files

Do you know the problem could be related my Mac with M1 chip or the halfpipe version?

Thanks

[HippocampusGirl]

Hi @LZhangCWRU,

• The warning message can be ignored I think.

• Could you try putting {subject} in place of the subject IDs? That means the path from the first screenshot

/Users/lzhang/Downloads/TestHC/sub01/sub01_T1.nii.gz

would become

/Users/lzhang/Downloads/TestHC/sub{subject}/sub{subject}_T1.nii.gz

This way, the program can extract the subject IDs from the filenames.

• I would also recommend creating a new folder for your working directory, because having the raw data and the outputs in the same directory can sometimes lead to problems down the line.

Hope this helps!

[LZhangCWRU]

Thanks HippocampusGirl
Now it has new error with "string index out of range" as attached, I also attach error file.

spec.json.txt

log.txt

Would you check what the problem could be?

Thanks

[LZhangCWRU]

Lea: Thanks for helping me with the missing subject problem. Now it has a new error with "string index out of range" as attached, I also attach an error file below. I ran halfpipe both on my Mac (using Docker) and our HPC with (singularity/3.8.1). Both show this string index error. I try to do the preprocessing step without the first-level feature. [image: error] <https://user-images.githubusercontent.com/125577571/237786056-56ee9e82-5b1a-45c0-b4bc-187d414cb37a.png> spec.json.txt <https://github.com/HALFpipe/HALFpipe/files/11455523/spec.json.txt> log.txt <https://github.com/HALFpipe/HALFpipe/files/11455524/log.txt> Would you check what the problem could be? Thanks Best

…

On Thu, May 11, 2023 at 12:04 PM Lea Waller ***@***.***> wrote: Hi @LZhangCWRU <https://github.com/LZhangCWRU>, - The warning message can be ignored I think. - Could you try putting {subject} in place of the subject IDs? That means the path from the first screenshot /Users/lzhang/Downloads/TestHC/sub01/sub01_T1.nii.gz would become /Users/lzhang/Downloads/TestHC/sub{subject}/sub{subject}_T1.nii.gz This way, the program can extract the subject IDs from the filenames. - I would also recommend creating a new folder for your working directory, because having the raw data and the outputs in the same directory can sometimes lead to problems down the line. Hope this helps! — Reply to this email directly, view it on GitHub <#548 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A56CSY5DPKDLZ3E5TVKQUDLXFUEXZANCNFSM6AAAAAAX6KCGEU> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[HippocampusGirl]

Hi @LZhangCWRU,
I'm out of the office this week but will have a look next week!

Best,
Lea