search

james-cole / brainageR

Software for generating a brain-predicted age value, using Gaussian Processes regression, implemented in R
GNU Lesser General Public License v3.0
74 stars 26 forks source link

Fatal error with slicesdir.braingeR #12

Open DustyGrooms opened 8 months ago

DustyGrooms commented 8 months ago

Hello,

Thank you for making an exceptional program and addition to the scientific literature on brain health! I have used brainageR before with no problem but we upgraded to a new MAC and new Matlab ect. and I have it working (it generates a brain age estimate), but right before it finishes I get this error below and I am not sure how to resolve it... or what the issue is? Could it be something with our T1s? Or my guess is something not 100% set up on the new machine MAC OS? Any thoughts much appreciated!

/Users/lab/Desktop/BrainAge_TestData//c1MPRAGE

Fatal error: cannot open file: - Function: (main)

/Users/lab/Desktop/brainageR//software/slicesdir.brainageR: line 149: [: -lt: unary operator expected

james-cole commented 8 months ago

Hi Dusty,

Thanks for your email and your interest in brainageR.

Sorry that you’re having issues. From the error, I doubt this is related to your data. It seems much more likely that it’s to do with your new Mac OS.

The error is related to the customised version of slicesdir. Can I suggest you comment out line #83 from the main brainageR script and see if it works? Slicesdir is mainly for QC, so should give you output of brain-age values without this line. You can also run brainageR in debug mode, so that the segmented niftis don’t get deleted, then do QC on them.

Let me know if that resolves your issue or not, and we can take it from there.

Best wishes, James

From: DustyGrooms @.> Date: Wednesday, 31 January 2024 at 3:05 pm To: james-cole/brainageR @.> Cc: Subscribed @.***> Subject: [james-cole/brainageR] Fatal error with slicesdir.braingeR (Issue #12)

⚠ Caution: External sender

Hello,

Thank you for making an exceptional program and addition to the scientific literature on brain health! I have used brainageR before with no problem but we upgraded to a new MAC and new Matlab ect. and I have it working (it generates a brain age estimate), but right before it finishes I get this error below and I am not sure how to resolve it... or what the issue is? Could it be something with our T1s? Or my guess is something not 100% set up on the new machine MAC OS? Any thoughts much appreciated!

/Users/lab/Desktop/BrainAge_TestData//c1MPRAGE

Fatal error: cannot open file: - Function: (main)

/Users/lab/Desktop/brainageR//software/slicesdir.brainageR: line 149: [: -lt: unary operator expected

— Reply to this email directly, view it on GitHubhttps://github.com/james-cole/brainageR/issues/12, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACCUV6HQ4RGDZ2FTBMQRKNLYRJMRZAVCNFSM6AAAAABCTHDQDGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGEYTAMZQHA2TSMI. You are receiving this because you are subscribed to this thread.Message ID: @.***>

DustyGrooms commented 8 months ago

Hi James,

Thanks for getting back to me so quickly! It is great how much you support your software!

You are correct, commenting that line out works (generates brainage estimate csv file, but no QC files). I think we will run it in debug mode with the line in though and just have the error so we can double check the data.

I can't imagine how much of a headache it is to keep the software operational with the pace of operating system and dependent program updates you have to deal with!

Dusty

On Thu, Feb 1, 2024 at 5:03 AM James Cole @.***> wrote:

Hi Dusty,

Thanks for your email and your interest in brainageR.

Sorry that you’re having issues. From the error, I doubt this is related to your data. It seems much more likely that it’s to do with your new Mac OS.

The error is related to the customised version of slicesdir. Can I suggest you comment out line #83 from the main brainageR script and see if it works? Slicesdir is mainly for QC, so should give you output of brain-age values without this line. You can also run brainageR in debug mode, so that the segmented niftis don’t get deleted, then do QC on them.

Let me know if that resolves your issue or not, and we can take it from there.

Best wishes, James

From: DustyGrooms @.> Date: Wednesday, 31 January 2024 at 3:05 pm To: james-cole/brainageR @.> Cc: Subscribed @.***> Subject: [james-cole/brainageR] Fatal error with slicesdir.braingeR (Issue

12)

⚠ Caution: External sender

Hello,

Thank you for making an exceptional program and addition to the scientific literature on brain health! I have used brainageR before with no problem but we upgraded to a new MAC and new Matlab ect. and I have it working (it generates a brain age estimate), but right before it finishes I get this error below and I am not sure how to resolve it... or what the issue is? Could it be something with our T1s? Or my guess is something not 100% set up on the new machine MAC OS? Any thoughts much appreciated!

/Users/lab/Desktop/BrainAge_TestData//c1MPRAGE

Fatal error: cannot open file: - Function: (main)

/Users/lab/Desktop/brainageR//software/slicesdir.brainageR: line 149: [: -lt: unary operator expected

— Reply to this email directly, view it on GitHub< https://github.com/james-cole/brainageR/issues/12>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/ACCUV6HQ4RGDZ2FTBMQRKNLYRJMRZAVCNFSM6AAAAABCTHDQDGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGEYTAMZQHA2TSMI>.

You are receiving this because you are subscribed to this thread.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/james-cole/brainageR/issues/12#issuecomment-1920952563, or unsubscribe https://github.com/notifications/unsubscribe-auth/BFXYN26HJ623EJ66PIHANO3YRNR5TAVCNFSM6AAAAABCTHDQDGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMRQHE2TENJWGM . You are receiving this because you authored the thread.Message ID: @.***>

james-cole commented 8 months ago

Hi Dusty,

Glad that helped. If you run debug mode and have the nifti files, you can of course run the original FSL slicesdir on those images, and you’ll have the QC files anyway. Or you can QC them using fsleyes or any other nifti viewer.

Best wishes, James

From: DustyGrooms @.> Date: Saturday, 3 February 2024 at 11:42 am To: james-cole/brainageR @.> Cc: Cole, James @.>, Comment @.> Subject: Re: [james-cole/brainageR] Fatal error with slicesdir.braingeR (Issue #12) Hi James,

Thanks for getting back to me so quickly! It is great how much you support your software!

You are correct, commenting that line out works (generates brainage estimate csv file, but no QC files). I think we will run it in debug mode with the line in though and just have the error so we can double check the data.

I can't imagine how much of a headache it is to keep the software operational with the pace of operating system and dependent program updates you have to deal with!

Dusty

On Thu, Feb 1, 2024 at 5:03 AM James Cole @.***> wrote:

Hi Dusty,

Thanks for your email and your interest in brainageR.

Sorry that you’re having issues. From the error, I doubt this is related to your data. It seems much more likely that it’s to do with your new Mac OS.

The error is related to the customised version of slicesdir. Can I suggest you comment out line #83 from the main brainageR script and see if it works? Slicesdir is mainly for QC, so should give you output of brain-age values without this line. You can also run brainageR in debug mode, so that the segmented niftis don’t get deleted, then do QC on them.

Let me know if that resolves your issue or not, and we can take it from there.

Best wishes, James

From: DustyGrooms @.> Date: Wednesday, 31 January 2024 at 3:05 pm To: james-cole/brainageR @.> Cc: Subscribed @.***> Subject: [james-cole/brainageR] Fatal error with slicesdir.braingeR (Issue

12)

⚠ Caution: External sender

Hello,

Thank you for making an exceptional program and addition to the scientific literature on brain health! I have used brainageR before with no problem but we upgraded to a new MAC and new Matlab ect. and I have it working (it generates a brain age estimate), but right before it finishes I get this error below and I am not sure how to resolve it... or what the issue is? Could it be something with our T1s? Or my guess is something not 100% set up on the new machine MAC OS? Any thoughts much appreciated!

/Users/lab/Desktop/BrainAge_TestData//c1MPRAGE

Fatal error: cannot open file: - Function: (main)

/Users/lab/Desktop/brainageR//software/slicesdir.brainageR: line 149: [: -lt: unary operator expected

— Reply to this email directly, view it on GitHub< https://github.com/james-cole/brainageR/issues/12>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/ACCUV6HQ4RGDZ2FTBMQRKNLYRJMRZAVCNFSM6AAAAABCTHDQDGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGEYTAMZQHA2TSMI>.

You are receiving this because you are subscribed to this thread.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/james-cole/brainageR/issues/12#issuecomment-1920952563, or unsubscribe https://github.com/notifications/unsubscribe-auth/BFXYN26HJ623EJ66PIHANO3YRNR5TAVCNFSM6AAAAABCTHDQDGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMRQHE2TENJWGM . You are receiving this because you authored the thread.Message ID: @.***>

— Reply to this email directly, view it on GitHubhttps://github.com/james-cole/brainageR/issues/12#issuecomment-1925295142, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACCUV6AYVZ4YUCBIDFNRUXTYRYPCLAVCNFSM6AAAAABCTHDQDGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMRVGI4TKMJUGI. You are receiving this because you commented.Message ID: @.***>