Yash refactor #254

ythackerCS · 2023-03-20T21:02:10Z

Finished refactoring PreFresurfer ready for others to test I did do one run seems to get through without variable errors

glasserm · 2023-03-20T21:14:07Z

Let's not change the setup script or the Batch script.

ythackerCS · 2023-03-20T21:16:51Z

Alright should I just replace them with the standard scripts that come with the pipeline? Thank you, Yash Thacker

…

________________________________ From: glasserm ***@***.***> Sent: Monday, March 20, 2023 4:14:32 PM To: Washington-University/HCPpipelines ***@***.***> Cc: Thacker, Yash ***@***.***>; Author ***@***.***> Subject: Re: [Washington-University/HCPpipelines] Yash refactor (PR #254) * External Email - Caution * Let's not change the setup script. — Reply to this email directly, view it on GitHub<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FWashington-University%2FHCPpipelines%2Fpull%2F254%23issuecomment-1476943735&data=05%7C01%7Cythacker%40wustl.edu%7C531488fe580d47f0892e08db29881a64%7C4ccca3b571cd4e6d974b4d9beb96c6d6%7C0%7C0%7C638149436804628272%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=%2B7FWOljmV0TmNYhPDxEpyNO%2BedDRMW%2BkiOK%2FN8kAZCs%3D&reserved=0>, or unsubscribe<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FALEHJY7I7XXKYEDUGBMOF6DW5DCDRANCNFSM6AAAAAAWBTQHFA&data=05%7C01%7Cythacker%40wustl.edu%7C531488fe580d47f0892e08db29881a64%7C4ccca3b571cd4e6d974b4d9beb96c6d6%7C0%7C0%7C638149436804628272%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=9QJ8hsMgbB0Q%2BF%2BGGwmrQwpNFAztJaeksV579iEa%2FsM%3D&reserved=0>. You are receiving this because you authored the thread.Message ID: ***@***.***>

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glasserm · 2023-03-20T21:21:28Z

I wouldn't have committed those two files to this pull request. I don't know the best way to back that out, perhaps Tim can help.

glasserm · 2023-03-20T21:28:35Z

Can you make a side by side comparison of the usage statements when you run the script without arguments/trigger the usage?

coalsont · 2023-03-20T22:26:13Z

I have removed the changes to other files. Please check that the changes to the pipeline are all of the changes you intended to commit.

ythackerCS · 2023-03-21T20:56:48Z

PreFreeSurfer_new.txt
PreFreeSurfer_old.txt
Here are the help's of the two scripts old and new.

glasserm · 2023-03-21T21:02:19Z

Thanks. I noticed a new parameter at the end for the new script (perhaps the last line of the old was just omitted) and also there are some places were there are too many spaces in the sentences, e.g.: "for hcp-style" has two spaces instead of one.

coalsont · 2023-03-21T22:12:25Z

I believe the old script accepted --usejacobian, but didn't list it in the help info:

HCPpipelines/PreFreeSurfer/PreFreeSurferPipeline.sh

Line 358 in 655e69b

UseJacobian=`opts_GetOpt1 "--usejacobian" $@`

HCPpipelines/PreFreeSurfer/PreFreeSurferPipeline.sh

Line 272 in 655e69b

glasserm · 2023-03-21T22:15:30Z

I see. Perhaps @demsarjure or @sivcek have some ideas on acceptance testing in their environment we could do to thoroughly test all the options?

coalsont · 2023-03-21T22:20:02Z

global/scripts/debug.shlib

-{    
-    if [ ! $HCP_DEBUG_USETRAP == 'OFF' ]; then        
+{
+    if [[ "$HCP_DEBUG_USETRAP" == "ON" ]]; then


FYI, these edits are from the branch I told him to use. This PR probably shouldn't go into master, but into the debug-function-enable branch. Once all of the pipelines have gone through testing, we can rebase that branch onto master.

I do think we want to do this expeditiously, as Misha needs to use the updated structural pipelines for longitudinal pipeline development.

Will Misha need all 3 structural pipelines converted before starting? If so, we should still do them into the debug-function-enable branch, test them with that change, and then I can rearrange the commits so the new versions are on master, debug-function-enable is based on that, and the rest of the PRs can continue the same way.

Even if he needs each one as soon as they are available, I can do that kind of rearrangement 3 times without much trouble, so that we don't have to test them twice (without, and then with) the debug.shlib changes.

I think it would be best if he had all three pipelines converted before doing any development on them. There is also the longitudinal pipeline. Perhaps I can convince Jure to convert that one too.

coalsont · 2023-03-21T22:51:27Z

The extra spaces look like they came from where the old help info had newlines. There is a style choice here, do we convert it into sentences by adding a period, or do we put in newlines, making it longer but with less line wrapping towards the start of each sentence? Looks like I kept the newlines when I converted hcp_fix_multi_run, but I don't care that much.

glasserm · 2023-03-22T00:03:33Z

I would rather we didn't have double spaces in the middle of sentences. I think letting your code do the wrapping is fine.

demsarjure · 2023-03-22T08:00:07Z

I see. Perhaps @demsarjure or @sivcek have some ideas on acceptance testing in their environment we could do to thoroughly test all the options?

I can build a develop QuNex container and acceptance test the refactored FS on our end. This acceptance test runs HCP MPP over 7 different datasets (3 HCP and 4 internal, from Siemens, GE and Phillips scanners).

glasserm · 2023-03-22T10:23:46Z

Would that test your legacy options thoroughly? Both SE and standard fieldmaps?

demsarjure · 2023-03-22T11:17:26Z

One of the datasets is legacy style, it has SE pairs though, but is not multi-band.

If there is something else/bespoke to test, we can discuss it.

glasserm · 2023-03-22T11:20:57Z

Well for now this is just HCP Structural Preprocessing and PreFreeSurfer. It would be good to test a dataset with standard field maps, another with SE fieldmaps, and any legacy options you guys find important.

demsarjure · 2023-03-22T11:24:46Z

OK, just to be clear the idea is to test PreFreeSurfer on the Yash_Refactor branch. We should test it on the standard data, SE fieldmaps and other possible legacy options.

What is the timeline here? If we do this by the end of next week, would this work?

glasserm · 2023-03-22T11:26:49Z

Yes, that's fine.

glasserm · 2023-04-11T02:01:36Z

@demsarjure were you able to do these tests?

demsarjure · 2023-04-11T06:09:24Z

@glasserm

Sorry, for not getting back to you sooner!

The command is not backwards compatible, what QuNex generates right now is missing a number of mandatory parameters. So it seems like many parameters that previously had defaults set in your scripts are now mandatory. See below for details. Please advise about how to proceed. The agreement we have is that we set only mandatory parameters QuNex side, while optional ones can be set through QuNex but use HCP defaults if not set.

/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/PreFreeSurfer/PreFreeSurferPipeline.sh --path="/gpfs/gibbs/pi/n3/Studies/QuNexAcceptTest/Results/jd2528/qunex_container/QuNex_acceptance_CNP_BIDS_20230310_030316/sessions/10159/hcp" --subject="10159" --t1="/gpfs/gibbs/pi/n3/Studies/QuNexAcceptTest/Results/jd2528/qunex_container/QuNex_acceptance_CNP_BIDS_20230310_030316/sessions/10159/hcp/10159/unprocessed/T1w/10159_T1w_MPR1.nii.gz" --t2="NONE" --t1template="/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm.nii.gz" --t1templatebrain="/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm_brain.nii.gz" --t1template2mm="/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/global/templates/MNI152_T1_2mm.nii.gz" --t2template="/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/global/templates/MNI152_T2_0.7mm.nii.gz" --t2templatebrain="/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/global/templates/MNI152_T2_0.7mm_brain.nii.gz" --t2template2mm="/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/global/templates/MNI152_T2_2mm.nii.gz" --templatemask="/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm_brain_mask.nii.gz" --template2mmmask="/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz" --brainsize="150" --fnirtconfig="/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/global/config/T1_2_MNI152_2mm.cnf" --seechospacing="NONE" --seunwarpdir="NONE" --t1samplespacing="NONE" --t2samplespacing="NONE" --unwarpdir="NONE" --gdcoeffs="NONE" --avgrdcmethod="NONE" --processing-mode="LegacyStyleData"

Test file: 
/gpfs/gibbs/pi/n3/Studies/QuNexAcceptTest/Results/jd2528/qunex_container/QuNex_acceptance_CNP_BIDS_20230310_030316/sessions/10159/hcp/10159/MNINonLinear/T1w_restore_brain.nii.gz
------------------------------------------------------------

Tue Apr 11 02:06:19 EDT 2023:PreFreeSurferPipeline.sh: While running '/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/PreFreeSurfer/PreFreeSurferPipeline.sh --path=/gpfs/gibbs/pi/n3/Studies/QuNexAcceptTest/Results/jd2528/qunex_container/QuNex_acceptance_CNP_BIDS_20230310_030316/sessions/10159/hcp --subject=10159 --t1=/gpfs/gibbs/pi/n3/Studies/QuNexAcceptTest/Results/jd2528/qunex_container/QuNex_acceptance_CNP_BIDS_20230310_030316/sessions/10159/hcp/10159/unprocessed/T1w/10159_T1w_MPR1.nii.gz --t2=NONE --t1template=/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm.nii.gz --t1templatebrain=/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm_brain.nii.gz --t1template2mm=/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/global/templates/MNI152_T1_2mm.nii.gz --t2template=/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/global/templates/MNI152_T2_0.7mm.nii.gz --t2templatebrain=/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/global/templates/MNI152_T2_0.7mm_brain.nii.gz --t2template2mm=/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/global/templates/MNI152_T2_2mm.nii.gz --templatemask=/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm_brain_mask.nii.gz --template2mmmask=/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz --brainsize=150 --fnirtconfig=/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/global/config/T1_2_MNI152_2mm.cnf --seechospacing=NONE --seunwarpdir=NONE --t1samplespacing=NONE --t2samplespacing=NONE --unwarpdir=NONE --gdcoeffs=NONE --avgrdcmethod=NONE --processing-mode=LegacyStyleData':
Tue Apr 11 02:06:19 EDT 2023:PreFreeSurferPipeline.sh: While running '/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/PreFreeSurfer/PreFreeSurferPipeline.sh --path=/gpfs/gibbs/pi/n3/Studies/QuNexAcceptTest/Results/jd2528/qunex_container/QuNex_acceptance_CNP_BIDS_20230310_030316/sessions/10159/hcp --subject=10159 --t1=/gpfs/gibbs/pi/n3/Studies/QuNexAcceptTest/Results/jd2528/qunex_container/QuNex_acceptance_CNP_BIDS_20230310_030316/sessions/10159/hcp/10159/unprocessed/T1w/10159_T1w_MPR1.nii.gz --t2=NONE --t1template=/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm.nii.gz --t1templatebrain=/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm_brain.nii.gz --t1template2mm=/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/global/templates/MNI152_T1_2mm.nii.gz --t2template=/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/global/templates/MNI152_T2_0.7mm.nii.gz --t2templatebrain=/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/global/templates/MNI152_T2_0.7mm_brain.nii.gz --t2template2mm=/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/global/templates/MNI152_T2_2mm.nii.gz --templatemask=/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm_brain_mask.nii.gz --template2mmmask=/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz --brainsize=150 --fnirtconfig=/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/global/config/T1_2_MNI152_2mm.cnf --seechospacing=NONE --seunwarpdir=NONE --t1samplespacing=NONE --t2samplespacing=NONE --unwarpdir=NONE --gdcoeffs=NONE --avgrdcmethod=NONE --processing-mode=LegacyStyleData':
Tue Apr 11 02:06:19 EDT 2023:PreFreeSurferPipeline.sh: ERROR: missing the following mandatory parameter(s): --fmapmag --fmapphase --fmapgeneralelectric --echodiff --SEPhaseNeg --SEPhasePos --topupconfig
Tue Apr 11 02:06:19 EDT 2023:PreFreeSurferPipeline.sh: ERROR: missing the following mandatory parameter(s): --fmapmag --fmapphase --fmapgeneralelectric --echodiff --SEPhaseNeg --SEPhasePos --topupconfig
Tue Apr 11 02:06:19 EDT 2023:PreFreeSurferPipeline.sh: ABORTING

glasserm · 2023-04-11T10:49:52Z

@ythackerCS @coalsont can you look at this? The goal here was not to change the requirements of the command, but just to simplify the I/O interface code.

demsarjure · 2023-04-11T10:58:52Z

Several parameters above should not be mandatory as they are connected with acquisition devices and protocols (e.g., fmapgeneralelectric, fmapphase, SEPhaseNeg). I think the issue might be just that some parameters were erroneously labeled as mandatory instead of as optional.

ythackerCS · 2023-04-11T16:48:36Z

Yes I can go ahead and make those not mandatory! Sorry about that some of them aren’t as clear to me if they are mandatory or not. Thank you, Yash Thacker

…

________________________________ From: Jure Demsar ***@***.***> Sent: Tuesday, April 11, 2023 5:59:04 AM To: Washington-University/HCPpipelines ***@***.***> Cc: Thacker, Yash ***@***.***>; Mention ***@***.***> Subject: Re: [Washington-University/HCPpipelines] Yash refactor (PR #254) * External Email - Caution * Several parameters above should not be mandatory as they are connected with acquisition devices and protocols (e.g., fmapgeneralelectric, fmapphase, SEPhaseNeg). I think the issue might be just that some parameters were erroneously labeled as mandatory instead of as optional. — Reply to this email directly, view it on GitHub<#254 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ALEHJY5XNU3TNZLIO6XFYQDXAU2PRANCNFSM6AAAAAAWBTQHFA>. You are receiving this because you were mentioned.Message ID: ***@***.***>

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ythackerCS · 2023-04-12T03:41:02Z

Do we have a list of all vars that are non mandatory? That way I can make sure they are correct. Also Jure, Matt said you wanted to convert longitudinal Freesurfer, I built a command converter for it to make it a bit easier to do the conversion to use Tim’s input library. I have attached it above it is a notebook. In the first cell where there’s command = replace the content between the triple quotes (“””) with the old command run the cell and the next one and it should give you a refactored command that should be close to what you need for Tim’s library! Let me know if you have any questions. From: Thacker, Yash ***@***.***> Date: Tuesday, April 11, 2023 at 11:48 AM To: Washington-University/HCPpipelines ***@***.***>, Washington-University/HCPpipelines ***@***.***> Cc: Mention ***@***.***> Subject: Re: [Washington-University/HCPpipelines] Yash refactor (PR #254) Yes I can go ahead and make those not mandatory! Sorry about that some of them aren’t as clear to me if they are mandatory or not. Thank you, Yash Thacker

…

________________________________ From: Jure Demsar ***@***.***> Sent: Tuesday, April 11, 2023 5:59:04 AM To: Washington-University/HCPpipelines ***@***.***> Cc: Thacker, Yash ***@***.***>; Mention ***@***.***> Subject: Re: [Washington-University/HCPpipelines] Yash refactor (PR #254) * External Email - Caution * Several parameters above should not be mandatory as they are connected with acquisition devices and protocols (e.g., fmapgeneralelectric, fmapphase, SEPhaseNeg). I think the issue might be just that some parameters were erroneously labeled as mandatory instead of as optional. — Reply to this email directly, view it on GitHub<#254 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ALEHJY5XNU3TNZLIO6XFYQDXAU2PRANCNFSM6AAAAAAWBTQHFA>. You are receiving this because you were mentioned.Message ID: ***@***.***>

________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

demsarjure · 2023-04-12T05:12:33Z

Hi @ythackerCS ,

Yes, I am waiting for the FreeSurfer refactor as that one is more similar to Longitudinal FreeSurfer than this one and it will save me a bunch of work. But if there is a conversion script then I will use that. Where can I find this script, I am unable to find it in this correspondence.

Thanks, Jure

coalsont · 2023-04-12T20:22:02Z

In the old-style code, the mandatory/optional logic is sometimes implemented deep in the processing code, in this case the fieldmap stuff is passed as-is to the T2wToT1wDistortionCorrectAndReg.sh sub-script and it deals with whether the arguments are valid. The --avgrdcmethod option is probably the only fieldmap-related option that is mandatory.

For cases like this, maybe we could borrow QuNex's understanding of what is mandatory vs optional?

ythackerCS · 2023-04-12T20:28:55Z

Sounds good! Yea from what I have implemented it usually just looks for square brackets. And if option arguments are passed in if not it’s considered mandatory. Also, Jure it should be attached in the email I just set yesterday. Let me know if you still can’t find it, I can message it through slack. Thank you, Yash Thacker

…

________________________________ From: Tim Coalson ***@***.***> Sent: Wednesday, April 12, 2023 3:22:13 PM To: Washington-University/HCPpipelines ***@***.***> Cc: Thacker, Yash ***@***.***>; Mention ***@***.***> Subject: Re: [Washington-University/HCPpipelines] Yash refactor (PR #254) * External Email - Caution * In the old-style code, the mandatory/optional logic is sometimes implemented deep in the processing code, in this case the fieldmap stuff is passed as-is to the T2wToT1wDistortionCorrectAndReg.sh sub-script and it deals with whether the arguments are valid. The --avgrdcmethod option is probably the only fieldmap-related option that is mandatory. For cases like this, maybe we could borrow QuNex's understanding of what is mandatory vs optional? — Reply to this email directly, view it on GitHub<#254 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ALEHJYYKCB4BRSPWAC7AMA3XA4FHLANCNFSM6AAAAAAWBTQHFA>. You are receiving this because you were mentioned.Message ID: ***@***.***>

________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

coalsont · 2023-04-12T20:39:04Z

So, PreFS is also one of the oldest scripts, and may be less consistent than others about the help info.

I also notice that the way to tell it not to do distortion correction is currently "any string that isn't recognized", which is not good design (not typo-safe). I think we should use something like "NONE" here to mean no distortion correction (though this is different than how other scripts unfortunately use "NONE" to represent an empty list), and the *) case should be an error of "unrecognized distortion correction method". This also suggests validating the value of --avgrdcmethod much earlier in the script, before it calls any sub-scripts or does any other processing.

global/scripts/TopupPreprocessingAll.sh

DeDriftAndResample/MSMRemoveGroupDrift.sh

Supplemental/MakeAverageDataset/MakeAverageDataset.sh

…les.

coalsont force-pushed the Yash_Refactor branch from b791810 to f0fd0b3 Compare March 20, 2023 22:24

ythackerCS force-pushed the Yash_Refactor branch from f0fd0b3 to 2863dc2 Compare March 21, 2023 20:40

coalsont reviewed Mar 21, 2023

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coalsont and others added 21 commits November 21, 2023 22:45

add set -E to debug.shlib, cleanup and style

ff2dff1

Finsihed testing of prefreesurfer, with updates to pipeline scripts

c9c2d82

Finished testing of fMRIVolume along with pipeline scripts.

8b78137

Cleaned up prefreesurfer comments that were unnecessary.

3d28db5

Removed unecessary commented lines.

cf3cf99

Removed commented out opts parsing lines from fMIRVolume scripts

d7fc50d

Finished testing of FMRISurface

bf1e3e3

Postfix and ReapplyFix tested and run successfully.

6f22468

Fixed all comments from github and commiting non-pipeline specific fi…

5bdc932

…les.

Addressed additional comments by Tim and removed old code.

e979b4a

Addressed last few comments by Tim on msm and make avg.

274c93f

various cleanup and fixes, help info displays at least

f7ba047

Additional cleanup

2b8668b

more cleanup

cc33ada

restore definition of script_name for info function

c128776

replace ls with glob, quoting

cdfa0c7

remove stay opts_DefaultOpt

3f19971

stop matlab from expecting binary .mat format from melodic_mix

94cfc83

set another load() to ascii, for safety

f011bf8

Fixed an unbound variable issue in PostFix.

48c123a

Make even/odd checking use Pos_Neg_b0

84a6729

coalsont force-pushed the Yash_Refactor branch from 400e7f1 to 84a6729 Compare November 22, 2023 04:47

coalsont marked this pull request as ready for review December 13, 2023 00:48

coalsont merged commit 15a9b0e into master Dec 19, 2023

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Yash refactor #254

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Yash refactor #254

Yash refactor #254

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