NODDI Analysis Issue with HCP Pipelines Example Data

[k5105880]

Dear Takuya Hayashi,

I attempted to analyze NODDI using the example data from HCP Pipelines, but I encountered an issue where ICVF was not calculated, and the process stopped midway.

I changed the AMICO parallel diffusivity value to 1.1E-3 mm²/s and set the RunMode in NoddiSurfaceMapping.sh to "1" (0: Matlab, 1: Python).

I am using HCP Pipelines version 5.0.0 (latest) and AMICO version 2.0.3 (latest).

Could you please advise me on how to address this issue?

Thank you for your assistance.

Best regards,
Toshiharu
NoddiSurfaceMapping_log.txt
NoddiSurfaceMapping.sh.txt

[takuya-hayashi]

Sorry about this. We have not used AMICO for a while, and the error is caused because the output names of AMICO are different from those expected in the code. Can you let me know what files are actually generated after running AMICO in the following folder? $AMICODATADIR/$protocol/$subjdir/AMICO/NODDI/ Cheers, Takuya 2025年1月6日(月) 17:49 Toshiharu Kamishikiryo ***@***.***>:

…

Dear Takuya Hayashi, I attempted to analyze NODDI using the example data from HCP Pipelines, but I encountered an issue where ICVF was not calculated, and the process stopped midway. I changed the AMICO parallel diffusivity value to 1.1E-3 mm²/s and set the RunMode in NoddiSurfaceMapping.sh to "1" (0: Matlab, 1: Python). I am using HCP Pipelines version 5.0.0 (latest) and AMICO version 2.0.3 (latest). Could you please advise me on how to address this issue? Thank you for your assistance. Best regards, Toshiharu NoddiSurfaceMapping_log.txt <https://github.com/user-attachments/files/18316895/NoddiSurfaceMapping_log.txt> NoddiSurfaceMapping.sh.txt <https://github.com/user-attachments/files/18316954/NoddiSurfaceMapping.sh.txt> — Reply to this email directly, view it on GitHub <#2>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AD57Y5SORHKCZ7VK7NHWUPD2JI7TPAVCNFSM6AAAAABUVFJIC6VHI2DSMVQWIX3LMV43ASLTON2WKOZSG43TAMJWGA3TKNY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[k5105880]

Dear Takuya Hayashi,

Thank you for your prompt response.
I have attached the output files from the following directory:
$AMICODATADIR/$protocol/$subjdir/AMICO/NODDI/

I was investigating the cause, and I wondered if it might be due to the different version of AMICO.
I found that starting from v2.0.0（https://github.com/daducci/AMICO/releases）,
there were changes to the NODDI map names:
from ICVF to NDI
from OD to ODI
from FISO to FWF
Could this be the reason?
Are the attached output files correctly computed?

Best regards,
Toshiharu

NODDI.zip

[takuya-hayashi]

Thanks Toshiharu, Here are suggested changes for you. Can you please give it a try? Line 255 From: if [ `imtest $AMICODATADIR/$protocol/$subjdir/AMICO/NODDI/FIT_ICVF` != 1 ] ; then To: if [ `imtest $AMICODATADIR/$protocol/$subjdir/AMICO/NODDI/fit_NDI` != 1 ] ; then Line 258 - 230 From: fslmaths $AMICODATADIR/$protocol/$subjdir/AMICO/NODDI/FIT_ICVF $DWIT1wFolder/noddi_ficvf fslmaths $AMICODATADIR/$protocol/$subjdir/AMICO/NODDI/FIT_ISOVF $DWIT1wFolder/noddi_fiso fslmaths $AMICODATADIR/$protocol/$subjdir/AMICO/NODDI/FIT_OD $DWIT1wFolder/noddi_odi To: fslmaths $AMICODATADIR/$protocol/$subjdir/AMICO/NODDI/fit_NDI $DWIT1wFolder/noddi_ficvf fslmaths $AMICODATADIR/$protocol/$subjdir/AMICO/NODDI/fit_FWF $DWIT1wFolder/noddi_fiso fslmaths $AMICODATADIR/$protocol/$subjdir/AMICO/NODDI/fit_ODI $DWIT1wFolder/noddi_odi Takuya 2025年1月6日(月) 20:08 Toshiharu Kamishikiryo ***@***.***>:

…

Dear Takuya Hayashi, Thank you for your prompt response. I have attached the output files from the following directory: $AMICODATADIR/$protocol/$subjdir/AMICO/NODDI/ I was investigating the cause, and I wondered if it might be due to the different version of AMICO. I found that starting from v2.0.0（ https://github.com/daducci/AMICO/releases）, there were changes to the NODDI map names: from ICVF to NDI from OD to ODI from FISO to FWF Could this be the reason? Are the attached output files correctly computed? Best regards, Toshiharu NODDI.zip <https://github.com/user-attachments/files/18318500/NODDI.zip> — Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AD57Y5WUNXIXBJZCTG2XQUD2JJP2PAVCNFSM6AAAAABUVFJIC6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKNZSHA4DKNJVGI> . You are receiving this because you commented.Message ID: ***@***.***>

[k5105880]

Dear Takuya Hayashi,

In addition to the corrections you provided, I tried the following, and it worked !!

Line 261
From:
fslmaths $AMICODATADIR/$protocol/$subjdir/AMICO/NODDI/FIT_dir $DWIT1wFolder/noddi_dir
To:
fslmaths $AMICODATADIR/$protocol/$subjdir/AMICO/NODDI/fit_dir $DWIT1wFolder/noddi_dir

Line 325
From:
${CARET7DIR}/wb_command -metric-resample $AtlasSpaceResultsDWIFolder/RibbonVolumeToSurfaceMapping/"$Subject"."$Hemisphere".${vol}.native.func.gii "$AtlasSpaceNativeFolder"/"$Subject"."$Hemisphere".sphere.${RegName}.native.surf.gii "$DownsampleFolder"/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA $AtlasSpaceResultsDWIFolder/"$Subject"."$Hemisphere".${vol}${Reg}."$LowResMesh"k_fs_LR.func.gii -area-surfs "$AtlasSpaceNativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$DownsampleFolder"/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii -current-roi "$AtlasSpaceNativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii

To:
${CARET7DIR}/wb_command -metric-resample $AtlasSpaceResultsDWIFolder/RibbonVolumeToSurfaceMapping/"$Subject"."$Hemisphere".${vol}.native.func.gii "$AtlasSpaceNativeFolder"/"$Subject"."$Hemisphere".sphere.${REGNAME}.native.surf.gii "$DownsampleFolder"/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA $AtlasSpaceResultsDWIFolder/"$Subject"."$Hemisphere".${vol}${Reg}."$LowResMesh"k_fs_LR.func.gii -area-surfs "$AtlasSpaceNativeFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$DownsampleFolder"/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii -current-roi "$AtlasSpaceNativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii

I truly appreciate your guidance and support. Thank you very much!

NoddiSurfaceMapping_log2.txt