From cecile.madjar at mcin.ca Tue Jun 4 12:44:28 2019 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Tue, 4 Jun 2019 12:44:28 -0400 Subject: [MINC-development] mnc2nii failure Message-ID: Hi MINC developers, I just QC'ed some images that went through mnc2nii and it results in either flipped NIfTI files or empty NIfTI files (mainly for 4D datasets apparently). I am using the latest MINC toolkit version but I believe mnc2nii has not be worked on in a while if I am not mistaken. We need mnc2nii to work to disseminate data that have been through a defacing algorithm that ran on the MINC files. Would it be possible to please fix this issue? Additionally, when converting DWI MINC files into NIfTI files, two additional files (.bvec and .bval) should be created to store the direction information. I can provide test MINC datasets on different modalities. Let me know. Thank you! C?cile Madjar MCIN lab -------------- next part -------------- An HTML attachment was scrubbed... URL: From gabriel.devenyi at mcgill.ca Fri Jun 7 12:20:59 2019 From: gabriel.devenyi at mcgill.ca (Gabriel Allan Devenyi, Dr) Date: Fri, 7 Jun 2019 16:20:59 +0000 Subject: [MINC-development] mnc2nii failure In-Reply-To: <2b5207ed6edc45be8c8828a4d1898d92@YQXPR0101MB0741.CANPRD01.PROD.OUTLOOK.COM> References: <2b5207ed6edc45be8c8828a4d1898d92@YQXPR0101MB0741.CANPRD01.PROD.OUTLOOK.COM> Message-ID: Hi, Can you please open up a github issue with full details (with verbose turned on). As well as the minchistory/mincheaders for working vs non-working conversions. -- Gabriel A. Devenyi B.Eng. Ph.D. Research Computing Associate Computational Brain Anatomy Laboratory Cerebral Imaging Center Douglas Mental Health University Institute Affiliate, Department of Psychiatry McGill University t: 514.761.6131x4781 e: gabriel.devenyi at mcgill.ca On Tue, 4 Jun 2019 at 12:45, Cecile Madjar > wrote: Hi MINC developers, I just QC'ed some images that went through mnc2nii and it results in either flipped NIfTI files or empty NIfTI files (mainly for 4D datasets apparently). I am using the latest MINC toolkit version but I believe mnc2nii has not be worked on in a while if I am not mistaken. We need mnc2nii to work to disseminate data that have been through a defacing algorithm that ran on the MINC files. Would it be possible to please fix this issue? Additionally, when converting DWI MINC files into NIfTI files, two additional files (.bvec and .bval) should be created to store the direction information. I can provide test MINC datasets on different modalities. Let me know. Thank you! C?cile Madjar MCIN lab -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Wed Jun 12 15:35:51 2019 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Wed, 12 Jun 2019 15:35:51 -0400 Subject: [MINC-development] mnc2nii failure In-Reply-To: References: <2b5207ed6edc45be8c8828a4d1898d92@YQXPR0101MB0741.CANPRD01.PROD.OUTLOOK.COM> Message-ID: Hi Gabriel, Thank you for the pointers. I created a Github issue with all the details you mentioned. On Fri, Jun 7, 2019 at 12:21 PM Gabriel Allan Devenyi, Dr < gabriel.devenyi at mcgill.ca> wrote: > Hi, > > Can you please open up a github issue with full details (with verbose > turned on). As well as the minchistory/mincheaders for working vs > non-working conversions. > > > -- > Gabriel A. Devenyi B.Eng. Ph.D. > Research Computing Associate > Computational Brain Anatomy Laboratory > Cerebral Imaging Center > Douglas Mental Health University Institute > Affiliate, Department of Psychiatry > McGill University > t: 514.761.6131x4781 > e: gabriel.devenyi at mcgill.ca > > > On Tue, 4 Jun 2019 at 12:45, Cecile Madjar wrote: > >> Hi MINC developers, >> >> I just QC'ed some images that went through mnc2nii and it results in >> either flipped NIfTI files or empty NIfTI files (mainly for 4D datasets >> apparently). >> >> I am using the latest MINC toolkit version but I believe mnc2nii has not >> be worked on in a while if I am not mistaken. >> >> We need mnc2nii to work to disseminate data that have been through a >> defacing algorithm that ran on the MINC files. Would it be possible to >> please fix this issue? >> >> Additionally, when converting DWI MINC files into NIfTI files, two >> additional files (.bvec and .bval) should be created to store the direction >> information. >> >> I can provide test MINC datasets on different modalities. >> >> Let me know. >> Thank you! >> >> C?cile Madjar >> MCIN lab >> > _______________________________________________ > MINC-development mailing list > MINC-development at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development > -------------- next part -------------- An HTML attachment was scrubbed... URL: