From louis.collins at McGill.Ca Mon May 13 08:36:57 2024 From: louis.collins at McGill.Ca (Louis Collins, Dr.) Date: Mon, 13 May 2024 12:36:57 +0000 Subject: [MINC-development] location of avg250 ? Message-ID: <5917131A-849A-4A14-B2DB-C7525074C249@mcgill.ca> Hi all, I was looking at our history of minc stereotaxic MRI average templates. I can?t seem to find the avg250.mnc (mni250.mnc ?) that is described in Evans, A., Collins, D. L., & Milner, B. (1992). An MRI-based stereotaxic atlas from 250 young normal subjects. Paper presented at the Society for Neuroscience. Anyone have any ideas where I can find it? -Louis From gabriel.devenyi at mcgill.ca Mon May 13 11:33:13 2024 From: gabriel.devenyi at mcgill.ca (Gabriel Allan Devenyi, Dr) Date: Mon, 13 May 2024 15:33:13 +0000 Subject: [MINC-development] location of avg250 ? In-Reply-To: <5917131A-849A-4A14-B2DB-C7525074C249@mcgill.ca> References: <5917131A-849A-4A14-B2DB-C7525074C249@mcgill.ca> Message-ID: According to https://en.wikibooks.org/wiki/MINC/Atlases/Atlases/History#Average_250_T1_model > This original MNI-space model has never been officially released from the MNI. This might make finding it difficult. ________________________________________ From: MINC-development on behalf of Louis Collins, Dr. Sent: May 13, 2024 08:36 To: minc-development at bic.mni.mcgill.ca Subject: [MINC-development] location of avg250 ? Hi all, I was looking at our history of minc stereotaxic MRI average templates. I can?t seem to find the avg250.mnc (mni250.mnc ?) that is described in Evans, A., Collins, D. L., & Milner, B. (1992). An MRI-based stereotaxic atlas from 250 young normal subjects. Paper presented at the Society for Neuroscience. Anyone have any ideas where I can find it? -Louis _______________________________________________ MINC-development mailing list MINC-development at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development From a.janke at gmail.com Tue May 14 06:08:47 2024 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 14 May 2024 20:08:47 +1000 Subject: [MINC-development] location of avg250 ? In-Reply-To: References: <5917131A-849A-4A14-B2DB-C7525074C249@mcgill.ca> Message-ID: Afternoon/morning/evening all, Louis, I did go through all the old archives when I was helping JF clean up the original shadow server before decom and movement to the first Linux ipl drives we built. Would have been around 2004? As part of this, I did find all the original models, source data and some of the scripts including the 250, the data was in a word, amusing. By 2006 standards, huge artifacts, but yet built a great model. I do wonder what the 2024 young pups would think. ? So, the data will be in one of the /data/ipl/iplxx drives in a rotor share. If I can recall my password I could take a crack at finding them if they haven't been reassigned. Thanks a On Tue, 14 May 2024, 01:33 Gabriel Allan Devenyi, Dr, < gabriel.devenyi at mcgill.ca> wrote: > According to > https://en.wikibooks.org/wiki/MINC/Atlases/Atlases/History#Average_250_T1_model > > > This original MNI-space model has never been officially released from > the MNI. > > This might make finding it difficult. > > ________________________________________ > From: MINC-development on > behalf of Louis Collins, Dr. > Sent: May 13, 2024 08:36 > To: minc-development at bic.mni.mcgill.ca > Subject: [MINC-development] location of avg250 ? > > Hi all, > > I was looking at our history of minc stereotaxic MRI average templates. I > can?t seem to find the avg250.mnc (mni250.mnc ?) that is described in > Evans, A., Collins, D. L., & Milner, B. (1992). An MRI-based > stereotaxic atlas from 250 young normal subjects. Paper presented at the > Society for Neuroscience. > > Anyone have any ideas where I can find it? > > -Louis > > > _______________________________________________ > MINC-development mailing list > MINC-development at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development > > _______________________________________________ > 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: From louis.collins at McGill.Ca Wed May 15 08:24:16 2024 From: louis.collins at McGill.Ca (Louis Collins, Dr.) Date: Wed, 15 May 2024 12:24:16 +0000 Subject: [MINC-development] location of avg250 In-Reply-To: References: Message-ID: HI all, I?ve checked again to try to find the original average of 250 manually registered T1w 1.5T (Philips) MRIs that are described in Alan?s 1992 abstract. Andrew - if you have time, could you poke around /data/ipl/ipl*/rotor ? I don?t have permissions to do so. I have managed to find a bunch of other templates and made a slide if anyone is interested. I?d love to add the avg250.mnc to complete the collection. -Louis > On May 14, 2024, at 12:00, minc-development-request at bic.mni.mcgill.ca wrote: > > [You don't often get email from minc-development-request at bic.mni.mcgill.ca. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] > > Send MINC-development mailing list submissions to > minc-development at bic.mni.mcgill.ca > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development > or, via email, send a message with subject or body 'help' to > minc-development-request at bic.mni.mcgill.ca > > You can reach the person managing the list at > minc-development-owner at bic.mni.mcgill.ca > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of MINC-development digest..." > > > Today's Topics: > > 1. Re: location of avg250 ? (Andrew Janke) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 14 May 2024 20:08:47 +1000 > From: Andrew Janke > To: "MINC development discussion & planning" > > Subject: Re: [MINC-development] location of avg250 ? > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Afternoon/morning/evening all, > > > Louis, I did go through all the old archives when I was helping JF clean up > the original shadow server before decom and movement to the first Linux ipl > drives we built. Would have been around 2004? > > As part of this, I did find all the original models, source data and some > of the scripts including the 250, the data was in a word, amusing. By 2006 > standards, huge artifacts, but yet built a great model. I do wonder what > the 2024 young pups would think. ? > > So, the data will be in one of the /data/ipl/iplxx drives in a rotor share. > If I can recall my password I could take a crack at finding them if they > haven't been reassigned. > > Thanks > > > a > > On Tue, 14 May 2024, 01:33 Gabriel Allan Devenyi, Dr, < > gabriel.devenyi at mcgill.ca> wrote: > >> According to >> https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fen.wikibooks.org%2Fwiki%2FMINC%2FAtlases%2FAtlases%2FHistory%23Average_250_T1_model&data=05%7C02%7Clouis.collins%40mcgill.ca%7C8f7d1ca0f52f4fc9cf0808dc742eee2d%7Ccd31967152e74a68afa9fcf8f89f09ea%7C0%7C0%7C638512992120641930%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=9Zj%2BSErYEymKtnZbkT5sHAjLmo%2B4W%2FNsiR3XZcKcMpg%3D&reserved=0 >> >>> This original MNI-space model has never been officially released from >> the MNI. >> >> This might make finding it difficult. >> >> ________________________________________ >> From: MINC-development on >> behalf of Louis Collins, Dr. >> Sent: May 13, 2024 08:36 >> To: minc-development at bic.mni.mcgill.ca >> Subject: [MINC-development] location of avg250 ? >> >> Hi all, >> >> I was looking at our history of minc stereotaxic MRI average templates. I >> can?t seem to find the avg250.mnc (mni250.mnc ?) that is described in >> Evans, A., Collins, D. L., & Milner, B. (1992). An MRI-based >> stereotaxic atlas from 250 young normal subjects. Paper presented at the >> Society for Neuroscience. >> >> Anyone have any ideas where I can find it? >> >> -Louis >> >> >> _______________________________________________ >> MINC-development mailing list >> MINC-development at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development >> >> _______________________________________________ >> 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: > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > MINC-development mailing list > MINC-development at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development > > > ------------------------------ > > End of MINC-development Digest, Vol 88, Issue 2 > *********************************************** -------------- next part -------------- An HTML attachment was scrubbed... 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Name: MNI templates.pptx Type: application/vnd.openxmlformats-officedocument.presentationml.presentation Size: 2780178 bytes Desc: MNI templates.pptx URL: From a.janke at gmail.com Mon May 20 18:56:29 2024 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 21 May 2024 08:56:29 +1000 Subject: [MINC-development] location of avg250 In-Reply-To: References: Message-ID: Hi all, Everything I have is in /home/bic/rotor/data >From a look around in there, I think it has what louis is looking for. login1:*data*$ ls ADNI-data01 als avgbrain icbm_recovery jacob_atlas.obj mni-models ms-mni-bu prism symatlas tle login1:*data*$ ls avgbrain/*/* avgbrain/avgbrain1/atlas: talairach wolforth_atlas avgbrain/avgbrain1/brain: autoreg brain-models male-female-diff males-low-Z ms-normal native-xfm temp-work-files-not-to-delete brain_mask images males-females-low-Z manreg native old_images avgbrain/avgbrain1/vasco: avgbrain.fx avgbrain/avgbrain2/brain: auto-corr brain-models manreg native avgbrain/avgbrain2/vasco: brain_mask.mnc.Z feature_t1.mnc.Z kollokian_vasco_t1.mnc.Z phantom10.mnc.Z t1.mnc.gz brain_mask_t.mnc.gz feature_t2.mnc.Z kollokian_vasco_t1tal.log phantom_doc.ps t2.mnc.gz brain_vein_dura_mask.mnc.Z fill_pd kollokian_vasco_t1tal.xfm phantom_pd.mnc.Z vasco_label.tag classified_brain_t.mnc.gz fill_t1 kollokian_vasco_t2.mnc.Z phantom_t1.mnc.Z vasco_stx_label.tag classified_t.mnc.gz fill_t2 make_brain_phantom.txt phantom_t2.mnc.Z vasco_stx.tag feature_pd.mnc.Z kollokian_vasco_pd.mnc.Z pd.mnc.gz readme.1st vasco_t2-t1.tag Thanks a On Thu, 16 May 2024 at 01:22, Louis Collins, Dr. wrote: > HI all, > > I?ve checked again to try to find the original average of 250 manually > registered T1w 1.5T (Philips) MRIs that are described in Alan?s 1992 > abstract. > > Andrew - if you have time, could you poke around /data/ipl/ipl*/rotor ? I > don?t have permissions to do so. > > I have managed to find a bunch of other templates and made a slide if > anyone is interested. I?d love to add the avg250.mnc to complete the > collection. > > -Louis > > > > On May 14, 2024, at 12:00, minc-development-request at bic.mni.mcgill.ca > wrote: > > > > [You don't often get email from > minc-development-request at bic.mni.mcgill.ca. Learn why this is important > at https://aka.ms/LearnAboutSenderIdentification ] > > > > Send MINC-development mailing list submissions to > > minc-development at bic.mni.mcgill.ca > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development > > or, via email, send a message with subject or body 'help' to > > minc-development-request at bic.mni.mcgill.ca > > > > You can reach the person managing the list at > > minc-development-owner at bic.mni.mcgill.ca > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of MINC-development digest..." > > > > > > Today's Topics: > > > > 1. Re: location of avg250 ? (Andrew Janke) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Tue, 14 May 2024 20:08:47 +1000 > > From: Andrew Janke > > To: "MINC development discussion & planning" > > > > Subject: Re: [MINC-development] location of avg250 ? > > Message-ID: > > < > CAG0CB20KzGEPOPcNbb4BE9YKOB7MeNphtiNRbG3wxTkW2vsXMA at mail.gmail.com> > > Content-Type: text/plain; charset="utf-8" > > > > Afternoon/morning/evening all, > > > > > > Louis, I did go through all the old archives when I was helping JF clean > up > > the original shadow server before decom and movement to the first Linux > ipl > > drives we built. Would have been around 2004? > > > > As part of this, I did find all the original models, source data and some > > of the scripts including the 250, the data was in a word, amusing. By > 2006 > > standards, huge artifacts, but yet built a great model. I do wonder what > > the 2024 young pups would think. ? > > > > So, the data will be in one of the /data/ipl/iplxx drives in a rotor > share. > > If I can recall my password I could take a crack at finding them if they > > haven't been reassigned. > > > > Thanks > > > > > > a > > > > On Tue, 14 May 2024, 01:33 Gabriel Allan Devenyi, Dr, < > > gabriel.devenyi at mcgill.ca> wrote: > > > >> According to > >> > https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fen.wikibooks.org%2Fwiki%2FMINC%2FAtlases%2FAtlases%2FHistory%23Average_250_T1_model&data=05%7C02%7Clouis.collins%40mcgill.ca%7C8f7d1ca0f52f4fc9cf0808dc742eee2d%7Ccd31967152e74a68afa9fcf8f89f09ea%7C0%7C0%7C638512992120641930%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=9Zj%2BSErYEymKtnZbkT5sHAjLmo%2B4W%2FNsiR3XZcKcMpg%3D&reserved=0 > > >> > >>> This original MNI-space model has never been officially released from > >> the MNI. > >> > >> This might make finding it difficult. > >> > >> ________________________________________ > >> From: MINC-development on > >> behalf of Louis Collins, Dr. > >> Sent: May 13, 2024 08:36 > >> To: minc-development at bic.mni.mcgill.ca > >> Subject: [MINC-development] location of avg250 ? > >> > >> Hi all, > >> > >> I was looking at our history of minc stereotaxic MRI average > templates. I > >> can?t seem to find the avg250.mnc (mni250.mnc ?) that is described in > >> Evans, A., Collins, D. L., & Milner, B. (1992). An MRI-based > >> stereotaxic atlas from 250 young normal subjects. Paper presented at the > >> Society for Neuroscience. > >> > >> Anyone have any ideas where I can find it? > >> > >> -Louis > >> > >> > >> _______________________________________________ > >> MINC-development mailing list > >> MINC-development at bic.mni.mcgill.ca > >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development > >> > >> _______________________________________________ > >> 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: < > http://mailman.bic.mni.mcgill.ca/pipermail/minc-development/attachments/20240514/0da0b2bb/attachment-0001.html > > > > > > ------------------------------ > > > > Subject: Digest Footer > > > > _______________________________________________ > > MINC-development mailing list > > MINC-development at bic.mni.mcgill.ca > > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-development > > > > > > ------------------------------ > > > > End of MINC-development Digest, Vol 88, Issue 2 > > *********************************************** > > _______________________________________________ > 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... 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