Thank you, Ashwati. I really don’t understand how this may have happened… Do you have the same problem with the new version in FreeSurfer 7? Cheers, /E

Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Ashwati Vipin (NNI)" ashwati_vipin@nni.com.sg Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, July 9, 2020 at 22:11 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer Digest, Vol 197, Issue 7 {Disarmed}

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Hi Eugenio!

Thank so much for your reply. Please find attached the following files you requested:

1. A single subject processed cross sectionally - lh.hippoSfVolumes-T1.v10.txt 2. The same subject process longitudinally - lh.hippoSfVolumes-T1.long.v10.txt

Best,

Ashwati

________________________________

________________________________ From: Ashwati Vipin (NNI) Sent: Monday, 6 July 2020 4:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: Freesurfer Digest, Vol 197, Issue 7

Hi Eugenio!

Thank so much for your reply. Please find attached the following files you requested:

1. A single subject processed cross sectionally - lh.hippoSfVolumes-T1.v10.txt 2. The same subject process longitudinally - lh.hippoSfVolumes-T1.long.v10.txt

Best,

Ashwati

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu freesurfer-request@nmr.mgh.harvard.edu Sent: Friday, 3 July 2020 9:52:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 197, Issue 7

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Today's Topics:

1. Destrieux atlas volume based in matlab (Gian Marco Duma) 2. Cerebellum segmentation (?lvaro Deleglise) 3. Re: Longitudinal Hippocampal Subfields - negative subfield volume values (Iglesias Gonzalez, Juan E.)

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Message: 1 Date: Fri, 3 Jul 2020 10:42:38 +0200 From: Gian Marco Duma gianmarco.duma@phd.unipd.it Subject: [Freesurfer] Destrieux atlas volume based in matlab To: freesurfer@nmr.mgh.harvard.edu Message-ID: CABaZGsdYPOVzFsztFw2ykE0J78vcXQ_RyPz25=C5fety0gZMNQ@mail.gmail.com Content-Type: text/plain; charset="utf-8"

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Dear Freesurfers experts, I need to obtain in the volume and not in the surface, in MNI space with voxels of 2mm. At this moment I do not need to obtain a parcellation of a single subject, even a parcellation in the volume from the MNI template would be great. Do you have any suggestions? thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: MailScanner has detected a possible fraud attempt from "imsva91-ctp.trendmicro.com:443" claiming to be https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=http%3a%2f...https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=http%3a%2f%2fmail.nmr.mgh.harvard.edu%2fpipermail%2ffreesurfer%2fattachments%2f20200703%2f6aae04e8%2fattachment%2d0001.html&umid=EF661599-A989-D805-85ED-26495DA1044B&auth=6e3fe59570831a389716849e93b5d483c90c3fe4-bc9d3995c614a970a19ac81b5e6309ca98dc1be9

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Message: 2 Date: Fri, 3 Jul 2020 10:14:37 -0300 From: ?lvaro Deleglise alvarodeleglise@gmail.com Subject: [Freesurfer] Cerebellum segmentation To: freesurfer@nmr.mgh.harvard.edu Message-ID: CAPq+_auo7VYdT193N1YotUm7A3UYgWFThToJmAHJ4uXwNW2KmQ@mail.gmail.com Content-Type: text/plain; charset="utf-8"

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Hi! I was wondering how can I run a segmentation of the cerebellum with a different strategy than the one provided by the default subcortical segmentation (which only differentiates lh and rh white and grey matter). I'm currently analyzing longitudinal data from a motor learning experiment in which the cerebellum it's very important, so I would like to have more cerebellar ROIs. I recently found an article by Makris et al., 2003, *Human Cerebellum- Surface-Assisted Cortical Parcellation and Volumetry with Magnetic Resonance Imaging,* but I'm not sure if there is any implementation of this strategy. Does anyone knows how can I use it? Or if there is another segmentation strategies available?

*Thanks in advance.*

* ?lvaro Deleglise * -------------- next part -------------- An HTML attachment was scrubbed... URL: MailScanner has detected a possible fraud attempt from "imsva91-ctp.trendmicro.com:443" claiming to be https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=http%3a%2f...https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=http%3a%2f%2fmail.nmr.mgh.harvard.edu%2fpipermail%2ffreesurfer%2fattachments%2f20200703%2f7658d9da%2fattachment%2d0001.html&umid=EF661599-A989-D805-85ED-26495DA1044B&auth=6e3fe59570831a389716849e93b5d483c90c3fe4-81a2656a4617dc3904e9b2831c302cc681ec2133

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Message: 3 Date: Fri, 3 Jul 2020 13:52:38 +0000 From: "Iglesias Gonzalez, Juan E." JIGLESIASGONZALEZ@mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal Hippocampal Subfields - negative subfield volume values To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: E2915099-787D-4ABC-B9AA-E2490734CBBB@mgh.harvard.edu Content-Type: text/plain; charset="utf-8"

Thank you Ashwati. This is very weird. Can you please send me a copy of the text files with the volumes for:

1. A single subject processed cross sectionally 2. The same subject process longitudinally Cheers, /E

Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) MailScanner has detected a possible fraud attempt from "imsva91-ctp.trendmicro.com:443" claiming to be https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=http%3a%2f...https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=http%3a%2f%2fwww.jeiglesias.com&umid=EF661599-A989-D805-85ED-26495DA1044B&auth=6e3fe59570831a389716849e93b5d483c90c3fe4-23e9a9cc1c5c427fca935fc1cd048afc3ac3ab36

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Ashwati Vipin (NNI)" ashwati_vipin@nni.com.sg Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, July 3, 2020 at 04:40 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Longitudinal Hippocampal Subfields - negative subfield volume values

External Email - Use Caution Dear FreeSurfer Developers,

I've run the longitudinal hippocampal subfield pipeline using the following command on freesurfer version 6.0:

longHippoSubfieldsT1.sh PAWS001_base_FS

I received no errors and everything seems to have run fine. But on computing the subfields using the following command:

quantifyHippocampalSubfields.sh T1.long PAWS_longitudinalhipsubfields.txt

I noticed that all of subfields have negative volume values. I checked the individual text files within each subject's timepoint and indeed the output is showing negative volumes as shown below:

[Inline image OWAPstImg380689]

I have also tested the same subject and run the cross-sectional hippocampal subfield pipeline using the following command:

recon-all -s PAWS001_TP1_FS -hippocampal-subfields-T1

I received the following output with volumes:

[Inline image OWAPstImg750361]

I'm really not sure why the longitudinal pipeline is showing negative values. Could it be a Freesurfer version issue? Am I doing something wrong? It is especially mind-boggling since I receive no error and the command is running smoothly! Please help.

Thank you so much!!

Best regards, Ashwati

[cid:image003.png@01D6511F.AE1499B0]nnitagl1

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End of Freesurfer Digest, Vol 197, Issue 7 ******************************************