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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"

        External Email - Use Caution       

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
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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>
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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 *
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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)
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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
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