External Email - Use Caution Dear Sir,
I was able to generate segmentations as cited in the module , I am able obtain segmentations for CA1 posterior Head and CA1 Posterior body , along with CA1 head and CA1 body , what does non posterior parcellations of CA1 head and body indicates, can these be assumed as anterior regions ?, is there any way to obtain CA1 head and CA1 body etc for both left and right hemispheres , as per segmentation results i can only see *[lr]h.hippoSfVolumes-T1.v2x.mgz files * . Not (lr)h.CA1_head and body , how can i split these subfields from *[lr]h.hippoSfVolumes-T1.v2x.mgz files.* *Thanks* *Vasudev* On Tue, Jul 3, 2018 at 11:49 AM, Iglesias Gonzalez, Eugenio < e.igles...@ucl.ac.uk> wrote: > Yes! > > > Juan Eugenio Iglesias > > Centre for Medical Image Computing (CMIC) > > University College London > > http://www.jeiglesias.com > > http://cmictig.cs.ucl.ac.uk/ > > > ------------------------------ > *From:* Dev vasu <vasudevamurthy.devulapa...@gmail.com> > *Sent:* Tuesday, July 3, 2018 12:22:27 AM > *To:* Iglesias Gonzalez, Eugenio > *Cc:* freesurfer@nmr.mgh.harvard.edu > > *Subject:* Re: Anterior / Posterior Partition in Hippocampus parcellation > atlas > > Dear Sir, > > I have another query if i use "export WRITE_POSTERIORS=1", will it > generate posterior CA1 and other substructures in the form as cited > *posterior_side_<substructure>_<T1>_<analysisID>_v2x.mgz > , * > > > Thanks > Vasudev > > On Mon, Jul 2, 2018 at 8:30 PM, Dev vasu <vasudevamurthy.devulapally@ > gmail.com> wrote: > > Dear Sir, > > Thanks for your reply Yes,i have run 6.0, Can you send me the link for > developmental version of freesurfer, also how can i obtain posterior > regions of subfields like CA1,CA2,CA3,CA4, as the link suggests only CA1 > head and CA1 body were segmented , i need posterior part of CA1 can i > assume CA1 body as posterior region. > > > Thanks > Vasudev > > On Mon, Jul 2, 2018 at 8:25 PM, Iglesias Gonzalez, Eugenio < > e.igles...@ucl.ac.uk> wrote: > > Ah, now I understand. > > To get the division in the wiki (https://surfer.nmr.mgh.harvar > d.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala), you need to run > the development version of FreeSurfer. The version you ran (6.0, I > presume), does not provide such subdivision. > > In principle, you could use Garikoitz’s code to subdivide the > segmentation, but his code is not part of FreeSurfer, so you would have to > contact him for support. Alternatively, you can also download the > development version of FreeSurfer, which will provide the segmentation that > I mentioned earlier. > > Kind regards, > > /Eugenio > > > > -- > > Juan Eugenio Iglesias > > ERC Senior Research Fellow > > Centre for Medical Image Computing (CMIC) > > University College London > > http://www.jeiglesias.com > > http://cmictig.cs.ucl.ac.uk/ > > > > > > *From: *Dev vasu <vasudevamurthy.devulapa...@gmail.com> > *Date: *Monday, 2 July 2018 at 19:22 > *To: *"Iglesias Gonzalez, Eugenio" <e.igles...@ucl.ac.uk> > *Cc: *"freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>, " > igles...@nmr.mgh.harvard.edu" <igles...@nmr.mgh.harvard.edu> > *Subject: *Re: Anterior / Posterior Partition in Hippocampus parcellation > atlas > > > > Dear sir, > > > > In the following journal published by you ,procedure for longitudinal > segmentation was highlighted (https://github.com/garikoitz/hippovol) , I > have run the module described in wiki and i have obtained > lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz and lh.hippoSfLabels-T1.v10.mgz > files , i would like to know how i can split the labels CA1 head, CA1 body > and CA1 tail from this file, since individual subfield label numbers for > CA1 head and CA1 body are not defined ,also can i assure CA1 body as > posterior region and CA1 head as anterior ?. > > > > > > Thanks > > Vasudev > > > > On Mon, Jul 2, 2018 at 7:39 PM, Iglesias Gonzalez, Eugenio < > e.igles...@ucl.ac.uk> wrote: > > Dear Vasudev, > > You can run the module described in that wiki page, and in the output file > [lr]h.hippoAmygLabels-T1.v2x.mgz you will find segmentations for CA1 > head, CA1 body, CA23 head, CA23 body, CA4 head, CA4 body, and hippocampal > tail (note that we don’t parcellate the tail). > > Cheers, > > /Eugenio > > > > -- > > Juan Eugenio Iglesias > > ERC Senior Research Fellow > > Centre for Medical Image Computing (CMIC) > > University College London > > http://www.jeiglesias.com > > http://cmictig.cs.ucl.ac.uk/ > > > > > > *From: *Dev vasu <vasudevamurthy.devulapa...@gmail.com> > *Date: *Monday, 2 July 2018 at 17:09 > *To: *"freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>, " > igles...@nmr.mgh.harvard.edu" <igles...@nmr.mgh.harvard.edu> > *Subject: *Anterior / Posterior Partition in Hippocampus parcellation > atlas > > > > * External Email - Use Caution * > > Dear Sir, > > > > > > I have reviewed your journal which detailed about hippocampus parcellation > ( https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfiel > dsAndNucleiOfAmygdala ) of subfields ( HBT - Head/body/Tail) , could you > please let me know how to partition the atlas along the lines of Anterior > CA1,CA3,CA4 and posterior CA1,CA3,CA4. > > > > > > Thanks > > Vasdudev > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > > > >
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