Re: [Freesurfer] TRACULA statistics concern

Ciao Stefano, can you be a bit more specific about what you're exactly trying to to? Am I correctly assuming that you are looking at differences between your groups? Are you looking at average FA/MD/RD/AD over whole tracts, or at values along them? Do you have any strong hypothesis on which tract

Re: [Freesurfer] R: Re: TRACULA statistics concern

Hi again, if you perform the same analysis over and over for each of the 18 tracts, then the Bonferroni corrected p-value would be 0.05/18 Cheers, /Eugenio On Mon, 2014-03-24 at 22:47 +0100, std...@virgilio.it wrote: Ciao Eugenio, thank you very much for your prompt and kind response. Yes,

Re: [Freesurfer] R: Re: TRACULA statistics concern

Unless you're comparing groups in a pairwise manner, i.e., A vs B, B vs C, and A vs C. In that case, you would have 18 x 3 comparisons and the threshold for significance would be 0.05 / (18 x 3) Cheers, /Eugenio On Mon, 2014-03-24 at 17:50 -0400, Juan Eugenio Iglesias wrote: Hi again, if you

Re: [Freesurfer] hippocampal subfields

Eugenio Iglesias On Mon, 2014-03-03 at 13:49 +0100, Gabor Perlaki wrote: Dear all, 1. Which is the suggested resolution for hippocampal subfields segmentation with freesurfer? I've seen articles with 0.5*0.5*0.5mm^3 and with 1.0*1.0*1.0mm^3 as well. Does the hippocampal subfields

Re: [Freesurfer] Extracting only hippo campus volume

Hi Saurabh, the volume of the hippocampal subfields can be computed with: cd $SUBJECTS_DIR/bert/mri kvlQuantifyPosteriorProbabilityImages \ $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt \ posterior_right_* posterior_Right-Hippocampus.mgz and the whole hippocampal volume is just the

Re: [Freesurfer] Hippocampal Subfield Segmentation

Dear Sierra, there's no direct correspondence between these subfields and head / body. If you want, you could create a geometric rule to subdivide the hippocampus into head / body / tail, e.g., by creating a coordinate system based on the major axis of the hippocampal shape. Kind regards, Eugenio

Re: [Freesurfer] longitudinal hippocampal subfields

Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center

Re: [Freesurfer] -hippo-subfields error

/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown

Re: [Freesurfer] hippocampal subfield segmentations

-- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A

Re: [Freesurfer] Hippocampal subfield segmentation paused

is the right command for computing subfields with high-res T2? Thank you very much!! This is not an option at this point, but we are working on it. Cheers, /Eugenio -Irene *From:* Juan Eugenio Iglesias igles

Re: [Freesurfer] Hippocampal subfield segmentation paused

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth

Re: [Freesurfer] Hippocampal Subfield Segmentation

-- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ Freesurfer mailing list Freesurfer

Re: [Freesurfer] hippocampal subfields question

/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown

Re: [Freesurfer] hippo_subfields atlas

to what labels/areas? Thanks for your time, Raja On Wed, Aug 7, 2013 at 4:26 PM, Rajapillai Pillai raja.i.pil...@gmail.com mailto:raja.i.pil...@gmail.com wrote: Thanks very much! On Wed, Aug 7, 2013 at 4:23 PM, Juan Eugenio Iglesias igles...@nmr.mgh.harvard.edu mailto:igles

Re: [Freesurfer] hippo_subfields atlas

question about the hippocampal subfields atlas--might be a silly one. Is there a way to extract volumes from the mesh collection? Thanks a lot, Raja On Wed, Jul 31, 2013 at 5:06 PM, Juan Eugenio Iglesias igles...@nmr.mgh.harvard.edu mailto:igles...@nmr.mgh.harvard.edu wrote: Sounds good

Re: [Freesurfer] hippo_subfields atlas

://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301

Re: [Freesurfer] hippo_subfields atlas

directory. Any idea what might have gone wrong and how I can try and fix it? Thanks, Raja On Wed, Jul 31, 2013 at 4:29 PM, Juan Eugenio Iglesias igles...@nmr.mgh.harvard.edu mailto:igles...@nmr.mgh.harvard.edu wrote: Hi Raja, I'm have a question regarding the GEMS hippocampal

Re: [Freesurfer] kvlQuantifyHippocampalSubfieldSegmentations.sh empty text files

right_hippocampal_fissure: 541.872 cd .. cd .. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio

Re: [Freesurfer] kvlQuantifyHippocampalSubfieldSegmentations.sh empty text files

. Thanks for your help. On Wed, Jul 17, 2013 at 11:16 AM, Juan Eugenio Iglesias igles...@nmr.mgh.harvard.edu mailto:igles...@nmr.mgh.harvard.edu wrote: Hi Jasmeet, what modification did you exactly make? Whih version of FreeSurfer is this? Cheers, /Eugenio On 07/17

Re: [Freesurfer] Question about running kvlQuantifyHippocampalSubfieldSegmentations.sh

reconed with the --hippo-subfields flag. Both of them have 20 output files. Cheers, Zoe *From:*Juan Eugenio Iglesias [mailto:igles...@nmr.mgh.harvard.edu] *Sent:* Monday, June 24, 2013 5:03 PM *To:* Yang, Zoe *Cc:* 'Freesurfer@nmr.mgh.harvard.edu' *Subject:* Re: [Freesurfer] Question about

Re: [Freesurfer] Question about running kvlQuantifyHippocampalSubfieldSegmentations.sh

. -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A

Re: [Freesurfer] Hippocampal subfields intensity

(postsub); The *postres.mgz files are nu, norm and T1 resampled as you suggested. And nMRIread is the workarounded version of MRIread I said in previous message. Cheers, Marcos Em Seg, 2013-06-10 às 16:58 -0400, Juan Eugenio Iglesias escreveu: Hi Marcos, 1. your fix of MRIread.m is great

Re: [Freesurfer] Hippocampal subfields intensity

this after the binarize step. Thank you in advance for any help. Marcos ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Juan Eugenio Iglesias, PhD http

Re: [Freesurfer] Hippocampal subfields intensity

help? Cheers, Marcos PS: I promised I will post the final solution to list. But I guess it is more didactic if these little problems are solved before. TY, again. Em Seg, 2013-06-10 às 14:19 -0400, Juan Eugenio Iglesias escreveu: Hi Marcos, the right way of doing this is using the soft

Re: [Freesurfer] subfield algorithm and subject intensity differences

/listinfo/freesurfer -- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ Freesurfer mailing

Re: [Freesurfer] hippocampal subfield segmentation

549-557 On Wed, 2013-06-05 at 10:54 +0200, Claudia Dacquino wrote: Thank you for your response. Would you suggest a reference I can refer to? 2013/6/4 Juan Eugenio Iglesias igles...@nmr.mgh.harvard.edu I would probably leave out the fissure, but not the fimbria... Cheers

Re: [Freesurfer] hippocampal subfield segmentation

list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts

Re: [Freesurfer] Freeview automation

://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A

Re: [Freesurfer] hipposubfields and data

) and upsamples it to .5mm? Josh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula

Re: [Freesurfer] QDEC and Hippocampal subfields

- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ Freesurfer mailing list Freesurfer

Re: [Freesurfer] Hippo-subfields

that right and left Ca1 dimensions did not match. Thank you again. Em Qui, 2013-04-18 às 11:29 -0400, Juan Eugenio Iglesias escreveu: I agree with Bruce. You can use MRIread.m to read in the data. Regarding the other question: first you need to combine the posteriors of all the subfields

Re: [Freesurfer] Hippo-subfields

about how to do it? Sorry, I am afraid I am a novice here and my questions are the best proof of this, so I would like to thank you for all your patience. Em Qua, 2013-04-17 às 21:19 -0400, Juan Eugenio Iglesias escreveu: Dear Marcos, 1- How do I save the combined 3D view I got

Re: [Freesurfer] Hippo-subfields

mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos

Re: [Freesurfer] R: Re: R: Re: hippo subfield

://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite

Re: [Freesurfer] R: Re: R: Re: R: Re: hippo subfield

://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301

Re: [Freesurfer] R: Re: hippo subfield

@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging

Re: [Freesurfer] question about hippocampus subfield segmentation flag

Hi Mehul, that should work. Let us know if you have any problems. Kind regards, Juan Eugenio Iglesias On Sat, 2013-03-16 at 14:29 -0700, Mehul Sampat wrote: Hi Folks, I had a question about the hippocampus subfield segmentations as described here : http://surfer.nmr.mgh.harvard.edu/fswiki

Re: [Freesurfer] Hippocampus volume calculations

! Gari ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http

Re: [Freesurfer] nb0 question

, Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - Juan Eugenio Iglesias, PhD http

Re: [Freesurfer] nb0 question

when you acquire the image. Hth, Shantanu On Thu, February 21, 2013 12:16 pm, Juan Eugenio Iglesias wrote: Isn't nb0 the *number* of b0 images? Therefore it should be 1 no matter where in the table it is. From the tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Step7.3

Re: [Freesurfer] Hippocampus volume

- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ Freesurfer

Re: [Freesurfer] Head, body and tail of hippocampus

___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles

Re: [Freesurfer] hippocampal subfield segmentation

-- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology, MGH, Harvard Medical School 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A

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