Re: [Freesurfer] LGI

Hi Greve, Thank you very much. I have another question about the whole brain volume. I want to compare the relation between age and the volume of the whole brain, total GM and total WM. I don't know where the whole brain volume is in aseg.stats. Is it segmentation brain volume? Sincerely,

Re: [Freesurfer] Qdec

I get it. Thank you very much. Best, Zheng At 2017-11-27 11:46:46, "Bruce Fischl" wrote: It’s because people have found empirically that surface area and volume are correlated with TIV, but thickness is not cheers Bruce On Nov 26, 2017, at 9:54 PM, 郑凤莲 <13181786...@163.com> wrote: Hi

Re: [Freesurfer] LGI

yes, that should work too On 11/26/17 8:38 PM, 郑凤莲 wrote: Hi Greve,     Tnahks for your reply. I used "mri_segstats --annot my_subject_id lh aparc --i $SUBJECTS_DIR/my_subject_id/surf/lh.pial_*lgi* --sum lh.aparc.pial_*lgi*.stats" and get a stats file. In this file, I can get mean value unde

Re: [Freesurfer] Qdec

It’s because people have found empirically that surface area and volume are correlated with TIV, but thickness is not cheers Bruce > On Nov 26, 2017, at 9:54 PM, 郑凤莲 <13181786...@163.com> wrote: > > Hi Bruce, > > Thanks for your help. But I have a doubt in why we should do in this way? > Ar

Re: [Freesurfer] Qdec

Hi Bruce, Thanks for your help. But I have a doubt in why we should do in this way? Are there any principles or mechanisms in Qdec? Sincerely, Zheng At 2017-11-27 10:47:49, "Bruce Fischl" wrote: Yes On Nov 26, 2017, at 9:40 PM, 郑凤莲 <13181786...@163.com> wrote: Hi Bruce, Tha

Re: [Freesurfer] Qdec

Yes > On Nov 26, 2017, at 9:40 PM, 郑凤莲 <13181786...@163.com> wrote: > > Hi Bruce, > That is, I should set eTIV at Nuisance Factors for volume and surface > area, not for thickness in qdec, is it right? > > > > > > At 2017-11-27 10:22:05, "Bruce Fischl" wrote: > >you should correct for

Re: [Freesurfer] Qdec

Hi Bruce, That is, I should set eTIV at Nuisance Factors for volume and surface area, not for thickness in qdec, is it right? At 2017-11-27 10:22:05, "Bruce Fischl" wrote: >you should correct for eTIV for volume (but not for thickness) >On Mon, 27 >Nov 2017, 郑凤莲 wrote: > >> Hi Greve,

Re: [Freesurfer] Qdec

you should correct for eTIV for volume (but not for thickness) On Mon, 27 Nov 2017, 郑凤莲 wrote: Hi Greve,     Only for age and surface area, no thickness or volume, is it right? Thanks! Zheng At 2017-11-26 03:04:26, "Douglas Greve" wrote: Yes, for age and surface area. On 1

Re: [Freesurfer] Qdec

Hi Greve, Only for age and surface area, no thickness or volume, is it right? Thanks! Zheng At 2017-11-26 03:04:26, "Douglas Greve" wrote: Yes, for age and surface area. On 11/23/17 2:05 AM, 郑凤莲 wrote: Hi professors, I am using Qdec in Freesurfer. I want to study the re

Re: [Freesurfer] LGI

Hi Greve, Tnahks for your reply. I used "mri_segstats --annot my_subject_id lh aparc --i $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats" and get a stats file. In this file, I can get mean value under the "Mean" volume. Is this the same as you say? Thanks a lot !

Re: [Freesurfer] CSF mask with aparc+aseg

If you just use 24, then you will see a small patch near cerebellum. The 257 is not part of the analysis yet. All the others are venticular On 11/26/17 3:40 PM, Sam D wrote: THanks for the response, Doug! So just to clarify, when I use mri_binarize with the 24 label, which indicates CSF, I sho

Re: [Freesurfer] CSF mask with aparc+aseg

THanks for the response, Doug! So just to clarify, when I use mri_binarize with the 24 label, which indicates CSF, I shouldn’t expect to see any CSF in my mask other than that within ventricles? The reason I ask is I’m trying to generate the mask from which to acquire my csf regressor. Would you in

Re: [Freesurfer] Back to native space after registration

does this answer your question? https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat On 11/22/17 9:29 AM, Bruce Fischl wrote: Hi Avi we do all our analysis in native space, so there is no "putting back". cheers Bruce On Wed, 22 Nov 2017, Avideh Gharehgazlou wrote: Hi experts, Wi

Re: [Freesurfer] Local white and gray matter measures

I've never seen them, so I don't think they are ours On 11/17/17 7:52 PM, Crocetti, Deana wrote: Freesurfer Developers, I recently received FS data from a collaborator which included measures such for which, I as a FS user, I am familiar (i.e. GrayVol.lh.Frontal and GrayVol.rh.Frontal).  Als

Re: [Freesurfer] LGI

use something like cd subject/surf mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.lgi.stats -t lh.lgi.mgh -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab subject lh white In the output, the mean LGI will be under the "ThickAvg" column On 11/

Re: [Freesurfer] data conversion

Hi Danny, If you want to cd into SUBJECTS_DIR, just run: export SUBJECTS_DIR=/downloads/buckner_data/tutorial_subjs cd $SUBJECTS_DIR “cd $downloads/buckner_data/tutorial_subjs” isn’t a valid command if you haven’t set a variable named “downloads" Andrew > On Nov 23, 2017, at 4:00 AM, Danny De

Re: [Freesurfer] Intracranial Volume

yes, that is correct On 11/23/17 2:43 PM, Tamara Tavares wrote: Hello, Just a quick question regarding the computed intracranial volume. I have ran Freesurfer version 5.1 and I have been using the intracranial volume from the aseg.stats file to correct for head size. I just want to ensure t

Re: [Freesurfer] inqiury

Hi Danny you need to follow the instructions on our wiki. Start with this: http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall then you can go through tthe getting started tutorial as well cheers Bruce On Fri, 24 Nov 2017, Danny Deng wrote: Dear FS developers, I wish to transform DIC