Re: [Freesurfer] subcortical structures volume

Hi Zheng For volume, usually including eTIV reduces the variance and increases power more than you lose for having one additional regressor. Not sure about gender - how unbalanced is your sample? You might be ok with just eTIV Bruce On Sat, 2 Dec 2017, 郑凤莲 wrote: Hi professor,    I am

Re: [Freesurfer] subcortical structures volume

Hi Bruce, I think I get it. I have 27 males and 28 females and 26 males. It isn't necessary to corrected by eTIV. Is it right? Thanks a lot ! Zheng At 2017-12-02 11:45:10, "Bruce Fischl" wrote: >Hi Zheng > >For volume, usually including eTIV reduces

[Freesurfer] [Re] medial wall label in Freesurfer 6

Hello, I have upload the data. Recipient mail was ahoo...@mgh.harvard.edu. Please, check you have received it. Thanks very much, M del Mar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Merging two groups

Dear Bruce, Thank you. Now its working fine. On Thu, Nov 30, 2017 at 3:46 PM, Ramesh Babu wrote: > Dear Bruce, > Thank you very much for reply. > > I have to link fsavarage also. Because recently I have formated my system, > the link between freesurfer and fsaverage

[Freesurfer] mri_vol2surf wrong hemisphere

Hi, I have a strange issue I can't figure out. I am currently trying to use the parcellation from Gordon et al. 2014 (download link here) to create ROIs for the frontoparietal network. They provided a volume of the parcellation in MNI152

[Freesurfer] mri_vol2surf wrong hemisphere

Hi, I have a strange issue I can't figure out. I am currently trying to use the parcellation from Gordon et al. 2014 (http://www.nil.wustl.edu/labs/petersen/Resources.html) to create ROIs for the frontoparietal network. They provided a volume of the parcellation in MNI152 space for public

Re: [Freesurfer] transformation matrix

See https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat On 12/1/17 10:57 AM, John Anderson wrote: Dear FS experts, Is there any transformation matrix between the files /mri/orig.mgz and the file /mri/rawavg.mgz Please advice! John

Re: [Freesurfer] [freesurfer] version differences for pial matter / skull strip?

Hi, I am confused by the instructions for the ftp. Once I am logged into the ftp and have navigated to the transfer/incoming directory, how am I supposed to find / access the file that I would ike to send through? Does terminal still recognize my working directory before I logged into the ftp?

Re: [Freesurfer]  hippocampus subfields

Dear Zheng, You can build a GLM with a single group, and then look at the residuals. Or, even easier: just divide the volumes of each subject by his/her ICV (the answers won’t be identical, but should definitely be quite similar). Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research

Re: [Freesurfer]  hippocampus subfields

Hi Bruce, I am sorry for asking you question as this, but I really don't know how to do it? It seems that GLM is suitable for there are two groups or more. But I only have one group, If I want to get the line trend with eTIV corrected for the relationship between age and volume, what

Re: [Freesurfer] Intracranial Volume

Hi Tamara, yes, it is in the aseg stats . You can extract that information for all subjects using asegstats2table Best, Martin Am 23.11.2017 um 20:43 schrieb Tamara Tavares: Hello, Just a quick question regarding the computed intracranial volume. I have ran Freesurfer version 5.1 and I

Re: [Freesurfer] FA to MNI

you can use mri_vol2vol with the --mni152reg flag. Run it with --help to get more info On 11/30/17 3:54 PM, Bruce Fischl wrote: > Hi John > > if your FA map is registered to the structurals (e.g. using bbregister) > then you would just compose that transform with the talairach.xfm in the >

[Freesurfer] transformation matrix

Dear FS experts, Is there any transformation matrix between the files /mri/orig.mgz and the file /mri/rawavg.mgz Please advice! John___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] [Re] medial wall label in Freesurfer 6

Thanks, I just received it - I’ll take a look Andrew On Dec 1, 2017, at 5:10 AM, M del Mar Velasco > wrote: Hello, I have upload the data. Recipient mail was ahoo...@mgh.harvard.edu. Please, check you have

[Freesurfer] create frontal lobe label

Dear freesurfer group, I tried to create a frontal lobe label but it gives the following error message. Do you have any idea what could be changed to make it run? mri_annotation2label --labelbase ./ --lobesStrict frontal --subject fsaverage --hemi lh subject = fsaverage annotation = aparc

Re: [Freesurfer] [freesurfer] version differences for pial matter / skull strip?

can you paste the full session text into the email (not as a screen shot)? On Fri, 1 Dec 2017, Michelle VanTieghem wrote: Hi, I am unsure whether this worked: see attached screenshot. Thanks! M On Fri, Dec 1, 2017 at 4:26 PM, Bruce Fischl wrote: yes, it

Re: [Freesurfer] [freesurfer] version differences for pial matter / skull strip?

yn-128-59-230-36:structural michellevantieghem2$ ftp surfer.nmr.mgh.harvard.edu Connected to surfer.nmr.mgh.harvard.edu. 220-This is the Martinos Center Anonymous FTP service. Use of this site 220-shows implicit consent to our Acceptable Use Policy outlined at

Re: [Freesurfer] [freesurfer] version differences for pial matter / skull strip?

try cd'ing to incoming not outgoing (the names are from our perspective I think :) On Fri, 1 Dec 2017, Michelle VanTieghem wrote: yn-128-59-230-36:structural michellevantieghem2$ ftp surfer.nmr.mgh.harvard.edu Connected to surfer.nmr.mgh.harvard.edu. 220-This is the Martinos Center

Re: [Freesurfer] [freesurfer] version differences for pial matter / skull strip?

Ok that worked. I sent the data for a subject with the skull stripping issue that is common in most of our dataset. Thanks, Michelle On Fri, Dec 1, 2017 at 4:56 PM, Bruce Fischl wrote: > try cd'ing to incoming not outgoing (the names are from our perspective I >

Re: [Freesurfer] [freesurfer] version differences for pial matter / skull strip?

yes, it should. You should just be able to do a "put" On Fri, 1 Dec 2017, Michelle VanTieghem wrote: Hi,  I am confused by the instructions for the ftp. Once I am logged into the ftp and have navigated to the transfer/incoming directory, how am I supposed to find / access the file that I

Re: [Freesurfer] [freesurfer] version differences for pial matter / skull strip?

Hi, I am unsure whether this worked: see attached screenshot. Thanks! M On Fri, Dec 1, 2017 at 4:26 PM, Bruce Fischl wrote: > yes, it should. You should just be able to do a "put" > > On Fri, 1 Dec 2017, Michelle VanTieghem wrote: > > Hi, >> I am confused by the

[Freesurfer] subcortical structures volume

Hi professor, I am using Freesurfer 6.0 and get the volume of subcortical structures. I want to get the relationship between age and volume. I only have one group, is it necessary to take gender and eTIV as a covariate? If it is necessary, Which statistical analysis should be used? I