[Freesurfer] Freeview error: Surface does not contain valid volume geometry information

Hi all, after doing GLM analysis I'm trying to run freeview to see results, but I get this warning: Surface does not contain valid volume geometry information. It may not align with volumes and other surfaces. What's wrong? I'm using 5.1 version. Thanks to all. Claudia -- D

[Freesurfer] make_average_volume problems

full and I have permissions. Any ideas? Thanks a lot. Claudia -- Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia Laboratorio di Neuropsichiatria Dipartimento di Neurologia Clinica e Comportamentale IRCCS Fondazione Santa Lucia via Ardeatina 306 - 00179 Roma Tel. +39 (0)6 51501358

[Freesurfer] cannot read white surface

/SUBJ/newtemplate/surf/lh.white ERROR: make_average_surface Any ideas on what the problem is? Why cannot find white surface? I'm using 5.1 version, but I got the same problem with version 5.3. Thanks to all. Claudia -- Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia Labo

[Freesurfer] cannot read white surface

/SUBJ/newtemplate/surf/lh.white ERROR: make_average_surface Any ideas on what the problem is? Why cannot find white surface? I'm using 5.1 version, but I got the same problem with version 5.3. Thanks to all. Claudia -- Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia Labo

[Freesurfer] Troubles witg GLM Surface-based Cluster Summary Table

uster Size (76467.08 mm2) greater than the Total Cortical Surface (65416.6 mm2). Are there some errors in this? Thanks a lot to all of you. Claudia -- Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia Laboratorio di Neuropsichiatria Dipartimento di Neurologia Clinica e Comportament

[Freesurfer] manually drawn ROI mean thickness extraction

Dear all freesurfers, I have manually drawn a region of interest and saved it as a label file in the /label folder and I now want to extract mean thickness of this ROI. How can I do it? Thanks a lot Claudia -- Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia Laboratorio di

Re: [Freesurfer] asegstat values pre and post editing

rsions reran the aseg for autorecon2-cp, but 5.3 does not > > n Wed, 24 Jul 2013, Claudia Dacquino wrote: > > Thanks Bruce,but I'm sure I ran autorecon2-cp autorecon3: >> >> >> recon-all -autorecon2-cp -autorecon3 -subjid. >> >> However, is it ok to use as

Re: [Freesurfer] asegstat values pre and post editing

gt; if you run autorecon2 you will rerun the aseg, which will use the control > points to change the subcortical intensity normalization. If you don't want > that to happen, you need to run -autorecon2-cp > > cheers > Bruce > > > On Wed, 24 Jul 2013, Claudia Dacquino wrote: &g

[Freesurfer] asegstat values pre and post editing

Dear Freesurfers, we recently processed a sample of adult patients and then we reran autorecon-2 and autorecon-3 after editing contol points, white matter and pial surface. We exported the asegstat table both pre and post editing, and we got different volumes for most of the subjects. How is that p

[Freesurfer] error in downloading tutorial dataset

Hi freesurfers, I'm trying downloading the tutorial dataset but after several attempts I still couldn't connect to the server and I recived this message repeately, even with the -c flag: "server response error, closing connection". I'm working on Linux Centos System and using the wget command.

Re: [Freesurfer] processing flow

everything the autorecon2-wm and autorecon2-pial would and more, > so you can just run that. > > cheers > Bruce > > > On Wed, 5 Jun 2013, Claudia Dacquino wrote: > > Hi everyone,I'm sorry, this is a probably very basic question, but I'm a >> >> li

[Freesurfer] processing flow

Hi everyone, I'm sorry, this is a probably very basic question, but I'm a little bit confused about the recon-all correct flowchart. I mean, the first step is recon-all -s -all (comprising autorecon1, autorecon2 and autorecon3), correct? After this step if I want to add control points then I hav

Re: [Freesurfer] hippocampal subfield segmentation

Thank you for your response. Would you suggest a reference I can refer to? 2013/6/4 Juan Eugenio Iglesias > I would probably leave out the fissure, but not the fimbria... > Cheers, > /Eugenio > > On Tue, 2013-06-04 at 14:33 +0200, Claudia Dacquino wrote: > > Hi guys!

[Freesurfer] hippocampal subfield segmentation

Hi guys! I have a dataset including hippocampal subfields obtained through the -hippo-subfields flag. I want to have a measure of total hippo volume and I'm not sure which structures should I include in the sum. I was thinking to exclude fimbria and fissure and sum the others. Am I right? Or shoul

Re: [Freesurfer] autorecon3 error

Ok. Thanks a lot! Cheers Claudia Il giorno lunedì 3 giugno 2013, Bruce Fischl ha scritto: > yes, you should be running > > recon-all -autorecon2-cp > > cheers > Bruce > > On Mon, 3 Jun 2013, Claudia Dacquino wrote: > > Is this the problem? Is there an incor

Re: [Freesurfer] autorecon3 error

Is this the problem? Is there an incorrect command? Thanks. Cheers Claudia Il giorno lunedì 3 giugno 2013, Bruce Fischl ha scritto: > Hi Claudia > > there is no autorecon3-cp, just autorecon2-cp > > cheers > Bruce > On Mon, 3 Jun 2013, Claudia Dacquino wrote: > >

Re: [Freesurfer] error loading volume brainmask.gcut.mgz

and my freesurfer version is 5.1. 2013/5/30 Claudia Dacquino > yes I did answer again to the list. > no it is no full at all. > > > > 2013/5/30 Bruce Fischl > >> is your disk partition full? And please cc the list so others can answer >> Bruce >> >>

Re: [Freesurfer] error loading volume brainmask.gcut.mgz

yes I did answer again to the list. no it is no full at all. 2013/5/30 Bruce Fischl > is your disk partition full? And please cc the list so others can answer > Bruce > > On Thu, 30 May 2013, Claudia Dacquino wrote: > > Yes I did run mri_info, these are the results: >>

Re: [Freesurfer] error loading volume brainmask.gcut.mgz

-0. 1. -0. 128.4031 0. 0. 0. 1. Cheers 2013/5/30 Claudia Dacquino > Yes I did run mri_info, these are the results: > > Volume information for brainmask.gcuts.mgz > type: MGH > dimensions:

[Freesurfer] error loading volume brainmask.gcut.mgz

Hi Freesurfers, I'm trying to remove some dura which affect my surfaces with the command recon-all -skullstrip -clean-bm -gcut -subjid but then I can't use tkmedit to check that. The message I get is: Error: Loading volume brainmask.gcut.mgz Couldn't read the anatomical volume. Tkmedit couldn't

[Freesurfer] error loading volume brainmask.gcut.mgz

Hi Freesurfers, I'm trying to remove some dura which affect my surfaces with the command recon-all -skullstrip -clean-bm -gcut -subjid but then I can't use tkmedit to check that. The message I get is: Error: Loading volume brainmask.gcut.mgz Couldn't read the anatomical volume. Tkmedit couldn't

Re: [Freesurfer] adding grey matter

my subjdir is on FTP server. thanks claudia 2013/4/29 Claudia Dacquino > I'm uploading my subjdir on FTP server. > Thanks a lot. > Claudia > > > 2013/4/29 Bruce Fischl > >> Hi Claudia >> >> if you upload your whole subject and send us some example

Re: [Freesurfer] adding grey matter

I'm uploading my subjdir on FTP server. Thanks a lot. Claudia 2013/4/29 Bruce Fischl > Hi Claudia > > if you upload your whole subject and send us some example voxel coords of > where you are looking we will take a look > > Bruce > > > On Mon, 29 Apr 2013,

Re: [Freesurfer] adding grey matter

y be incorrect if the > white surface is incorrect, so the first thing to do is make sure it is > right > > > Bruce > > > On Mon, 29 Apr 2013, Claudia Dacquino wrote: > > But in "brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white >> -segmentation aseg.mgz&q

Re: [Freesurfer] adding grey matter

But in "brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation aseg.mgz" it's labeled as white matter, could it be possible? 2013/4/29 Claudia Dacquino > Actually it could not be WM, but I'm quite sure that there is grey matter > excluded by pial bo

Re: [Freesurfer] adding grey matter

Actually it could not be WM, but I'm quite sure that there is grey matter excluded by pial bounaries as well, how can I add that? 2013/4/29 Bruce Fischl > visually is the only way. Do you think it is white matter? > > On Mon, 29 Apr 2013, Claudia Dacquino wrote: > > Yes it

Re: [Freesurfer] adding grey matter

Yes it's my doubt too, but how can I check this? 2013/4/29 Bruce Fischl > then it's not rerunning the -cp. And is it really wm if it's that dark? > > On Mon, 29 Apr 2013, Claudia Dacquino wrote: > > Bruce,no the intensity is lesser then 110 at those voxels, it&

Re: [Freesurfer] adding grey matter

Bruce, no the intensity is lesser then 110 at those voxels, it's like 60-70. Claudia 2013/4/29 Bruce Fischl > is the intensity at those voxels 110 after you have processed with > autorecon2-cp? > > On Mon, 29 Apr 2013, Claudia Dacquino wrote: > > The problem is that a

Re: [Freesurfer] adding grey matter

Claudia 2013/4/29 Bruce Fischl > Hi Claudia > > can you describe the problems? And cc the list so that others can help? > thanks > > Bruce > > On Mon, 29 Apr 2013, Claudia Dacquino wrote: > > Hi Bruce,I think wm.mgz it's accurate enough, but what you mean? &

Re: [Freesurfer] adding grey matter

Hi Bruce, I think wm.mgz it's accurate enough, but what you mean? I'm trying to upload data, but I've problems with your server. Cheers, Claudia 2013/4/29 Claudia Dacquino > Hi Bruce, > I think wm.mgz it's accurate enough, but what you mean? > I'm trying to u

[Freesurfer] adding grey matter

Hi Freesurfers, I have a question about pial editing. I have some reconructions in which there's a lot of grey matter excluded, and consequently white metter too. I did correct these images manually by control points editing, and then autorecon2-cp autorecon3, but some cortical grey matter continue

Re: [Freesurfer] autorecon2-cp error

dramatically wrong. Did you check any of the outputs (wm.mgz, filled.mgz, > lh.orig, etc...)? > > cheers > Bruce > > On Thu, 18 Apr 2013, Claudia Dacquino wrote: > > Hi freesurfer, >> my autorecon2-cp after ctrl pts edits exited with this error message: >> >>

[Freesurfer] autorecon2-cp error

Hi freesurfer, my autorecon2-cp after ctrl pts edits exited with this error message: CORRECTING DEFECT 0 (vertices=176788, convex hull=8149) Excessive topologic defect encountered: could not allocate -776253752 edges for retessellation Cannot allocate memory Could anyone help me with this, please

Re: [Freesurfer] cortical recontruction error

ig to email. You can either use our ftp site or file >> drop >> >> cheers >> Bruce >> On Mon, 25 Mar 2013, Claudia Dacquino wrote: >> >> I'm sorry, I did mean the moderator of Freesurfer mailing list. >>> >>> 2

Re: [Freesurfer] cortical recontruction error

I'm sorry, I did mean the moderator of Freesurfer mailing list. 2013/3/25 Bruce Fischl > you should be able to use our ftp site or file drop. Which administrator > do you mean? > > On Mon, 25 Mar 2013, Claudia Dacquino wrote: > > I was trying, but the administrator did r

Re: [Freesurfer] cortical recontruction error

I was trying, but the administrator did reject that, because the file is too big. 2013/3/25 Claudia Dacquino > I was trying, but the administrator did reject that, because the file is > too big. > > > 2013/3/25 Claudia Dacquino > >> Hi Bruce, >> I'

[Freesurfer] cortical recontruction error

Dear Freesurfers, I'm new and I'm starting using Freesurfer. I'm having a problem with one subject, during the cortical reconstruction (recon-all) the process stops at this stage: mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz at this point:

Re: [Freesurfer] editing Cts an pial surface

nterventions you can take to correct them, that > are detailed on our wiki > > > cheers > Bruce > > > On Mon, 18 Mar 2013, Claudia Dacquino wrote: > > Thaks a lot Bruce, >> so I have to edit WM first, and then, what about grey matter? Do I have >&g

[Freesurfer] editing Cts an pial surface

Hi everyone, I'm a very new fresurfer user and I have to understand the very simple basis of its use yet. So I have some maybe stupid questions about that. I heve to work on cortical thickness, so I suppose I have to complete the segmentation and then correcting CPs and Pial surface. The first ques

[Freesurfer] Correcting CPs and Pial

Hi everyone, I'm a very new fresurfer user and I have to understand the very simple basis of its use yet. So I have some maybe stupid questions about that. I heve to work on cortical thickness, so I suppose I have to complete the segmentation and then correcting CPs and Pial surface. The first ques