Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Start a nNew thread

% threshold in mri_segment
by Bai Xue 17 Feb '09

17 Feb '09

Hi, What's the use of the % threshold (-p option) in mri_segment? Thanks. Bai

2 1

brazil course
by Sam Torrisi 17 Feb '09

17 Feb '09

hello there, i have questions for Pedro Paulo de M. Oliveira regarding the upcoming Brazilian FS course but cannot find his email address anywhere in the archives or his announcement. also, do you know if there is another upcoming course in the states, preferably on the west coast? thank you -Sam Torrisi Neuroscience IDP PhD student University of California Los Angeles

2 1

(no subject)
by carl＠nmr.mgh.harvard.edu 17 Feb '09

17 Feb '09

As far as the first, This happens sometimes when you make your own average subject. You just need to inflate it more. I will try to dig up an old email I have on the commands. As for the second, just click the redraW BUTTON CARL SCHWARTZ On 2/17/09 12:44 PM, "Devdutta W" <devdutta.w(a)gmail.com> wrote: Oops, forgot the attachment. On Tue, Feb 17, 2009 at 11:42 AM, Devdutta W <devdutta.w(a)gmail.com> wrote: Hello again, My questions refer to the attached image. The image is of the average subject I created from our subjects using the "make_average_subject" command. As you can see, in an inflated view there are many gyri and sulci looking structures that shouldn't be there. Clearly something is not right. My first question is what aspect of our subjects' brains could be causing this? I have inspected the brains in tksurfer and have not found any defects that could account for this. My second question refers to the oddness at the bottom left of the image. That is something I notice happening all the time. Everytime I drag any window across the tksurfer or tkmedit window that happens. It goes away once I rotate the brain or zoom in or out or anything like that. Is this something that people have encountered before or is this an anomaly unique to our system? Once again, I really appreciate any help these matters. Thank you, Devdutta

3 2

mri_convert crash
by Kirk Gregory R. 17 Feb '09

17 Feb '09

I have epi data with a single slice at each time point and am trying to convert it. get MRIresample(): error inverting matrix; determinant is nan, matrix is: when it tries to resample the data. seems the single slice blows a fuse. i don't see a flag to turn off the resampling ? or other way ? Greg.

1 0

Qdec area measure
by Devdutta W 17 Feb '09

17 Feb '09

Hi, In Qdec, what exactly does the area option measure? As I understand, qdec does its calculations vertex by vertex, which makes sense in case of cortical thickness. But if area refers to surface area how does that change from vertex to vertex? Or is it calculating the area by ROI? Is my understanding of this correct? Also, as regards to the volume option, I was told that it is not working. But when I ran it it seems to work fine. Should I take that to mean that the calculation has bugs and that the results it displays are incorrect? Or has it been fixed? I greatly appreciate any help in this matter. Thank you, Devdutta

4 7

more inflation of average subject
by carl＠nmr.mgh.harvard.edu 17 Feb '09

17 Feb '09

below worked for us carl schwartz ---------- Forwarded message ---------- From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Date: Fri, Sep 5, 2008 at 1:26 PM Subject: Re: more inflation To: Doug Greve <greve(a)nmr.mgh.harvard.edu> two things: 1. use -n <i>, where the default <i> is 10 (try 20) 2. -dist <l>, where the default l is 0.1 (try something smaller, or 0) you could also dl -f <rms> where default <rms> is 0.015 (try smaller for smoother surfaces) for example: mris_inflate -n 20 -f 0.001 -dist 0 lh.white lh.inflated_more should make a smoother surface On Fri, 5 Sep 2008, Doug Greve wrote: Bruce, off the top of your head, do you know how an inflated surface can be inflated more? I've tried mris_inflate, but it does not seem to help. It's just for display, but a little annoying. thanks doug >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > > > As far as the first, This happens sometimes when you make your own average > subject. You just need to inflate it more. I will try to dig up an old > email I have on the commands. > > As for the second, just click the redraW BUTTON > > > CARL SCHWARTZ > > On 2/17/09 12:44 PM, "Devdutta W" <devdutta.w(a)gmail.com> wrote: > > Oops, forgot the attachment. > > On Tue, Feb 17, 2009 at 11:42 AM, Devdutta W <devdutta.w(a)gmail.com> wrote: > Hello again, > My questions refer to the attached image. > The image is of the average subject I created from our subjects using the > "make_average_subject" command. As you can see, in an inflated view there > are many gyri and sulci looking structures that shouldn't be there. > Clearly something is not right. > > My first question is what aspect of our subjects' brains could be causing > this? I have inspected the brains in tksurfer and have not found any > defects that could account for this. > > My second question refers to the oddness at the bottom left of the image. > That is something I notice happening all the time. Everytime I drag any > window across the tksurfer or tkmedit window that happens. It goes away > once I rotate the brain or zoom in or out or anything like that. Is this > something that people have encountered before or is this an anomaly unique > to our system? > > Once again, I really appreciate any help these matters. > > Thank you, > Devdutta > > > > > > > > Carl E. Schwartz, M.D. Harvard Medical School Director, Developmental Neuroimaging & Psychopathology Laboratory Psychiatric Neuroscience Program Massachusetts General Hospital tel 617-726-8965 fax 617-726-4078

1 0

Re: Freesurfer Digest, Vol 60, Issue 30
by Daniel Wakeman 17 Feb '09

17 Feb '09

Hi Devdutta, I'm fairly certain (i.e. correct me if I'm wrong people) that this average brain looks correct. Some of the gyri and sulci are more pronounced on the group inflated cortex than on the individuals, because in the averaging process these are more consistent across participants (like the central sulcus for example). If you load the curvature and binarize it, you will see what looks like a normal brain, but with much fewer gyri and sulci (due to gyri and sulci not matching across brains, from the normal intersubject variability). You can also check this by loading up the labels for the group participant As to your second question, this is a common bug experienced on many systems. Freesurfer has a few implemented techniques to deal with this without changing your image i.e. rotating etc.. The simplest is just right clicking the image. Next there is the refresh button on the toolbar. There is also a setting you can change to have the windows refresh more frequently, but this is very costly in computing power. Dan freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: Freesurfer visuals (Devdutta W) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 17 Feb 2009 11:44:05 -0600 > From: Devdutta W <devdutta.w(a)gmail.com> > Subject: [Freesurfer] Re: Freesurfer visuals > To: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <95b61cf50902170944u29ba6278nf4e16822af92916(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Skipped content of type multipart/alternative

1 0

Freesurfer visuals
by Devdutta W 17 Feb '09

17 Feb '09

Hello again, My questions refer to the attached image. The image is of the average subject I created from our subjects using the "make_average_subject" command. As you can see, in an inflated view there are many gyri and sulci looking structures that shouldn't be there. Clearly something is not right. My first question is what aspect of our subjects' brains could be causing this? I have inspected the brains in tksurfer and have not found any defects that could account for this. My second question refers to the oddness at the bottom left of the image. That is something I notice happening all the time. Everytime I drag any window across the tksurfer or tkmedit window that happens. It goes away once I rotate the brain or zoom in or out or anything like that. Is this something that people have encountered before or is this an anomaly unique to our system? Once again, I really appreciate any help these matters. Thank you, Devdutta

1 1

still exiting with errors
by Dankner, Nathan (NIH/NIMH) [F] 17 Feb '09

17 Feb '09

Sorry to post this again, but I am still having issues with surfaces exiting with errors. These are the two outputs that I have gotten: MRI_fill: could not read segmentation from aseg.auto_noCC.mgz reading segmented volume aseg.auto_noCCseg.mgz... ERROR: cannot find [subject path]/aseg.auto_noCCseg.mgz No such file or directory and ERROR: cannot find [subject path]/mri/aseg.mgz Mr. Schmansky indicated that this may be due to 2 different versions being used. I have been running recon-all on version 4.1.0 on a 64 bit linux machine, and editing on the same version but on a mac. Also, I attempted to use the -clean-aseg command as directed, but this doesn't seem to have fixed the problem. I'm currently in the process of updating both machines to version 4.2.0, so I don't know how this will affect things. Any suggestions? Thanks in advance, Nathan

3 5

bbregister: PET and MRI
by Rafa x 16 Feb '09

16 Feb '09

Dear FS Team, I have a problem with the bbregister command. I used it for coregister a MRI with a PET. My first step is set the same origin and orientation for both images (approximately) (I use SPM or tkregister2). After, I write in the terminal "bbregister --mov s24PET.img --t1 --s sr24 --init-fsl --reg register.dat"(s24 is the name of my patient) The result of the process is a bad corregister (see the included file). I would like to improve this result. Maybe the number of iterations is too less (I'm not sure of that) I probed with the flags SPM, FSL and HEADER but they don't provide good result. Thank you all in advance.

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer