Freesurfer February 2009

freesurfer@nmr.mgh.harvard.edu

86 participants
126 discussions

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

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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

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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

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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

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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.

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Qdec question
by Devdutta W 16 Feb '09

16 Feb '09

Hi, I am using qdec for analysis and noticed that in addition to thickness measures I can select others such as area and volume. I have been trying to figure out what exactly the area measure refers to (surface area, etc.). I did not find it on the website. Can someone clarify that for me? If this is a repeat question, I apologize and ask that you point me to the archived post. Thank you, Dev

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In common stereotactic space?
by Jürgen Hänggi 16 Feb '09

16 Feb '09

Dear FS experts I had run recon-all -long on two time points and would like to subtract the cortical thickness maps of the two time points. Do the two ?h.thickness maps of the different time points are already in the same space so that they can be directly subtracted in MATLAB? Or Do I have to use mri_surf2surf to register them before I can subtract them? Thanks Regards Jürgen ---------------------------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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manual segmentation of subcortical structures
by Jose Luis Cantero Lorente 16 Feb '09

16 Feb '09

Hi there, we have a bunch of MRI scans already segmented by using the typical FS recons protocol. Now we would like to improve the hippocampus and thalamus delimitation by manual segmentation, but several basic questions arose: 1. Are there radiological protocols (commonly used) to segment these subcortical structures from FS? Any help with this issue will be very welcome. 2. Is there any tutorial to manually segment subcortical structures from FS? We just performed cortical segmentation and are not familiar at all with manual subcortical segmentation menus and steps to follow. 3. Will these subcortical changes affect to our cortical thickness values and cortical parcellation? Thanks for your help. Best regards, Jose --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cellular Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/es/

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Wrong Red Line and Yellow Line
by Haobo Zhang 16 Feb '09

16 Feb '09

Hi all, After running with Freesurfer, I found the red line cutting through the superior temporal gyrus in the coronal view slice. And the yellow line excluded part of the white matter in this area. Please check the attachment. Does anyone have experience in fixing this type of problems? Thank you for your help! Cheers, Haobo Zhang School of Psychiatry, University of New South Wales

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Version re-run
by Martin Ystad 16 Feb '09

16 Feb '09

Hi all, I have 100-something scans already run on a FreeSurfer version from 2005 that I'd like to re-run with the newest version of FreeSurfer. The subjects contain manual edits to the brainmask.mgz and wm.mgz, as well as control points. As far as I have understood, when running autorecon2 my manual edits will be saved by default. However, is there any need to re-run the autorecon1-steps for my subjects? Also: when do you plan to release the next version of FreeSurfer? Many thanks, Martin Ystad

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Freesurfer February 2009