Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30128 discussions

two questions
by Joongnam Yang 05 Jan '05

05 Jan '05

Hi, Sounds like trivial questions... (1) How do you check if the talairach.xfm is OK? (2) Either during the command-line option of recon-all -stage 1 thru 4, when do you use tkregister2 for registeration? Thanks for the help. Nam.

2 1

not symmetrical
by Joongnam Yang 05 Jan '05

05 Jan '05

Hi, For another subject, the inflated surfaces for left and right are not right after "create surface" in csurf GUI. They are not symmetrically cut. The brain seems to have been cut not through the midline, but a notch toward left hemisphere. When I looked at wm or T1 surfaces, they show that they are not symmetrical, the right hemisphere taking some of the left hemisphere. When the cut is not right, what should I do? Comments appreciated. Nam.

2 1

Re: [Freesurfer] unpredictable
by evelina＠nmr.mgh.harvard.edu 05 Jan '05

05 Jan '05

Nam, did the command-lines work for those same subjects for which the GUI failed? I prefer the command-line operation, in any case. > Hi Nam, > > this depends on the quality of the scans, the subject positioning, and > the quality of the MNI talairaching. > > Bruce > > On Wed, 5 Jan 2005, Joongnam Yang > wrote: > > > Hi, > > > > For some subjects' data, pure Csurf GUI works, while for other subjects > > Csurf GUI complains, giving errors during "create surface", upon which I > > have to run the command-line option "recon-all -stage1" with CC and pons > > coordinates. > > > > Is it ture, I mean the Csurf GUI is unpredictable, because of the nature of > > the algorithm? > > > > Comments appreciated. > > > > Nam. > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

1 0

unpredictable
by Joongnam Yang 05 Jan '05

05 Jan '05

Hi, For some subjects' data, pure Csurf GUI works, while for other subjects Csurf GUI complains, giving errors during "create surface", upon which I have to run the command-line option "recon-all -stage1" with CC and pons coordinates. Is it ture, I mean the Csurf GUI is unpredictable, because of the nature of the algorithm? Comments appreciated. Nam.

2 1

CC and pons
by Joongnam Yang 04 Jan '05

04 Jan '05

Hi all, recon-all -stage1 gives me an error on "could not find corpus callosum". So, I used Tkmedit to find xyz talairach coordinates of the two structures and ran stage1 again, many times with different coordinates. "surfaces" are twisted and "filled" volume didn't look like a brain. How can I find correct coordinates? The way I did: I loaded T1 volume and aux volume and picked the approximate center of each structure. Any wise words? Thanks. Nam.

2 1

tkmedit problem
by Kapdoskar, Shweta (NIH/CC/DRD) 04 Jan '05

04 Jan '05

Hello, I am using freesurfer on suse 9.0. I have run into problem while using tkmedit tool. When I click on the volume button in csurf , it initially turns purple and then again becomes white without doing anything. It does not spit out error messege either. Using the log messege generated , tran the following line from shell: /usr/local/freesurfer/bin/Linux/tkmedit CAM T1 -csurf (where CAM is the subject directory) .Even now it does not do anything. Plz help Shweta Kapdoskar Diagnostic Radiology Clinical Center , Rm : 1C 534 National Institutues Of Health , 9000 Rockville Pike, Bethesda , MD- 20892 Ph: 301-402-2896 Fax: 301-496-9933

1 0

Freesurfer on Latitude X300?
by Kristine Beate Walhovd 03 Jan '05

03 Jan '05

Hi We've had some trouble with displaying the Freesurfer graphics correctly on some new stationary Dell PCs recently. I now need a new laptop, and I'm considering buying a Dell Latitude X300. I won't use it as an analysis machine, mostly just for travel, but I need to be able to display images and work with Freesurfer on it. Most features on this light-weight model are integrated so that they can't be changed, including the graphics card (855GM integrated graphics shipset - up to 64MB), so I was wondering if any of you have any expericence with running Freesurfer on this model, and if so, does it work OK? I'd be grateful for any comments. Thanks, Kristine

3 2

fix topology
by Joongnam Yang 03 Jan '05

03 Jan '05

Hi happy new year everybody, "fix topology" in Freesurfer takes 57 hours on my machine, which has a speed of 1 GHz and RAM of 1 Gbytes, a pretty fast machine. 57 hours sounds TOO long for me; other processes take less than an hour. Does it sound OK, or something wrong? Any comments are appreciated. Nam.

2 1

FSL analyze to bfloat
by Jyrki Ahveninen 30 Dec '04

30 Dec '04

Hi, I tried to convert analyze (FSL) img files to bfloat (for group analysis) using spm2bfloat. It complains about the header size. Is there a fix for this? Same problem occurred with spm_to_bfloat.m Thanks, Jyrki header_key sizeof_hdr = 1543569408 data_type = db_name = extents = 4194304 session_error = 0 regular = r hkey_un0 = image_dimension dim = 1024 16384 16384 5120 256 0 0 0 datatype = 4096 bitpix = 8192 dim_un0 = 0 pixdim = 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 compressed = 0.000000 verified = 0.000000 glmax = 167772160 glmin = 0 data_history descrip = Externally created avw->header aux_file = orient = originator = 0 0 0 0 0 0 0 0 0 0 generated = scannum = patient_id = exp_date = exp_time = hist_un0 = views = 0 vols_added = 0 start_field = 0 field_skip = 0 omax = 0 omin = 0 smax = 0 smin = 0 incorrect header size in analyze file -- Jyrki Ahveninen, PhD MGH/MIT/HMS - Athinoula A. Martinos Center for Biomedical Imaging CNY 149-2301, 13th Street Charlestown, MA 02129 email: jyrki(a)nmr.mgh.harvard.edu

1 0

tklib8.3.so
by Kevin DeSimone (kdesimon＠Princeton.EDU) 27 Dec '04

27 Dec '04

hi-- i've recently installed the February 18th 2004 (561M) snapshot on my linux. when trying to run any process requiring graphical display of surfaces/volumes, i get the following error: "/usr/local/freesurfer/bin/Linux/tkmedit: error while loading shared libraries: libtk8.3.so: cannot open shared object file: No such file or directory" i was able to run these processes just fine w/ the older version of freesurfer (i believe it was the june 27 2003 snapshot) also, i noticed someone posted to the list w/ this problem in April, and the response gave link to .rpm of this missing library. however, that library is dependent on yet another library (libtcl.so.0)-- which i can't find. what's an easy fix for this, so i don't have install libraries for libraries? kevin desimone

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Freesurfer