Freesurfer January 2005

freesurfer@nmr.mgh.harvard.edu

23 participants
50 discussions

topology of vertices in cortical reconstructions
by Glenn Lawyer 26 Jan '05

26 Jan '05

Hi, We are experimenting with statistical methods for analyzing cortical thickness differences in a case/control study. After doing the cortical reconstructions and running mris_glm, we will have the significance (p-value) of the t-ratio of the contrast between case and control. What we want to do is first apply some spatial smoothing to the p-values, and use a false discovery rate controlling method on the resulting smoothed p-values to find an appropriate significance level. We can run mris_glm, save the output in bfloat format, and load into Matlab using 'fread'; no problems. What we are lacking is a description of the topology of the vertices, and the mapping from the vector of floats to this topology. I assume a triangulation implies a 6-connect structure. Correct? Assume the vertices are numbered 1:163842 (as in the output of mris_glm --sigt), which vertices are neighbors (what are the six neighbors of vertex 100) ?? Are distances between neighbors (nearly) constant, or do they vary??? Very much appreciative of your reply, +glenn -- I want to go farther, farther! A. E. L. > Glenn Lawyer < > Instituttgruppe for psykiatri < > Postboks 1130 Blindern < > 0318 Oslo < < http://folk.uio.no/davidgl > <><><><><><><><><><><><><><><><><:)

2 1

how to seed points
by Wan Park 25 Jan '05

25 Jan '05

when i try to create the surface, i receive this message: /usr/local/freesurfer_package/freesurfer/bin/Darwin/mri_fill -lval 255 -rval 80 -ccmask -T 1 -L /usr/local/freesurfer_package/freesurfer/subjects/23963/mri/tmp/ ponscall.dat /usr/local/freesurfer_package/freesurfer/subjects/23963/mri/wm /usr/local/freesurfer_package/freesurfer/subjects/23963/mri/filled using 255 as fill val for left hemisphere. using 80 as fill val for right hemisphere. not using corpus callosum to mask possible location of pons. logging cutting plane coordinates to /usr/local/freesurfer_package/freesurfer/subjects/23963/mri/tmp/ ponscall.dat... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; /usr/local/freesurfer_package/freesurfer/bin/Darwin/mri_fill: could not find valid seed for the cc No such file or directory Looking for area (min, max) = (350, 1400) area[0] = 2435 (min = 350, max = 1400), aspect = 0.88 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... using +/- offset search region where offset is 24..... using +/- offset search region where offset is 27..... using +/- offset search region where offset is 30..... using +/- offset search region where offset is 33..... using +/- offset search region where offset is 36..... using +/- offset search region where offset is 39..... using +/- offset search region where offset is 42..... using +/- offset search region where offset is 45..... using +/- offset search region where offset is 48..... Looking for area (min, max) = (350, 1400) area[0] = 2001 (min = 350, max = 1400), aspect = 0.99 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... using +/- offset search region where offset is 24..... using +/- offset search region where offset is 27..... using +/- offset search region where offset is 30..... using +/- offset search region where offset is 33..... using +/- offset search region where offset is 36..... using +/- offset search region where offset is 39..... using +/- offset search region where offset is 42..... using +/- offset search region where offset is 45..... using +/- offset search region where offset is 48..... /usr/local/freesurfer_package/freesurfer/bin/Darwin/mri_fill: could not find corpus callosum No such file or directory INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in structure! Searching neighborhood... could you please teach me how to solve the problem? thanks, wan park

2 1

manual parcellation of labels
by Ketwaroo, Gyanprakash Avinash 25 Jan '05

25 Jan '05

Hello, I guess my main question is are the volume tal coordinates in tkmedit equivalent to the vertex Tal in tksurfer. That is, can I ignore drawing the line in tkmedit and converting with csurf, and just trace out the Tal = 0 line in tksurfer? I think this is what you are implying but just want to make sure. Also, the cingulate labels are in RAS coordinates. Is there a quick way to convert the Tal=0 coordinate to a RAS coordinate so that I can just divide the cingulate label by applying a condition (eg RAS < x) rather than tracing it out in tksurfer. Thank you for all your help. Avinash Hi Aviinas, you could draw the label directly on the inflated surfaces, then use mri_label2label to map it from one subject (or the average) to the others. cheers, Bruce

1 0

manual parcellation of labels
by Ketwaroo, Gyanprakash Avinash 25 Jan '05

25 Jan '05

Hi, I want to divide my cingulate labels into anterior and posterior cingulate labels. This divison is based on a line perpendicular to the AC-PC axis, and through the AC. Currently, I am trying to do this by using csurf and clicking and saving points along the Tal = 0 coordinate within the midsagittal plane of the tkmedit view. I then go to the points in the tksurfer view and then draw a line here to create a new label. It seems that there must be an easier way of doing this using the code that csurf employs to link the volume and surface coordinates. If you could suggest a method for automating this, I would greatly appreciate it. Thanks, Avinas

2 1

Functional Overlay
by Ruth Smans 25 Jan '05

25 Jan '05

Hi, I am having problems with functional overlays onto my anatomical. When I go to set functional sessions directory an Alert message appears saying : session:left_down (functional name) scripts subdir not found using /tmp make scripts dir to save session_specific params. What exactly is this refering too? Thanks alot Ruth Smans

1 0

TKSURF ERROR
by Ajay Pillai 20 Jan '05

20 Jan '05

I recently upgraded my fedora to fedora core 3 I am getting the following error when I try to use tksurf /user/freesurfer/bin/Linux/tksurfer: error while loading shared libraries: libtk8.3.so: cannot open shared object file: No such file or directory How do I fix this Ajay

2 1

how to visualize the parcellation
by Wan Park 20 Jan '05

20 Jan '05

hi, after doing: recon-all -stage4b -subjid 40032 -hemi lh recon-all -stage4b -subjid 40032 -hemi rh, i did: parcellate_subject 40032 and it seems to have finished without problems. now, how can i visualize the different areas? thanks, wan

4 4

full surface cuts
by Joongnam Yang 19 Jan '05

19 Jan '05

Hi, I followed the manual instructions on full surface cuts, but not working. Here is what I did. (1) cut five relaxation cuts. (2) right-click. (3) left-click one of regions that are to be kept. (4) select "Fill Uncut Area" button, The image refrehses, but no change is made on the image. The circular midline region is supposed to be cut off. (I looked at the archive; someone had this problem, but she just said later she figured it out and no comment on it was given) Thanks. Nam.

2 1

Re: [Freesurfer] manual editting not implemented
by Joongnam Yang 14 Jan '05

14 Jan '05

Thanks Brian, Does that mean csurf interface is useless for "creating surfaces" to implement the editting of major topological defects? Nam. >>> "Brian T. Quinn" <btquinn(a)nmr.mgh.harvard.edu> 01/14/05 3:22 PM >>> hi Nam- please refrain from using the csurf interface to create surfaces. instead, run through the command line: recon-all -stage2 -subjid <subject_name> this will create a log file($SUBJECTS_DIR/subject_name/scripts/recon-all.log) include this with your email so we can better assist you with your difficulties. thanks, brian On Fri, 14 Jan 2005, Joongnam Yang wrote: > Hi, > > I did manual editting for lateral ventricles, fornix, basal ganglia, optic > nerve, > as illustrated in the cortical reconstruction tutorial, for both left and > right hemispheres, and DID save them in the "wm" volume. > Then I ran "create surface", but nothing is changed. > > What could have been wrong? > > Comments are appreciated. > Nam. > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- brian t. quinn

3 2

manual editting not implemented
by Joongnam Yang 14 Jan '05

14 Jan '05

Hi, I did manual editting for lateral ventricles, fornix, basal ganglia, optic nerve, as illustrated in the cortical reconstruction tutorial, for both left and right hemispheres, and DID save them in the "wm" volume. Then I ran "create surface", but nothing is changed. What could have been wrong? Comments are appreciated. Nam.

2 1

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Freesurfer January 2005