Freesurfer November 2004

freesurfer@nmr.mgh.harvard.edu

22 participants
53 discussions

Re: [Freesurfer] functional combo box
by Joongnam Yang 15 Nov '04

15 Nov '04

When I clicked "Volume-Stats" button on the top right corner of the window that shows up after I clicked "View Functional Data" button of csurf, I got the tksurfer window, but with the following error Error: Parsing command line options Option -invphaseflag not recognized This option was not recognized and ignored. Could someone let me know how to fix it? Nam.

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functional combo box
by Joongnam Yang 15 Nov '04

15 Nov '04

Hi everyone, For functional overlay, In csurf GUI window, on the right-most side, there is a "functional" combo box, where you are to set two items "session" and "scandir". Would someone tell what I am supposed to type in for those two? Thanks Joongnam Yang

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Flattening section of the Cortex
by Ajay Pillai 15 Nov '04

15 Nov '04

Hello Everyone, I have the following problem. I have a section/patch of the Cortical Surface (Auditory area.) which I would like to unfold/flatten. The data is in matlab and I have it as vertex and faces of the cortical surface. I know how to write it to a ?h.pial.asc file format from matlab. I also have activation maps from SPM2. My questions are : 1. Can I read this surface in freesurfer and an unfold/flatten it ? If yes how ? 2. Can I overlay the activation maps in freesurfer on to the cortial patch I described above? If so could some one list the possible steps please? 3. Finally if I can indeed ufold the above mentioned cortical surface will I be able to export it back to .asc file format? Thank you Ajay

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vertex "area"
by Doug Greve 14 Nov '04

14 Nov '04

I have just fixed a bug in FreeSurfer that involves computing the area of some surface structures. For those of you who care, this was a bug that emerged after converting our surface meshes from quadralaterals to triangles. This change was made a few years ago. This change should have little effect on the reconstruction. It will have an effect on programs that report the area of subsections of cortex (but not total cortical area). At least three such programs that are affected are: mris_compute_overlap, mris_label_area, and mri_surfcluster. The bug causes the reported area to appear to be 1.5 times what it really is. For example, in mri_surfcluster, a cluster threshold of 300 mm^2 would actually be a threshold of 200 mm^2. For those in the NMR center, these three programs have been updated. For those outside, you can get these programs from ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve New versions of freesurfer will, of course, have the update. Sorry for any inconvenience. doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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Re: [Freesurfer] functional overlay
by Joongnam Yang 12 Nov '04

12 Nov '04

Thanks Doug, So, "structural data registration" "functional data registration" "co-registration" have to be done separately? How do I do the first two? The manual is pretty murky on that. Please enlighten me... I am trying to do functional overlay using csurf and there are so many hidden things when I use the manual. I appreciate your help, Doug. Nam.

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Re: [Freesurfer] functional overlay
by Joongnam Yang 12 Nov '04

12 Nov '04

Thanks Doug, When I run tkregister2 --targ structuralimage --mov functionalimage --reg register.dat I got the following error. ====================== target volume XXXXX.img movable volume XXXXXX.img reg file register.dat LoadVol 1 $Id: tkregister2.c,v 1.22 2003/11/05 21:30:50 greve Exp $ Diagnostic Level -1 regio_read_register(): No such file or directory Could not open register.dat Segmentation fault (core dumped) ========================== What could have been wrong? Thanks. Nam.

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Re: [Freesurfer] functional overlay
by Joongnam Yang 12 Nov '04

12 Nov '04

Hi Bruce, I co-registered functional and structural images using SPM, the results of which looked normal. Then, I used spmmat2register to produce register.dat file. But "register.dat" contained only following two lines. subjectname 0.3000 It is supposed to have 8 lines. Could you guess what went wrong? Nam.

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functional overlay
by Joongnam Yang 11 Nov '04

11 Nov '04

Hi all, If someone can give me help, it would be greately appreciated. in csurf GUI, I choose "New Functional", and I give it a name. (1) The name is entirely new for analysis or is it the directory that contains functional scan. If I give it a name, it asks for "Now, locate the single subject directory that matches this functional scan" (2) Is it the structural scan direcotory or the directory that includes the actual functional scan image, or something other? Nam.

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Problems installing freesurfer on Mac OS X (Darwin)
by Catherine Schevon 11 Nov '04

11 Nov '04

Hi, I have been trying to get freesurfer installed on my Mac, and ran into a problem getting csurf to run. I figured out to put the correct path to tclsh into csurf (it's in /usr/bin, not /bin), but now I get an error message: $ tcsh % source fs_setup Setting up enviroment for FreeSurfer/FS-FAST $ Id: FreeSurferEnv.csh,v 1.3 2003/08/05 19:19:16 kteich Exp $ FREESURFER_HOME /freesurfer FSFAST_HOME /freesurfer/fsfast AFNI_DIR /freesurfer/afni FSL_DIR /freesurfer/fsl SUBJECTS_DIR /freesurfer/subjects WARNING: /freesurfer/afni/Darwin does not exist. WARNING: /freesurfer/fsl/bin does not exist. [mccec-061135:/freesurfer] cschevon% csurf tix not found--setenv problem? % Also, I notice that the "tixwish" command doesn't seem to execute when it's run from csurf, although it does create a window when I run it from the command line. Any suggestions would be most welcome! Cathy

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mri_convert orientation problem
by Goldman, Aaron (NIH/NIMH) 11 Nov '04

11 Nov '04

Hi, I'm planning to use mri_convert to convert a large number of analyze images into COR format. To test the orientation, I first ran the command on an image with a pill marking the right side. When I did this, the resulting COR files were reversed in the left-right dimension (in tkmedit, the r coordinates got lower as I moved the cursor towards the side with the pill, and when I ran recon-all stage1, the side with the pill was created as the left-hemisphere surface). What option should I add to the mri_convert command to correct the left & right orientation? Right now, I'm using: mri_convert --in_type analyze subj/mri/orig/file.img subj/mri/orig Thanks, -Aaron- Aaron L. Goldman Post-Bacc IRTA Genes, Cognition and Psychosis Program, NIMH Building 10, Room 3C108 Phone: (301) 435-0944 Email: <mailto:aarong@mail.nih.gov> aarong(a)mail.nih.gov

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Freesurfer November 2004