Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30063 discussions

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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Preprocessing steps of freesurfer on Macs
by Kushal Koolwal 10 Nov '04

10 Nov '04

Greetings, Let me apologize in advance for bothering you all agian with a technical question, but we seem to have reached an impasse and I am hopeful that you might be able to point us in the correct direction. We are struggling to get freesurfer up and running on Mac OS X, and have encountered difficulties with several of the preprocessing steps as mentioned in the Freesurfer tutorial(the steps for averaging and motion correcting Bert's data). I am wondering if you know anyone who has successfully ported the application to the Mac and that might be willing to suggest a fix or two? Also earlier someone had suggest using mri_motion_correct utility but to my surprise there was no such thing in the Mac installaion of freesurfer. All I could find was mri_motion_correct2 utility but even that didn't work. Can anyone please give proper pointers and directions in this matter. We are in a process of almost setting our lab with Mac so that we can start our work on freesurfer. Thanks Kushal __________________________________ Do you Yahoo!? Check out the new Yahoo! Front Page. www.yahoo.com

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Another question
by Calabrese Massimiliano 08 Nov '04

08 Nov '04

I'm sorry but I have another question for you. Sometimes the cutting planes are not correct and it doesn't delete the cerebellum. Whay can I do? Manual editing is my only chance? Thanks a lot Massimiliano Calabrese Neuroimaging Group Neuroimmunology Branch NINDS, NIH

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Re: [Freesurfer] FsFast file conversion/preprocessing
by Margaret Duff 08 Nov '04

08 Nov '04

Hi, so, instead of converting the files, i unpacked them into bshort and it gave me, i think, the right amount of files. then i used the command preproc-sess --sf sessid --df sesspar --fwhm 6. it ran for a while, gave me the sections converting input to afni, motion correcting, and matlab file. after it opens matlab it has the errors saying the mc-sess failed. i am running this from /space/troy. it does create the file fmc.mcdat and it looks like its complete. it just stops after that and doesn't make the actual motion corrected files. thanks for your help. margaret SPM stores each *frame* in a separate file, but all slices for a given frame in the same file. Thus, the number of files will equal the number of frames. bshort/bfloat stores each *slice* in a separate file, but all frames for a given slice in the same file. Thus the number of files will equal the number of slices. Does this resolve the difference? It sounds like your bshorts are not being converted to AFNI properly. Can you send me your preproc-sess command-line and the location you are running it from? doug Margaret Duff wrote: > > Hi, I have 12 runs of functional data I am trying to convert to FSFast > formats and then preprocess. I have been using mri_convert to make my > .img files into bshorts. However mri_convert makes only 30 files when my > folders originally contained 37 or 73 files. Is this what it is supposed > to do? I am also then trying to run preproc-sess on these files but i > keep getting an error during the motion correction of the first run. it > says can't register a 1 brick dataset to itself, and ERROR: 3dvolreg > existed with status 1. I am using the command "preproc-sess -sf sessid > -df sesspar -fwhm 6" for preprocessing and "mri_convert 028/f001.img > 028/f_001.bshort" for file conversion. Does anyone know why my steps > aren't working or knows of a better way to do these steps? Thank you so > much, Margaret Duff > > _______________________________________________ > Freesurfer mailing list > [EMAIL PROTECTED] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 _______________________________________________ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer