Freesurfer

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30070 discussions

Re: Files uploaded for you on Martinos Center FileDrop site
by Anil Roy 14 Feb '07

14 Feb '07

Nick, The files were acquired axially(120 slices) on a GE scanner. These scans are a couple of years old. I should also inform you that I converted the orginal 120 slices into afni brik format (afni was able to read them) and then used mri_convert to convert the BRIK to cor. Freesurfer then used this cor to run the recon-all pipeline. The original files could not be read by Freesurfer which is why I did that. Also, this may be obvious to you but cannot the contrast be simply changed by Freesurfer. In tkmedit, the brightness and contrast can be adjusted so isn't there a way that recon-all can use this change while running the brain. Thanks - Anil On 2/14/07, Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> wrote: > > Anil, > > The image has almost no contrast. I've attached a TIFF of one slice. > How was this acquired? Bruce, any idea why it would be so white? > > Nick > > > On Wed, 2007-02-14 at 16:10 -0500, aroy85(a)gmail.com wrote: > > The following files have been uploaded to the Martinos Center FileDrop > site > > by Anil Roy for you to download: > > > > (1) orig.mgz > > > > > > > > These files will expire in 30 days. > > > > To view or download these files, go in your web browser to: > > > > > https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/5010/426/7389dc… > > > > DO NOT SHARE this web address with anyone else. It is your personal > access key to the files. > > > > Overall Comment about files from Anil Roy: > > > > Hi, > > > > Attached is the orig.mgz file for the subject that quits at the > watershed step. > > > > Thanks, > > > > Anil. > > > > > >

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longitudinal analysis - error
by Chacko Cherian 14 Feb '07

14 Feb '07

Hello all, This is an error I got while running the longitudinal analysis on one of our subjects.It didnt create the filled.mgz volume and so the surfaces weren't created. #@# Fill Tue Feb 13 20:59:04 MST 2007 /ud/chacko/freesurfer/subjects/apoe/1279MRI4/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.mgz -topofix norm.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.mgz... fill: could not scan threshold from 'norm.mgz'Linux snuffy 2.6.17-10-generic #2 SMP Tue Dec 5 22:28:26 UTC 2006 i686 GNU/Linux recon-all-long exited with ERRORS at Tue Feb 13 20:59:04 MST 2007 THanks in advance Chacko. ____________________________________________________________________________________ It's here! Your new message! Get new email alerts with the free Yahoo! Toolbar. http://tools.search.yahoo.com/toolbar/features/mail/

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recon-all error
by Anil Roy 14 Feb '07

14 Feb '07

Hello all, I have some raw data and I'm not sure of the format. Its definitely not dicom. I ran recon-all on these files but I get an error saying it can't read the files. I have posted the output below. I tried to convert the files to afni format (BRIK + HEAD), and tried recon-all again. It ran for a while but gave an error that I've attached to a text file. Can someone please tell me how I can get Freesurfer to read these files. I can also upload the raw files if you'd like to take a look at them. Thanks a lot - Anil. [root@dhcp-129-105-146-127 freesurfer]# recon-all -force -i /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 -subjid Nl-TA1-001 -sd /root/Freesurfer/Tone_Acquisition -all INFO: SUBJECTS_DIR is /root/Freesurfer/Tone_Acquisition INFO: /root/Freesurfer/Tone_Acquisition/Nl-TA1-001 exists with -i, but -force specified. Deleting any previous source volumes Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 root root 76880 Feb 8 13:25 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/scripts/recon-all.log Linux dhcp-129-105-146-127.speech.northwestern.edu 2.6.17-1.2157_FC5smp #1 SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux strings: Command not found. WM removal version /root/Freesurfer/Tone_Acquisition/Nl-TA1-001 mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz mri_convert /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 /root/Freesurfer/Tone_Acquisition/Nl-TA1-001/mri/orig/001.mgz reading from /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001... genesisRead(): can't determine file name format for /root/U_Chicago/Tone_Acquisition/Nl-TA1-001/I.001 Linux dhcp-129-105-146-127.speech.northwestern.edu 2.6.17-1.2157_FC5smp #1 SMP Tue Jul 11 23:24:16 EDT 2006 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Thu Feb 8 13:52:57 CST 200

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64bit centos utilities: mris_wm_volume & mris_volume
by Juranek, Jenifer 14 Feb '07

14 Feb '07

Recently (7 Feb 2007) mris_wm_volume for 32bit centos was posted in /pub/dist. Is there any possibility of posting 64bit centos versions of mris_wm_volume & mris_volume? I'm running Freesurfer 3.0.4 Many Thanks, Jenifer

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pial editing
by Derin Cobia 14 Feb '07

14 Feb '07

I have a question regarding editing the pial surface. Many times it includes bright spots, such as fat or vessels. Should I be editing this out? I'm pretty clear on getting rid of included dura, but if I spent the time to edit out every little bright spot, it would be pretty time intensive. Would leaving these little "extras" skew my data? Is there some balance I can strike when editing? Thanks! -Derin

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WM vol
by Nurunisa Neyzi 14 Feb '07

14 Feb '07

Hi, when I use mri_anatomical stats - I get a total WM value 503450 for left and right hemispheres that's the same number in the stats file in the stats folder. but when I use mris_wm_volume - I get 174896 and 178464 which one is the accurate one? also, is the GM volume I get from mris_anatomical_stats accurate? thanks, n. 174896 17464

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average thickness overlay per group
by Marie Schaer 14 Feb '07

14 Feb '07

Hello, I have a two groups comparison design, and I was wondering if there is any easy way to compute an average thickness file per group (in order to be able to overlay mean thickness values on my average subject). Is there an existing command or matlab function to do it? If yes, would I also be able to do a standard deviation file using the same command? Many thanks, Marie Schaer

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Reconstruction problems
by Fornito, Alexander 13 Feb '07

13 Feb '07

Hi, I'm having problems reconstructing the surface for one individual on an older version of recon-all (v. 1.104). It always seems to exit with no error message during mris_fix_topology. I've tried to re-run this subject several times, and even starting from scratch does not seem to help. I'm not sure why this is happening, as I've used this version of recon-all on hundreds of other images without any problem. There's no obvious difference between this image and any of the others that I can see by looking at the T1 (e.g., no apparent artifacts, etc.). I've attached recon-all.log. Any suggestions? Thanks, Alex Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1861 Fax: +61 3 9348 0469 email: alexander.fornito(a)wh.org.au

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(no subject)
by Nurunisa Neyzi 13 Feb '07

13 Feb '07

Hi, I am trying to color code my labels according to the stats associated with each label. I was playing with the colortable but that did not work. I will appreciate any guidance/ help on that. How can I give to a given label the color I want to? thanks, Nurunisa

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smoothing with mris_preproc
by Lars M. Rimol 12 Feb '07

12 Feb '07

Hi, If I don't specify any smoothing level when running mris_preproc, with --fwhm or --niters, does that mean that it won't apply any smoothing or is there a default smoothing level? -- yours, LMR

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