Freesurfer

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30080 discussions

Problems on MAC 10.5
by Martin Kavec 01 Feb '08

01 Feb '08

Hi, I have upgraded my Mac OS X to 10.5 and after that nu_correct says: Can't locate MNI/Startup.pm .... $FREESURFERHOME/mni/bin/nu_correct line 37 Anybody has an idea, what could be wrong? Obviously, the file is there. Thanks, Martin

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Freesurfer qcache error
by William R Mcgarry 01 Feb '08

01 Feb '08

When running qcache (on a recent version of freesurfer) after running recon-all -s 4964-14_recon -all command, I get the following error: ERROR: number of vertices in /usr/local/freesurfer/subjects/4964-14_recon/surf/lh.thickness does not match surface (138139,137319)ERROR: reading curvature file Linux localhost.localdomain 2.6.23.14-107.fc8 #1 SMP Mon Jan 14 22:07:11 EST 2008 x86_64 x86_64 x86_64 GNU/Linux Any ideas? This happens for multiple subjects without any known cause or covariance. --------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-rh9-stable-pub-v4.0.2 RedHat release: Fedora release 8 (Werewolf) Kernel info: Linux 2.6.23.14-107.fc8 x86_64

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mris_wm_volume
by Gallo, Antonio (NIH/NINDS) [F] 01 Feb '08

01 Feb '08

Hello All, We are trying to obtain an accurate measurement of the total WM volume (cerebral WM + WM hypointensities) in a group of patients with multiple sclerosis (MS). As per Bruce's suggestion, we are now using mris_wm_volume that gives more accurate measures than aseg.stats. When looking at our data we have noticed that within the WM surface (yellow line) there are many voxels labeled as Cerebral-Cortex (mainly in places where we put cp to expand the WM surface), and some others labeled as None (mainly in places of iuxtacortical MS lesions). As expected basing on how mris_wm_volume works, we have noticed that WM volume actually change upon manual editing of these mislabeled voxels in the aseg.mgz (i.e. relabeling them as actual WM). Thus, we were wondering if there is any way to capture and correct for all these mislabeled voxels in a more automated manner (i.e. automatically considering Cerebral-Cortex and None voxels included in the WM surface as actual WM in the mris_wm_volume computation). In this way it should be possible to get more accurate measures of WM volumes as well as save a lot of time in manual editing. Thanks a lot in advance, Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5C203B Bethesda, MD, 20892 - USA ph #: 001-301-496.7368 fax #: 001-301-402.0373 ***********************

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thresholding problems/visualizing .curv files
by swallace＠nmr.mgh.harvard.edu 01 Feb '08

01 Feb '08

Warm greetings from the first floor- I am having an issue with my .curv files, similar to what Adam from the archives had a little over a year ago: On Tue, 25 Apr 2006, adam walczak wrote: Hello, I am testing the output of some data I ran through the reconstruction process. While attempting to view the rh.sphere volume with the rh.curv overlay, I only could see the red lines, not the green lines. I noticed that I had to adjust the settings (view--configure--curvature display). I had to change the value of the threshold midpoint to .2 and the threshold slope to 3.5. Only then could I see both. Is this normal, or maybe is something wrong...all of the processes said they finished without error. Thanks. Adam I know Bruce replied and said that there looked to be something wrong, and to include the screen shots of what default thresholding looks like. I am running this on a Centos 4 machine with a frozen version of Freesurfer from Nov 2005. Thanks for the assistance! Stuart

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alloc: invalid block
by George He 31 Jan '08

31 Jan '08

Hi, I am following the tutorial http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OverlayFeatStatisticalM… At this command, tksurfer bert lh inflated -overlay ./fbert1.feat/stats/zstat1.nii.gz -overlay-reg ./fbert1.feat/reg/freesurfer/anat2exf.register.dat -fthresh 2.3 -fmid 3.3 -fslope 1 -annot aparc.annot tksurfer runs OK but when I click on any button between "show curvature" and "draw outlined labels", it crashes and gives this error: % alloc: invalid block: 0xbb6c80: 0 0 0 Here is the section copied from bugr output: --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/packages/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.1 RedHat release: Fedora release 8 (Werewolf) Kernel info: Linux 2.6.23.9-85.fc8 x86_64 --------------------------------------------------------------------- any suggestions how to correct this? Thanks, George

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displaying the result of group analysis in thickness or p-value
by Woo-Suk, Tae 30 Jan '08

30 Jan '08

.Bold { font-weight: bold; } .Title { font-weight: bold; font-size: 18px; color: #cc3300; } .Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color: #000066; font-family: 'Courier New' , Monospace;background-color: #ff9933; } Dear FreeSurfer experts.I have finished the FreeSurfer analysis using (version 3.04) in the patients with depression.But, the result using qdec was displayed only in T-value.I'd like to know how can I display the result of group analysis in thickness (mm) and statistical p value.Best regards.Woo-Suk, Tae Ph.DChucheon, Korea

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recon-all error @ mris_volmask...
by Cameron Ellis 30 Jan '08

30 Jan '08

Hi, I am receiving this error for every subject I send through recon-all. I am checking for edits that need to be made but it seems very odd that 30 subjects or so would all error out at the same step. Any suggestions? Cameron Subject 'Ponce_033d2': make all recon-all -s /autofs/space/grouch_004/users/ponce/Ponce_033d2 -hemi lh -cortribbon INFO: SUBJECTS_DIR is /autofs/space/grouch_004/users/ponce Actual FREESURFER_HOME /autofs/space/freesurfer/centos4.0_x86_64/stable4 -rw-rw-r-- 1 cameo zenuwgp 1257898 Jan 29 17:38 /autofs/space/grouch_004/users/ponce/Ponce_033d2/scripts/recon-all.log Linux node0325 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:28:26 CDT 2006 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# Cortical ribbon mask Wed Jan 30 11:41:19 EST 2008 /autofs/space/grouch_004/users/ponce/Ponce_033d2/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance Ponce_033d2 Segmentation fault Linux node0325 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:28:26 CDT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Jan 30 11:41:42 EST 2008

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Aseg.stats file
by Jared Conley 30 Jan '08

30 Jan '08

FreeSurfer Community, Is there an easy, quick way to regenerate the aseg.stats file? This particular file was deleted accidentally for a few subjects and we wondered if we could quickly recreate this file without having to run recon-all again. All the other files in the subject directory are present. Thanks in advance, Jared

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midline errors in pial and white matter boundary
by nima＠nmr.mgh.harvard.edu 29 Jan '08

29 Jan '08

Hi Guys, In few recons, I noitced that in the midline, pial and white matter boundaries are not the way they are supposed to be; i.e., they sometimes diverge toward the ventricles instead of following the midline and these divergences are not symmetrical either. I thought maybe I should add some cp...but that does not make sense because in actuality there is not white matter there as it is underneath the cortical gray matter... Any suggestion? The new version of the freesurfer fills the 3rd ventricle adjacent to the fornices. Should I leave the fornices in? or I should clean it up like old versions? ps. is there any way to add control points for pial surface? cheers nima

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Creating average overlays for time-varying data (MEG)
by Pádraig Kitterick 29 Jan '08

29 Jan '08

Dear list, I am trying to use freesurfer to visualise MEG data (minimum norm) overlayed on the cortical surface, both at an individual and group level. I have successfully processed all of the participants MRIs using recon-all, and have decimated the cortical surface (white) to compute the MEG solution. I would be grateful if anyone could help with the following issues I have run into: 1) I would like to know how to view the time-varying solution over the cortex using tksurfer. I have successfully exported the overlay for a single sample to a .w file (using matlab), and then smoothed it (mri_surf2surf) and viewed it on the cortical surface, which works great. But I am aware that .w format only supports a single 'frame' of data. Some previous posts on the list suggest that exporting the data in .mgh format as a nverts x 1 x 1 x nsamples volume would allow visualisation of the timecourse in tksurfer. My question is: is there a way to only write out the data for the vertices with values (i.e. left after decimation) when using the mgh format, and not a matrix of the total vertices in the original cortex? For example, if the surface has N vertices, and after decimation I have M vertices left, using the .w format I only need to write out data for the M vertices, along with a list of the vertex numbers to place them on the original surface. Can I do this with .mgh? It is difficult to get matlab to write out an mgh file with a 140000x1x1x500 volume! 2) I wish to view the average data across several subjects, mapped onto the fsaverage subject template. I have seen that mris_preproc can warp one or more overlays onto a single subject. My question is: will mris_preproc work with the type of .mgh files I described above, i.e. containing multiple frames of data overlay? Or am I better trying to do the whole operation with .w files, with one per timepoint? Many thanks in advance, Padraig -- Pádraig Kitterick Graduate Student Department of Psychology University of York Heslington York YO10 5DD UK Tel: +44 (0) 1904 43 3170 Email: p.kitterick(a)psych.york.ac.uk

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