Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30080 discussions

Cortical thickness issues
by Ryan Scotton 10 Jul '08

10 Jul '08

Hi all, I am fairly new to FreeSurfer and I've just finished initial runs on about 140 MRI images. Now, my job is to go through and do a little QC that helps ensure that the cortical thickness values are as accurate as possible. Now, I have a few questions: 1. Am I right in assuming that cortical thickness values are calculated as a function of the distance between the white and pial surfaces? 2. How exactly are the white and pial surfaces calculated? Do they utilize the wm segmentation? 3. Since I thought this was the case, I have tried cleaning up a couple images by using control points (using case 4 in the tutorial as a guide), hoping that the white and pial surfaces would be redrawn in a more accurate way. However, the problem remains. The surfaces are not including parts that are obviously white matter and gray matter. So basically, I'm thinking I'm missing something on the best way to fix white and pial surfaces when they're not accurate enough. Could anyone offer me some advice/a link to a site which explains the best way to handle such problems? Thanks, and sorry for the looooong post. Ryan

3 2

change in default GCA file
by Michael Harms 10 Jul '08

10 Jul '08

Hello, Comparing the recon-all script for FS v4.0.2 against FS v4.0.5, I noticed that somewhere between those versions the "default" GCA files changed from ones dated 2007-08-08 to 2008-03-26. Is this related to the "new feature" of FS v4.0.3 described on the Release Notes as "talairach_with_skull.lta generation is now robust in presence of increased background noise levels." ? What are the implications (if any) of this change in the GCA for the intermingling of data processed under early version 4 releases (4.0.2 or earlier) with later version 4 releases (4.0.3 or later)? Is the difference in the GCA minor enough that it would be reasonable to intermix data processed under 4.0.5 and 4.0.2, without needing to update the v4.0.2 data? e.g., Does the difference have any relevant impact on the subcortical segmentation? thanks, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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mri_glmfit tutorial data problem
by Ming Hsu 09 Jul '08

09 Jul '08

Hi, I have been using mri_glmfit to analyze my data because of qdec display problems on Tiger. So far though I do not appear to be getting the same result from the buckner group analysis sample data as those on the wiki. I've attached a couple of screenshots of the differences. There are some similarities, but the differences are pretty large. It is not a thresholding problem as the distribution of the threshold values are very different (screenshot also attached). We followed the wiki tutorials pretty closely so we're not sure what is behind the apparent differences. Best, Ming Hsu

1 0

major lobes of cerebellum
by Juranek, Jenifer 09 Jul '08

09 Jul '08

Is there any interest in parcellation of the cerebellum into its major regions: corpus medullare, anterior, superior-posterior, inferior-posterior regions? Any easy approaches available for testing out? Would a volume-based approach be sufficient, or would a surface-based approach be necessary? Anyone's input is greatly appreciated Jenifer

3 2

path error on cluster super-computer
by Woo-Suk, Tae 09 Jul '08

09 Jul '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 had a error message when I ran a subjects on cluter super-computer.It seemed that the error was caused by permission on "/usr" directory.How can I correct this problem?Woo-Suk, TaeChuncheon, Korea-------------------------------------------------------------------------------------------Iteration 1 Mon Jul 7 08:51:03 KST 2008nu_correct -clobber ./tmp.mri_nu_correct.mni.25070/nu0.mnc ./tmp.mri_nu_correct.mni.25070/nu1.mnccouldn't create "/usr/tmp/nu_correct_25115/": Permission denied[a174tws@tachyond:/home01/a174tws/freesurfer/subjects/001/mri/] [2008-07-07 08:51:04] running: /home01/a174tws/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_25115/ ./tmp.mri_nu_correct.mni.25070/nu0.mnc ./tmp.mri_nu_correct.mni.25070/nu1.imp nccreate: filename "/usr/tmp/nu_correct_25115/nu0.mnc": No such file or directorymicreate: MINC package entry pointnu_estimate_np_and_em: crashed while running mincresample (termination status=768)nu_correct: crashed while running nu_estimate_np_and_em (termination status=768)ERROR: nu_correctLinux tachyond 2.6.9-67.0.4.ELsmp #1 SMP Wed Mar 19 15:45:32 KST 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Jul 7 08:51:05 KST 2008-------------------------------------------------------------------------------------------

3 5

Re: registration issue
by Satrajit Ghosh 09 Jul '08

09 Jul '08

I have 4 files: F1. anatomical image 1 F2. anatomical image 2 F3. T-map coregistered with anat img 2 F4. xfm file that coregisters anat img 2 to anat img 1. If I load all of these in scuba and apply the xfm inside scuba to the data from F2 and F3, everything aligns up nicely with the data from F1. However, if I run mri_convert as: mri_convert F2 --apply_transform F4 newF2 mri_convert F3 --apply_transform F4 newF3 and then run scuba, newF2 is in alignment with F1 but newF3 is still in alignment with F3. Any suggestions would be most helpful. Thanks, Satra

1 0

Re: [Freesurfer] error message of mris_register
by Jan Kalkus 09 Jul '08

09 Jul '08

I have also been having similar trouble with mris_register: [dynamic-oit-vapornet-c-124:Data/monkey_surface_data/bu_edited] work% mris_register surf/rh.sphere $SUBJECTS_DIR/monk_temp0.tif surf/ rh.sphere.reg $Id: mris_register.c,v 1.48 2007/07/19 15:58:50 fischl Exp $ $Id: mrisurf.c,v 1.557.2.13 2008/05/23 00:06:05 nicks Exp $ reading surface from surf/rh.sphere... reading template parameterization from /Volumes/Data/ monkey_surface_data/monk_temp0.tif... /Volumes/Data/monkey_surface_data/monk_temp0.tif: Deflate compression support is not configured. TiffReadImage: TIFFReadScanline returned error No such file or directory MRISPread(/Volumes/Data/monkey_surface_data/monk_temp0.tif): could not open file No such file or directory mris_register: could not open template file /Volumes/Data/ monkey_surface_data/monk_temp0.tif No such file or directory - Jan Kalkus

2 2

mgh2 stc
by nima＠nmr.mgh.harvard.edu 09 Jul '08

09 Jul '08

Hi Does anybody have a code to convert mgh format to stc? best Nima Nima Dehghani MD.

1 0

deflate compression support
by Jan Kalkus 09 Jul '08

09 Jul '08

Hi everyone, I'm trying to make a monkey template using mris_make_template. So far, every time I run the mris_make_template, I get this error: [jkalkus:~] work% /Volumes/Data/monkey_surface_data/mris_make creating new parameterization... processing subject bu_edited (1 of 1) reading spherical surface /Volumes/Data/monkey_surface_data//bu_edited/ surf/rh.sphere... curvature mean = 0.000, std = 1.000 computing parameterization for surface /Volumes/Data/ monkey_surface_data//bu_edited/surf/rh.inflated.H... curvature mean = 0.000, std = 0.592 computing parameterization for surface /Volumes/Data/ monkey_surface_data//bu_edited/surf/rh.sulc... curvature mean = -0.100, std = 1.787 computing parameterization for surface /Volumes/Data/ monkey_surface_data//bu_edited/surf/rh.smoothwm... writing updated template with 1 subjects to monk_temp0.tif... monk_temp0.tif: Deflate compression support is not configured. TiffWrite: TIFFWriteScanline returned error I am working on an intel MacBook with OS X 10.5.4 and I'm running freesurfer-Darwin-leopard-i686-stable-pub-v4.0.5. Has anyone else encountered this problem? Does anyone have any suggestions? Thanks - Jan Kalkus

3 3

seg edits
by Juranek, Jenifer 09 Jul '08

09 Jul '08

Running Freesurfer v4.0.5 on RHEL5 linux system. General Question: after using the "Edit Segmentation" tool and saving edits by overwriting the aseg.mgz file generated during $recon-all -autorecon-all...which command should I pass to re-enter the analysis pipeline at the most appropriate spot? I understand that after edits to the wm.mgz file, it is fine to re-enter the pipeline with $recon-all -autorecon2-wm -autorecon3. But unable to find much in the Wiki wrt *aseg.mgz* edits and subsequent re-processing (other than "how to" accomplish edits). Specific info: Unusual case with enlarged lateral ventricles (particularly posteriorly). Review of the aseg.mgz after completing $recon-all -autorecon-all indicated that the right lateral ventricle (posterior portion) was partially incorrectly labeled in a range of slices (COR: 86-48) with a "cocktail" of labels, including the following: Right-Lateral-Ventricle; Right-Cerebral-White-Matter; Right-Cerebral-Cortex; None; WM-hypointensities. After editing *wm.mgz* to fill-in missing voxels in the problem areas and re-running $recon-all -autorecon2-wm -autorecon3, segmentation labels of problem areas still required edits. After using the "Edit Segmentation" tool, I have now saved my edits by overwriting *aseg.mgz*. So which command should I pass to re-enter the pipeline? Many Thanks for any advice you can provide. Jenifer

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