Freesurfer June 2009

freesurfer@nmr.mgh.harvard.edu

94 participants
140 discussions

Re: [Freesurfer] scuba bus error on MacBook
by Nick Schmansky 10 Jun '09

10 Jun '09

its included in the distribution. On Wed, 2009-06-10 at 15:48 -0400, Satrajit Ghosh wrote: > Hi Nick, > > I hadn't heard of freeview. Is there a place we can download it? > > Cheers, > > Satra > > On Wed, Jun 10, 2009 at 3:34 PM, Nick Schmansky > <nicks(a)nmr.mgh.harvard.edu> wrote: > Will Freeview work for you? Support for scuba has ended > because work on > Freeview to replace has been ongoing. > > Nick > > > On Wed, 2009-06-10 at 15:24 -0400, akram(a)nmr.mgh.harvard.edu > wrote: > > Hello, > > I remember I had this same issue last summer, and I can't > find a record of > > the solution. > > I installed freesurfer-Darwin-leopard-i686-stable-pub-v4.3.1 > on a MacBook > > running Mac OS X 10.5.7 with specs: 2.4 GHz Intel Core 2 > Duo, 2 GB 667 MHz > > DDR2 SDRAM. > > > > I set my FREESURFER_HOME to /Applications/freesurfer and > sourced my > > SetUpFreeSurfer.csh > > I type scuba to bring up the scuba gui, but it returns "Bus > error" > > tkmedit/tksurfer/qdec work fine. > > Is this due to a 32 vs 64 bit issue and is there an easy > fix? > > I suppose we can always VNC in, but I was hoping we could do > some work > > offline. > > Thanks for the help! > > Akram > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

2 1

rebuild_gca_atlas/mri_ca_train error
by Kevin Scheibel 10 Jun '09

10 Jun '09

I am trying to run rebuild_gca_atlas to create an atlas from my segmented vervet sample. I'm pretty sure I've got everything set up correctly, but am getting an error: ERROR: mri_ca_train: talairach.xfm not found in seg_edited.mgz I'm using vervet (primte) MRIs, so I didn't think a talairach transform for my subjects would be useful. Also, it seems that this script points at seg_edited.mgz as a directory, even though I have it set up in my directory as a file. Kevin Scheibel k.scheibel(a)ucla.edu

1 0

how to to redo the analysis after recon-all
by karlkarl 10 Jun '09

10 Jun '09

Hello, experts: I have finished autorecon1-3 on the data. But now when I am examining the data, some images need skull stripping and white matter editing. So I need to rerun the steps. If I strip the skull after autoreon1 and want to put it to autorecon2, This should be: recon-all �Cs <participants> -autorecon2 And after fixing white matter problem from autorecon2 This should be: recon-all �Cs <participants> -autorecon3 All the old files will be automatically overwritten? What is the most efficient way to redo the analysis after recon-all? Thanks a lot! Karl _________________________________________________________________ Լ��˵��ط��΢��ͼ��msn��ܣ� http://ditu.live.com/?form=TL&swm=1

2 1

Re: Error in Analyze
by Toh Hock Wong 10 Jun '09

10 Jun '09

On 10/06/2009, at 9:51 PM, Toh Hock Wong wrote: > Hi all, > I have reconstructed 12 paediatric subjects aged 4-13 and managed > to load qdec as well as generating stats. The factors are age, > diagnosis, gender and a continuos factor such as lh temporalpole > thickness. When i click analyze, the return is a list of errors as > follow. > UseMaskWithSmoothing 1 > > OneSampleGroupMean 0 > > y /Applications/freesurfer/subjects/qdec/ > lh_temporalpole_thickness/y.mgh > > logyflag 0 > > usedti 0 > > FSGD /Applications/freesurfer/subjects/qdec/ > lh_temporalpole_thickness/qdec.fsgd > > labelmask /Applications/freesurfer/subjects/fsaverage/label/ > lh.cortex.label > > maskinv 0 > > glmdir /Applications/freesurfer/subjects/qdec/ > lh_temporalpole_thickness > > DoFFx 0 > > Creating output directory /Applications/freesurfer/subjects/qdec/ > lh_temporalpole_thickness > > Loading y from /Applications/freesurfer/subjects/qdec/ > lh_temporalpole_thickness/y.mgh > > Matrix condition is 1e+08 > > ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 > > Possible problem with experimental design: > > Check for duplicate entries and/or lack of range of > > continuous variables within a class. > > 1.000 0.000 0.000 0.000 3.701 0.000 0.000 0.000; > > 0.000 0.000 1.000 0.000 0.000 0.000 4.554 0.000; > > 1.000 0.000 0.000 0.000 4.044 0.000 0.000 0.000; > > 0.000 0.000 1.000 0.000 0.000 0.000 4.459 0.000; > > 0.000 0.000 1.000 0.000 0.000 0.000 3.857 0.000; > > 0.000 0.000 1.000 0.000 0.000 0.000 3.537 0.000; > > 0.000 0.000 1.000 0.000 0.000 0.000 3.652 0.000; > > 1.000 0.000 0.000 0.000 2.870 0.000 0.000 0.000; > > 0.000 0.000 1.000 0.000 0.000 0.000 3.736 0.000; > > 0.000 0.000 1.000 0.000 0.000 0.000 3.636 0.000; > > 1.000 0.000 0.000 0.000 4.102 0.000 0.000 0.000; > > 1.000 0.000 0.000 0.000 3.755 0.000 0.000 0.000; > > 0.000 0.000 0.000 1.000 0.000 0.000 0.000 2.816; > > > > > > Error in Analyze: command failed: mri_glmfit --y /Applications/ > freesurfer/subjects/qdec/lh_temporalpole_thickness/y.mgh --fsgd / > Applications/freesurfer/subjects/qdec/lh_temporalpole_thickness/ > qdec.fsgd dods --glmdir /Applications/freesurfer/subjects/qdec/ > lh_temporalpole_thickness --surf fsaverage lh --label /Applications/ > freesurfer/subjects/fsaverage/label/lh.cortex.label --C / > Applications/freesurfer/subjects/qdec/lh_temporalpole_thickness/ > contrasts/lh-Avg-Intercept-thickness.mat --C /Applications/ > freesurfer/subjects/qdec/lh_temporalpole_thickness/contrasts/lh-Avg- > thickness-lh_temporalpole_thickness-Cor.mat --C /Applications/ > freesurfer/subjects/qdec/lh_temporalpole_thickness/contrasts/lh-Diff- > nonepileptic-epilepsy-Intercept-thickness.mat --C /Applications/ > freesurfer/subjects/qdec/lh_temporalpole_thickness/contrasts/lh-Diff- > nonepileptic-epilepsy-Cor-thickness-lh_temporalpole_thickness.mat -- > C /Applications/freesurfer/subjects/qdec/lh_temporalpole_thickness/ > contrasts/lh-Diff-Male-Female-Intercept-thickness.mat --C / > Applications/freesurfer/subjects/qdec/lh_temporalpole_thickness/ > contrasts/lh-Diff-Male-Female-Cor-thickness- > lh_temporalpole_thickness.mat --C /Applications/freesurfer/subjects/ > qdec/lh_temporalpole_thickness/contrasts/lh-X-diagnosis-gender- > Intercept-thickness.mat --C /Applications/freesurfer/subjects/qdec/ > lh_temporalpole_thickness/contrasts/lh-X-diagnosis-gender-Cor- > thickness-lh_temporalpole_thickness.mat > > What do i need to do from here? > > Do i have to write a fsgd file/contrast etc? Any suggestions will be > most appreciated! > > If i wish to use freesurfer for a paediatric group less than 10 > years old, what errors or difficulties should i be anticipating? > > Thanks! Toh Wong > > > > > >

2 1

using cortical thickness values
by Kai Lutz 09 Jun '09

09 Jun '09

Dear List, in an attempt to divide grey matter segments into an outer and inner layer, I am currently using the vertex coordinates for pial surface (in Matlab>> read_surf('lh.pial') ) and vertex coordinates for white matter surface (MATLAB>>read_surf('lh.white') ). Perhaps naively, I assume, that the order of the two coordinate matrices is identical and calculate the wanted coordinates of a point on a line (say half way) in between the corresponding pial and white matter vertices. What puzzles me is that the distances between corresponding (?) white matter and pial surface vertices are not equal to the cortical thickness values given by >>read_curv('lh.thickness') (GM-WM distances up to 9.3 mm are found, whereas cortical thickness values vary between -0.24 and 5 mm in the data set I am working on) --> To determine a layer, separating outer from inner half of the cortex, would it be a more valid to A: determine vertex normals of pial surface and travel along them by a distance 1/2 the cortical thickness? (Q: which thickness value belongs to which vertex? where do the negative thickness values come from?) or B: determine points half way in between vertex coordinates of corresponding pial and WM vertices? (Q: how can I assure their correspondence?) Is anyone working on / has solved a related problem? Any hint would be greatly appreciated! Cheers, Kai -- Dr. Kai Lutz Neuropsychology Institute for Psychology University of Zurich Binzmühlestrasse 14 /Box 25 CH-8050 Zürich Switzerland _________________________ Diese E-Mail (ggf. nebst Anhang) enthält vertrauliche und/oder rechtlich geschützte Informationen. Wenn Sie nicht der richtige Adressat sind, oder diese E-Mail irrtümlich erhalten haben, informieren Sie bitte sofort den Absender und vernichten Sie diese Mail. Das unerlaubte Kopieren sowie die unbefugte Weitergabe dieser Mail ist nicht gestattet. This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. _________________________

2 1

error estimates
by Dana W. Moore 09 Jun '09

09 Jun '09

I was wondering if there is any output in stats that generates an error estimate for the calculated stats for an individual subject? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

2 1

FW: RE: [Freesurfer] vtkMultiThreader error
by Christopher Nunez 09 Jun '09

09 Jun '09

I am getting similar error messages when running on our grid and pipeline systems (see below). Our tech people had previously thought this could be related to memory capacity issues, but after increasing memory to 8gb when submitting my jobs with a qsub command, the problem is still not resolved. I'm beginning to have doubts about this being related to memory capacity. Could somebody please provide instructions on disabling the ribbon processing? Thank you. #@# Cortical ribbon mask Sun May 31 18:21:54 PDT 2009 /ifs/edevel/CN_SAN_DIEGO/FREESURFER/OUTPUT/164/mri \n mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance 164 \n ERROR: In /usr/pubsw/packages/vtk/5.1.0-CVS/src/VTK/Common/vtkMultiThreader.cxx, line 372 vtkMultiThreader (0x3279bb60): Unable to create a thread. pthread_create() returned 12 ERROR: In /usr/pubsw/packages/vtk/5.1.0-CVS/src/VTK/Common/vtkMultiThreader.cxx, line 372 vtkMultiThreader (0x3279bb60): Unable to create a thread. pthread_create() returned 12 ERROR: In /usr/pubsw/packages/vtk/5.1.0-CVS/src/VTK/Common/vtkMultiThreader.cxx, line 372 vtkMultiThreader (0x3279bb60): Unable to create a thread. pthread_create() returned 12 ERROR: In /usr/pubsw/packages/vtk/5.1.0-CVS/src/VTK/Common/vtkMultiThreader.cxx, line 372 vtkMultiThreader (0x3279bb60): Unable to create a thread. pthread_create() returned 12 ERROR: In /usr/pubsw/packages/vtk/5.1.0-CVS/src/VTK/Common/vtkMultiThreader.cxx, line 372 vtkMultiThreader (0x3279bb60): Unable to create a thread. pthread_create() returned 12 ERROR: In /usr/pubsw/packages/vtk/5.1.0-CVS/src/VTK/Common/vtkMultiThreader.cxx, line 372 vtkMultiThreader (0x3279bb60): Unable to create a thread. pthread_create() returned 12 ERROR: In /usr/pubsw/packages/vtk/5.1.0-CVS/src/VTK/Common/vtkMultiThreader.cxx, line 372 vtkMultiThreader (0x3279bb60): Unable to create a thread. pthread_create() returned 12 ------------------------------------------------------------------- S. Christopher Nuñez, PhD Postdoctoral Fellow Developmental Cognitive Neuroimaging Group Laboratory of Neuro Imaging UCLA Dept of Neurology Neuroscience Research Building 1, Suite 225 635 Charles Young Drive South Los Angeles, CA 90095-7334 (310) 267-5555 ------------------------------------------------------------------- ________________________________________ From: hranilovich(a)ucla.edu [hranilovich(a)ucla.edu] Sent: Monday, June 08, 2009 12:13 PM To: Christopher Nunez Subject: Fwd: RE: [Freesurfer] vtkMultiThreader error Pretty much what I was saying the other day. It looks like maybe you can disable this step if you don't want this output, though? ----- Forwarded message from dhaglerjr(a)hotmail.com ----- Date: Mon, 8 Jun 2009 11:19:43 -0700 From: Don Hagler <dhaglerjr(a)hotmail.com> Reply-To: Don Hagler <dhaglerjr(a)hotmail.com> Subject: RE: [Freesurfer] vtkMultiThreader error To: nicks(a)nmr.mgh.harvard.edu, martin.kavec(a)gmail.com Cc: freesurfer maillist <freesurfer(a)nmr.mgh.harvard.edu> Hi Nick, Thanks for the reply. I will look into the memory limit issue some more (we recently instituted per job memory limits), but I have done a test run with a 16GB memory limit (running one job per node). Meanwhile, thanks for the novtk suggestion. Our fallback option is to just disable the ribbon generation. I don't think we ever use them for anything. Don > Subject: Re: [Freesurfer] vtkMultiThreader error > From: nicks(a)nmr.mgh.harvard.edu > To: martin.kavec(a)gmail.com; dhaglerjr(a)hotmail.com > Date: Mon, 8 Jun 2009 11:15:51 -0400 > CC: freesurfer(a)nmr.mgh.harvard.edu > > Don and Martin, > > I dont have a good solution for you to this problem. The error code > indicates an 'out-of-memory' error returned by pthread_create, and I do > know the mris_vol_mask uses a lot of memory (at least 1GB). > > I have not been able to find any clues to the source of this problem on > the web either. The only curious thing to it is that in the source > code, that section is conditionally compiled to ignore the return code > if 'VTK_HP_PTHREADS' is defined, which implies some sort of odd behavior > on some special HP platform build. > > mris_vol_mask has been a real thorn in the side of the recon-all stream, > but its not easy to replace because it does a subjectively better job of > finding the voxels which intersect the pial and white surfaces. For > comparison, or even to solve your problem, you can use > mris_vol_mask_novtk to create the ribbon.mgz files. The output is not > the same as that produced by mris_vol_mask though. Perhaps you can run > it, and compare the results side-by-side and give us your opinion on > which is the better ribbon (as there is no objective measure on what a > 'correct' ribbon.mgz should like like, ie, should it include voxels that > intersect more than half way through a surface, or not at all?). > > Nick > > > On Mon, 2009-06-08 at 09:16 +0200, Martin Kavec wrote: > > Hi Don, > > > I am in a similar situation. I am on a IBM BladeCenter cluster > (though with > one blade only) with 2 Quad core Intels, and I > experience intermittent > crashes of mri_volmask as well. Similarly > as you, when I run the mri_volmask > on the crashed subject on a > desktop, this passes perfectly fine and sometimes > also on the > cluster as well. > > > I am wonder whether how do you obtain the debug information > about the cause of > the crash (being in the vtkMultiThreader)? > > > I also wonder, whether the crashes could be due to different > compilation > environments of the VTK libraries used in teh FS > distribution (centos) and > your redhat. I went on the bug-report > site of VTK and there really isn't > anythink major reported on this > class. > > In my experience the mri_volmask runs fine for quite a > while and then crashes. > >From the debug messages you show it would > thus could be that the process may > hit some limit of the threads > which could be allocated to a process. > > > What do you think? > > > Martin > > On Saturday 06 June 2009 04:19:51 Don Hagler wrote: > > > When we run v430 on our cluster, running rocks redhat 4.3, we > get the error > > > message below when mris_volmask is run. From a google search, I see that > > > someone had the same error message back in Oct 2007. Was a > solution found > > > for this? It runs fine on our desktop machines as well as when we log in > > > directly to a node and run the job interactively. > > > > > > > > > > > > mris_volmask --label_left_white 2 --label_left_ribbon 3 > > > --label_right_white 41 --label_right_ribbon 42 --save_ribbon > > > --save_distance FREESURFERRECON_NTNU_PRE_095v2_20071126.173245.968000_1 > > > > > > SUBJECTS_DIR is /home/dhagler/data_test > > > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, > > > line 372 vtkMultiThreader (0x1306ec80): Unable to create a > thread. > > pthread_create() returned 12 > > > > > > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, > > > line 372 vtkMultiThreader (0x1306ec80): Unable to create a > thread. > > pthread_create() returned 12 > > > > > > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, > > > line 372 vtkMultiThreader (0x1306ec80): Unable to create a > thread. > > pthread_create() returned 12 > > > > > > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, > > > line 372 vtkMultiThreader (0x1306ec80): Unable to create a > thread. > > pthread_create() returned 12 > > > > > > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, > > > line 372 vtkMultiThreader (0x1306ec80): Unable to create a > thread. > > pthread_create() returned 12 > > > > > > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, > > > line 372 vtkMultiThreader (0x1306ec80): Unable to create a > thread. > > pthread_create() returned 12 > > > > > > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, > > > line 372 vtkMultiThreader (0x1306ec80): Unable to create a > thread. > > pthread_create() returned 12 > > > > > > Segmentation fault > > > Linux compute-0-12.local 2.6.9-55.0.2.ELsmp #1 SMP Tue Jun 26 > 14:14:47 EDT > > > 2007 x86_64 x86_64 x86_64 GNU/Linux > > > > > > recon-all exited with ERRORS at Fri Jun 5 18:58:09 PDT 2009 > > > > > > > > > > > > > > > > > > _________________________________________________________________ > > > Hotmail® has ever-growing storage! Don't worry about storage limits. > > > > http://windowslive.com/Tutorial/Hotmail/Storage?ocid=TXT_TAGLM_WL_HM_Tutori > > >al_Storage_062009 > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _________________________________________________________________ Insert movie times and more without leaving Hotmail®. http://windowslive.com/Tutorial/Hotmail/QuickAdd?ocid=TXT_TAGLM_WL_HM_Tutor… ----- End forwarded message ----- n

3 2

Anatomical stats for fsaverage
by Alex Fornito 09 Jun '09

09 Jun '09

Hi, I'm playing around with different ways of generating custom annotation files using the fsaverage surface, and would like to estimate the surface area of each ROI. I tried running mris_anatomical stats, but it seems to required wm.mgz, which is not contained in the fsaverage directories (please see below). Is there any way around this? I'm really just interested in extracting the surface area for each label in my .annot file. Thanks for your help, Alex mris_anatomical_stats -a lh.test.aparc.annot -f stats_table.txt -log logfile.txt fsaverage lh white computing statistics for each annotation in lh.test.aparc.annot outputting results to logfile.txt... reading volume /work/imaging5/af397/twins/fsaverage/mri/wm.mgz... ERROR: cannot find /work/imaging5/af397/twins/fsaverage/mri/wm.mgz mris_anatomical_stats: could not read input volume /work/imaging5/af397/twins/fsaverage/mri/wm.mgz No such file or directory

3 7

problem with spmregister
by Hesheng Liu 09 Jun '09

09 Jun '09

Hi, Guys, I am trying to coregister a CT image with MRI using spmregister, however I am getting the following error message. I have run the same command on many subjects before and never had a problem. Is there any update that I am not aware of? Any thoughts will be greatly appreciated. Hesheng Adding my matlab commands... >> >> >> >> >> >> >> >> >> /usr/pubsw/common/spm/spm5/spm_coreg.m >> >> >> >> >> INFO: Assuming RAS coordinate system >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> using ./tmp.spmreg.7057/refvol.spmregister.img as the target image >> using ./tmp.spmreg.7057/movvol.spmregister.img as the source image >> >> >> >> >> >> >> >> >> >> >> >> >> >> INFO: ignore warnings about scalefactor >> >> determining coregistration parameters... >> >> >> ERROR: spm_coreg >> ??? Undefined function or variable 'x'. >> Finished after 0.258371 sec >> >> Parameters >> ??? Undefined function or variable 'x'. >> >> >> >> >> ??? Undefined function or variable 'x'. >> >> Using spm_get_space ??? Undefined function or variable 'M'. >> >> >> ERROR: matlab exited with errors ERROR: spm_coreg /usr/pubsw/common/spm/spm5/spm_coreg.m

2 1

FW: fsaverage, posterior slices missing
by Sharmili 57 09 Jun '09

09 Jun '09

From: sharmili75(a)hotmail.com To: freesurfer(a)nmr.mgh.harvard.edu Subject: fsaverage, posterior slices missing Date: Tue, 9 Jun 2009 12:01:48 +0000 Hi, I tried to run make_average_suject with 22 Subjects (11 Schizophrenia and 11 controls). In tkmedit I checked the result. the posterior slices seem to be missing in fsaverage orig.mgz but tksurfer ist complete. I've attached a screenshot. Has anyone have an idea, how to solve this problem. Thanks Sharmili Posteingang immer voll? Der erste Speicher, der mitwächst: Unbegrenzter Speicher bei Windows Live Hotmail! _________________________________________________________________ http://redirect.gimas.net/?n=M0906xIE8_MSN4 Internet Explorer 8 jetzt für MSN - kostenlos!

2 1

← Newer
1
...
6
7
8
9
10
11
12
13
14
Older →

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer June 2009