Freesurfer January 2011

freesurfer@nmr.mgh.harvard.edu

99 participants
144 discussions

discrepant outputs from recon-all/mri_ca_normalize
by Tossi Ikuta 25 Jan '11

25 Jan '11

Hi everyone, I'm wondering whether there are multiple versions of recon-all v 1.313.2.6 (2010/08/04 15:50:56), and/or mri_ca_normalize stable5. I have been testing recon-all and compared our output against the sample processed-data in FS/TUtorial. I found that the output obtained was different from the sample, despite the fact that I ran recon-all with the same options as the sample outputs, on the same input files. recon-all -s bert -i /analysis/Tests/FSTest_Tossi/Samples2/buckner_data/tutorial_subjs/bert/mri/orig/001.mgz -i /analysis/Tests/FSTest_Tossi/Samples2/buckner_data/tutorial_subjs/bert/mri/orig/002.mgz -i /analysis/Tests/FSTest_Tossi/Samples2/buckner_data/tutorial_subjs/bert/mri/orig/003.mgz -all -debug -clean -norandomness -allowcoredump -time -subjid BertByTossi20110119A I performed a line-by-line comparison of the recon-all log between the sample and one from my run and found that our log differs from the sample (buckner_data/tutorial_subjs/bert/scripts/recon-all.log) at line 1034, where mri_ca_normalize runs the first path of smoothing (with sigma=0.200). Whereas the sample has 38 recursions, my run had 18 recursions for this section. The outputs hereafter differed from each other. I used the same version as the sample was processed, recon-all: v 1.313.2.6 (2010/08/04 15:50:56), and mri_ca_normalize: stable5. Not to mention, the input files are identical. Also, I ran the exact same line of the command more than three times, and obtained the exact same result. Therefore, I believe this is not due to any randomization introduced (if any) in normalization/smoothing. I used an x86_64 processor, the same as the sample. Thus, I do not believe this is due to any floating point resolution difference between architectures, either. The only possible reason I can think of that might account for the discrepancy is that there are multiple versions or compiles "stable5" mri_ca_normalize. I obtained the sample input and result from; ftp://surfer.nmr.mgh.harvard.edu/pub/data/bert.recon.tgz Our download md5sum matches the one posted. Here's a list of input files; $ls -l /analysis/Tests/FSTest_Tossi/Samples2/buckner_data/tutorial_subjs/bert/mri/orig/ total 17776 -rw-rw-r-- 1 tossi mrilab 5996899 2010-08-09 13:01 001.mgz -rw-rw-r-- 1 tossi mrilab 6077242 2010-08-09 13:01 002.mgz -rw-rw-r-- 1 tossi mrilab 6083164 2010-08-09 13:01 003.mgz Thank you very much in advance. Tossi /********************************************* Tossi Ikuta, Ph.D. Research Scientist The Feinstein Institute for Medical Research The Zucker Hillside Hospital (718) 470-4486 <tikuta(a)nshs.edu> *********************************************/

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Bbregister for fsl tractography
by Lena Palaniyappan 25 Jan '11

25 Jan '11

Dear Doug & others The FSL page on fa to freesurfer registration ( http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html) contain info that uses tkregister2. To determine freesurfer_to_fa space registration file, do we need to go through the freesurfer_to_struc and then struc_to_fa rooutine given in fsl pages.? I wonder if the registration can be done using the bbregister currently. If that is the case how to get the fsl-type registration file? tkregister2 had an option for this but it is not working with bbregister Cheers Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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CUDA installation and configuration...
by Gonzalo Rojas Costa 25 Jan '11

25 Jan '11

Hi: I am currently configuring Freesurfer 5 in a new workstation that we received... That workstation has Ubuntu 10.10, and a NVIDIA Quadro FX 1800 graphics card... Could you please send me the detailed steps necessary to install and configure CUDA support ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica Las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Which surface to mesh_vertex_nearest
by Gabriele Arnulfo 25 Jan '11

25 Jan '11

Hi again, looking in previous emails in the list i found that the best way to find the nearest vertex number to a certain point is by using the matlab script mesh_vertex_nearest. So far I've used it with input parameters: the vertices read through read_surf(rh_pial) and a matrix of Cartesian Coordinates. In this context I'd like to know which surface is the right choice, if there should be a choice. I've inserted either the pial and inflated surface having different result (vertex index) for the same point (RAS xyz). Cheers, g. -- In a world without wall, how needs WINDOWS??

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freesurfer and VBM
by Ritobrato Datta 25 Jan '11

25 Jan '11

Hello All, Are there any papers comparing freesurfer to VBM ? Can anyone point me to them ? Thanks Ri

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Re: [Freesurfer] freesurfer and VBM
by a.cerasa＠isn.cnr.it 25 Jan '11

25 Jan '11

In our last imaging genetic study (Cerasa et al., Dysbindin C-A-T haplotype is associated with thicker medial orbitofrontal cortex in healthy population. Neuroimage 2011 in press) we showed similar findings between Freesurfer and VBM analyses. ----- Original Message ----- From: Douglas N Greve To: Ritobrato Datta <ridatta(a)mail.med.upenn.edu> Cc: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Sent: Tue, 25 Jan 2011 10:43:37 -0500 Subject: Re: [Freesurfer] freesurfer and VBM Try looking at Voets, et al, 2008, in Neuroimage vol 43, pg 665-675. doug Ritobrato Datta wrote: > Hello All, > > Are there any papers comparing freesurfer to VBM ? > > Can anyone point me to them ? > > Thanks > > Ri > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- This message was scanned by ESVA and is believed to be clean. Click here to report this message as spam. http://smtp.isn.cnr.it/cgi-bin/learn-msg.cgi?id=B67D828015.63D0A

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color scale bar in freeview
by tulu＠ms36.hinet.net 25 Jan '11

25 Jan '11

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mri_gcut killed
by Michelle Umali 24 Jan '11

24 Jan '11

Dear All, recon-all was killed during mri_gcut. Here is the error: mri_gcut -110 -mult brainmask.auto.mgz T1.mgz brainmask.auto.mgz Killed. How does one deal with this? Thanks in advance for any help. Michelle

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ERROR: flag --tablefile not recognized
by Jesse Bledsoe 24 Jan '11

24 Jan '11

Hi FreeSurfer team, After running: asegstats2table --subjects *subject1 subject2... *--meas volume --tablefile aseg.stats.txt I receive the following error: ERROR: flag --tablefile not recognized Stamp: freesurfer-Linuxcentos4-stable-pub-v4.2.0 Any suggestions are greatly appreciated, Jesse

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asegstats2table in version 4.2.0 error?
by Jesse Bledsoe 24 Jan '11

24 Jan '11

Hello FreeSurfer group, I am unable to run asegstats2table and cannot view asegstats2table --help. I did some looking in the archives and it seems like there were bugs in previous versions that were fixed before version 4.2.0. Any ideas on how to fix this? At this point I have been creating my own tables and viewing each individual aseg.stats file for each participant. When I use the following: asegstats2table --subjects *subject1 subject 2* --meas volume --tablefile aseg_stats.txt I get the following error: 'import site' failed; use -v for traceback Traceback (most recent call last): File "/usr/local/freesurfer/bin/ > > asegstats2table", line 4, in ? > import os; > ImportError: No module named os > Thank you for your time, Jesse (Linux-centos4-stable-pub-v4.2.0) On Tue, Nov 30, 2010 at 3:43 PM, Jesse Bledsoe <bledsoej(a)msu.edu> wrote: > Hello, > > I am having difficulty generating an aseg_stats.txt table. > > When I use the following: > > asegstats2table --subjects *subject1 subject 2* --meas volume --tablefile > aseg_stats.txt > > I get the following error: > > 'import site' failed; use -v for traceback > Traceback (most recent call last): > File "/usr/local/freesurfer/bin/asegstats2table", line 4, in ? > import os; > ImportError: No module named os > > > I am on Linux-centos4-stable-pub-v4.2.0 > > Any suggestions are much appreciated, > Jesse > -- Jesse Bledsoe, M.A. Clinical Psychology Graduate Student Assistant Director, Consortium for Neurodevelopmental Study Department of Psychiatry Michigan State University 321 W. Fee Hall East Lansing, MI 48824 ______________________________________ Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments.

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Freesurfer January 2011