[Freesurfer] Virtual Box crashes
Dear all, Please help with the following problem: I am trying to run the FreeSurfer disk image on Virtual Box 4.1.6. I start it, I get: GRUB loading please wait... and then the Virtual Box crashes. It has 2048 MB base memory, 12 MB video memory. Thank you! Veronica ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] mri_nu_correct error
Hello everybody, I am trying to use mri_nu_correct.mni function in freesurfer on the XUbuntu system installed on the VirtualBox on a Windows 7 machine. I converted Siemens IMA into analyze format .img (with function; mri_convert -i input_file_name.IMA -ot analyze -o output_file_name.img), then when I called the function mri_nu_correect for the inhomogeneity correction, it gave me an error message (see below). What is wrong? Cheers, Baris FreeSurfer:~/Documents/EEGLAB/NFT/MPRAGE/7031 mri_nu_correct.mni --i S1.img --o S1inh.img --n 2/home/virtualuser/Documents/EEGLAB/NFT/MPRAGE/7031/home/virtualuser/freesurfer/bin/mri_nu_correct.mni--i S1.img --o S1inh.img --n 2nIters 2$Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/LinuxMon Nov 21 10:53:06 EST 2011Program nu_correct, built from:Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13tmpdir is ./tmp.mri_nu_correct.mni.3086/home/virtualuser/Documents/EEGLAB/NFT/MPRAGE/7031mri_convert S1.img ./tmp.mri_nu_correct.mni.3086/nu0.mnc -odt floatmri_convert S1.img ./tmp.mri_nu_correct.mni.3086/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $reading from S1.img...TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-0.0286335, -0.999213, 0.0274527)j_ras = (-0.00717244, -0.0272578, -0.999603)k_ras = (-0.999564, 0.028819, 0.00638633)changing data type from short to float (noscale = 0)...writing to ./tmp.mri_nu_correct.mni.3086/nu0.mnc... Iteration 1 Mon Nov 21 10:53:10 EST 2011nu_correct -clobber ./tmp.mri_nu_correct.mni.3086/nu0.mnc ./tmp.mri_nu_correct.mni.3086/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.3086/0/[virtualuser@FreeSurfer:/home/virtualuser/Documents/EEGLAB/NFT/MPRAGE/7031/] [2011-11-21 10:53:11] running: /home/virtualuser/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 ./tmp.mri_nu_correct.mni.3086/0/ ./tmp.mri_nu_correct.mni.3086/nu0.mnc ./tmp.mri_nu_correct.mni.3086/nu1.imp Assertion failed at line 827 in file templates/CachedArray.ccnu_estimate_np_and_em: crashed while running volume_stats (termination status=256)nu_correct: crashed while running nu_estimate_np_and_em (termination status=256)ERROR: nu_correct -- Ş. Barış Demiral, PhD. Department of Psychiatry Washington University School of Medicine 660 S. Euclid Avenue Box 8134 Saint Louis, MO 63110 Phone: +1 (314) 7477 1603 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Virtual Box crashes
Sounds like a virtualbox problem. Try reinstalling Virtualbox.. Try adding a bit more video memory to the vm. BTW, is there an error message, or does it just silently shut down? - Joshua On Mon, Nov 21, 2011 at 2:05 AM, Popescu, V. v.pope...@vumc.nl wrote: Dear all, Please help with the following problem: I am trying to run the FreeSurfer disk image on Virtual Box 4.1.6. I start it, I get: “GRUB loading please wait…” and then the Virtual Box crashes. It has 2048 MB base memory, 12 MB video memory. Thank you! Veronica ** ** ** ** ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Virtual Box crashes
Hi, Joshua! This is what I get on screen: [cid:image001.jpg@01CCA877.F24CDD40] I'll try reinstalling the VB and see what happens. Thank you! Best, Veronica From: nimzodisas...@gmail.com [mailto:nimzodisas...@gmail.com] On Behalf Of Joshua Lee Sent: maandag 21 november 2011 17:20 To: Popescu, V. Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Virtual Box crashes Sounds like a virtualbox problem. Try reinstalling Virtualbox.. Try adding a bit more video memory to the vm. BTW, is there an error message, or does it just silently shut down? - Joshua On Mon, Nov 21, 2011 at 2:05 AM, Popescu, V. v.pope...@vumc.nlmailto:v.pope...@vumc.nl wrote: Dear all, Please help with the following problem: I am trying to run the FreeSurfer disk image on Virtual Box 4.1.6. I start it, I get: GRUB loading please wait... and then the Virtual Box crashes. It has 2048 MB base memory, 12 MB video memory. Thank you! Veronica ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@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. inline: image001.jpg___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] use of --a2009s flag
hi everyone i am trying to use the mri_aparc2aseg command with the --a2009s flag to have the aparc.a2009s labels and i have the following message Option --a2009s unknown thanks ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] use of --a2009s flag
What version are you using? You can accomplish the same thing with --annot aparc.a2009s doug LAOUCHEDI MAKHLOUF wrote: hi everyone i am trying to use the mri_aparc2aseg command with the --a2009s flag to have the aparc.a2009s labels and i have the following message Option --a2009s unknown thanks ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@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.
[Freesurfer] T1 mapping, mri_ms_fitparms and flip angle map
Dear all, For a structural study, I would like to determine cortical T1 values. T1 map generation from two FLASH images works like a charm, and I would like to add B1 correction now. I have acquired flip angle maps for my subjects (using the Yarnykh method with interleaved FLASH and two TRs), and would like to correct my T1 maps accordingly. Looking at the online help of mri_ms_fitparms, I think the parameter -afi should do the trick. However, I'm not sure about the properties of the flip angle map that I need to supply to mri_ms_fitparms. Does that programme expect absolute flip angle values? Or can I feed in my two AFI FLASH volumes in some way? If anyone can point me in the right direction, that would be great! Thanks for you help, Johannes ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] T1 mapping, mri_ms_fitparms and flip angle map
Hi Johannes you should give it a flip angle map in degrees. We assume that the nominal flip angle (that is, if B1 was homogeneous) would be 60 deg. cheers Bruce On Mon, 21 Nov 2011, Dr.med. Johannes C. Klein wrote: Dear all, For a structural study, I would like to determine cortical T1 values. T1 map generation from two FLASH images works like a charm, and I would like to add B1 correction now. I have acquired flip angle maps for my subjects (using the Yarnykh method with interleaved FLASH and two TRs), and would like to correct my T1 maps accordingly. Looking at the online help of mri_ms_fitparms, I think the parameter -afi should do the trick. However, I'm not sure about the properties of the flip angle map that I need to supply to mri_ms_fitparms. Does that programme expect absolute flip angle values? Or can I feed in my two AFI FLASH volumes in some way? If anyone can point me in the right direction, that would be great! Thanks for you help, Johannes ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] T1 mapping, mri_ms_fitparms and flip angle map
Hi Bruce, Thanks a lot for your (very speedy) help! Cheers, Johannes Am 21 Nov 2011 um 18:21 schrieb Bruce Fischl: Hi Johannes you should give it a flip angle map in degrees. We assume that the nominal flip angle (that is, if B1 was homogeneous) would be 60 deg. cheers Bruce On Mon, 21 Nov 2011, Dr.med. Johannes C. Klein wrote: Dear all, For a structural study, I would like to determine cortical T1 values. T1 map generation from two FLASH images works like a charm, and I would like to add B1 correction now. I have acquired flip angle maps for my subjects (using the Yarnykh method with interleaved FLASH and two TRs), and would like to correct my T1 maps accordingly. Looking at the online help of mri_ms_fitparms, I think the parameter -afi should do the trick. However, I'm not sure about the properties of the flip angle map that I need to supply to mri_ms_fitparms. Does that programme expect absolute flip angle values? Or can I feed in my two AFI FLASH volumes in some way? If anyone can point me in the right direction, that would be great! Thanks for you help, Johannes ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] when to invoke reg-feat2anat in fsl ppi
Hi Michelle, the time series is an average over the ROI right? If so, then it should be independent of any future registration. In any case, aseg2feat will create an ROI in the native functional space which is where FEAT does its analysis, so I think you're fine in any case. doug Michelle Umali wrote: Dear Freesurfers, I am using seeds based on Freesurfer masks to run a PPI analysis and am wondering if I am using reg-feat2anat at the right fsl feat registration step. First, I ran an fsl analysis to generate a feat directory. Then I ran reg-feat2anat using that feat directory. Next I ran aseg2feat and fslmaths to generate binary masks Next I extracted the timeseries by using the filtered func of the feat and the binary masks from aseg2feat. So now I want to do another feat analysis, but this time using the extracted timeseries But this timeseries is based on the first feat and associated masks from the reg-feat2anat registration. 1) Is it still valid to use this timeseries in this new feat since FSL will be running another registration? 2) Do I have to run reg-feat2anat again? Thanks. Michelle ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@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.
[Freesurfer] control points didn't work
Dear FreeSurfer list, I was trying to edit wm surface by adding control points. After saving them and re-running recon-all -autorecon2-cp -autorecon3, the control points are still there, but wm is not edited (although cp worked in other places for the same brain). The intensity there is around 95-98 depending on slice. Could you please suggest what could go wrong? Thank you, Tanja. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] T1 mapping, mri_ms_fitparms and flip angle map
sure On Mon, 21 Nov 2011, Dr.med. Johannes C. Klein wrote: Hi Bruce, Thanks a lot for your (very speedy) help! Cheers, Johannes Am 21 Nov 2011 um 18:21 schrieb Bruce Fischl: Hi Johannes you should give it a flip angle map in degrees. We assume that the nominal flip angle (that is, if B1 was homogeneous) would be 60 deg. cheers Bruce On Mon, 21 Nov 2011, Dr.med. Johannes C. Klein wrote: Dear all, For a structural study, I would like to determine cortical T1 values. T1 map generation from two FLASH images works like a charm, and I would like to add B1 correction now. I have acquired flip angle maps for my subjects (using the Yarnykh method with interleaved FLASH and two TRs), and would like to correct my T1 maps accordingly. Looking at the online help of mri_ms_fitparms, I think the parameter -afi should do the trick. However, I'm not sure about the properties of the flip angle map that I need to supply to mri_ms_fitparms. Does that programme expect absolute flip angle values? Or can I feed in my two AFI FLASH volumes in some way? If anyone can point me in the right direction, that would be great! Thanks for you help, Johannes ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] control points didn't work
Hi Tanja, if you upload the subject we can take a look. Does the aseg look ok in those regions? cheers Bruce On Mon, 21 Nov 2011, Tetiana Dadakova wrote: Dear FreeSurfer list, I was trying to edit wm surface by adding control points. After saving them and re-running recon-all -autorecon2-cp -autorecon3, the control points are still there, but wm is not edited (although cp worked in other places for the same brain). The intensity there is around 95-98 depending on slice. Could you please suggest what could go wrong? Thank you, Tanja. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] Running 2 versions of Freesurfer on same computer
Hello, I have been successfully running FreeSurfer 4.5 on my MacOSX 10.5.8 with no issues. I recently installed FreeSurfer 5.1 to a separate directory on the same laptop to analyze a new dataset but I am now having various issues using FreeSurfer version 4.5. For Version 4.5, I path the freesurfer directories as follows (identical to before installing version 5.1): setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir source $FREESURFER_HOME/SetUpFreeSurfer.csh - freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir MNI_DIR /Applications/freesurfer/mni The issue is that now various commands no longer function in version 4.5. For example when typing tkmedit, tksurfer or qdec, I get the following type of error: tkmedit.bin: Command not found. Is it possible that although I installed version 5.1 in a separate directory, that some files were deleted or moved in version 4.5? Is my 4.5 license no longer valid now that I have installed version 5.1 with a new license? It is confusing since some commands appear to function, such as mri_convert and recon-all, but anything involving a GUI seems not to function. Any help would be appreciated. thanks, Jennifer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] reg-feat2anat
you can just copy it doug Michelle Umali wrote: Dear Freesurfers, I've previoiusly run reg-feat2anat on some fsl feat data, but now my advisor things i should re-preprocess my fsl data with a larger kernel size. Since it's the same dataset , do I have to re-run reg-feat2anat on this or can I just copy the registration folder from the old analysis? Thanks. Michelle ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@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.
Re: [Freesurfer] use of --a2009s flag
does that file exist? LAOUCHEDI MAKHLOUF wrote: hi doug i am using the v5.0.0 version, the massage i have when running mri_aparc2aseg --s ctr12 --a2009s is : ( SUBJECTS_DIR makh_free subject ctr12 outvol makh_free/ctr12/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface makh_free/ctr12/surf/lh.white Reading lh pial surface makh_free/ctr12/surf/lh.pial Loading lh annotations from makh_free/ctr12/label/lh.aparc.a2009s.annot could not read annot file makh_free/ctr12/label/lh.aparc.a2009s.annot No such file or directory ERROR: MRISreadAnnotation() failed makh_free/ctr12/label/lh.aparc.a2009s.annot) same thing when using : --annot aparc.a2009s thanks for your help --- En date de : *Lun 21.11.11, Douglas N Greve /gr...@nmr.mgh.harvard.edu/* a écrit : De: Douglas N Greve gr...@nmr.mgh.harvard.edu Objet: Re: [Freesurfer] use of --a2009s flag À: LAOUCHEDI MAKHLOUF laouma...@yahoo.fr Cc: Freesurfer@nmr.mgh.harvard.edu Date: Lundi 21 novembre 2011, 18h18 What version are you using? You can accomplish the same thing with --annot aparc.a2009s doug LAOUCHEDI MAKHLOUF wrote: hi everyone i am trying to use the mri_aparc2aseg command with the --a2009s flag to have the aparc.a2009s labels and i have the following message Option --a2009s unknown thanks ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu /mc/compose?to=Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu /mc/compose?to=gr...@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@nmr.mgh.harvard.edu /mc/compose?to=Freesurfer@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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Running 2 versions of Freesurfer on same computer
are you certain that v5.1 was installed in a separate directory? does v5.1 work properly, including tkmedit and qdec? the license should not be the problem in this case, you can use the same license in both versions. one option is to re-install v4.5. you can get it from here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/4.5.0/ also, check the directory /Applications/freesurfer/bin for tkmedit.bin. n. On Mon, 2011-11-21 at 12:58 -0500, Jennifer Addicks wrote: Hello, I have been successfully running FreeSurfer 4.5 on my MacOSX 10.5.8 with no issues. I recently installed FreeSurfer 5.1 to a separate directory on the same laptop to analyze a new dataset but I am now having various issues using FreeSurfer version 4.5. For Version 4.5, I path the freesurfer directories as follows (identical to before installing version 5.1): setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir source $FREESURFER_HOME/SetUpFreeSurfer.csh - freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /MRIData/Root/freesurfer/TRDsubjects_dir MNI_DIR /Applications/freesurfer/mni The issue is that now various commands no longer function in version 4.5. For example when typing tkmedit, tksurfer or qdec, I get the following type of error: tkmedit.bin: Command not found. Is it possible that although I installed version 5.1 in a separate directory, that some files were deleted or moved in version 4.5? Is my 4.5 license no longer valid now that I have installed version 5.1 with a new license? It is confusing since some commands appear to function, such as mri_convert and recon-all, but anything involving a GUI seems not to function. Any help would be appreciated. thanks, Jennifer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] fs-fast tutorial data
I don't know why it's not there. I'm copying it over now, but it might take a half an hour. Try back in a while (making sure to refresh your browser window). doug Verena Gramse wrote: Hi, I am trying to follow the FS-FAST tutorial but I cant find the required data for it under the links specified on the tutorial site: ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz, ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-tutorial.subjects.tar.gz Could you tell me where I find the data? Thanks so much, Verena ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@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.
[Freesurfer] question about thickness file
Hi all: After finishing recon-all steps, there are some thickness files generated such as lh.thickness and lh.thickness.fwhm10.fsaverage.mgh which contain cortical thickness values at each vertex. Are the thickness values in lh.thickness file calculated in individual space ,that is , they are absolute values and values in lh.thickness.fwhm10.fsaverage.mgh file computed based on fsaverage template, that is, they represent relative values ? Any suggestions appreciated.___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] question about thickness file
They are all absolute in the sense that they are in real millimeters Bruce On Nov 21, 2011, at 9:27 PM, ZhiLiangLong lagosslong1...@163.com wrote: Hi all: After finishing recon-all steps, there are some thickness files generated such as lh.thickness and lh.thickness.fwhm10.fsaverage.mgh which contain cortical thickness values at each vertex. Are the thickness values in lh.thickness file calculated in individual space ,that is , they are absolute values and values in lh.thickness.fwhm10.fsaverage.mgh file computed based on fsaverage template, that is, they represent relative values ? Any suggestions appreciated. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Virtual Box crashes
Sorry, your error message image is too small to read. - Josh On Mon, Nov 21, 2011 at 9:04 AM, Popescu, V. v.pope...@vumc.nl wrote: Hi, Joshua! This is what I get on screen: I’ll try reinstalling the VB and see what happens. Thank you! Best, Veronica ** ** ** ** -- *From:* nimzodisas...@gmail.com [mailto:nimzodisas...@gmail.com] *On Behalf Of *Joshua Lee *Sent:* maandag 21 november 2011 17:20 *To:* Popescu, V. *Cc:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Virtual Box crashes ** ** Sounds like a virtualbox problem. Try reinstalling Virtualbox.. Try adding a bit more video memory to the vm. BTW, is there an error message, or does it just silently shut down? - Joshua ** ** On Mon, Nov 21, 2011 at 2:05 AM, Popescu, V. v.pope...@vumc.nl wrote:*** * Dear all, Please help with the following problem: I am trying to run the FreeSurfer disk image on Virtual Box 4.1.6. I start it, I get: “GRUB loading please wait…” and then the Virtual Box crashes. It has 2048 MB base memory, 12 MB video memory. Thank you! Veronica ___ Freesurfer mailing list Freesurfer@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. ** ** ___ Freesurfer mailing list Freesurfer@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.
