Re: [Freesurfer] AAL and freesurfer atlas concordance
External Email - Use Caution Dear All I have seen posts discussing about bringing AAL to freesurfer etc. I am wondering whether anyone has created a table of concordance between the regions in AAL to the freesurfer or the vice versa. If so can you please share with me. For my work I just want to know the mapping between the two atlases. Or is there any software or website (like the brain atlas concordance one) from where I can find the concordance between the two atlas regions Any help is greatly appreciated Thanks Venkat ___ 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] AAL and freesurfer atlas concordance
External Email - Use Caution Dear All I have seen posts discussing about bringing AAL to freesurfer etc. I am wondering whether anyone has created a table of concordance between the regions in AAL to the freesurfer or the vice versa. If so can you please share with me. For my work I just want to know the mapping between the two atlases. Or is there any software or website (like the brain atlas concordance one) from where I can find the concordance between the two atlas regions Any help is greatly appreciated Thanks Venkat ___ 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] Fwd: mpr2mni305 failed, see transforms/talairach_avi.log
Nick, Thanks for your kind help. I uploaded my orig.mgz i.e. 001.mgz using Martinos center file drop. Thanks Venkat On Mon, Jun 23, 2014 at 11:42 PM, Nick Schmansky, MGH ni...@nmr.mgh.harvard.edu wrote: Venkat, Can you send me your orig.mgz so that I can attempt to replicate? Nick On Mon, 2014-06-23 at 08:46 +0530, Venkateswaran Rajagopalan wrote: Hi Bruce, Thanks very much. I will wait for Avi Synder's response. Thanks a lot Venkat On Sat, Jun 21, 2014 at 8:23 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Venkat I'll cc Avi Snyder. Avi: do you know what this error message means? thanks Bruce On Sat, 21 Jun 2014, Venkateswaran Rajagopalan wrote: Dear All, I am sorry to post this again. Any help will be greatly appreciated. I am struck as I am unable to run the recon-all step. Thanks Venkat -- Forwarded message -- From: Venkateswaran Rajagopalan venkateswa...@hyderabad.bits-pilani.ac.in Date: Fri, Jun 20, 2014 at 5:14 PM Subject: mpr2mni305 failed, see transforms/talairach_avi.log To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Hi All, I am getting the the following error when I run recon-all -subjid E368 -autorecon1 ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Here is what talairach_avi.log says /home/administrator/Desktop/freesurfer/subjects_dir/E368/mri /usr/local/freesurfer/bin/talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ Linux administrator-HP-Pro-3330-MT 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux Fri Jun 20 17:06:38 IST 2014 mri_convert orig_nu.mgz talsrcimg.img $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to talsrcimg.img... Analyze Output Matrix -1.000 0.000 0.000 129.000; 0.000 0.000 1.000 -129.000; 0.000 -1.000 0.000 122.500; 0.000 0.000 0.000 1.000; INFO: set hdr.hist.orient to -1 mpr2mni305 talsrcimg Fri Jun 20 17:06:39 IST 2014 /usr/local/freesurfer/bin/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ target=711-2C_as_mni_average_305 - analyzeto4dfp talsrcimg -O0 -y - $Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Fri Jun 20 17:06:40 2014 Writing: talsrcimg.4dfp.hdr $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $ Reading: talsrcimg.hdr header size 348 bytes hdr.dime.datatypeoffset=70value=2 hdr.dime.bitpixoffset=72value=8 hdr.hist.orientoffset=252value=-1 dimensionality 4 dimensions 256 256 256 1 Reading: talsrcimg.img Writing: talsrcimg.4dfp.img Writing: talsrcimg.4dfp.ifh ifh2hdr talsrcimg -r0to255 ori=2 - gauss_4dfp talsrcimg 1.1 - $Id: gauss_4dfp.c,v 1.3 2009/05/15 21:43:46 nicks Exp $ Reading: talsrcimg.4dfp.img Writing: talsrcimg_g11.4dfp.img image dimensions 256 256 256 padded to 288 288 288 processing volume 1$Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Fri Jun 20 17:06:46 2014 Writing: talsrcimg_g11.4dfp.hdr
Re: [Freesurfer] Fwd: mpr2mni305 failed, see transforms/talairach_avi.log
Hi Bruce, Thanks very much. I will wait for Avi Synder's response. Thanks a lot Venkat On Sat, Jun 21, 2014 at 8:23 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Venkat I'll cc Avi Snyder. Avi: do you know what this error message means? thanks Bruce On Sat, 21 Jun 2014, Venkateswaran Rajagopalan wrote: Dear All, I am sorry to post this again. Any help will be greatly appreciated. I am struck as I am unable to run the recon-all step. Thanks Venkat -- Forwarded message -- From: Venkateswaran Rajagopalan venkateswa...@hyderabad.bits- pilani.ac.in Date: Fri, Jun 20, 2014 at 5:14 PM Subject: mpr2mni305 failed, see transforms/talairach_avi.log To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Hi All, I am getting the the following error when I run recon-all -subjid E368 -autorecon1 ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Here is what talairach_avi.log says /home/administrator/Desktop/freesurfer/subjects_dir/E368/mri /usr/local/freesurfer/bin/talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ Linux administrator-HP-Pro-3330-MT 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux Fri Jun 20 17:06:38 IST 2014 mri_convert orig_nu.mgz talsrcimg.img $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to talsrcimg.img... Analyze Output Matrix -1.000 0.000 0.000 129.000; 0.000 0.000 1.000 -129.000; 0.000 -1.000 0.000 122.500; 0.000 0.000 0.000 1.000; INFO: set hdr.hist.orient to -1 mpr2mni305 talsrcimg Fri Jun 20 17:06:39 IST 2014 /usr/local/freesurfer/bin/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ target=711-2C_as_mni_average_305 - analyzeto4dfp talsrcimg -O0 -y - $Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Fri Jun 20 17:06:40 2014 Writing: talsrcimg.4dfp.hdr $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $ Reading: talsrcimg.hdr header size 348 bytes hdr.dime.datatypeoffset=70value=2 hdr.dime.bitpixoffset=72value=8 hdr.hist.orientoffset=252value=-1 dimensionality 4 dimensions 256 256 256 1 Reading: talsrcimg.img Writing: talsrcimg.4dfp.img Writing: talsrcimg.4dfp.ifh ifh2hdr talsrcimg -r0to255 ori=2 - gauss_4dfp talsrcimg 1.1 - $Id: gauss_4dfp.c,v 1.3 2009/05/15 21:43:46 nicks Exp $ Reading: talsrcimg.4dfp.img Writing: talsrcimg_g11.4dfp.img image dimensions 256 256 256 padded to 288 288 288 processing volume 1$Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Fri Jun 20 17:06:46 2014 Writing: talsrcimg_g11.4dfp.hdr Writing: talsrcimg_g11.4dfp.ifh including: talsrcimg.4dfp.img.rec in talsrcimg_g11.4dfp.img.rec - imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 none talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 4355 - $Id: imgreg_4dfp.c,v 1.4 2010/02/27 01:41:53 nicks Exp $ imgreg_4dfp: /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img read error /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img 256 256 256 1 1.00 1.00 1.00 orientation T byte_order littleendian Reading image: /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img dimensions: 256 256 256 mmppix: 1. -1. -1. center: 128. -129. -129. ERROR: 'imgreg_4dfp /usr/local/freesurfer/average/ 711-2C_as_mni_average_305 none talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 4355' failed! status=255 ERROR: mpr2mni305 execution aborted Any help will be greatly appreciated. Thanks Venkat ___ 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] Can some send me rh.average.curvature.filled.buckner40.tif file
Dear All, when I run recon-all I encounter errro saying that rh.average.curvature.filled.buckner40.tif file is missing. I found this file missing in my average folder so if someone can send it as an attachment or guide me to where I can find it it will be great help. Many thanks in advance Venkat ___ 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] mpr2mni305 failed, see transforms/talairach_avi.log
Hi All, I am getting the the following error when I run recon-all -subjid E368 -autorecon1 ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Here is what talairach_avi.log says /home/administrator/Desktop/freesurfer/subjects_dir/E368/mri /usr/local/freesurfer/bin/talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ Linux administrator-HP-Pro-3330-MT 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux Fri Jun 20 17:06:38 IST 2014 mri_convert orig_nu.mgz talsrcimg.img $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to talsrcimg.img... Analyze Output Matrix -1.000 0.000 0.000 129.000; 0.000 0.000 1.000 -129.000; 0.000 -1.000 0.000 122.500; 0.000 0.000 0.000 1.000; INFO: set hdr.hist.orient to -1 mpr2mni305 talsrcimg Fri Jun 20 17:06:39 IST 2014 /usr/local/freesurfer/bin/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ target=711-2C_as_mni_average_305 - analyzeto4dfp talsrcimg -O0 -y - $Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Fri Jun 20 17:06:40 2014 Writing: talsrcimg.4dfp.hdr $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $ Reading: talsrcimg.hdr header size 348 bytes hdr.dime.datatypeoffset=70value=2 hdr.dime.bitpixoffset=72value=8 hdr.hist.orientoffset=252value=-1 dimensionality 4 dimensions 256 256 256 1 Reading: talsrcimg.img Writing: talsrcimg.4dfp.img Writing: talsrcimg.4dfp.ifh ifh2hdr talsrcimg -r0to255 ori=2 - gauss_4dfp talsrcimg 1.1 - $Id: gauss_4dfp.c,v 1.3 2009/05/15 21:43:46 nicks Exp $ Reading: talsrcimg.4dfp.img Writing: talsrcimg_g11.4dfp.img image dimensions 256 256 256 padded to 288 288 288 processing volume 1$Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Fri Jun 20 17:06:46 2014 Writing: talsrcimg_g11.4dfp.hdr Writing: talsrcimg_g11.4dfp.ifh including: talsrcimg.4dfp.img.rec in talsrcimg_g11.4dfp.img.rec - imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 none talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 4355 - $Id: imgreg_4dfp.c,v 1.4 2010/02/27 01:41:53 nicks Exp $ imgreg_4dfp: /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img read error /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img 256 256 256 1 1.00 1.00 1.00 orientation T byte_order littleendian Reading image: /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img dimensions: 256 256 256 mmppix: 1. -1. -1. center: 128. -129. -129. ERROR: 'imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 none talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 4355' failed! status=255 ERROR: mpr2mni305 execution aborted Any help will be greatly appreciated. Thanks Venkat ___ 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] Fwd: mpr2mni305 failed, see transforms/talairach_avi.log
Dear All, I am sorry to post this again. Any help will be greatly appreciated. I am struck as I am unable to run the recon-all step. Thanks Venkat -- Forwarded message -- From: Venkateswaran Rajagopalan venkateswa...@hyderabad.bits-pilani.ac.in Date: Fri, Jun 20, 2014 at 5:14 PM Subject: mpr2mni305 failed, see transforms/talairach_avi.log To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Hi All, I am getting the the following error when I run recon-all -subjid E368 -autorecon1 ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Here is what talairach_avi.log says /home/administrator/Desktop/freesurfer/subjects_dir/E368/mri /usr/local/freesurfer/bin/talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ Linux administrator-HP-Pro-3330-MT 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux Fri Jun 20 17:06:38 IST 2014 mri_convert orig_nu.mgz talsrcimg.img $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to talsrcimg.img... Analyze Output Matrix -1.000 0.000 0.000 129.000; 0.000 0.000 1.000 -129.000; 0.000 -1.000 0.000 122.500; 0.000 0.000 0.000 1.000; INFO: set hdr.hist.orient to -1 mpr2mni305 talsrcimg Fri Jun 20 17:06:39 IST 2014 /usr/local/freesurfer/bin/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ target=711-2C_as_mni_average_305 - analyzeto4dfp talsrcimg -O0 -y - $Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Fri Jun 20 17:06:40 2014 Writing: talsrcimg.4dfp.hdr $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $ Reading: talsrcimg.hdr header size 348 bytes hdr.dime.datatypeoffset=70value=2 hdr.dime.bitpixoffset=72value=8 hdr.hist.orientoffset=252value=-1 dimensionality 4 dimensions 256 256 256 1 Reading: talsrcimg.img Writing: talsrcimg.4dfp.img Writing: talsrcimg.4dfp.ifh ifh2hdr talsrcimg -r0to255 ori=2 - gauss_4dfp talsrcimg 1.1 - $Id: gauss_4dfp.c,v 1.3 2009/05/15 21:43:46 nicks Exp $ Reading: talsrcimg.4dfp.img Writing: talsrcimg_g11.4dfp.img image dimensions 256 256 256 padded to 288 288 288 processing volume 1$Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Fri Jun 20 17:06:46 2014 Writing: talsrcimg_g11.4dfp.hdr Writing: talsrcimg_g11.4dfp.ifh including: talsrcimg.4dfp.img.rec in talsrcimg_g11.4dfp.img.rec - imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 none talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 4355 - $Id: imgreg_4dfp.c,v 1.4 2010/02/27 01:41:53 nicks Exp $ imgreg_4dfp: /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img read error /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img 256 256 256 1 1.00 1.00 1.00 orientation T byte_order littleendian Reading image: /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img dimensions: 256 256 256 mmppix: 1. -1. -1. center: 128. -129. -129. ERROR: 'imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 none talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 4355' failed! status=255 ERROR: mpr2mni305 execution aborted Any help will be greatly appreciated. Thanks Venkat ___ 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] Freesurfer installation problem
Nick, Thanks very much. I will do as per your suggestion. I am new to Linux and Ubuntu. If I am not bothering you too much. I read an article where they compared the results from Freesurfer's different versions and about using different OS and concluded saying that use the same version and do not upgrade while in the middle of the study. My collaborators are using Freesurfer 5.0 and I will be helping them in processing the data (sharing the data processing and analysis) so is it ok to use use 5.3.0 or 5.0 is recommended. Thanks very much again Venkat On Wed, Jun 11, 2014 at 12:50 AM, Nick Schmansky, MGH ni...@nmr.mgh.harvard.edu wrote: Venkat, Your system appears to be 32bit distribution, as indicated by 'i686' in your output string, but the freesurfer you installed is 64b, indicated by 'x86_64' in our filename. So you will need the 32b dist: freesurfer-Linux-centos4-stable-pub-v5.3.0.tar.gz Also, v5.0.0 is pretty old, I'd recommend v5.3.0. Nick On Tue, 2014-06-10 at 13:23 +0530, Venkateswaran Rajagopalan wrote: Dear All, I looked into the archives extensively but could not find a solution to my problem. I am having Ubuntu Linux administrator-HP-Pro-3330-MT 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux. I tried installing freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0.tar.gz. But I get the following error message mri_convert /usr/local/freesurfer/bin/mri_convert: Exec format error. Binary file not executable. tkmedit /usr/local/freesurfer/tktools/tkmedit.bin: Exec format error. Binary file not executable. I followed the instruction steps as given in freesurfer wiki. What am I doing wrong here?. Is there a installation wiki page for giving guidelines for ubuntu freesurfer installation. Thanks, any help will be greatly appreciated as I am trying to install freesurfer for the past 3 days without success. Thanks Venkat ___ 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 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] Freesurfer installation problem
Dear All, I looked into the archives extensively but could not find a solution to my problem. I am having Ubuntu Linux administrator-HP-Pro-3330-MT 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux. I tried installing freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0.tar.gz. But I get the following error message mri_convert /usr/local/freesurfer/bin/mri_convert: Exec format error. Binary file not executable. tkmedit /usr/local/freesurfer/tktools/tkmedit.bin: Exec format error. Binary file not executable. I followed the instruction steps as given in freesurfer wiki. What am I doing wrong here?. Is there a installation wiki page for giving guidelines for ubuntu freesurfer installation. Thanks, any help will be greatly appreciated as I am trying to install freesurfer for the past 3 days without success. Thanks Venkat ___ 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] Freesurfer installation problem
Hi Bruce, Thanks very much What hardware platform are you running on? Memory: 3.8 GiB Processor Intel core i3-3220 cpu @3.30 GHz*4 Graphics Intel Ivybridge Desktop x86/MMX/SSE2 OS type 32-bit Disk 103.1 GB And can you run: ls -l /usr/local/freesurfer/bin/mri_convert I get the following when the run the above -rwxr-xr-x 1 root root 4015444 May 14 2013 /usr/local/freesurfer/bin/mri_convert Thanks a lot Venkat On Tue, Jun 10, 2014 at 6:29 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Venkat What hardware platform are you running on? And can you run: ls -l /usr/local/freesurfer/bin/mri_convert cheers Bruce On Tue, 10 Jun 2014, Venkateswaran Rajagopalan wrote: Dear All, I looked into the archives extensively but could not find a solution to my problem. I am having Ubuntu Linux administrator-HP-Pro-3330-MT 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux. I tried installing freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0.tar.gz. But I get the following error message mri_convert /usr/local/freesurfer/bin/mri_convert: Exec format error. Binary file not executable. tkmedit /usr/local/freesurfer/tktools/tkmedit.bin: Exec format error. Binary file not executable. I followed the instruction steps as given in freesurfer wiki. What am I doing wrong here?. Is there a installation wiki page for giving guidelines for ubuntu freesurfer installation. Thanks, any help will be greatly appreciated as I am trying to install freesurfer for the past 3 days without success. Thanks Venkat ___ 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.
