Re: [Freesurfer] convert FS volume in scanner space
My command line was cd $SUBJECTS_DIR/subjid/mri mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o brain-in-rawavg.mgz --no-save-reg according to fswiki/FsAnat-to-NativeAnat. As I mentioned, I am happy with the results but the coordinates are still RAS (from my understanding) and different from the original dicom-coordinates (that my manual segmentations are in). When I use mri_convert, the coordinates are in dicom-space (0 in center of image/ coil; offset and z-axis identical with original dicoms), but the segmentation seems different/ more prone to artifacts, also when I use rt- nearest. Georg -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas Greve Gesendet: Mittwoch, 8. Juli 2015 04:20 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] convert FS volume in scanner space what was your vol2vol command line? What wiki page were you referencing? What was the problem with the coordinates? On 7/7/15 8:11 PM, Bruce Fischl wrote: I think you meant you want nearest neighbor interpolation, not trilinear, since you are mapping labels. Try using -rt nearest insted On Wed, 8 Jul 2015, von Polier, Georg wrote: Thanks for your reply. I tried mri_convert with -rt interpolate (resulting in trilinear interpolation), however, the results were partially prone to artifacts and different from those I get with mir_vol2vol (but in dicom space). Is there a way using mir_vol2vol with results in dicom space, or a second step that gives a vox2vox from conformed/anatomical space to dicom space? I use the .mgz-output of hippo_subfields (FS_dev). Thanks again, Georg Am 07.07.2015 um 02:34 schrieb Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Georg if you have a volume (like the 001.mgz) that is in scanner coordinates you can use the reslice like and resample type flags in mri_convert: mri_convert -rl 001.mgz -rt trilinear input.mgz output.mgz cheers Bruce On Mon, 6 Jul 2015, von Polier, Georg wrote: Dear FreeSurfers, I need to convert an FS-volume back in scanner space (to calculate overlap with manual segmentation). I went through the wiki-entry and converted to native space with mir_vol2vol, however the coordinates are still RAS and not identical with the original Scanner-coordinates. I tried mri_convert, however, the results were not as good as mri_vol2vol (apparently need trilinear interpolation, not available in mri_convert). Any help would be greatly appreciated, Cheers, Georg ___ 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 ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] wm- volume limitations
Great - just what I was looking for - thanks. Regards, Don [Signature0001] Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: Tuesday, July 07, 2015 10:18 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] wm- volume limitations the wmparc gets the cortical parcellation of the closest cortical parcellation (not necessarily normal to the surface). I think it has to be within 5mm of cortex or else it gets Unsegmented White Matter. The method is described here http://www.ncbi.nlm.nih.gov/pubmed/19027860 On 7/7/15 8:36 PM, Krieger, Donald N. wrote: Freesurfer provides ctx- and wm- volumes on either side of the white labelled sheet, all for a particular cortical region. What is the idea which is used to limit the extent of the wm- volume which is adjacent to a particular ctx- volume? Is it as simple as a maximum distance normal to the white matter sheet? I'm sure this is documented somewhere but I haven't been able to find it. Thanks. Don ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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] Make liberal ROI masks
Dear all, I've created non-overlapping ROI masks using mri_label2vol --seg aparc.a2009s+aseg.mgz --regheader orig.mgz --o rois.nii --temp sub.nii --subject 01 Now these ROI masks are actually quite conservative concerning grey matter vs. other structures, i.e. they are only on the grey matter. I've seen more liberal masks e.g. here: https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011 I would like to create similarly liberal non-overlapping ROI masks for all ROIs in the voxel size defined by the image in --temp, but excluding specific tissue types such as white matter, CSF, and other non-grey matter tissue. What would be the best way to do so? Cheers, Martin ___ 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] mris_fill on HCP data
Hi all, I have been trying to use the mris_fill function on some Human connectome project data. I firstly convert the .gii file containing the pial surface using mris_convert. When visualising the converted mesh into FreeView everything looks normal. After the first step (“mris_fill -c -r 1”), though, the reconstructed filled volume does not look correct. The axes are flipped (anterior-posterior becomes superior-inferior) and the volume itself is “cut” at the edges. Does anybody know why that happen? Best, Matteo ___ 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] Cannot launch tkmedit in Ubuntu
Hello, When trying to use tkmedit, I got the following error message: No protocol specified No protocol specified GLUT: Fatal error in tkmedit.bin: could not open display: :0.0 In addition, when I tried to switch to freeview instead, I also got an error message: No protocol specified No protocol specified Freeview.bin: cannot connect to X server: 0.0 I'm running Ubuntu 12.04 LTS. Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Debian version: wheezy/sid Kernel info: Linux 3.2.0-60-generic x86_64 Please let me know if there is other info that you need. Any suggestion is very much appreciated. Thanks, Yifan -- Yifan Hu PhD Student | Social, Cognitive, Personality, and Emotional (SCoPE) Neuroscience Laboratory 3414/2436 Beckman Institute for Advanced Science and Technology Cognitive Neuroscience Division, Department of Psychology University of Illinois at Urbana-Champaign 405 North Mathews Ave Urbana, IL 61801 USA Phone: +1 (217) 607-4536 Email: yifan...@illinois.edumailto:yifan...@illinois.edu Website: http://dolcoslab.beckman.illinois.edu/ ___ 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] convert FS volume in scanner space
what do you mean the coords are still in RAS? On 7/8/15 8:25 AM, von Polier, Georg wrote: My command line was cd $SUBJECTS_DIR/subjid/mri mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o brain-in-rawavg.mgz --no-save-reg according to fswiki/FsAnat-to-NativeAnat. As I mentioned, I am happy with the results but the coordinates are still RAS (from my understanding) and different from the original dicom-coordinates (that my manual segmentations are in). When I use mri_convert, the coordinates are in dicom-space (0 in center of image/ coil; offset and z-axis identical with original dicoms), but the segmentation seems different/ more prone to artifacts, also when I use rt- nearest. Georg -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas Greve Gesendet: Mittwoch, 8. Juli 2015 04:20 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] convert FS volume in scanner space what was your vol2vol command line? What wiki page were you referencing? What was the problem with the coordinates? On 7/7/15 8:11 PM, Bruce Fischl wrote: I think you meant you want nearest neighbor interpolation, not trilinear, since you are mapping labels. Try using -rt nearest insted On Wed, 8 Jul 2015, von Polier, Georg wrote: Thanks for your reply. I tried mri_convert with -rt interpolate (resulting in trilinear interpolation), however, the results were partially prone to artifacts and different from those I get with mir_vol2vol (but in dicom space). Is there a way using mir_vol2vol with results in dicom space, or a second step that gives a vox2vox from conformed/anatomical space to dicom space? I use the .mgz-output of hippo_subfields (FS_dev). Thanks again, Georg Am 07.07.2015 um 02:34 schrieb Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Georg if you have a volume (like the 001.mgz) that is in scanner coordinates you can use the reslice like and resample type flags in mri_convert: mri_convert -rl 001.mgz -rt trilinear input.mgz output.mgz cheers Bruce On Mon, 6 Jul 2015, von Polier, Georg wrote: Dear FreeSurfers, I need to convert an FS-volume back in scanner space (to calculate overlap with manual segmentation). I went through the wiki-entry and converted to native space with mir_vol2vol, however the coordinates are still RAS and not identical with the original Scanner-coordinates. I tried mri_convert, however, the results were not as good as mri_vol2vol (apparently need trilinear interpolation, not available in mri_convert). Any help would be greatly appreciated, Cheers, Georg ___ 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 ___ 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 ___ 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
Re: [Freesurfer] mris_fill on HCP data
Nope. On 8 Jul 2015, at 17:06, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: do you have access to the surfaces before they were converted to gii? On Wed, 8 Jul 2015, Matteo Bastiani wrote: Hi Bruce, yes. With both surfaces (the original hcp '*.pial.surf.gii’ and the one I obtain using mris_converted '*.pial') I have the same results. To convert the original hcp gift surface into freesurfer format, I use: mris_convert subjId.surf,gii subjId.pial Is that the correct way? Cheers, Matteo On 8 Jul 2015, at 16:52, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Matteo what happens if you use our surface format? Does it work properly? Bruce On Wed, 8 Jul 2015, Matteo Bastiani wrote: Hi all, I have been trying to use the mris_fill function on some Human connectome project data. I firstly convert the .gii file containing the pial surface using mris_convert. When visualising the converted mesh into FreeView everything looks normal. After the first step (“mris_fill -c -r 1”), though, the reconstructed filled volume does not look correct. The axes are flipped (anterior-posterior becomes superior-inferior) and the volume itself is “cut” at the edges. Does anybody know why that happen? Best, Matteo ___ 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 ___ 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] mris_fill on HCP data
Hi Matteo what happens if you use our surface format? Does it work properly? Bruce On Wed, 8 Jul 2015, Matteo Bastiani wrote: Hi all, I have been trying to use the mris_fill function on some Human connectome project data. I firstly convert the .gii file containing the pial surface using mris_convert. When visualising the converted mesh into FreeView everything looks normal. After the first step (“mris_fill -c -r 1”), though, the reconstructed filled volume does not look correct. The axes are flipped (anterior-posterior becomes superior-inferior) and the volume itself is “cut” at the edges. Does anybody know why that happen? Best, Matteo ___ 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] Cannot launch tkmedit in Ubuntu
Hi Yifan are you on the console of that machine or are you remotely logging in from somewhere else? Can you run standard x apps (like xclock)? cheers Bruce On Wed, 8 Jul 2015, Hu, Yifan wrote: Hello, When trying to use tkmedit, I got the following error message: No protocol specified No protocol specified GLUT: Fatal error in tkmedit.bin: could not open display: :0.0 In addition, when I tried to switch to freeview instead, I also got an error message: No protocol specified No protocol specified Freeview.bin: cannot connect to X server: 0.0 I’m running Ubuntu 12.04 LTS. Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Debian version: wheezy/sid Kernel info: Linux 3.2.0-60-generic x86_64 Please let me know if there is other info that you need. Any suggestion is very much appreciated. Thanks, Yifan -- Yifan Hu PhD Student | Social, Cognitive, Personality, and Emotional (SCoPE) Neuroscience Laboratory 3414/2436 Beckman Institute for Advanced Science and Technology Cognitive Neuroscience Division, Department of Psychology University of Illinois at Urbana-Champaign 405 North Mathews Ave Urbana, IL 61801 USA Phone: +1 (217) 607-4536 Email: yifan...@illinois.edu Website: http://dolcoslab.beckman.illinois.edu/ ___ 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] mris_fill on HCP data
do you have access to the surfaces before they were converted to gii? On Wed, 8 Jul 2015, Matteo Bastiani wrote: Hi Bruce, yes. With both surfaces (the original hcp '*.pial.surf.gii’ and the one I obtain using mris_converted '*.pial') I have the same results. To convert the original hcp gift surface into freesurfer format, I use: mris_convert subjId.surf,gii subjId.pial Is that the correct way? Cheers, Matteo On 8 Jul 2015, at 16:52, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Matteo what happens if you use our surface format? Does it work properly? Bruce On Wed, 8 Jul 2015, Matteo Bastiani wrote: Hi all, I have been trying to use the mris_fill function on some Human connectome project data. I firstly convert the .gii file containing the pial surface using mris_convert. When visualising the converted mesh into FreeView everything looks normal. After the first step (“mris_fill -c -r 1”), though, the reconstructed filled volume does not look correct. The axes are flipped (anterior-posterior becomes superior-inferior) and the volume itself is “cut” at the edges. Does anybody know why that happen? Best, Matteo ___ 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 ___ 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] mris_fill on HCP data
Hi Bruce, yes. With both surfaces (the original hcp '*.pial.surf.gii’ and the one I obtain using mris_converted '*.pial') I have the same results. To convert the original hcp gift surface into freesurfer format, I use: mris_convert subjId.surf,gii subjId.pial Is that the correct way? Cheers, Matteo On 8 Jul 2015, at 16:52, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Matteo what happens if you use our surface format? Does it work properly? Bruce On Wed, 8 Jul 2015, Matteo Bastiani wrote: Hi all, I have been trying to use the mris_fill function on some Human connectome project data. I firstly convert the .gii file containing the pial surface using mris_convert. When visualising the converted mesh into FreeView everything looks normal. After the first step (“mris_fill -c -r 1”), though, the reconstructed filled volume does not look correct. The axes are flipped (anterior-posterior becomes superior-inferior) and the volume itself is “cut” at the edges. Does anybody know why that happen? Best, Matteo ___ 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
Re: [Freesurfer] Help with V6
Thanks Noah. It doea say on the website that you need the 2012b runtime, but its definitely buried among too much other, less critical stuff Cheers E Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Noah Markowitz noahb.markow...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Sat, 04 Jul 2015 13:57:53 +0200 (CEST) Subject: Re: [Freesurfer] Help with V6 Hey Eugenio, I was able to resolve it with the help of another expert. One of the problems definitely was that 2014b doesn’t run on the hippocampal-subfields module. Maybe try adding that as a note to the website as numerous people have access to the 2014b version and 2015a was just released. Thanks again for all the help. Cheers, Noah On Jul 3, 2015, at 5:12 PM, Eugenio Iglesias e.igles...@bcbl.eu wrote: Hi Noah, this error is pretty weird. Can you please send us the exact command you executed? Regarding the runtime: your 2014b runtime won't work. You need to follow the instructions here: https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Noah Markowitz noahb.markow...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, July 3, 2015 4:20:02 AM Subject: [Freesurfer] Help with V6 Hi, I’m trying to run the ‘beta’ version of FS6, centos4, and encountered the error: ‘ERROR: Flag -hippocampal-subfields-T1 unrecognized’. I setenv and source just as described for previous versions. Also, I have Matlab 2014b downloaded on the computer (obviously comes with runtime) but am unsure if the runtime folder needs to be placed in the FS folder or is fine where it is. Any FS experts help with these two problems and concerns? Much appreciated if you do. Cheers, Noah Markowitz ___ 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 ___ 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
Re: [Freesurfer] mris_fill on HCP data
If you can you upload your subject on our website and email us the exact command lines you used, we will take a look. Bruce On Wed, 8 Jul 2015, Matteo Bastiani wrote: Nope. On 8 Jul 2015, at 17:06, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: do you have access to the surfaces before they were converted to gii? On Wed, 8 Jul 2015, Matteo Bastiani wrote: Hi Bruce, yes. With both surfaces (the original hcp '*.pial.surf.gii’ and the one I obtain using mris_converted '*.pial') I have the same results. To convert the original hcp gift surface into freesurfer format, I use: mris_convert subjId.surf,gii subjId.pial Is that the correct way? Cheers, Matteo On 8 Jul 2015, at 16:52, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Matteo what happens if you use our surface format? Does it work properly? Bruce On Wed, 8 Jul 2015, Matteo Bastiani wrote: Hi all, I have been trying to use the mris_fill function on some Human connectome project data. I firstly convert the .gii file containing the pial surface using mris_convert. When visualising the converted mesh into FreeView everything looks normal. After the first step (“mris_fill -c -r 1”), though, the reconstructed filled volume does not look correct. The axes are flipped (anterior-posterior becomes superior-inferior) and the volume itself is “cut” at the edges. Does anybody know why that happen? Best, Matteo ___ 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 ___ 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 ___ 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] 3 Group comparison
There is not a --meas option for mri_glmfit, you need to give it a --y option explicity, though it may be trying to read a yfile if you have one in the FSGD. How did you make g3v0.fsgd? Can you send it? The second command looks like you are doing the right thing, you just need to tell mri_glmfit that this is surface data by adding --surface fsaverage hemi where hemi is lh or rh doug On 07/07/2015 06:45 AM, pablo najt wrote: Dear FS experts, I am trying to run a 3 group comparison with FS. I have run preproc ( script from ENIGMA Cortical protocol) on my first fsgd file. As I have three groups I have prepared my second fsgd file as g3v0.fsgd and all my desired contrasts, rather than using QDEC. I run this second stage as follows: mri_glmfit \ --glmdir g3v0 \ --meas thickness ../SURF/lh.thickness.mgh \ --fsgd g3v0.fsgd \ --C HC-BD_fam.mtx \ --C HC-BD.mtx \ --C BD-BD_fam.mtx \ --C group.effect.mtx \ --C HC+BD-vs-BD_fam.mtx and I get: Loading y from /Volumes/NEW_VOLUME/Familial_FS_Final/FSGD/y.mgh mghRead(/Volumes/NEW_VOLUME/Familial_FS_Final/FSGD/y.mgh, -1): could not open file ERROR: loading y /Volumes/NEW_VOLUME/Familial_FS_Final/FSGD/y.mgh As far as I understand y.mgh is a stack data that is made after using QDEC is run. But I have been prompted to not use QDEC, so I am now wondering how I am supposed to run my glm design. Also I tried to change the y.mgh to any of the outputs of the mris_preproc (lh.white.mgh, lh.volume.mgh, lh.thickness.mgh, etc), and it says: Creating output directory g3v0 Loading y from /Volumes/NEW_VOLUME/Familial_FS_Final/SURF/rh.white.mgh ERROR: you must use '--surface subject hemi' with surface data Any suggestion would be greatly appreciated. Thanks a lot. Pablo ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] longitudinal analysis
Hi Martin, Now clear. Thanks. Yawu On Mon, Jul 6, 2015 at 8:50 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Yawu, no, that would be the simple average. Temporal average is the linear fit (within each subject) evaluated at the mid time. So if you had 10 time points at the same day and 1 a year later, it would look like a .5 years time point. This is used to compute symmetrized percent change, representing the change with respect to the temporal average to make it more symmetric. Cheers, Martin On 07/03/2015 08:43 AM, Liu Y wrote: Dear Freesurfer experts In the command long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR, Do-avg will compute the temporal average. I do not quite understand the temporal average Is the average of baseline and followup thicknesses? Best regards, Yawu ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ 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.
