Re: [Freesurfer] trac-all -stat
OK, thanks Amelia. That's interesting - keep me posted if you run into this with 6.0 in any new data set. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Versace, Amelia [versa...@upmc.edu] Sent: Thursday, April 13, 2017 10:24 AM To: Freesurfer support list Subject: Re: [Freesurfer] trac-all -stat Thanks, Anastasia!! It should be it. I had run the same command before with slightly fewer subjects in my "set subjlist" and it did work fine. Then I rerun the -path (and added extra 18 subjects) to update the tracts with the recent implementation that you have done (FS 6). After, started having this issue with -stat However, I ended up running the dmri_group after manually creating the *inputs.txt files and it did work fine... ;-) Thanks, Amelia -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Wednesday, April 12, 2017 5:04 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] trac-all -stat Hi Amelia - This means that it can't find any of the tracts that you've specified (or any tracts period, if you haven't specified a list) for the subjects that you've specified in your config file. It'd be looking under: /data/dprojects/BIOS/tracula/$subj/dpath/ Best, a.y From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Versace, Amelia [versa...@upmc.edu] Sent: Wednesday, April 12, 2017 5:00 PM To: Freesurfer support list Subject: [Freesurfer] trac-all -stat Hi Anastasia, I am having some issues with the -stat option. Below is the error. I am not sure of what's causing the issue. Any idea? Thanks a lot!! Amelia - trac-all -c scripts/dmrirc.stats -stat INFO: SUBJECTS_DIR is /data/dprojects/BIOS/freesurfer INFO: Diffusion root is /data/dprojects/BIOS/tracula Actual FREESURFER_HOME /data/software/freesurfer6 ERROR: no pathway reconstructions found - ___ 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
Re: [Freesurfer] trac-all -stat
Thanks, Anastasia!! It should be it. I had run the same command before with slightly fewer subjects in my "set subjlist" and it did work fine. Then I rerun the -path (and added extra 18 subjects) to update the tracts with the recent implementation that you have done (FS 6). After, started having this issue with -stat However, I ended up running the dmri_group after manually creating the *inputs.txt files and it did work fine... ;-) Thanks, Amelia -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Wednesday, April 12, 2017 5:04 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] trac-all -stat Hi Amelia - This means that it can't find any of the tracts that you've specified (or any tracts period, if you haven't specified a list) for the subjects that you've specified in your config file. It'd be looking under: /data/dprojects/BIOS/tracula/$subj/dpath/ Best, a.y From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Versace, Amelia [versa...@upmc.edu] Sent: Wednesday, April 12, 2017 5:00 PM To: Freesurfer support list Subject: [Freesurfer] trac-all -stat Hi Anastasia, I am having some issues with the -stat option. Below is the error. I am not sure of what's causing the issue. Any idea? Thanks a lot!! Amelia - trac-all -c scripts/dmrirc.stats -stat INFO: SUBJECTS_DIR is /data/dprojects/BIOS/freesurfer INFO: Diffusion root is /data/dprojects/BIOS/tracula Actual FREESURFER_HOME /data/software/freesurfer6 ERROR: no pathway reconstructions found - ___ 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] trac-all -stat
Hi Anastasia, I am having some issues with the -stat option. Below is the error. I am not sure of what's causing the issue. Any idea? Thanks a lot!! Amelia - trac-all -c scripts/dmrirc.stats -stat INFO: SUBJECTS_DIR is /data/dprojects/BIOS/freesurfer INFO: Diffusion root is /data/dprojects/BIOS/tracula Actual FREESURFER_HOME /data/software/freesurfer6 ERROR: no pathway reconstructions found - ___ 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] trac-all -stat
Hi Amelia - This means that it can't find any of the tracts that you've specified (or any tracts period, if you haven't specified a list) for the subjects that you've specified in your config file. It'd be looking under: /data/dprojects/BIOS/tracula/$subj/dpath/ Best, a.y From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Versace, Amelia [versa...@upmc.edu] Sent: Wednesday, April 12, 2017 5:00 PM To: Freesurfer support list Subject: [Freesurfer] trac-all -stat Hi Anastasia, I am having some issues with the -stat option. Below is the error. I am not sure of what's causing the issue. Any idea? Thanks a lot!! Amelia - trac-all -c scripts/dmrirc.stats -stat INFO: SUBJECTS_DIR is /data/dprojects/BIOS/freesurfer INFO: Diffusion root is /data/dprojects/BIOS/tracula Actual FREESURFER_HOME /data/software/freesurfer6 ERROR: no pathway reconstructions found - ___ 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] Trac-all -stat
Thanks for the response. When looking at pathstats.overall.txt, I did a similar rh-lh name flip. But is this ok for pathstats.byvoxel.txt, where the tracts are moved from the subjects' diffusion space to MNI space? The stat log file shows it uses the reference volume from ...base/dlabel/anatorig/aparc+aseg_mask.nii.gz and affine registration from ...base/dmri/xfms/anatorig2mni.mat. Maybe these should be ones after they've been left-right reversed using xhemi registration? Peggy On Fri, Aug 7, 2015 at 6:05 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Peggy - That's a good question and yet another great feature request. I can think of one completely inelegant hack for doing this right now in the absence of an actual feature. Let's say the path to the lh.cst stats of your subject is: subj1/blah...lh...blah/pathstats.byvoxel.txt Then you can create a fake subject with the same directory structure as your real subject so that you can create a fake lh.cst output directory for your fake subject that's really a symbolic link to the rh.cst output directory of your real subject: ln -s subj1/blah...rh...blah/pathstats.byvoxel.txt \ subj1-fake/blah...lh...blah/pathstats.byvoxel.txt Then you put all subjects, real and fake, into your subjlist and run trac-all -stat. It's ugly but it might just work! a.y On Thu, 23 Jul 2015, Peggy Skelly wrote: Hi, I'm using tracula with stroke subjects with a mixture which hemisphere is lesioned, so I'd like to compare all contra- or ipsilesional hemis together. trac-all -stat combines pathstats.byvoxel.txt for group analysis. Is there a way to combine some subjects' LH tract and other subjects' RH tract? Thanks, Peggy ___ 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] Trac-all -stat
Hi Peggy - That's a good question and yet another great feature request. I can think of one completely inelegant hack for doing this right now in the absence of an actual feature. Let's say the path to the lh.cst stats of your subject is: subj1/blah...lh...blah/pathstats.byvoxel.txt Then you can create a fake subject with the same directory structure as your real subject so that you can create a fake lh.cst output directory for your fake subject that's really a symbolic link to the rh.cst output directory of your real subject: ln -s subj1/blah...rh...blah/pathstats.byvoxel.txt \ subj1-fake/blah...lh...blah/pathstats.byvoxel.txt Then you put all subjects, real and fake, into your subjlist and run trac-all -stat. It's ugly but it might just work! a.y On Thu, 23 Jul 2015, Peggy Skelly wrote: Hi, I'm using tracula with stroke subjects with a mixture which hemisphere is lesioned, so I'd like to compare all contra- or ipsilesional hemis together. trac-all -stat combines pathstats.byvoxel.txt for group analysis. Is there a way to combine some subjects' LH tract and other subjects' RH tract? Thanks, Peggy ___ 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] Trac-all -stat
Hi, I'm using tracula with stroke subjects with a mixture which hemisphere is lesioned, so I'd like to compare all contra- or ipsilesional hemis together. trac-all -stat combines pathstats.byvoxel.txt for group analysis. Is there a way to combine some subjects' LH tract and other subjects' RH tract? Thanks, Peggy ___ 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] trac-all -stat option
Hi Kathryn - The -stat option was added in the latest tracula update, see here: http://freesurfer.net/fswiki/Tracula/#Updates You need to download this update, after installing freesurfer 5.3, to be able to do what is described in the tutorials. a.y On Wed, 4 Jun 2014, Kathryn Cullen wrote: Hello, I am trying to examine FA along the trajectory of the white matter tract, as described in the wiki: http://freesurfer.net/fswiki/FsTutorial/TraculaStatistics (half way down the page). I am using the FreeSurfer version 3.0. The wiki says: The pathstats.byvoxel.txt files will generally not contain the same number of positions (rows) for each subject because the tracts are reconstructed in each subject's native diffusion space and not in a template space. Thus they are not ready for performing group analyses yet. To combine these files from multiple subjects, interpolating the anisotropy and diffusivity values at corresponding positions along the tract for all subjects, run the following: trac-all -stat -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial However, when I try to use the -stat option, it says it is not recognized. There is no -stat option described in the help, either. Am I using the wrong version, or do I need to upload something differently? Thanks very much, Katie -- Kathryn R. Cullen, M.D. Assistant Professor University of Minnesota Medical School Department of Psychiatry Division of Child and Adolescent Psychiatry F268 West Building 2450 Riverside Avenue Minneapolis, MN 55454 (612) 273-9762 ___ 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] trac-all -stat option
Hello, I am trying to examine FA along the trajectory of the white matter tract, as described in the wiki: http://freesurfer.net/fswiki/FsTutorial/TraculaStatistics (half way down the page). I am using the FreeSurfer version 3.0. The wiki says: The pathstats.byvoxel.txt files will generally not contain the same number of positions (rows) for each subject because the tracts are reconstructed in each subject's native diffusion space and not in a template space. Thus they are not ready for performing group analyses yet. To combine these files from multiple subjects, interpolating the anisotropy and diffusivity values at corresponding positions along the tract for all subjects, run the following: trac-all -stat -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial However, when I try to use the -stat option, it says it is not recognized. There is no -stat option described in the help, either. Am I using the wrong version, or do I need to upload something differently? Thanks very much, Katie -- Kathryn R. Cullen, M.D. Assistant Professor University of Minnesota Medical School Department of Psychiatry Division of Child and Adolescent Psychiatry F268 West Building 2450 Riverside Avenue Minneapolis, MN 55454 (612) 273-9762 ___ 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.
