Re: [Freesurfer] Making a custom experimental template
Hi doug, I read your instructions on how to make an average subject, it looks quite streamlined. But I still have two questions about the procedure. 1. During the processing, every subject's surface need to register to a common target, and where the target comes from, it is an existed template in FreeSurfer or randomly selected from the pool of subjects, or something else? 2. In order to get a well-established or accurate average template, how many times does the function make_average_subject need to run? Thanks in advance, Lijie Huang On Tue, May 10, 2011 at 3:28 AM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Hi Joakim, here are some instructions on what to do (some of which you've already done): doug # Create an average subject (Creates $SUBJECTS_DIR/newtemplate) make_average_subject --out newtemplate --subjects subj1 subj2 subj3 ... # Register each subject to the new template (do for both lh and rh) # Creates lh.sphere.reg.newtemplate and rh.sphere.reg.newtemplate foreach subject (subj1 subj2 subj3 ...) cd $SUBJECTS_DIR/subject mris_register -curv surf/lh.sphere \ $SUBJECTS_DIR/newtemplate/lh.reg.template.tif \ surf/lh.sphere.reg.newtemplate end # Get thickness values in the newtemplate space for GLM analysis mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2 --s subj3 ... # Create another average template based on the previous one: # (Creates $SUBJECTS_DIR/newnewtemplate) make_average_subject --out newnewtemplate --surf-reg sphere.reg.newtemplate \ --subjects subj1 subj2 subj3 ... Joakim Vinberg wrote: Doug, Thanks! I just took a look at make_average_subject, and that looks quite a bit more streamlined--I think I'll just do that. Looking at make_average_subject, this should make the replacement for fsaverage. Following that, I would want to run mri_surf2surf to generate all of the surfaces in our new template space? Thanks! Joakim *From:* Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] *Sent:* Fri 5/6/2011 9:46 AM *To:* Joakim Vinberg *Cc:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Making a custom experimental template You are correct. If you run make_average_subject, it will create the template for you (as well as all the other files in a typical subject dir -- you'll need these to do a simple replacement for fsaverage). doug Joakim Vinberg wrote: Hi FS crowd, I just want to make sure that I have the process correctly described for setting up a custom experimental template. I am basing this off of the SurfaceRegAndTemplates (http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates), and a hypothetical experiment with 10 subjects (s1, s2, …s10). I apologize if this has been well-covered—I couldn’t quite match it on the website or the archives. For the prep step, I believe my commands would be: mris_make_template lh sphere s1 custom_template_lh_0.tif mris_make_template rh sphere s1 custom_template_rh_0.tif which would result in two new template files names custom_template_lh_0.tif and custom_template_rh_0.tif For Round 1, I would first create another registration for each subject: mris_register s1/surf/lh.sphere custom_template_lh_0.tif s1/surf/lh.sphere.regcustom_0 mris_register s1/surf/rh.sphere custom_template_rh_0.tif s1/surf/rh.sphere.regcustom_0 … mris_register s10/surf/lh.sphere custom_template_lh_0.tif s10/surf/lh.sphere.regcustom_0 mris_register s10/surf/rh.sphere custom_template_rh_0.tif s10/surf/rh.sphere.regcustom_0 And then create another custom template: mris_make_template lh sphere s1 s2 s3 … s10 custom_template_lh_1.tif mris_make_template rh sphere s1 s2 s3 … s10 custom_template_rh_1.tif For round 2, I would repeat Round 1, generating a new set of sphere.reg files, and then a new template, except substitute the custom template from round 1 (custom_template_lh_1.tif and custom_template_rh_1.tif). Then, I would register all of my data to the custom_template_lh_2.tif and custom_template_rh_2.tif generated at the end of round 2. From there, I am assuming that I could be able to use this new template as I would fsaverage. Am I correct, or have I missed a step? Thanks in advance for all of your help! Joakim ___ 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 The information
[Freesurfer] Mris_anatomical_stats
Dear FS experts I tried to read out in each subject the surface area values of some clusters derived from a group comparison. For that purpose, I used mri_surf2surf and mris_anatomical_stats. Everything worked fine, but in some clusters the direction of the effects reversed. A first guess was that this might have to do with the smoothing that we applied to the group comparison. Therefore, I smoothed the individual area files to get the smoothed surface area in each subject using the following command: mris_anatomical_stats -a area_p01.annot -t rh.area -nsmooth 15 -f $s/stats/rh.aparc.a2005s.stats $s rh But the surface area of this smoothed data gives the same values as the unsmoothed data. Any idea what is wrong here? Thanks in advance Regards Jürgen Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ___ 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] Neuroscience software survey: What is popular, what has problems? Immediate results
[Apologies for cross-posting] Dear neuroscience researchers and IT staff We invite you to participate in a survey on software usage and computing environments in neuroscience research. It will take no more than five minutes to fill it out. Immediately after sending your answers you will get to see a summary of how other participants have responded before. This data will eventually be made available to software vendors and distributors to determine advantages and issue of popular computing environments in neuroscience research. Learn about what fellow neuroscientists are doing to address their computing demands -- take the survey! http://goo.gl/euIMc Thanks, -- PyMVPA/NeuroDebian Team: Yaroslav O. Halchenko Michael Hanke Postdoctoral Fellows, Department of Psychological and Brain Sciences Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 ___ 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_anatomical_stats problem
Dear FS experts I tried to read out in each subject the surface area values of some clusters derived from a group comparison. For that purpose, I used mri_surf2surf and mris_anatomical_stats. Everything worked fine, but in some clusters the direction of the effects reversed. A first guess was that this might have to do with the smoothing that we applied to the group comparison. Therefore, I smoothed the individual area files to get the smoothed surface area in each subject using the following command: mris_anatomical_stats -a area_p01.annot -t rh.area -nsmooth 15 -f $s/stats/rh.aparc.a2005s.stats $s rh But the surface area of this smoothed data gives the same values as the unsmoothed data. Any idea what is wrong here? Thanks in advance Regards Jürgen PS: sorry for posting this message twice, but the first post did not appeared in the archives Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ___ 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_anatomical_stats problem
Juegen, can you send the full terminal output? Also, you can try explicitly smoothing the file with mri_surf2surf and then run anatomical stats on the smoothed file. doug Jürgen Hänggi wrote: Dear FS experts I tried to read out in each subject the surface area values of some clusters derived from a group comparison. For that purpose, I used mri_surf2surf and mris_anatomical_stats. Everything worked fine, but in some clusters the direction of the effects reversed. A first guess was that this might have to do with the smoothing that we applied to the group comparison. Therefore, I smoothed the individual area files to get the smoothed surface area in each subject using the following command: mris_anatomical_stats -a area_p01.annot -t rh.area -nsmooth 15 -f $s/stats/rh.aparc.a2005s.stats $s rh But the surface area of this smoothed data gives the same values as the unsmoothed data. Any idea what is wrong here? Thanks in advance Regards Jürgen PS: sorry for posting this message twice, but the first post did not appeared in the archives Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ___ 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] Making a custom experimental template
soft.join Huang wrote: Hi doug, I read your instructions on how to make an average subject, it looks quite streamlined. But I still have two questions about the procedure. 1. During the processing, every subject's surface need to register to a common target, and where the target comes from, it is an existed template in FreeSurfer or randomly selected from the pool of subjects, or something else? I would recommend starting off with fsaverage, then you can use your new average for the next iteration. 2. In order to get a well-established or accurate average template, how many times does the function make_average_subject need to run? I don't know for sure. Probably two iterations are enough. doug Thanks in advance, Lijie Huang On Tue, May 10, 2011 at 3:28 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Joakim, here are some instructions on what to do (some of which you've already done): doug # Create an average subject (Creates $SUBJECTS_DIR/newtemplate) make_average_subject --out newtemplate --subjects subj1 subj2 subj3 ... # Register each subject to the new template (do for both lh and rh) # Creates lh.sphere.reg.newtemplate and rh.sphere.reg.newtemplate foreach subject (subj1 subj2 subj3 ...) cd $SUBJECTS_DIR/subject mris_register -curv surf/lh.sphere \ $SUBJECTS_DIR/newtemplate/lh.reg.template.tif \ surf/lh.sphere.reg.newtemplate end # Get thickness values in the newtemplate space for GLM analysis mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2 --s subj3 ... # Create another average template based on the previous one: # (Creates $SUBJECTS_DIR/newnewtemplate) make_average_subject --out newnewtemplate --surf-reg sphere.reg.newtemplate \ --subjects subj1 subj2 subj3 ... Joakim Vinberg wrote: Doug, Thanks! I just took a look at make_average_subject, and that looks quite a bit more streamlined--I think I'll just do that. Looking at make_average_subject, this should make the replacement for fsaverage. Following that, I would want to run mri_surf2surf to generate all of the surfaces in our new template space? Thanks! Joakim *From:* Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu] *Sent:* Fri 5/6/2011 9:46 AM *To:* Joakim Vinberg *Cc:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Making a custom experimental template You are correct. If you run make_average_subject, it will create the template for you (as well as all the other files in a typical subject dir -- you'll need these to do a simple replacement for fsaverage). doug Joakim Vinberg wrote: Hi FS crowd, I just want to make sure that I have the process correctly described for setting up a custom experimental template. I am basing this off of the SurfaceRegAndTemplates (http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates), and a hypothetical experiment with 10 subjects (s1, s2, …s10). I apologize if this has been well-covered—I couldn’t quite match it on the website or the archives. For the prep step, I believe my commands would be: mris_make_template lh sphere s1 custom_template_lh_0.tif mris_make_template rh sphere s1 custom_template_rh_0.tif which would result in two new template files names custom_template_lh_0.tif and custom_template_rh_0.tif For Round 1, I would first create another registration for each subject: mris_register s1/surf/lh.sphere custom_template_lh_0.tif s1/surf/lh.sphere.regcustom_0 mris_register s1/surf/rh.sphere custom_template_rh_0.tif s1/surf/rh.sphere.regcustom_0 … mris_register s10/surf/lh.sphere custom_template_lh_0.tif s10/surf/lh.sphere.regcustom_0 mris_register s10/surf/rh.sphere custom_template_rh_0.tif s10/surf/rh.sphere.regcustom_0 And then create another custom template: mris_make_template lh sphere s1 s2 s3 … s10 custom_template_lh_1.tif mris_make_template rh sphere s1 s2 s3 … s10 custom_template_rh_1.tif For round 2, I would repeat Round 1, generating a new set of sphere.reg files, and then a new template, except substitute the custom template from round 1 (custom_template_lh_1.tif and custom_template_rh_1.tif). Then, I would register all of my data to the custom_template_lh_2.tif and
Re: [Freesurfer] CORRELATION VALUE
Hi Cleo, the mc correction will generate a segmentation file (something like cache.th20.abs.sig.ocn.mgh). The value at each vertex/voxel in this file correspond to the cluster that the vertex/voxel belongs to (if any). You can use this as the segmentation for mri_segstats and specify the gamma.mgh from your slope contrast to give you the average slope in each cluster. doug cgo...@bidmc.harvard.edu wrote: Hi all, My design is very simple: 1-group,1-variable 2-nuisance (age,gender). I just want to see the correlation between Cth and my variable. I obtain one cluster after mc-correction. (using freesurfer5) There is any way to get the intercept,slope or r-pearson (in average) values of this particular cluster. What I've done is transform this cluster in a label to then visually inspect the Graph Average ROI, but I want the numerical results. Thanks in advance for your useful help. Cleo. ___ 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] Freesurfer Average Subject
Hi Massieh, try adding --meas thickness doug mmoay...@uhnres.utoronto.ca wrote: Dear Dr. Fischl, We have been following the steps you have laid out on the listserv (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg17601.html) to make an average subject. However, we are not able to proceed with the mris_preproc step. It requires an output file and the hemisphere. When we include these, it asks for an input file. The command we are inputting is: mris_preproc --surfreg sphere.reg.avgsubject --s nc_001 --s ... and mris_preproc --surfreg sphere.reg.avgsubject --hemi rh --s nc_001 --out avgsubject.mgz Could you please advise us on how to proceed? Thank you. Regards, Massieh Moayedi ___ 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] HippSubregions File Missing
Hi All, I tried a runnings some recons (one recon entirely in Stable 5.1.0 using the -hippo-subregions flag, and one recon in Stable 4.5.0 followed by recon-all -hippo-subregions in 5.1.0), and I am running into a small problem in that the posterior_Left-Hippocampus.mgz file does not seem to be created (in either case). It looks like all of the other subregion files are there, but it is missing the one file, which is causing the kv1* quantification script and viewing the left hippo subregions to fail (I can view the right ones just fine though). However, the recon did not exit with errors, and I don't see any errors in the log file. Any thoughts? Thanks, Garth ___ 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] ERROR: gdfOffsetSlope:
Hi there, When i load he group descriptor file i get the following error: cannot determine the offset and slope for the given group descriptor because the design matrix creation method is unknown Why is that? Thanks ilana -- *** peligro! flaca pero mala! ** ___ 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] ERROR: gdfOffsetSlope:
which fsgd file are you loading? You should load the y.fsgd in the glm output dir. doug Ilana Hairston wrote: Hi there, When i load he group descriptor file i get the following error: cannot determine the offset and slope for the given group descriptor because the design matrix creation method is unknown Why is that? Thanks ilana -- *** peligro! flaca pero mala! ** ___ 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] CORRELATION VALUE
Hi Doug, Thank you for your quick answer. However, there are some points that are still not clear for me: 1-I would like to know also the correlation value (r-pearson; Cth-Variable) of my significant cluster. This is something that I can get directly or I have to do some additional analysis? If yes, which ones?? 2-I would know the intercept of this cluster. 3-I’m using mri_segstats to get the average slope, I use: mri_segstats --seg mc-z.abs.th13.sig.ocn.mgh --sum proof But with this I only obtain the NVtx, I think I’m missing something…. Cleo. De: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Enviado el: miércoles, 18 de mayo de 2011 10:25 Para: Gomez,Cleofe P. (BIDMC - Neurology) CC: freesurfer@nmr.mgh.harvard.edu Asunto: Re: [Freesurfer] CORRELATION VALUE Hi Cleo, the mc correction will generate a segmentation file (something like cache.th20.abs.sig.ocn.mgh). The value at each vertex/voxel in this file correspond to the cluster that the vertex/voxel belongs to (if any). You can use this as the segmentation for mri_segstats and specify the gamma.mgh from your slope contrast to give you the average slope in each cluster. doug cgo...@bidmc.harvard.edu wrote: Hi all, My design is very simple: 1-group,1-variable 2-nuisance (age,gender). I just want to see the correlation between Cth and my variable. I obtain one cluster after mc-correction. (using freesurfer5) There is any way to get the intercept,slope or r-pearson (in average) values of this particular cluster. What I've done is transform this cluster in a label to then visually inspect the Graph Average ROI, but I want the numerical results. Thanks in advance for your useful help. Cleo. ___ 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 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] recon-all tutorial data
Hi, I'm new to the software and I'm having trouble finding the following file: ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tar.gz How can I download the recon-all tutorial data? Has it been replaced/relocated? Thanks a lot, Gabriel Obregon ___ 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.
