Freesurfer

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30088 discussions

HippSubregions File Missing
by Garth Coombs 18 May '11

18 May '11

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

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Freesurfer Average Subject
by mmoayedi＠uhnres.utoronto.ca 18 May '11

18 May '11

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

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Re: [Freesurfer] Making a custom experimental template
by Douglas N Greve 18 May '11

18 May '11

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:greve@nmr.mgh.harvard.edu] > *Sent:* Fri 5/6/2011 9:46 AM > *To:* Joakim Vinberg > *Cc:* freesurfer(a)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(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)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. > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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

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Mris_anatomical_stats problem
by Jürgen Hänggi 18 May '11

18 May '11

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. ----------------------------------------------------------------------------

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Neuroscience software survey: What is popular, what has problems? Immediate results
by Yaroslav Halchenko 18 May '11

18 May '11

[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

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Mris_anatomical_stats
by Jürgen Hänggi 18 May '11

18 May '11

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. ----------------------------------------------------------------------------

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MRI Signal Dropout
by Victor Yee 17 May '11

17 May '11

Hello, We have some signal dropout at the top of the brain in some scans, possibly similar to Rutvik Desai's 02/18/10 post. However, in our case, FreeSurfer is not including any of the regions affected by the dropout in both its subcortical segmentation and cortical parcellation. Instead, FreeSurfer essentially begins to treat the gray/white boundary as the CSF/gray surface, and classifies white matter as gray matter. The severity of this issue seems to correlate with how severe the dropout is. I have tried running nu_correct (normalization) for up to 256 iterations. This produces a noticeable effect when visualizing the volumes in tkmedit, but has no effect on FreeSurfer's output. I can upload a sample subject, if desired. We are using FreeSurfer 5.0 x64 on a Sun Grid Engine operating servers running CentOS 4.5. Thank you, Victor Yee

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No inflated brain...
by jim kroger 17 May '11

17 May '11

Hello, I am following the sequence in the "FreeSurfer Troubleshooting Reconstruction Work Flow" instructions, and am at step 8, FsTutorial/WhiteMatterEdits. It looks like the thalamus and corpus callosum are included as white matter, and the pial surface surrounds some subcortical structures. Assuming this is not correct, I decided to look at the inflated surface as suggested in the referenced page " Making Edits to the White Matter." Unfortunately when I issue: tksurfer wm1_edits_before rh inflated I only see what looks like a very small fraction of an egg shell for the rh, and nothing for lh. Can I check somehow to see why I have almost no inflated brain? Thanks, Jim -- Cell: 575-571-8274 Email: jkk251(a)gmail.com

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ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
by Pedro Paulo de Magalhães Oliveira Junior 17 May '11

17 May '11

I'm having this error in the recon-all #-------------------------------------------- #@# Talairach Mon May 16 16:38:01 EDT 2011 /usr/local/freesurfer/subjects/GAGRICOLA/mri talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm ERROR: mpr2mni305 failed, see transforms/talairach_avi.log I've uploaded to the ftp at surfer.nmr.mgh.harvard.edu the talairach_avi.log, the orig.mgz (as ppj_orig.mgz) and the original nifti image as ga_2010.nii Any hints?

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different V1 sizes for same subject in two different sessions
by Ritobrato Datta 17 May '11

17 May '11

Hello All, I have estimated V1 using Hinds and Fischl method for some subjects scanned on two different days. I've been going through the V1 surface area data for these. One thing that concerns me is that is seems that very different V1 sizes are reported for the same subject when scanned on different dates and each run through the cross sectional stream. I am trying to check the test-re-test values for these. Any idea why this is so and whats a better method to do the comparison ? Thanks Ri

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