Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Temporal lobe tracing abnomality uncorrected by control points
by Moiyadi, Ammar 10 May '11

10 May '11

Dear Freesurfers, Freesurfer's autorecon is having trouble tracing both gray and white matter boundaries in the temporal region of one of my subjects (even after I added control points for the white matter). I have attached a png screen shot of this abnormality and was wondering if anyone has any ideas to correct this since I have never seen such a large tracing error before. Your input is much appreciated! Ammar

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Testing FreeSurfer recon-all with 2 different head coils
by Gullett,Joseph M 10 May '11

10 May '11

Hello, Our University's MRI facility recently upgraded from an 8 channel to a 32 channel head coil. I have been doing some QC analyses to determine if this will affect our results with T1 enough to warrant a regression for the number of RF channels in the final study analysis. I ran FreeSurfer recon-all cortical measurements two times on the 8 channel T1's (I always do the recon-all with two consecutively acquired T1's), and two times on the 32 channel T1's. I did it twice on each because some members in our lab have mentioned that in the past they have re-ran the same analysis and got different results. This was not the case for me as I got identical results for both runs. I ran a t-test on all of the cortical results for 32 vs 8 channels and there is a significant difference p<.019 between the two in the LH aparc measurements, but no significant difference between the 8 and 32 channel scans in the RH aparc measurements (p<.280). Is there anything inherent to the method FreeSurfer uses for its' cortical measurements that would result in an inconsistency only in the left hemisphere, or is it safe to chalk this up to a difference between head coils? Also of note, the two sets of scans were done only 6 months apart on the same individual (me). Here is what I ran if it helps at all: recon-all -s FShc12_redo -i /data/birc/RESEARCH/DFITZGERALD_projects/664-2008/HC12/acqfiles/DICOM/T1-1/DICOM/o20101113_104703IM_0001T1W3DTFESENSE664-2008-HC12s601a1006.nii.gz -i /data/birc/RESEARCH/DFITZGERALD_projects/664-2008/HC12/acqfiles/DICOM/T1-2/DICOM/o20101113_104703IM_0001T1W3DTFESENSE664-2008-HC12s701a1007.nii.gz -autorecon-all and then, aparcstats2table --subjects FShc12_redo --hemi rh --meas thickness --tablefile aparc_rh_thickness_stats_May_10_2011.txt and aparcstats2table --subjects FShc12_redo --hemi lh --meas thickness --tablefile aparc_lh_thickness_stats_May_10_2011.txt Thank you in advance, Joe

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Re: [Freesurfer] Making a custom experimental template
by Douglas N Greve 10 May '11

10 May '11

That is not unusual. It attempts to create an aseg by merging all the asegs from the individuals. To do this, it has to load all of them in memory, which often too big. doug Joakim Vinberg wrote: > > Doug, > > I figured that would be a little weird. Thanks again for guiding me > through this process. > > An additional follow-up question: this was the output from > make_average_subject this morning. I have started mris_register, and > it appears to be running just fine. Is this a normal error? If not, > how best to get around it? I was running this on a MacPro with 8 cores > and 16GB of memory—I’m surprised it would have ran out. > > Thanks! > > Joakim > > nframestot = 307 > > Allocing output > > mri_concat(32631) malloc: *** mmap(size=262144) failed (error code=12) > > *** error: can't allocate region > > *** set a breakpoint in malloc_error_break to debug > > MRIalloc(256, 256, 256): could not allocate 262144 bytes for 13726th slice > > Cannot allocate memory > > WARNING: could not create average segmentation for aseg ... > > ... but continuing > > Tue May 10 06:31:38 PDT 2011 > > make_average_volume done > > *From:* Douglas Greve [mailto:greve@nmr.mgh.harvard.edu] > *Sent:* Monday, May 09, 2011 8:00 PM > *To:* Joakim Vinberg; free surfer > *Subject:* Re: [Freesurfer] Making a custom experimental template > > No, unfortunately not. If all you want is the template, you can run > mris_make_template to get the tif files. I think that's pretty fast. > doug > > On 5/9/11 10:42 PM, Joakim Vinberg wrote: > > Doug, > > This is awesome--thank you! > > I have one final follow-up question, and maybe a bit of a long-shot: > given that this process is a little time intensive, is > make_average_subject able to "add in" extra subject to the existing > template? E.g. If I've collected 10 subjects currently, but will > shortly collect another 10--is the intermediate alignment information > from the first 10 subjects saved anywhere that can be usefully used > for the average subject of the final 20? > > Thanks again! > > Joakim > > ------------------------------------------------------------------------ > > *From:* Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] > *Sent:* Mon 5/9/2011 12:28 PM > *To:* Joakim Vinberg; freesurfer > *Subject:* Re: [Freesurfer] Making a custom experimental template > > 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 > <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 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 <mailto:Freesurfer@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 <mailto:greve@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 > <http://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 <mailto:greve@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 > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > -- 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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Re: [Freesurfer] Making a custom experimental template
by Douglas Greve 09 May '11

09 May '11

No, unfortunately not. If all you want is the template, you can run mris_make_template to get the tif files. I think that's pretty fast. doug On 5/9/11 10:42 PM, Joakim Vinberg wrote: > Doug, > This is awesome--thank you! > I have one final follow-up question, and maybe a bit of a long-shot: > given that this process is a little time intensive, is > make_average_subject able to "add in" extra subject to the existing > template? E.g. If I've collected 10 subjects currently, but will > shortly collect another 10--is the intermediate alignment information > from the first 10 subjects saved anywhere that can be usefully used > for the average subject of the final 20? > Thanks again! > Joakim > > ------------------------------------------------------------------------ > *From:* Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] > *Sent:* Mon 5/9/2011 12:28 PM > *To:* Joakim Vinberg; freesurfer > *Subject:* Re: [Freesurfer] Making a custom experimental template > > 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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retinotopy sig.nii file
by Thomas Janssens 09 May '11

09 May '11

Hi, I performed a retinotopy analyses with freesurfer using selxavg3-sess. One of the nii-files that is created with this command is sig.nii. How is the significance map in sig.nii calculated for retinotopy? which p-values are used in this calculation? Thanks! Thomas

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Re: [Freesurfer] subcortical volume and qdec
by 汪贵宏 09 May '11

09 May '11

Thanks for your reply,doctor Nick: I have done the subcortical volume analysis simply by working with the "aseg.volume.stats" txt in the "stats_tables" file with the SPSS soft . But it results no difference,so, as this analysis was done based on the ROI,if the analysis can be done by each voxel ,if can ,how? As I can see ,I think it can not ,not as the situation in the analysis of cortical thickness ,the subcotical volume is an entirety,such as the amygdala or hippocampus , if it has difference,it will be the total volume difference ,not some part of the the area.But I am not sure about it,is it right? thanks , wang At 2011-05-04 22:32:18，"Nick Schmansky" <nicks(a)nmr.mgh.harvard.edu> wrote: >wang, > >qdec doesnt yet support analysis of subcortical structures in the way i >think you were expecting. that is, currently only surface measures (by >default thickness), is selectable as the independent variable. a >subcort volume is not yet selectable (its output results would be bar >charts, not a surface display). you can do a subcortical volume >analysis by working with the aseg.stats file directly in some stats >program (or mri_glmfit). > >so if a particular volume measure is selected via the stats import >option, and it is selected as a possible factor, and that factor is >selected as a regressor in the Design window, then when an analysis is >run, it is entirely possible (and very likely) that there is no change >in thickness value given a particular subcortical volume. the one >exception i have seen for this is hippocampal volume, which does have an >effect on cortical thickness between controls and AD patients. > >n. > > >On Wed, 2011-05-04 at 11:18 +0800, 汪贵宏 wrote: >> Dear freesurfer experts: >> >> I had processed my data with recon-all, and also ,I had compared >> the cortical thickness difference between the con and pat with >> qdec .however,when i I try to compare the sub-cortical volume >> difference between con and pat ,the results were the same as the >> thickness,even in Analysis Results window,the option is not changed,as >> the "Does the average thickness differ between con and pat?" So, I >> have no idea about it,because I chose the ASEG.VOLUME in the "Stats >> Data Import" window. >> >> In addition ,I wander whether the volume differ comparison is >> processed based on ROI or vertex? >> >> Did anyone can help me with any suggestion. >> >> thank you >> wang >> >> >> >> >> ______________________________________________________________________ >> 体验网易邮箱2G超大附件，轻松发优质大电影、大照片，提速3倍! >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)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.

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cvs_register: missing surf2vol on MAC
by Martin Kavec 09 May '11

09 May '11

Hi all, I am trying to run mri_cvs_register on MAC distribution o Freesurfer 5.0, but it is failing on surf2vol. Looking into the $FREESURFER_HOME/bin, surf2vol is completely missing. Could you please provide this file? Thanks, Martin

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optimal voxel size
by Wenger, Elisabeth 09 May '11

09 May '11

Dear Freesurfer experts, I am currently planning a study in which I want to investigate changes in gray matter due to training on structural MR images. I heard some rumors that although FreeSurfer can of course process images with different voxel sizes, it always somehow "transforms" the voxel size to 1 x 1 x 1, irrespective of the originally obtained image resolution. I've been wondering if something has changed in this regard, that is, whether FreeSurfer is now capable of maintaining a higher resolution (eg, 0.8 mm) throughout all the analysis steps? As I am looking for very very tiny changes I would like to acquire images with 0.8mm resolution. But if FreeSurfer has to convert these images with the help of some estimation processes at some point of the reconstruction, I would rather like to acquire 1 x 1 x 1 images in the first place. Thank you so much for your help! All the best, Elisabeth

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mailing list
by shahriar ahadpour 08 May '11

08 May '11

Dear i got some problems with downloading the software,is it possible recieving the package by attachment?

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Flattened surface visualization using matlab
by Gabriele Arnulfo 07 May '11

07 May '11

Dear freesurfer experts, I've surfed the web looking for some example on how to visualize the flattened surface using matlab, but none has appeared so far. Does this task have been already addressed by someone? Cheers, -- Gabriele Arnulfo PhD Student Bioengineering Department of Systemistic, Telematic and Informatic University of Genoa, Italy Viale Causa 13, 16100

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