Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

non-white residuals in ROI-based contrast
by Pablo Polosecki 12 May '11

12 May '11

Hello List, I want to run an F-test on a ROI (I selected the voxels with some criterion). If I understand correctly the way to do it is by computing the F-statistic using: F=(roi_betas'*X'*M*X*roi_betas)/(Y'*R*Y)*(J-p)/p1 where: roi_betas are the average beta values across the roi X is the design matrix M is the projection matrix to the space generated by the reduced model given by my contrast matrix Y is the average time course of the ROI R is the residual generating matrix. J-p are the total degrees of freedom, and p1 are the degrees of freedom given by my contrast matrix I am noticing that the residuals are not whitened (the is noticeable auto-correlation in the ROI-averaged residuals that lasts ~10 timepoints). Could someone recommend a relatively simple way to correct for this auto-correlation (and avoid reinventing the weel in matlab)? Thanks in advance! Pablo

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mri_nu_correct.mni segmentation fault
by Nikolas Borrel-Jensen 11 May '11

11 May '11

Hi all. I have two subjects where the mri_nu_correct.mni in the autorecon1 step is aborting: $Id: mri_nu_correct.mni,v 1.12 2009/12/16 20:15:41 greve Exp $ mri_convert orig.mgz ./tmp.mri_nu_correct.mni.16617/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.16617/nu0.mnc -odt float ncendef: ncid 3: No space left on device Error outputting volume: possibly disk full? Segmentation fault ... and there is plenty of space on the disk. Trying to run the command afterwards with mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2, I get a bit further mri_convert orig.mgz ./tmp.mri_nu_correct.mni.22259/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.22259/nu0.mnc -odt float mri_convert: posixio.c:210: px_pgin: Assertion `*posp == ((off_t)(-1)) || *posp == lseek(nciop->fd, 0, 1)' failed. $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.22259/nu0.mnc... Abort ERROR: converting to minc It works for all other subjects. Can anybody help me with that? The orig.mgz file can be found here: http://freesurfer.nikolasborrel.com/ Kind regards, Nikolas

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Memory problem with mri_glmfit
by Ed Gronenschild 11 May '11

11 May '11

Hi, We are on a Intel Mac and are facing a memory problem with mri_glmfit. We want to apply it to a 4D volume consisting of 72 3D volumes of 256 * 256 * 256 voxels each, with 1 byte per voxel. During processing we get the error message that it could not allocate 262144 bytes for the 9313th slice. We noticed the info "changing y type to float" that was issued. We are wondering if there is a workaround for this. Ed

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Error when loading qdec project file
by Natalia Francisca 11 May '11

11 May '11

Dear freesurfer list, I have got this message while trying to load the saved project file ln -s /Volumes/FreeSurfer_ALL/CorticalThickness/IZQUIERDA/fsaverage/label/*.aparc.annot /tmp/qdec_project_archive/fsaverage/label ln -s /Volumes/FreeSurfer_ALL/CorticalThickness/IZQUIERDA/qdec/lh-curva_aprendizaje-thickness-fwhm10 /tmp/qdec_project_archive ln -s /Volumes/FreeSurfer_ALL/CorticalThickness/IZQUIERDA/qdec/qdec.table.dat /tmp/qdec_project_archive cp /Volumes/FreeSurfer_ALL/CorticalThickness/IZQUIERDA/qdec/*.levels /tmp/qdec_project_archive cd /tmp; zip -r /Volumes/FreeSurfer_ALL/CorticalThickness/IZQUIERDA/qdec/lh-thickness-fwhm10.qdec qdec_project_archive > /dev/null rm -rf /tmp/qdec_project_archive Saving project file done. Loading data table /tmp/qdec_project_archive/qdec.table.dat... ERROR: could not open /tmp/qdec_project_archive/qdec.table.dat Error loading the project file. When saving there is no error message, but when trying to load the saved project file, then the error pops up, any idea is appreciated. Natalia.

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freeview
by swoodman＠nmr.mgh.harvard.edu 11 May '11

11 May '11

Hello all! I have a question regarding using freeview. When doing a 3D rengering of t-maps, there is a setting that allows you to view clusters with peak t scores. When we do this peak t scores are included in two clusters. We wish to only show ONE cluster for an image we are creating. How does one get rid of a cluster, ie only show the one of interest? Thank you! Sandra

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Support for PPC Mac
by Ed Gronenschild 11 May '11

11 May '11

Hi, A while ago we were asked if still support was needed for FreeSurfer on a PPC Mac. I was one of the "happy" few who needed this. But I now can inform you that as far as I'm concerned you can discontinue this support. Thank you for all your support sofar. Ed

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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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