Freesurfer

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30132 discussions

restoring wm.mgz
by Jason Tourville 07 Oct '13

07 Oct '13

Hi there, I'm working on a project in which I manually "erased" voxels (changed to '1') in the optic chiasm region in the wm.mgz and brainmask.mgz. This was done to eliminate those voxels from the surface reconstructions. We've since realized that this isn't necessary...our results are largely unaffected by the edit. So we've skipped that edit on most (110+) scans. For the few scans that have the optic chiasm edits, I'd like to regenerate the original surfaces but would like to retain the numerous other edits I've made to the brainmask.mgz and wm.mgz volumes outside the optic chiasm region. I have tried to do this by "cloning" the voxels from the original brainmask and wm volumes to the edited version, thereby restoring the original voxel values in only this region. When I then rerun recon all from the autorecon2-cp option, the "restored" voxels in the wm volume are set set to "0" (so no longer the original values and not even the "erased" value of "1") before the surfaces are generated. The result is that the surfaces in the optic chiasm area remain "clipped." I've tried this on a couple different scans and after moving the wm.seg.mgz volume out of the mri/ directory. Any idea why this is happening? Is there a solution that does not require me to edit these scans from scratch? Thanks, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755

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[FreeSurfer] control points
by Francesco Siciliano 07 Oct '13

07 Oct '13

Hello, I am still having issues getting all of my control points to be effective. When I load my original point set (control.dat) and add control points to the set (using the control points edit tool), the new control points are visible but are not taken into account when I re-run recon-all (recon-all -autorecon2 -autorecon3 -s Subject1). I have also tried saving multiple control points (control2.dat, etc) and that does not seem to work either. It appears as though I am unable to add control points after saving the first set during my first edit of a brain. This is problematic because one edit of a brain is rarely sufficient, and I typically need to edit my control point set. Yet there seems to be no way to do this. The only other thing that I think may be causing the problem is that I am running freeview 5.3 and freesurfer 5.2 (to keep our data consistent with the same version). Any ideas how to resolve this issue? -Francesco Francesco Siciliano, B.A. Research Assistant Department of Child and Adolescent Psychiatry The New York State Psychiatric Institute Columbia University 1051 Riverside Drive, Unit 74 New York, NY 10032 (212) 543-6155

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Re: [Freesurfer] Binary stats
by Douglas N Greve 07 Oct '13

07 Oct '13

Not from the mri_cluster. If you run mri_binarize --i mask.nii --count count.dat --min 0.5 the total volume of the mask will be in the count file (along with some other numbers). doug ps. Please remember to post to the list instead of me directly. thanks! On 10/07/2013 12:53 PM, pfotiad(a)nmr.mgh.harvard.edu wrote: > Hi Doug, > > Thanks for your reply. Besides getting the volume of each cluster > separately, would you happen to know a way to get the sum of the volumes > (in mm^3) of all the clusters that come out in the summary file? > > Thanks, > Panos > >> If you save a segmentation from mri_volcluster (--ocn), then you can >> feed that into mri_segstats as the segmentation and it will create >> another summary file with the volumes of each cluster >> >> doug >> >> On 10/07/2013 10:12 AM, pfotiad(a)nmr.mgh.harvard.edu wrote: >>> Hi FS Community, >>> >>> I have a binary mask and have used the mri_volcluster command to come up >>> with different clusters and their volumes based on that binary mask. >>> However, I was wondering if it would be possible to come up with the sum >>> of the sizes (in mm3) of all the different clusters that come out of the >>> sum file as well. I could do it by writing a script that reads the >>> separate values from the summary file output of the mri_volcluster and >>> then adding them, but I was wondering whether there was an easier way. >>> >>> Thanks in advance, >>> Panos >>> _______________________________________________ >>> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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trouble with pial surface in v5.1
by Caspar M. Schwiedrzik 07 Oct '13

07 Oct '13

Hi Freesurfer Experts, I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having trouble getting the pial surface to go all the way through the grey matter. Please see screenshot attached. These data were acquired with a surface coil and the grey matter varies a lot in intensity. Interestingly, the pial surface growing process fails where the grey matter is fairly dark. I have tried several rounds of normalizing using the N3 tool but that didn't change anything. Thanks for any advice on this, Caspar

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Re: [Freesurfer] Global thickness calculation
by Kayle Sawyer 07 Oct '13

07 Oct '13

If you want the global thickness for all your subjects in a single table, use asegstats2table, e.g. aparcstats2table --subjects bert ernie fred margaret --hemi rh --meas thickness --tablefile rh.aparc_stats.txt The first column will be the rh thickness, which you can average with the lh in a spreadsheet. Or, you can use aparcstats2table again with "--meas area", and then in your spreadsheet use the equation you described to give additional weight to the hemisphere with larger area. Because it's in a table, you can then use this as a covariate in your FSGD, but I thought I read that some people do not recommend using global thickness as a covariate. -Kayle > Date: Fri, 04 Oct 2013 19:25:07 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Global thickness calculation > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <524F4E53.3020802(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > you can do something like this > > cd $SUBJECTS_DIR/$subject > > mri_segstats --slabel $subject lh label/lh.cortex.label --i > surf/lh.thickness --id 1 --sum stats/lh.meanthickness.dat > > > On 10/04/2013 05:22 PM, Mollie Bayda wrote: >> Hi, >> I am trying to calculate whole-brain mean cortical thickness in each >> individual subject for correction of regional mean thicknesses. >> I see on the wiki that this is recommended to be done by: >> bh.thickness = (lh.thickness X lh.area) + (rh.thickness X rh.area) / >> (lh.area +rh.area) >> In my table I see lh and rh total area but I do not see lh and rh >> thickness. All I see is mean thicknesses for each region. Are the >> total rh and lh mean thicknesses supposed to appear in the table? >> Thanks!

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Binary stats
by pfotiad＠nmr.mgh.harvard.edu 07 Oct '13

07 Oct '13

Hi FS Community, I have a binary mask and have used the mri_volcluster command to come up with different clusters and their volumes based on that binary mask. However, I was wondering if it would be possible to come up with the sum of the sizes (in mm3) of all the different clusters that come out of the sum file as well. I could do it by writing a script that reads the separate values from the summary file output of the mri_volcluster and then adding them, but I was wondering whether there was an easier way. Thanks in advance, Panos

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Re: [Freesurfer] statistically truncate negative values
by Maya Rosen 07 Oct '13

07 Oct '13

Hi Doug, Thanks for your response. I implemented what you suggested, but I'm unclear as to what I should use as the value for --min when i use mri_binarize? At first I used 1.3, but that masked out almost all the activation. I lowered it to 0.1 just to see what would happen. That looked overall more reasonable (i.e. showing differences where there is activation and not where there are differences in deactivation). However, there are a couple of very small regions that are still showing up as having a significant difference between Condition A and Condition B, when in fact that difference is due to differences in deactivation (i.e. more deactivation in Condition B than Condition A --> shows up as A greater than B). I'd like to know what a reasonable value for the --min flag and if you have any insight into why I am still seeing some regions that show differences in deactivation. Here's what I ran: mri_binarize --i CONDITION_Avpassive/ces.nii.gz --mask CONDITION_Bvpassive/ces.nii.gz --mask-thresh 0.00001 --o ConditionAvsConditionB/point1.ces.nii --min 0.1 mri_glmfit --y ConditionAvsConditionB/ces.nii.gz --osgm --mask ConditionAvsConditionB/point1.ces.nii --glmdir point1_masked.rfx --nii --surf fsaverage lh Thanks for the help! Maya Message: 1 Date: Tue, 10 Sep 2013 15:37:01 -0400 From: Maya Rosen <mayalrosen(a)gmail.com> Subject: [Freesurfer] statistically truncate negative values To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CAJzkiyGEMzm1GUke-XV0Ko5qYH3QdQAuPmZWO8Rqm-0RyTOiew(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hi All, I have two conditions of interest in my GLM analysis, Condition A and Condition B. I would like to make a contrast of Condition A and Condition B that includes only those vertices that are significantly positively activated when compared to the Passive Viewing baseline. In other words, I would like to mask anything that is Passive > Condition A or Passive > Condition B and only include Condition A > Passive and Condition B > Passive when contrasting Condition A and Condition B, so as to limit my contrast to changes in *activation *in the two conditions, not *deactivation *. I see that in an older version, when isxavg-re-sess was used, there was a flag --trunc that would allow you to set the negative values to 0. If there is a way to do this in the v 5.1.0, I could then perform a second level contrast of positively activated Condition A and Positively activated condition B. Is there a way to exclude the negatively activated voxels from the Condition A vs Passive and Condition B vs Passive contrasts when looking at Condition A vs Condition B? I would like to do this statistically, not just at the map level. Thank you for your help! Maya

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Re: [Freesurfer] missing eTIV in asegstats2table
by Daniel Ferreira 07 Oct '13

07 Oct '13

Dear Douglas and Martin, Thanks for your replies. So far I have always been able to get eTIV when running asegstats2table (last column on the spreadsheet). But my current FreeSurfer version (5.3.0) is not grabbing it. I can found eTIV in the header and extract it for all the subjects with mri_segstats (as below in blue), but output is quite messy. I would rather prefer to get it as in asegstats2table format. Any idea? Thanks a lot, Dani for i in FAD*; do echo $i; mri_segstats --subject $i --etiv-only >> table_eTIV; done

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Re: [Freesurfer] FSL masks applied to Freesurfer surfaces? 116(14)
by Ruth Carper 07 Oct '13

07 Oct '13

Doug, I'd like to get them into the individual's space, but I assume I have to get there by way of fsaverage? Final goal is to have a regional thickness measure for each individual subject. Ruth Carper ________________________________ From: "freesurfer-request(a)nmr.mgh.harvard.edu" <freesurfer-request(a)nmr.mgh.harvard.edu> To: freesurfer(a)nmr.mgh.harvard.edu Sent: Saturday, October 5, 2013 9:00 AM Subject: Freesurfer Digest, Vol 116, Issue 14 ---------------------------------------------------------------------- Message: 1 Date: Fri, 04 Oct 2013 12:21:32 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FSL masks applied to Freesurfer surfaces? To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <524EEB0C.8050400(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Do you want to transfer them to fsaverage space or to the individual anatomical space? doug On 10/04/2013 01:42 AM, Ruth Carper wrote: > Hi, > I'd like to take some masks that I have in MNI standard space in FSL > and map them to Freesurfer surface space. The goal is to extract > measures of average cortical thickness (or area or etc) for those > regions for each subject. Is there a standard way to do this? > > >

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hippocampal subfield segmentations
by Gregory Kirk 07 Oct '13

07 Oct '13

I heard from Koen a while back that a new improved version was in the works. I have several projects I would be interested in using it for. Any info on timelines for release or a publication ? thank You

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