Freesurfer October 2013

freesurfer@nmr.mgh.harvard.edu

136 participants
244 discussions

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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FW: Consistency between volumes in fsaverage and subject data?
by Jensen, Sarah 07 Oct '13

07 Oct '13

Hi Bruce, Thanks for getting back to me! I am using my own ROIs, created based on an ALE (Activation Likelihood Estimation) conducted in the gingerALE software, and dividing the ALE map into smaller clusters in Marsbar (SPM). I then applied the ROIs to the surface based registration(fsaverage registration) and turned these into label files (mri_cor2label) and extracted volumes from my participants (mri_label2label) I noticed that some of my biggest ROIs didn't come out with the larges volumes in my final data and started looking at the correlations of my volumes across the different steps. I found the volumes of my templates in SPM (Marsbar) and after the projection to fsaverage were highly correlated although the ROIs where much smaller in fsavarage. But there was no correlation between my ROIs in fsaverage and my extracted data (based on 500 participants). I did not correct for the reduced surface area in these analyses, so thanks a lot for making me aware of this. Can you by any chance direct me to a reference for this? And do you think I should expect a correlation between the templates in fsaverage my data if I do this? I am not interested in there correlations as such, but ran these analyses to check my data because I am worried something might have gone wrong. Thanks a lot! Best, Sarah ________________________________________ From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Sent: 07 October 2013 13:21 To: Jensen, Sarah Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Consistency between volumes in fsaverage and subject data? Hi Sarah what ROIs do you mean? And did you correct for the reduced surface area in fsaverage w.r.t. the individual surfaces? If not, it's not surprising that fsaverage ROIs have less surface area. It is an average surface and less folded than any individual. cheers Bruce On Mon, 7 Oct 2013, Jensen, Sarah wrote: > > Hi Freesurfer users, > > > I am analysing some volumetric data and have noticed that the volumes I > extract from my participants are very different from the volumes of my > templates in fsaverage space. I for instance have two ROIs that stand out as > big (about 6-8 times larger that the other ROIS) in fsaverage space, but > come out as almost indistinguishable from the other ROIs in my data. When I > sort my ROIs according to size there seems to be no consistency between the > size in fsaverage space and my subjects, and the correlation between the > volume in fsaverage and my subjects is about .05 - 0.1. > > > I am new to freesurfer, and would intuitively expect greater consistency > between the ROIs in fsaverage and the subjects. Has anyone else had similar > experiences, and is this lack of consistency between volumes in fsaverage > space and participant data perfectly normal? > > > Thanks, > > > Sarah > > > 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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Consistency between volumes in fsaverage and subject data?
by Jensen, Sarah 07 Oct '13

07 Oct '13

Hi Freesurfer users, I am analysing some volumetric data and have noticed that the volumes I extract from my participants are very different from the volumes of my templates in fsaverage space. I for instance have two ROIs that stand out as big (about 6-8 times larger that the other ROIS) in fsaverage space, but come out as almost indistinguishable from the other ROIs in my data. When I sort my ROIs according to size there seems to be no consistency between the size in fsaverage space and my subjects, and the correlation between the volume in fsaverage and my subjects is about .05 - 0.1. I am new to freesurfer, and would intuitively expect greater consistency between the ROIs in fsaverage and the subjects. Has anyone else had similar experiences, and is this lack of consistency between volumes in fsaverage space and participant data perfectly normal? Thanks, Sarah

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Re: [Freesurfer] DOSS contrast - one group, 3 covariates
by Anita van Loenhoud 07 Oct '13

07 Oct '13

Thank you Doug!

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Freesurfer October 2013