Freesurfer May 2012

freesurfer@nmr.mgh.harvard.edu

137 participants
209 discussions

Re: [Freesurfer] surfaceRAS to Talairach
by Douglas N Greve 18 May '12

18 May '12

What do you mean by "ras matlab subscripts"? Those looks like indices, not RAS. Assuming those are indices, then that looks right. doug On 05/18/2012 02:02 PM, Jordan L. Poppenk wrote: > Dear Doug, > > To generalize from this earlier conversion question, to interpret the coordinate space of a file loaded by freesufer/matlab/MRIread.m, would one use the following transform to move from ras matlab subscripts (e.g., 1:256,1:256,1:256) to mni coords? > > mni = talairach.xfm * vox2ras1 * [r a s 1] > > The coordinates I get out of this transform do not seem quite right. > > Cheers, > Jordan > > > On May 3, 2012, at 5:40 PM, Jordan Poppenk wrote: > >> Dear Douglas, >> >> That's exactly the information I was looking for. This worked perfectly. Thank you for your help! >> >> Cheers, >> Jordan >> >> >>> Here's how to convert from surface RAS to mni305 >>> >>> mni305ras = X*S*inv(K)*ras >>> X = talairach.xfm >>> S = scanner vox2ras (mri_info --vox2ras orig.mgz) >>> K = tkreg vox2ras (mri_info --vox2ras-tkr orig.mgz) >>> ras = surface ras >>> >>> If you want to go from mni305 to approximate talairach, you can use this >>> transform from Matthew Brett: >>> >>> >>> function outpoints = mni2tal(inpoints) >>> % Converts coordinates from MNI brain to best guess >>> % for equivalent Talairach coordinates >>> % FORMAT outpoints = mni2tal(inpoints) >>> % Where inpoints is N by 3 or 3 by N matrix of coordinates >>> % (N being the number of points) >>> % outpoints is the coordinate matrix with Talairach points >>> % Matthew Brett 10/8/99 >>> >>> dimdim = find(size(inpoints) == 3); >>> if isempty(dimdim) >>> error('input must be a N by 3 or 3 by N matrix') >>> end >>> if dimdim == 2 >>> inpoints = inpoints'; %' >>> end >>> >>> % Transformation matrices, different zooms above/below AC >>> upT = spm_matrix([0 0 0 0.05 0 0 0.99 0.97 0.92]); >>> downT = spm_matrix([0 0 0 0.05 0 0 0.99 0.97 0.84]); >>> >>> tmp = inpoints(3,:)<0; % 1 if below AC >>> inpoints = [inpoints; ones(1, size(inpoints, 2))]; >>> inpoints(:, tmp) = downT * inpoints(:, tmp); >>> inpoints(:, ~tmp) = upT * inpoints(:, ~tmp); >>> outpoints = inpoints(1:3, :); >>> if dimdim == 2 >>> outpoints = outpoints'; %' >>> end >>> >>> >>> >>> >>> >>> >>> On 05/02/2012 12:54 PM, Jordan Poppenk wrote: >>> Dear FreeSurfer experts, >>> >>>> >>> How does one properly convert from surfaceRAS coords, as provided by fs_read_surf.m, to talairach coords? I have tried using freesurfer_surf2tal.m posted on the web by Darren Weber, supplying it with transform data from transforms/talairach.xfm, but the values returned often differ from those in tksurfer by as much as 20mm (and are clearly wrong). What I would like to do is match the coordinate system in tksurfer (which is clearly right). How does tksurfer do it? >>> >>>> >>> Cheers, >>> >>> Jordan >>> >>>> >>>> >>> _______________________________________________ >>> >>> Freesurfer mailing list >>> >>>> Freesurfer at nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> >>> greve at 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 > > -- 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

1 0

Surface Area aparc from pial surface
by Inês Violante 18 May '12

18 May '12

Hi, I need to know the surface area of the structures in the aparc file but I want to obtain this measurement from the pial surface and not the white matter surface. How can I do that? Thank you a lot for your help. ines

3 6

MEMPRAGE sequence.
by Zheng Hui 18 May '12

18 May '12

2 1

Re: [Freesurfer] How to use aparcstats2table and asegstats2table for rois generated from QDEC group analyses
by Vy Dinh 17 May '12

17 May '12

Hi Josh, Thanks for the sample script. With a few modifications to the variable definitions I got your script to work. However, my stats file looks like this: # Table of FreeSurfer cortical parcellation anatomical statistics # # CreationTime 2012/05/10-17:03:40-GMT # generating_program mris_anatomical_stats # cvs_version $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ # mrisurf.c-cvs_version $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ # cmdline mris_anatomical_stats -l 051012_thickness_halluc_fwhm10_lh.fusiform.label -t lh.thickness -b -f 1014/stats/*051012_thickness_halluc_fwhm10_lh.fusiform.stats* 1014 lh # sysname Darwin # hostname skip-macpro-lab.rush.edu # machine i386 # user skip # # SUBJECTS_DIR /Users/skip/Desktop/harlow_mount/JenG/ResearchAssistant/data/freesurfer_v5.1 # anatomy_type surface # subjectname 1014 # hemi lh # AnnotationFile *051012_thickness_halluc_fwhm10_lh.fusiform.label* # AnnotationFileTimeStamp 2012/05/10 10:18:26 # Measure Cortex, NumVert, Number of Vertices, 119152, unitless # Measure Cortex, WhiteSurfArea, White Surface Total Area, 76575.4, mm^2 # NTableCols 10 # TableCol 1 ColHeader StructName # TableCol 1 FieldName Structure Name # TableCol 1 Units NA # TableCol 2 ColHeader NumVert # TableCol 2 FieldName Number of Vertices # TableCol 2 Units unitless # TableCol 3 ColHeader SurfArea # TableCol 3 FieldName Surface Area # TableCol 3 Units mm^2 # TableCol 4 ColHeader GrayVol # TableCol 4 FieldName Gray Matter Volume # TableCol 4 Units mm^3 # TableCol 5 ColHeader ThickAvg # TableCol 5 FieldName Average Thickness # TableCol 5 Units mm # TableCol 6 ColHeader ThickStd # TableCol 6 FieldName Thickness StdDev # TableCol 6 Units mm # TableCol 7 ColHeader MeanCurv # TableCol 7 FieldName Integrated Rectified Mean Curvature # TableCol 7 Units mm^-1 # TableCol 8 ColHeader GausCurv # TableCol 8 FieldName Integrated Rectified Gaussian Curvature # TableCol 8 Units mm^-2 # TableCol 9 ColHeader FoldInd # TableCol 9 FieldName Folding Index # TableCol 9 Units unitless # TableCol 10 ColHeader CurvInd # TableCol 10 FieldName Intrinsic Curvature Index # TableCol 10 Units unitless # ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd *051012_thickness_halluc_fwhm10_lh.fusiform.label* 85 76 435 3.697 0.350 0.325 0.129 6 0.5 I want to concatenate the last line for each subject, but since the string shows up 3 times in the stat file, I get more output info than I need. Is there a way to echo a line in the script only (using grep or some other command)? In other words, how can I only extract the last line from the stats file? Thanks, Vy On Thu, May 17, 2012 at 5:32 PM, Joshua Lee <jkilee(a)ucdavis.edu> wrote: > Here is a little script I wrote. It isn't very refined, and can be > improved. It is also attached. It references a file you muct make in which > you put all your subject names, one on each line of the text file like this: > > sub001 > sub002 > sub003 > ... > > Here is the script. > > #run this script from the Freesurfer Subjects Directory...alterntively, > you can modify the script to work automatically > #from the the FreeSurfer Subjects Directory Variable. However, since you > might not be using the bash shell, maybe that variable wont be available. > Anyway.. > filename=/home/local/AD3/jlee31/Desktop/NORA/segmentz #This points to > a file you will make in which every line contains a subject directory name. > > #The script will read this file line by line to get the data from each > subject listed in the script > statsfile=rh.curv.stats #Tells the scipt which kind of stat files you want > to collect > > #Name the file you want to put your results into > resultsFileName=results.txt > > #Ok here we go > while read line; do > > sub=`echo $line | cut -d\. -f1` #gets the subject name from the > file in the first line of this script > > currentStatsFile=./"$sub"/stats/$statsfile #puts together the fullpath > of the stats file > > #Next Grep finds a line in the file (stored in the variable > $myStatsFile) that mathces the criteria > #(for example here I find the line "Raw Total Surface Area:" and echos > that out to a result text file > echo $sub" "`grep "Raw Total Surface Area:" $currentStatsFile` #>> > $resultsFileName #creates a results txt file > > > done < "$filename" > > > - > Joshua Lee > Graduate Student > Center for Mind and Brain & > Department of Psychology > University of California, Davis > 530.747.3805 > > > > On Thu, May 17, 2012 at 2:37 PM, Vy Dinh <vy_dinh(a)rush.edu> wrote: > > Thanks for the suggestion Josh! I have definitely thought about this, but > > since I'm a total novice bash programmer, I thought that it would be > quicker > > to learn which option to add to asegstats2table and aparcstats2table. I > > would really appreciate it if you could help me come up with this code? > What > > shell function could I use to open each .stats file? How do I use grep to > > call, say line 53 in the stats file? > > > > Many thanks, > > > > Vy > > > > > > On Thu, May 17, 2012 at 4:19 PM, Joshua Lee <jkilee(a)ucdavis.edu> wrote: > >> > >> Why not use a bash or csh script that loops through your subjects stat > >> files, and use grep read the appropriate lines to a single text file > >> with >>. > >> > >> - > >> Josh > >> > >> > >> On Thu, May 17, 2012 at 1:04 PM, Vy Dinh <vy_dinh(a)rush.edu> wrote: > >> > Dear Freesurfer Experts, > >> > > >> > I've created a couple of ROIs from qdec comparisons of thickness and > >> > volume > >> > between two groups. We extracted the data from these ROIs for each > >> > subject > >> > using mris_anatomical_stats. > >> > > >> > The stat files are located within each subjects folder: > >> > sub/stats/rh.roi.stats > >> > > >> > Now, we would like to combine the data from each stat file to a text > >> > file > >> > using aparcstats2table and asegstats2table (for volume measures). I > >> > already > >> > have batch scripts that call these functions for multiple subjects. > The > >> > script basically concatenates all of the subject ids and inputs the > >> > concatenated string into the aparcstats2table (or asegstats2table) > >> > command. > >> > > >> > EX: > >> > asegstats2table -s s1 -s s2 -s s3 -s s4 --hemi lh --meas volume > >> > -tablefile > >> > test_stats.txt > >> > > >> > I would like to modify my script so that I can extract the data from > the > >> > roi.stats file. This is only a matter of entering the correct inputs > for > >> > aparcstats2table and asegstats2table but I have tried with little > >> > success. > >> > The problems with each command are explained below. > >> > > >> > For asegstats2table: > >> > According to documentation > >> > (http://surfer.nmr.mgh.harvard.edu/fswiki/asegstats2table) I have > tried > >> > running "asegstats2table $STRING --meas volume --skip --tablefile > >> > $OUTFILE " where string is "-i s1/stats/lh.roi.stats -i > >> > s2/stats/lh.roi.stats ......etc" but get the error message: > >> > > >> > Building the table.. > >> > Traceback (most recent call last): > >> > File > >> > > >> > > "/Users/skip/Desktop/harlow_mount/apps/fmri_progs/freesurfer_v51/freesurfer/bin/asegstats2table", > >> > line 513, in <module> > >> > rows, columns, table = sanitize_table(options, pretable) > >> > File > >> > > >> > > "/Users/skip/Desktop/harlow_mount/apps/fmri_progs/freesurfer_v51/freesurfer/bin/asegstats2table", > >> > line 412, in sanitize_table > >> > _specs, _id_name_map, _measl = _t[0] > >> > IndexError: list index out of range > >> > > >> > > >> > For aparcstats2table: > >> > when I run the command: > >> > > >> > aparcstats2table $STRING --hemi lh --parc roi_name --skip --tablefile > >> > $OUTFILE > >> > > >> > where string is "-s s1 -s s2 -s s3 ", I get a text file with 3 > columns. > >> > The > >> > first column lists the subject ids, but what are the values for the > 2nd > >> > and > >> > 3rd columns? Also, is it possible to input more than 2 .stats file for > >> > the > >> > command? > >> > > >> > > >> > Looking forward to your responses, > >> > > >> > > >> > Vy > >> > > >> > > >> > Vy T.U. Dinh > >> > Neurological Sciences > >> > Rush University Medical Center > >> > Phone: (312) 563-3853 > >> > Fax: (312) 563-4660 > >> > Email: Vy_dinh(a)rush.edu > >> > > >> > > >> > _______________________________________________ > >> > 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. > >> > > > > > > >

2 1

Re: [Freesurfer] How to use aparcstats2table and asegstats2table for rois generated from QDEC group analyses
by Vy Dinh 17 May '12

17 May '12

Thanks for the suggestion Josh! I have definitely thought about this, but since I'm a total novice bash programmer, I thought that it would be quicker to learn which option to add to asegstats2table and aparcstats2table. I would really appreciate it if you could help me come up with this code? What shell function could I use to open each .stats file? How do I use grep to call, say line 53 in the stats file? Many thanks, Vy On Thu, May 17, 2012 at 4:19 PM, Joshua Lee <jkilee(a)ucdavis.edu> wrote: > Why not use a bash or csh script that loops through your subjects stat > files, and use grep read the appropriate lines to a single text file > with >>. > > - > Josh > > > On Thu, May 17, 2012 at 1:04 PM, Vy Dinh <vy_dinh(a)rush.edu> wrote: > > Dear Freesurfer Experts, > > > > I've created a couple of ROIs from qdec comparisons of thickness and > volume > > between two groups. We extracted the data from these ROIs for each > subject > > using mris_anatomical_stats. > > > > The stat files are located within each subjects folder: > > sub/stats/rh.roi.stats > > > > Now, we would like to combine the data from each stat file to a text file > > using aparcstats2table and asegstats2table (for volume measures). I > already > > have batch scripts that call these functions for multiple subjects. The > > script basically concatenates all of the subject ids and inputs the > > concatenated string into the aparcstats2table (or asegstats2table) > command. > > > > EX: > > asegstats2table -s s1 -s s2 -s s3 -s s4 --hemi lh --meas volume > -tablefile > > test_stats.txt > > > > I would like to modify my script so that I can extract the data from the > > roi.stats file. This is only a matter of entering the correct inputs for > > aparcstats2table and asegstats2table but I have tried with little > success. > > The problems with each command are explained below. > > > > For asegstats2table: > > According to documentation > > (http://surfer.nmr.mgh.harvard.edu/fswiki/asegstats2table) I have tried > > running "asegstats2table $STRING --meas volume --skip --tablefile > > $OUTFILE " where string is "-i s1/stats/lh.roi.stats -i > > s2/stats/lh.roi.stats ......etc" but get the error message: > > > > Building the table.. > > Traceback (most recent call last): > > File > > > "/Users/skip/Desktop/harlow_mount/apps/fmri_progs/freesurfer_v51/freesurfer/bin/asegstats2table", > > line 513, in <module> > > rows, columns, table = sanitize_table(options, pretable) > > File > > > "/Users/skip/Desktop/harlow_mount/apps/fmri_progs/freesurfer_v51/freesurfer/bin/asegstats2table", > > line 412, in sanitize_table > > _specs, _id_name_map, _measl = _t[0] > > IndexError: list index out of range > > > > > > For aparcstats2table: > > when I run the command: > > > > aparcstats2table $STRING --hemi lh --parc roi_name --skip --tablefile > > $OUTFILE > > > > where string is "-s s1 -s s2 -s s3 ", I get a text file with 3 columns. > The > > first column lists the subject ids, but what are the values for the 2nd > and > > 3rd columns? Also, is it possible to input more than 2 .stats file for > the > > command? > > > > > > Looking forward to your responses, > > > > > > Vy > > > > > > Vy T.U. Dinh > > Neurological Sciences > > Rush University Medical Center > > Phone: (312) 563-3853 > > Fax: (312) 563-4660 > > Email: Vy_dinh(a)rush.edu > > > > > > _______________________________________________ > > 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. > > >

2 1

Re: [Freesurfer] aseg.stats not matching up
by Joshua Lee 17 May '12

17 May '12

Yes, I'm glad that Bruce confirmed this. Good. The majority had deviations that were in the range of 20-40 voxels which seems intuitively in the right range. The ones that concerned me were those that inexplicably deviated in the range of 600 to 1000 voxels out of 4000 or so voxels in the hippocampus. Notably, the large deviations occurred in subjects with some motion artifacts says my colleague, although the hippocampal segmentation itself seemed fairly representative of Freesurfer. However this last point seems different that the one raised in my first post, since we are getting deviations with the exact same voxels after relabeling. I hope Doug gets a chance to chime in; our lab is somewhat concerned about this right now because we are in the middle of a revision for a journal submission. Best, and thank you, Joshua - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805 Joshua On Thu, May 17, 2012 at 2:05 PM, Joshua . <nimzodisaster(a)gmail.com> wrote: > Yes. Good. The majority had deviations that were in the range of 20-40 > voxels which seems intuitively in the right range. The ones that concerned > me were those that inexplicably deviated in the range of 600 to 1000 voxels > out of 4000 or so voxels in the hippocampus. Notably, the large deviations > occurred in subjects with some motion artifacts says my colleague, although > the hippocampal segmentation itself seemed fairly representative of > Freesurfer. > > However this last point seems different that the one raised in my first > post, since we are getting deviations with the exact same voxels after > relabeling. I hope Doug gets a chance to chime; our lab is somewhat > concerned about this right now because we are in the middle of a revision > for a journal submission. > > Best, and thank you, > > Joshua > > > On Thu, May 17, 2012 at 12:39 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: >> >> yes, that is a consequence of partial volume correction. If you have a 3 >> class boundary (two of which are hippocampal subdivisions), we will compute >> different partial volume fractions than if you have a 2 class boundary. I >> wouldn't expect it to be a huge effect, but they definitely won't be >> identical >> >> >> >> On Thu, 17 May 2012, Joshua Lee wrote: >> >>> We discovered this while subdividing the hippocampus into several >>> subregions using tkmedit to relabel voxels, and finding that these >>> subregions were not adding up to the original volume. I expected some >>> differences, but many deviated more than I had expected. This led me to the >>> test I discussed at the beginning of the thread. >>> >>> >>> Joshua >>> >>> >>> >>> >>> >>> >>> On May 16, 2012, at 1:55 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>> wrote: >>> >>>> hmmm, that is convincing. I don't think there's anything in mri_segstats >>>> that knows about the meaning of any of the indices, but maybe Doug can >>>> correct me? >>>> >>>> On Wed, 16 May 2012, Joshua Lee wrote: >>>> >>>>> Hi Bruce, >>>>> First, let me add that if I run the mri_segstats without the --pv flag, >>>>> the >>>>> two will have identical volumes. This indicates to me that we captured >>>>> all >>>>> the voxels into the new label. >>>>> Joshua >>>>> - >>>>> Joshua Lee >>>>> Graduate Student >>>>> Center for Mind and Brain & >>>>> Department of Psychology >>>>> University of California, Davis >>>>> 530.747.3805 >>>>> On Wed, May 16, 2012 at 1:38 PM, Bruce Fischl >>>>> <fischl(a)nmr.mgh.harvard.edu> >>>>> wrote: >>>>> Hi Joshua >>>>> >>>>> probabilities are computed internally, but not stored nor used >>>>> in volume calcualtions. Are you actually doing a 3D fill? I >>>>> don't think the hippocampus label is guaranteed to be connected. >>>>> Can you try instead replacing every voxel in matlab with the >>>>> hippocampus index to your new one? That I think should give you >>>>> the same results. >>>>> >>>>> cheers >>>>> Bruce >>>>> >>>>> On Wed, 16 May 2012, Joshua Lee wrote: >>>>> >>>>> Suppose I were to open a subject aseg.mgz in >>>>> tkmedit, and use the 3D fill >>>>> tool to relabel the entire left hippocampus >>>>> segmentation to >>>>> 'MyNewImaginaryLabel'. If I then re-run the aseg >>>>> stats, should the left >>>>> hippocampus volume from the original aseg.stats be >>>>> identical to the volume >>>>> of MyImaginaryLabel in the newly generated >>>>> aseg.stats? >>>>> >>>>> Every voxel from the prior label is now assigned to >>>>> the new label; yet, I >>>>> am getting different results (by about 100 voxels in >>>>> the ones I've tried). >>>>> >>>>> The command Im using to recalculate: >>>>> mri_segstats --seg >>>>> /usr/local/freesurfer/subjects/s02/new_MRI/new/aseg.auto.mgz >>>>> --sum >>>>> >>>>> /usr/local/freesurfer/subjects/s02/stats/NEWmethod1aseg_Hipp.stats >>>>> --pv >>>>> /usr/local/freesurfer/subjects/s02/mri/norm.mgz >>>>> --excludeid 0 >>>>> --brain-vol-from-seg --brainmask >>>>> /usr/local/freesurfer/subjects/s02/mri/brainmask.mgz >>>>> --in >>>>> /usr/local/freesurfer/subjects/s02/mri/norm.mgz >>>>> --in-intensity-name norm >>>>> --in-intensity-units MR --etiv --surf-wm-vol --ctab >>>>> /usr/local/freesurfer/8regions.txt --subject s02; >>>>> >>>>> Now if I were to relabel 'MyNewImaginaryLabel' to >>>>> 'AthirdLabel', and again >>>>> changing every voxel in 'MyNewImaginaryLabel' to the >>>>> new label, the computed >>>>> volumes do not change. This led me to suspect that >>>>> aseg.mgz contains >>>>> probability estimates at each voxel that are then >>>>> subsequently overwritten >>>>> by my tkmedits. However, per a previous conversation >>>>> from a year ago or so >>>>> with Bruce and also the relevant Freesurfer >>>>> documentation this does not seem >>>>> to be the case. Partial volume information is not >>>>> contained within the >>>>> aseg.mgz (right!?), but is computed by mri_segstats >>>>> by comparing border >>>>> voxels with intensities in the norm.mgz. So I am at >>>>> a loss on why these >>>>> should be different. >>>>> >>>>> This has been replicated in version 4.5 and 5.1 >>>>> - >>>>> Joshua Lee >>>>> Graduate Student >>>>> Center for Mind and Brain & >>>>> Department of Psychology >>>>> University of California, Davis >>>>> 530.747.3805 >>>>> 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. >>> >>> >>> >>> >>> >

1 0

Re: [Freesurfer] aseg.stats not matching up
by Bruce Fischl 17 May '12

17 May '12

yes, that is a consequence of partial volume correction. If you have a 3 class boundary (two of which are hippocampal subdivisions), we will compute different partial volume fractions than if you have a 2 class boundary. I wouldn't expect it to be a huge effect, but they definitely won't be identical On Thu, 17 May 2012, Joshua Lee wrote: > We discovered this while subdividing the hippocampus into several subregions using tkmedit to relabel voxels, and finding that these subregions were not adding up to the original volume. I expected some differences, but many deviated more than I had expected. This led me to the test I discussed at the beginning of the thread. > > > Joshua > > > > > > > On May 16, 2012, at 1:55 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > >> hmmm, that is convincing. I don't think there's anything in mri_segstats that knows about the meaning of any of the indices, but maybe Doug can correct me? >> >> On Wed, 16 May 2012, Joshua Lee wrote: >> >>> Hi Bruce, >>> First, let me add that if I run the mri_segstats without the --pv flag, the >>> two will have identical volumes. This indicates to me that we captured all >>> the voxels into the new label. >>> Joshua >>> - >>> Joshua Lee >>> Graduate Student >>> Center for Mind and Brain & >>> Department of Psychology >>> University of California, Davis >>> 530.747.3805 >>> On Wed, May 16, 2012 at 1:38 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>> wrote: >>> Hi Joshua >>> >>> probabilities are computed internally, but not stored nor used >>> in volume calcualtions. Are you actually doing a 3D fill? I >>> don't think the hippocampus label is guaranteed to be connected. >>> Can you try instead replacing every voxel in matlab with the >>> hippocampus index to your new one? That I think should give you >>> the same results. >>> >>> cheers >>> Bruce >>> >>> On Wed, 16 May 2012, Joshua Lee wrote: >>> >>> Suppose I were to open a subject aseg.mgz in >>> tkmedit, and use the 3D fill >>> tool to relabel the entire left hippocampus >>> segmentation to >>> 'MyNewImaginaryLabel'. If I then re-run the aseg >>> stats, should the left >>> hippocampus volume from the original aseg.stats be >>> identical to the volume >>> of MyImaginaryLabel in the newly generated >>> aseg.stats? >>> >>> Every voxel from the prior label is now assigned to >>> the new label; yet, I >>> am getting different results (by about 100 voxels in >>> the ones I've tried). >>> >>> The command Im using to recalculate: >>> mri_segstats --seg >>> /usr/local/freesurfer/subjects/s02/new_MRI/new/aseg.auto.mgz >>> --sum >>> /usr/local/freesurfer/subjects/s02/stats/NEWmethod1aseg_Hipp.stats >>> --pv >>> /usr/local/freesurfer/subjects/s02/mri/norm.mgz >>> --excludeid 0 >>> --brain-vol-from-seg --brainmask >>> /usr/local/freesurfer/subjects/s02/mri/brainmask.mgz >>> --in >>> /usr/local/freesurfer/subjects/s02/mri/norm.mgz >>> --in-intensity-name norm >>> --in-intensity-units MR --etiv --surf-wm-vol --ctab >>> /usr/local/freesurfer/8regions.txt --subject s02; >>> >>> Now if I were to relabel 'MyNewImaginaryLabel' to >>> 'AthirdLabel', and again >>> changing every voxel in 'MyNewImaginaryLabel' to the >>> new label, the computed >>> volumes do not change. This led me to suspect that >>> aseg.mgz contains >>> probability estimates at each voxel that are then >>> subsequently overwritten >>> by my tkmedits. However, per a previous conversation >>> from a year ago or so >>> with Bruce and also the relevant Freesurfer >>> documentation this does not seem >>> to be the case. Partial volume information is not >>> contained within the >>> aseg.mgz (right!?), but is computed by mri_segstats >>> by comparing border >>> voxels with intensities in the norm.mgz. So I am at >>> a loss on why these >>> should be different. >>> >>> This has been replicated in version 4.5 and 5.1 >>> - >>> Joshua Lee >>> Graduate Student >>> Center for Mind and Brain & >>> Department of Psychology >>> University of California, Davis >>> 530.747.3805 >>> 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. > > > >

1 0

Slice Viewer
by Antonella Kis 17 May '12

17 May '12

Dear FS experts, I was using FreeView to see all my FA's clusters position from my DTI data that survived after correction by multiple comparisons. This clusters are locate in different slices and I would like to know if there is a way to print out in the same time different slices not only one by one so I can save this image for an article. If this is not possible using FreeView can you please recommend me any software which I can use? I know there is xjview for SPM but is there any software that will allow me to have a similar view (image with multiple slices) for my DTI data? Many thanks, Antonella

2 2

New data point for longitudinal processing.
by Zheng Hui 17 May '12

17 May '12

2 1

Re: [Freesurfer] Freesurfer 1mm Isotropic standard and the Future
by Michael Waskom 16 May '12

16 May '12

Oops i just realized I only sent this to Bruce: Thanks! It looks like this involves some manual intervention. Matt., I assume you're not manually making control points on 1000s of subjects (I imagine this is for the human connectcome project). Is your code public somewhere? Cheers, Michael On Tue, May 15, 2012 at 7:36 PM, Michael Waskom <mwaskom(a)stanford.edu>wrote: > Thanks! It looks like this involves some manual intervention. Matt., I > assume you're not manually making control points on 1000s of subjects (I > imagine this is for the human connectcome project). Is your code public > somewhere? > > Cheers, > Michael > > > On Tue, May 15, 2012 at 9:14 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > >> sure, here's mine. Matt's is probably a lot more polished as they intend >> to run it on hundreds or thousands of subjects >> >> On Tue, 15 May 2012, Michael Waskom wrote: >> >> Hi Bruce, >>> Sounds cool, I'd be very interested in checking out the script. >>> >>> Cheers, >>> Michael >>> >>> On Tue, May 15, 2012 at 5:29 AM, Bruce Fischl < >>> fischl(a)nmr.mgh.harvard.edu> >>> wrote: >>> you need to call mris_make_surfaces directly. It's a bit >>> complicated as you need to intensity normalize and register the >>> hires volume to the surfaces first. I have an example script if >>> anyone is interested, but no one has used it yet but me I don't >>> think (unless Matt Glasser has gotten his version working, which >>> on second thought he probably has) >>> >>> On Mon, 14 May 2012, Michael Waskom wrote: >>> >>> Hi Bruce, >>> Is there a flag for this on recon-all? Or do you >>> need to use >>> mri_make_surfaces directly? >>> >>> Best, >>> Michael >>> >>> On Mon, May 14, 2012 at 2:09 PM, Bruce Fischl >>> <fischl(a)nmr.mgh.harvard.edu> >>> wrote: >>> Hi Joshua >>> >>> yes, we already have upgraded >>> mris_make_surfaces to take higher >>> res data >>> and refine the surfaces with it. Haven't tried >>> it on the aseg >>> yet, but if >>> you upload a sample dataset I could see how >>> hard it is. >>> >>> cheers >>> Bruce >>> On Mon, 14 May 2012, >>> Joshua Lee wrote: >>> >>> > Dear Freesurfers, >>> > >>> > Over the last years, MR imaging technology >>> hasimproved such >>> that sub 1-mm >>> > isotropic scans can be obtained with good >>> signal to noise >>> characteristics. >>> > For example, our lab uses 0.7mm isotropic >>> structural MR >>> images. I understand >>> > that the Freesurfer pipeline will up-sample >>> these to 1mm >>> isotropic, but it >>> > seems a shame that so much information is >>> left unused which >>> could be used to >>> > improve the accuracy of sub-cortical and >>> cortical >>> segmentation. My question >>> > is whether there are any plans at Freesurfer >>> to change the >>> reference >>> > standard resolution from 1mm isotropic, or >>> provide another >>> solution that can >>> > help researchers make the most of your >>> technology. >>> > >>> > Sincerely, >>> > >>> > >>> > Joshua >>> > - >>> > Joshua >>> > >>> > >>> > >>> ______________________________**_________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** >>> freesurfer<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<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. >>> >>> >>> >>> >>> >>> >

2 1

← Newer
1
...
7
8
9
10
11
12
13
...
21
Older →

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer May 2012