Freesurfer

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30089 discussions

how to edit the pial surface
by 李盟 19 May '12

19 May '12

Hi FreeSurfer Experts, I had 2 question about the output troubleshooting. 1) when I used the mri_convert command, the format of the input image I choosed was 4D nii format, but not the original dicom format, which would affect the result of reconstruction? 2) When I checked the quality of output using tksurfer, I found the color line representing the surface (pial and white) were not along the folding pattern, and the distance between the two sufaces was rather short. Whether or not it was caused by the bad GM/WM contrast? What is the best way to deal with them? Thanks. Meng Li

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How to use aparcstats2table and asegstats2table for rois generated from QDEC group analyses
by Vy Dinh 18 May '12

18 May '12

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

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make check => mris_expand FAILED
by Akio Yamamoto 18 May '12

18 May '12

Hi, When I run 'make check' after successfully completing 'make' command, I get the following message: ...... ./mris_expand -v 111706 -thickness lh.white 0.5 lh.midgray mris_expand FAILED FAIL: test_mris_expand ========================================= 1 of 1 tests failed Please report to freesurfer(a)nmr.mgh.harvard.edu ========================================= How can I fix this error? Any help would be appreciated. Thanks, -- Akio Yamamoto The University of Tokyo

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How to calculate Total Brain Volume from aseg.stats
by Goldman, Aaron (NIH/NIMH) [C] 18 May '12

18 May '12

Hello, For an analysis, we're trying to calculate a Total Brain Volume covariate based on the data in aseg.stats, generated using version 5.0.0. Basically, we want to include all WM and GM but not CSF. I was thinking of doing Total GM + Cortical WM + L&R Cerebellum WM. Would this be the correct way to do it, or should we use some other combination? Thanks, Aaron

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splitting data into virtual runs
by Guthormsen, Amy M 18 May '12

18 May '12

Hello, I would like to use fsfast to analyze retinotopic data that I collected. I used the traditional 4 stimulus types (clockwise, counterclockwise, expanding, and contracting), but rather than collect each one in its own run, I took data from one long run that contained all the stimuli. Based on the logs, I can associate the pulse number/dicom file number with a stimulus type. However, when I tried to just move the sets of dicom files into sub-directories, which I set up as run directories, freesurfer still saw them as belonging to one run (which I assume is taken from meta-data). My question is, how can I best split up these files so that I can subject them to the FsFastIndividualRetinotopyAnalysis<http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis…> process? Thank you, Amy Guthormsen

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Question about DODS model and DOSS model
by ZhiLiangLong 18 May '12

18 May '12

Hi all: I'm a little confused about the DODS model and DOSS model. I have two groups (patient and control) and one covariate (age), and I want to compare the diffirence of thickness between the groups with age as the covariate. In DODS model, is the process the analysis of variance substantially (group is a factor and age is another factor)? Generally, if there is no interaction between age and group, then i can re-run with the DOSS model to increase the statistical power.But i don't know how to determine whether there is no interaction . I hope someone give me some suggestions.

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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

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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

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MEMPRAGE sequence.
by Zheng Hui 18 May '12

18 May '12

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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. > >> > > > > > > >

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