Freesurfer

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30132 discussions

Pial error on lesioned brain
by octavian lie 20 May '12

20 May '12

Dear All, > > I processed a MR brain after temporal lobe resection. While brainmask.mgz, > and brain.mgz include the temporal remnant (correctly), the calculated pial > surface excludes it (see attached). How, and at what step can I edit the > image so that the pial surface (red line) is inclusive of the postop > temporal lobe? Again, this is not a problem with skull extraction, and > overall I am happy with brainmask.mgz as is, but not with subsequent pial > calculations. Setting the volume brush to clone from brainmask.mgz the > temporal remnant does not seem to help, I may be doing smth wrong. > Please advise, thank you very much. > > Octavian. >

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Re: [Freesurfer] ERROR: comparison in expression (FS with SGE)
by Xue, Feng 19 May '12

19 May '12

Sorry, I didn't notice that the reply address was not the list, I've done re-post it. Is there any method to check whether it is ok? For SGE, it might only write errors to dot e files instead of warnings. It seemed like a shell syntax error, however, I don't have that experience to check the recon-all script. On Sun, Mar 14, 2010 at 11:24 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > can you post this to the list? There are others better qualified to say > what's going on. But if everything finished ok is there really a problem? > Maybe this is just a warning? > On Sun, 14 Mar 2010, Xue, Feng wrote: > >> Hi Bruce, >> >> Thanks for your reply. The recon-all.log said it finished without >> error. please find the whole scripts root in the attachment. >> I'm also running a raw testing with one subject and without SGEяяMaybe >> I can report the result the day after tomorrow. >> >> BTW, I found in my 64bit Debian nodes, I repeated got the error as below >> (standard_in) 2: Error: comparison in expression >> but in 32bit, I met both. >> >> for the GMail security restriction, I changed recon-all.cmd in the >> attachment to recon-all.cmds. >> >> On Sat, Mar 13, 2010 at 11:58 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> wrote: >>> >>> what does the recon-all.log say? Did the recon finish correctly? Does >>> this >>> happen if you just run it on the command line? >>> Bruce >>> >>> On Sat, 13 Mar 2010, Xue, Feng wrote: >>> >>>> Dear Bruce & FS experts, >>>> >>>> Please forgive my re-post, for I havn't got any response from last post. >>>> I do appreciate if anyone could give me a hint or suggestion. >>>> >>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>> >>>> We are running freesurfer with Sun GridEngine. Currently, we >>>> repeatedly got this error in SGE's job error log file on some data >>>> when doing recon_all: >>>> >>>> $ cat recon_xf.e437 >>>> (standard_in) 2: Error: comparison in expression >>>> $ cat recon_xf.e431 >>>> (standard_in) 2: comparison in expression >>>> >>>> I also checked the recon-all-status.log file, but not error was found. >>>> >>>> Has anyone met this problem? Is it critical? >>>> Thanks in advance. >>>> >>>> -- >>>> Best Regards >>>> >>>> Xue, Feng Phd. candidate >>>> Major in Developmental Cognitive Neuroscience >>>> >>>> National Key Laboratory of Cognitive Neuroscience and Learning >>>> Beijing Normal University >>>> Beijing, China. 100875 >>>> Tel: +86-13810154455 >>>> web: http://psychbrain.bnu.edu.cn >>>> ============================================== >>>> Welcome to MuDuo JinSheng BBS @ Beijing Normal University >>>> telnet://bbs.mdjs.org >>>> http://bbs.mdjs.org >>>> _______________________________________________ >>>> 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. >>> >>> >> >> >> > -- Best Regards Xue, Feng Phd. candidate Major in Developmental Cognitive Neuroscience National Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China. 100875 Tel: +86-13810154455 web: http://psychbrain.bnu.edu.cn ============================================== Welcome to MuDuo JinSheng BBS @ Beijing Normal University telnet://bbs.mdjs.org http://bbs.mdjs.org

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Re: [Freesurfer] 回复: Re: how to edit the pial surface
by Bruce Fischl 19 May '12

19 May '12

p.s. looks like an intensity normalization failure. Can you give us details of the acquisition? Sequence name, voxel resolution, etc....? If you upload the subject I'll take a look cheers Bruce On Sat, 19 May 2012, limengsecret wrote: > Hi Professor, > The image blow shows the problems which occur. > color lines representing the surfaces (pial and white) were not along the > folding pattern, and the distance between the two sufaces was rather short. > How to deal with these problems? > [IMAGE] > Thanks. > > Meng Li > > > ____________________________________________________________________________ > limengsecret > > From: Bruce Fischl > Date: 2012-05-19 22:08 > To: ?? > CC: freesurfer > Subject: Re: [Freesurfer] how to edit the pial surface > Hi Meng > > 1. Not positive I understand, but I don't think it should matter. > > 2. we'll need to see some data to diagnose this. > > cheers > Bruce > > > On Sat, 19 May 2012, ?? wrote: > > > > > 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 shor > t. > > Whether or not it was caused by the bad GM/WM contrast? What is the best ?? ?way > > to deal with them? > > > > ? > > > > Thanks. > > > > ? > > > > Meng Li > > > > > > > > > > > > > The information in this e-mail is intended only for the person to whom it i > s > addressed. If you believe this e-mail was sent to you in error and the e-ma > il > contains patient information, please contact the Partners Compliance HelpLi > ne at > http://www.partners.org/complianceline . If the e-mail was sent to you in e > rror > but does not contain patient information, please contact the sender and pro > perly > dispose of the e-mail. > > >

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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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