Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

Export .mgh files to volume
by Holly Bridge 26 Aug '09

26 Aug '09

We have performed a GLM analysis on pial_lgi surface data between 2 subject groups. We would like to transform the sig.mgh file back from the average subject surface space to the average subject volume (brainmask.mgz). It would appear we should use mri_surf2vol, but are not clear what our volume registration file should be in this case. Thanks for the help Holly ------------------------------------------------------------------------ --------------------------- Dr Holly Bridge Royal Society University Research Fellow FMRIB Centre Tel: +44-1865-222582 John Radcliffe Hospital Headington Oxford OX3 9DU Email: hb(a)fmrib.ox.ac.uk Lecturer and JRF, New College ------------------------------------------------------------------------ ---------------------------

2 1

Extraction of WM + GM Volumes
by Ed Gronenschild 26 Aug '09

26 Aug '09

Hi, I would like to extract the WM and GM segmentations used for the final cortical thickness calculations as nifti files. How can I do that? Ed

3 3

a question about mri_convert and mri_vol2vol
by Guang Zeng 26 Aug '09

26 Aug '09

Hi, there, I used FreeSurfer pipeline to study a subject, I convert my .nii file to .mgz file, and then send it to FreeSurfer pipeline.Everything works well. Now I want to convert the wmparc.mgz back to the space that the original volume was. I tried two command mri_covert wmparc.mgz -rl orig.nii new.nii and mri_vol2vol --mov wmparc.mgz --targ orig.nii --regheader --o new.ii Both of them gave me the same problem. My original volume is : qform_name Aligned Anat qform_code 2 qto_xyz:1 -1.198313 -0.049354 0.044215 94.332878 qto_xyz:2 -0.041108 1.237333 0.172261 -131.942123 qto_xyz:3 0.048546 -0.170504 1.237284 -105.448372 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 qform_xorient Right-to-Left qform_yorient Posterior-to-Anterior qform_zorient Inferior-to-Superior sform_name Aligned Anat sform_code 2 sto_xyz:1 -1.198313 -0.049354 0.044217 94.332878 sto_xyz:2 -0.041108 1.237333 0.172261 -131.942108 sto_xyz:3 0.048547 -0.170504 1.237284 -105.448372 sto_xyz:4 0.000000 0.000000 0.000000 1.000000 sform_xorient Right-to-Left sform_yorient Posterior-to-Anterior sform_zorient Inferior-to-Superior Now the new resampled volume is: qform_name Scanner Anat qform_code 1 qto_xyz:1 1.198313 -0.049354 0.044217 -96.198837 qto_xyz:2 0.041108 1.237333 0.172261 -138.478333 qto_xyz:3 -0.048547 -0.170504 1.237284 -97.729370 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 qform_xorient Left-to-Right qform_yorient Posterior-to-Anterior qform_zorient Inferior-to-Superior sform_name Scanner Anat sform_code 1 sto_xyz:1 1.198313 -0.049354 0.044217 -96.198837 sto_xyz:2 0.041108 1.237333 0.172261 -138.478333 sto_xyz:3 -0.048547 -0.170504 1.237284 -97.729370 sto_xyz:4 0.000000 0.000000 0.000000 1.000000 sform_xorient Left-to-Right sform_yorient Posterior-to-Anterior sform_zorient Inferior-to-Superior When I use fslview to view these two volumes, their orientations were swapped. Could you help me fix this problems? Thanks a lot! Guang _________________________________________________________________ Windows Live: Make it easier for your friends to see what you’re up to on Facebook. http://windowslive.com/Campaign/SocialNetworking?ocid=PID23285::T:WLMTAGL:O…

2 1

Re: [Freesurfer] Input/Output to specific atlas space/dimensions?
by Alexander Li Cohen 25 Aug '09

25 Aug '09

Yes, I am currently giving freesurfer an atlas (711-2B / TRIO_Y_NDC to be specific) transformed 111 MP-RAGE file. The concern is that if I use mri_convert, I want to specifically return to the same 111 volume size and space and I provided as accurately as possible (hopefully using the inverse of the total transform applied to the image during processing). I know Matt Glasser has worked out a way to convert (and apparently re-register?) surfaces to caret, and I will talk with him later this week to walk through this procedure, but I was hoping that freesurfer could directly output the surfaces in the original space. -Alex ~)------------- ---------------------------------------------------------------------- Alexander Li Cohen alexc(a)npg.wustl.edu (WORK Email) alexcohen(a)gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine ---------------------------------------------------------------------- This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the intended recipient, you are hereby notified that any use, dissemination, disclosure or copying of this communication is strictly prohibited. If you have received this communication in error, please destroy all copies of this message and its attachments and notify us immediately. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. On Aug 25, 2009, at 11:57 AM, Donna Dierker wrote: > Alan: Alex is detecting areal boundaries with functional > connectivity on lots of subjects: > > Cohen, A.L., Fair, D.A., Dosenbach, N.U.F., Miezin, F.M., Dierker, > D., Van Essen, D.C., Schlaggar, B.L., and Petersen, S.E. (2008) > Defining functional areas in individual human brains using resting > functional connectivity MRI. http://dx.doi.org/10.1016/j.neuroimage.2008.01.066 > > Alex: Freesurfer can write surfaces (and possibly volumes) out in > multiple ways. See output of mri_convert and mris_convert for > helpful details. I have also found this web site very helpful: > > http://www.wideman-one.com/gw/brain/fs/coords/fscoords.htm > > Just double-checking: So you are giving Freesurfer a T1 that has > already been put through Avi's imgreg (i.e., in 711-2* space)? > > Donna > > On 08/25/2009 11:40 AM, Alan Anticevic wrote: >> Alex, >> >> We ran into the same problem a while ago for some of our studies. >> We did the following: >> >> 1. Convert an Avi preprocessed T1 MPRAGE into a FreeSurfer-native >> format and provided it the appropriate orientation and image center. >> 2. Next, we simply ran recon-all on this file (single MPRAGE). Then >> we take the the final segmentation output (at least the aseg file) >> and convert it back to a 4dfp file, which is perfectly aligned >> with the original T1 image. >> >> It is my understanding that FreeSurfer completes the segmentation >> on the orignal image in it's native space, hence the alignment. >> >> However, the FreeSurfer surfaces we get are misaligned with the T1 >> and I am assuming this is what you need for your work. Donna >> Dierker and I have a script that may make your life a lot easier >> by converting surfaces from FreeSurfer into Caret including >> creating a mid-thickness surface. However, I would need to know a >> bit more about what you are trying to accomplish and I can help >> you use the tools we have. >> Best, >> Alan >> >> On Aug 25, 2009, at 11:23 AM, Alexander Li Cohen wrote: >> >> >>> Hi all, >>> Just starting using Freesurfer, and while I did search the mailing >>> list archive, I didn't see a ready answer for this question: >>> >>> I would like to use Freesurfer to generate surfaces for my subjects >>> (currently using Caret's SureFit routine), however I need to >>> maintain >>> a specific atlas space for my subjects (in this case, the WU 711-2B, >>> T88-derived space). >>> I can imagine two possibilities, but not how to do them, nor which >>> is >>> more accurate/appropriate: >>> >>> 1. Input the raw T1 for my subject in scanner space (1x1x1 >>> isovolumetric) and then convert the Freesurfer surface and volume >>> outputs to my atlas space using a previously defined linear affine >>> transform (using local scripts written by Avi). This requires >>> Freesurfer to back-convert all results to the original supplied >>> space, >>> then for me to additionally learn how to transform the surfaces. >>> >>> 2. Input the T1 for my subject already in my atlas space, and have >>> Freesurfer output all results in the original supplied space. This, >>> however, will be providing Freesurfer with data that has undergone >>> an >>> additional transform, but is obviously simpler.... >>> >>> in either case, the methodological question becomes simply: how >>> can I >>> tell recon-all to output all files in the original space provided. >>> Given that it must perform the necessary transforms to get into the >>> internal MNI305 space (I'm assuming), I'm simply wanting to undo all >>> of the applied transforms. For obvious reasons, I want to use the >>> same >>> affine transform and transform routine consistently across this >>> and my >>> other datatypes. >>> >>> As a side note, there appears to be a switch for recon-all: >>> -washu_mprage : assume scan parameters are Wash.U. MP-RAGE protocol >>> yet there is no documentation as to what this determines, nor >>> whether >>> the raw, or locally atlas-aligned data should be provided. (Avi >>> didn't >>> know either...) >>> >>> Many Thanks! >>> >>> -Alex Li Cohen >>> ~)----------------- >>> >>> ---------------------------------------------------------------------- >>> Alexander Li Cohen >>> alexc(a)npg.wustl.edu (WORK Email) >>> alexcohen(a)gmail.com (Non-secure / rapid-response Email) >>> Petersen/Schlaggar Lab >>> Medical Scientist Training Program >>> Washington University in St. Louis School of Medicine >>> ---------------------------------------------------------------------- >>> >>> This message is intended only for the exclusive use of the intended >>> recipient(s) named herein and may contain information that is >>> PRIVILEGED and/or >>> CONFIDENTIAL. If you are not the intended recipient, you are hereby >>> notified >>> that any use, dissemination, disclosure or copying of this >>> communication is >>> strictly prohibited. If you have received this communication in >>> error, please >>> destroy all copies of this message and its attachments and notify us >>> immediately. >>> >>> The materials in this message are private and may contain Protected >>> Healthcare Information or other information of a sensitive nature. >>> If >>> you are not the intended recipient, be advised that any unauthorized >>> use, disclosure, copying or the taking of any action in reliance on >>> the contents of this information is strictly prohibited. If you have >>> received this email in error, please immediately notify the sender >>> via >>> telephone or return mail. >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> >> Alan Anticevic >> -------------------------------------------------------------------- >> Department of Psychology - CCP Lab >> Washington University in St. Louis >> One Brookings Dr., Campus Box 1125 >> St. Louis, MO 63110 >> Phone: 314-935-8547 >> -------------------------------------------------------------------- >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>

2 1

Labeling surface to get thickness from a region
by Pierson, Ronald K 25 Aug '09

25 Aug '09

I am following up on some issues where we see some effects we really don't expect when analyzing our data with qdec. They look like they could be some slightly bad data from scan issues, segmentation problems, etc. This is a large set of scans so I would like to script out a routine to get the thickness values for each vertex in a region, then look for outliers to help us understand if this is real or a problem. How can I retrieve the thickness values for all of the vertices in a region? I am using the routine below, but the labels don't seem to be the same across subjects - apparently I need to understand how the label numbers/lists match with the various surfaces. What surfaces, annot files and label numbers would be the appropriate ones to use for this? Does the rest make sense? I have been loading the pial surface and using Labl_import_annotation aparc.annot Labl_save 30 l_ROI1 Then in matlab something like: l_thick = read_curv ('$path/$subject/surf/lh.thickness') l_roiverts = read_label('$subject,'l_ROI1') nvert1 = size(l_roiverts) for k = 1:nvert1(1,1) ind = l_roiverts(k,1) l_ROI1Thick(k,1) = l_thick(ind,1); end hist(l_ROI1Thick,100) print -djpeg -f1 -r150 l_ROI1Thick_$subj Thanks for your time, Ronald Pierson Chair of Imaging, PREDICT-HD Manager, Research and Development Department of Psychiatry, Carver College of Medicine W-278 GH, 200 Hawkins Dr Iowa City, IA 52242

1 0

bbregister: seg fault
by Victoria Williams 25 Aug '09

25 Aug '09

Hi, I have successfully run 126 subjects through bbregister and mri_vol2vol in order to translate the wmparc volume into TBSS space. However, there are 2 subjects that exited prematurely from bbregister. I think it may have to do with my naming system? 126 of the subjects have the subjid CVRAM_###_recon. But these 2 subjects that exited in error have 4 numbers: CVRAM_####_recon. I don't know how that would make a difference, but I've attached the bbregister logs. Although it doesn't say this in the log itself, in the terminal window right before it stops it gives me this message: "Loading mov Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting LH Surfs Projecting RH Surfs Loading rh.white surf Loading rh.thickness Segmentation fault" I'm running the following commands in the dev environment: naming example: subject = CVRAM_####_recon (FS subjdir) basename = CVRAM_#### Commands: bbregister --s $subject --mov $DTI_DIR/${basename}_dti/preTBSS_0.4thresh-LAS/lowb-swap.nii.gz --dti --init-fsl --reg $DTI_DIR/${basename}_dti/${basename}_lowb-to-anat.reg mri_vol2vol --targ $SUBJECTS_DIR/$subject/mri/wmparc.mgz --mov $DTI_DIR/${basename}_dti/preTBSS_0.4thresh-LAS/lowb-swap.nii.gz --o $DTI_DIR/${basename}_dti/${basename}_wmparc-in-lowb.nii.gz --reg $DTI_DIR/${basename}_dti/${basename}_lowb-to-anat.reg --inv --interp nearest Thank you very much! Tori

2 1

Re: [Freesurfer] thickness map
by Feng-Xian Yan 25 Aug '09

25 Aug '09

2009/8/25 Feng-Xian Yan <mimigirln(a)gmail.com> > Hi, > > First, I use mri_surf2surf (as follows) to map our subjects to > fsaverage. > > mri_surf2surf –srcsubject subject --sval-tal-xyz white --hemi lh > --trgsubject fsaverage --tval-xyz --tval lh.subject.tal > > > > Next step, I use mris_convert to show the cortical thickness value of this > subject on this MNI coordinates. But, this has an error as follows. > mris_convert -c subject/surf/lh.thickness fsaverage /surf/lh.white > lh.subject.thickness.asc > > > ERROR: number of vertices in subject/surf/lh.thickness does not match > surface (154962,163842) > > I know what’s happen, but I don’t know how to solve. > > I want to obtain the asc file containing the same vertices as fsaverage and > with the cortical thickness value and their coordinates in the file. Could > you teach me how to obtain the match fsaverage surface file? > > Thank you in advance! > > Feng-Xian > > > > > > > 2009/8/20 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > > you can use mri_surf2surf to map them all the fsaverage, then mris_convert >> to convert each one to asciii. >> >> cheers >> Bruce >> >> On Thu, 20 Aug 2009, Feng-Xian Yan wrote: >> >> Hi, >>> >>> But I want to obtain the asc file or other files containing the same >>> vertices and with the cortical thickness value and their coordinates in >>> the >>> file. >>> >>> Could some ways to obtain? >>> >>> >>> >>> Thank you in advance! >>> >>> >>> >>> Feng-Xian >>> >>> >>> >>> >>> 2009/8/20 Doug Greve <greve(a)nmr.mgh.harvard.edu> >>> >>> >>>> Yes, this is what our group analysis tools do. You can find tutorials >>>> on the wiki. You'll probably start with mris_preproc. >>>> >>>> doug >>>> >>>> >>>> >>>> >>>> On Thu, 20 Aug 2009, Feng-Xian Yan wrote: >>>> >>>> Hi, >>>> >>>>> >>>>> Thank you for your responses before. >>>>> >>>>> >>>>> >>>>> I have another problem want to solve. I check the number of vertex for >>>>> all >>>>> subjects, but I found that the number of vertex for each subjects and >>>>> each >>>>> hemispheres is different. Because I want to compare cortical thickness >>>>> using >>>>> vertex-by-vertex, I would to obtain the same vertex number. >>>>> >>>>> Therefore, have something to do to obtain the same vertex number, i.e. >>>>> template the cortical thickness at each vertex for each subject on the >>>>> fsaverage surface, or other methods? >>>>> >>>>> >>>>> >>>>> How can I do? Would you get me a hand? >>>>> >>>>> >>>>> >>>>> Thank you in advance! >>>>> >>>>> >>>>> >>>>> Feng-Xian >>>>> >>>>> >>>>> >>>>> >>>>> 2009/8/18 Feng-Xian Yan <mimigirln(a)gmail.com> >>>>> >>>>> >>>>> Thank s for your response. >>>>>> >>>>>> So, the coordinates are MNI coordinates, not Talairach coordinates. >>>>>> >>>>>> >>>>>> >>>>>> Thank you in advance. >>>>>> >>>>>> >>>>>> >>>>>> Feng-Xian >>>>>> >>>>>> >>>>>> >>>>>> 2009/8/18 Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >>>>>> >>>>>> The values in the asc file are in MNI305 space. You can see this in >>>>>> >>>>>>> tksurfer with View->Configure->Information and select the mni305 >>>>>>> button. >>>>>>> >>>>>>> Feng-Xian Yan wrote: >>>>>>> >>>>>>> >>>>>>> Thank you for your response. >>>>>>>> >>>>>>>> So, you mean that I have to do "mris_convert" two times. One for >>>>>>>> lh.white.tal.asc, another for lh.thickness.asc. And the Tal >>>>>>>> coordinates >>>>>>>> in >>>>>>>> lh.white.tal.asc file corresponds to the cortical thickness value in >>>>>>>> lh.thickness.asc file. >>>>>>>> >>>>>>>> >>>>>>>> But, the Tal coordinates in lh.white.tal.asc is difference from the >>>>>>>> result in the tksurfer tool box. That is to say, when I open this >>>>>>>> subject by >>>>>>>> tksurfer, I look at the coordinate of the vertex Tal in the tksurfer >>>>>>>> tool >>>>>>>> box, and the coordinate is difference from the coordinates that >>>>>>>> obtain >>>>>>>> from >>>>>>>> the command ?mris_convert ?c lh.thickness lh.white >>>>>>>> lh.thickness.asc?. >>>>>>>> >>>>>>>> >>>>>>>> What do have some problems? >>>>>>>> >>>>>>>> >>>>>>>> Thank you in advance! >>>>>>>> >>>>>>>> >>>>>>>> Feng-Xian >>>>>>>> >>>>>>>> >>>>>>>> 2009/8/18 Douglas N Greve <greve(a)nmr.mgh.harvard.edu <mailto: >>>>>>>> greve(a)nmr.mgh.harvard.edu>> >>>>>>>> >>>>>>>> You have convert the thickness file (lh.thickness) to ascii like >>>>>>>> you did >>>>>>>> with the surface (with mris_convert). You will then have two >>>>>>>> files, and >>>>>>>> the second file will have the thickness values. >>>>>>>> >>>>>>>> doug >>>>>>>> >>>>>>>> Feng-Xian Yan wrote: >>>>>>>> > >>>>>>>> > Hi, >>>>>>>> > >>>>>>>> > Sorry, I don't know what you mean. I know each lines is a vertex >>>>>>>> and >>>>>>>> > represent a Tal coordinate, but each lines only contain xyz, but >>>>>>>> not >>>>>>>> > contain cortical thickness value of these coordinates. That is >>>>>>>> to say, >>>>>>>> > the following is >>>>>>>> > >>>>>>>> > Tal x Tal y Tal z >>>>>>>> > >>>>>>>> > -13.424789 -125.068245 12.671550 0 >>>>>>>> > >>>>>>>> > What?s wrong do I think? >>>>>>>> > >>>>>>>> > Thank you in advance. >>>>>>>> > >>>>>>>> > Feng-Xian >>>>>>>> > >>>>>>>> > 2009/8/18 Douglas N Greve <greve(a)nmr.mgh.harvard.edu >>>>>>>> <mailto:greve@nmr.mgh.harvard.edu> >>>>>>>> > <mailto:greve@nmr.mgh.harvard.edu >>>>>>>> <mailto:greve@nmr.mgh.harvard.edu>>> >>>>>>>> > >>>>>>>> > Just convert the lh.thickness to ascii as well. Each line of >>>>>>>> the >>>>>>>> > xyz coords corresponds to a line in the thickness ascii >>>>>>>> (each line >>>>>>>> > is a vertex). >>>>>>>> > >>>>>>>> > >>>>>>>> > doug >>>>>>>> > >>>>>>>> > Feng-Xian Yan wrote: >>>>>>>> > >>>>>>>> > >>>>>>>> > Hi, >>>>>>>> > >>>>>>>> > I try it again with you recommend me, but the produced asc >>>>>>>> > file (lh.white.tal.asc) only contain x, y, z >>>>>>>> coordinates. (The >>>>>>>> > following shows that.) >>>>>>>> > >>>>>>>> > >>>>>>>> > #!ascii version of lh.white.tal >>>>>>>> > >>>>>>>> > 155006 310008 >>>>>>>> > >>>>>>>> > -13.424789 -125.068245 12.671550 0 >>>>>>>> > >>>>>>>> > -13.939213 -125.063232 12.714314 0 >>>>>>>> > >>>>>>>> > -14.861158 -125.268639 12.404987 0 >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > But, I want to have cortical thickness value with Tal >>>>>>>> > coordinates. This file doesn?t satisfy our demand. >>>>>>>> > >>>>>>>> > >>>>>>>> > Our demand should contain two points. >>>>>>>> > >>>>>>>> > 1) Each vertex across the mantle was represented with an >>>>>>>> > estimated value of cortical thickness and these estimated >>>>>>>> > values of cortical thickness should have their >>>>>>>> coordinates. >>>>>>>> > >>>>>>>> > 2) We want to analysis the cortical thickness difference >>>>>>>> of >>>>>>>> > three groups, so we want to the cortical thickness value >>>>>>>> of >>>>>>>> > each vertex across each subjects should be matched. That >>>>>>>> is to >>>>>>>> > say, the cortical thickness should superimposed on a >>>>>>>> template >>>>>>>> > surface like fsaverage. >>>>>>>> > >>>>>>>> > Therefore, how do we do to obtain the asc file matching >>>>>>>> our >>>>>>>> > demands? >>>>>>>> > >>>>>>>> > >>>>>>>> > Thank you in advance. >>>>>>>> > >>>>>>>> > >>>>>>>> > Feng-Xian >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > 2009/8/14 Douglas N Greve <greve(a)nmr.mgh.harvard.edu >>>>>>>> <mailto:greve@nmr.mgh.harvard.edu> >>>>>>>> > <mailto:greve@nmr.mgh.harvard.edu >>>>>>>> <mailto:greve@nmr.mgh.harvard.edu>> >>>>>>>> > <mailto:greve@nmr.mgh.harvard.edu >>>>>>>> <mailto:greve@nmr.mgh.harvard.edu> >>>>>>>> > <mailto:greve@nmr.mgh.harvard.edu >>>>>>>> <mailto:greve@nmr.mgh.harvard.edu>>>> >>>>>>>> > >>>>>>>> > >>>>>>>> > Try these commands: >>>>>>>> > >>>>>>>> > mri_surf2surf --s subject --hemi lh --sval-tal-xyz white >>>>>>>> > --tval-xyz --tval lh.white.tal >>>>>>>> > mris_convert lh.white.tal lh.white.tal.asc >>>>>>>> > >>>>>>>> > doug >>>>>>>> > >>>>>>>> > Feng-Xian Yan wrote: >>>>>>>> > >>>>>>>> > >>>>>>>> > Hi, >>>>>>>> > >>>>>>>> > I have some problems want to understand. >>>>>>>> > >>>>>>>> > (1) I want to analysis the cortical thickness difference >>>>>>>> of >>>>>>>> > three groups. But, three groups (one factor/three levels) >>>>>>>> of >>>>>>>> > Freesurfer is not satisfied with our demand. Because we >>>>>>>> want >>>>>>>> > to get a thickness difference map that satisfied with >>>>>>>> the many >>>>>>>> > voxels containing A group > B group > C group and A >>>>>>>> group < B >>>>>>>> > group < C group, Freesurfer can?t do that. So, we want >>>>>>>> to get >>>>>>>> > this map by myself and use Matlab or other tool to obtain >>>>>>>> > that. And, now I want to obtain a file that containing >>>>>>>> the Tal >>>>>>>> > coordinate and the thickness value of this coordinate >>>>>>>> for all >>>>>>>> > subjects. >>>>>>>> > >>>>>>>> > Would you tell me how to get the file that containing >>>>>>>> the Tal >>>>>>>> > coordinate and the thickness value of this coordinate? >>>>>>>> > >>>>>>>> > (2) Before, I want to use the following command to get the >>>>>>>> > thickness value. >>>>>>>> > >>>>>>>> > The command line is "mri_surf2surf --srcsubject noise0.5_0 >>>>>>>> > --srcsurfval thickness --sfmt surface --trgsubject >>>>>>>> noise0.5_0 >>>>>>>> > --trgsurfval noise0.5_0_tal.xfm --tfmt surface --hemi lh >>>>>>>> > --sval-tal-xyz orig --tval-xyz", and then i type >>>>>>>> ?mris_convert >>>>>>>> > lh.noise0.5_0_tal.xfm lh.white lh.thickness.asc?. >>>>>>>> > >>>>>>>> > But, the result file(lh.thickness.asc) does not contain >>>>>>>> the >>>>>>>> > thickness value of this coordinate. >>>>>>>> > >>>>>>>> > So, I think these commands have some error. >>>>>>>> > >>>>>>>> > (3) Use the command ?mris_convert ?c lh.thickness lh.white >>>>>>>> > lh.thickness.asc? to obtain the thickness value of the RAS >>>>>>>> > coordinates. But, I?m confused about that if I change >>>>>>>> lh.white >>>>>>>> > to lh.pail or lh.inflated. >>>>>>>> > What?s difference for the three? >>>>>>>> > >>>>>>>> > (4) And, I ask some problem before. >>>>>>>> > >>>>>>>> > Everyone said the result file(lh.thickness.asc) is using >>>>>>>> RAS >>>>>>>> > coordinates through ?mris_convert ?c lh.thickness lh.white >>>>>>>> > lh.thickness.asc?. But, I have confused about this. When I >>>>>>>> > open this subject by tksurfer, I look at the coordinate >>>>>>>> of the >>>>>>>> > vertex RAS in the tksurfer tool box, and the coordinate is >>>>>>>> > difference from the coordinates that obtain from the >>>>>>>> command >>>>>>>> > ?mris_convert ?c lh.thickness lh.white lh.thickness.asc?. >>>>>>>> > So, which one is right? >>>>>>>> > >>>>>>>> > Thank you in advance! >>>>>>>> > >>>>>>>> > Feng-Xian >>>>>>>> > >>>>>>>> >>>>>>>> >>>>>>>> ------------------------------------------------------------------------ >>>>>>>> > >>>>>>>> > _______________________________________________ >>>>>>>> > Freesurfer mailing list >>>>>>>> > Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>>>>>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu >>>>>>>> <mailto:Freesurfer@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 >>>>>>>> <mailto:greve@nmr.mgh.harvard.edu> >>>>>>>> <mailto:greve@nmr.mgh.harvard.edu <mailto: >>>>>>>> greve(a)nmr.mgh.harvard.edu >>>>>>>> >>>>>>>>> >>>>>>>>>> > <mailto:greve@nmr.mgh.harvard.edu >>>>>>>> <mailto:greve@nmr.mgh.harvard.edu> >>>>>>>> > <mailto:greve@nmr.mgh.harvard.edu >>>>>>>> <mailto:greve@nmr.mgh.harvard.edu>>> >>>>>>>> > >>>>>>>> > Phone Number: 617-724-2358 Fax: 617-726-7422 >>>>>>>> > >>>>>>>> > In order to help us help you, please follow the steps in: >>>>>>>> > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>>>>>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>>>>>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > -- >>>>>>>> > Douglas N. Greve, Ph.D. >>>>>>>> > MGH-NMR Center >>>>>>>> > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>>>>>>> <mailto:greve@nmr.mgh.harvard.edu <mailto: >>>>>>>> greve(a)nmr.mgh.harvard.edu >>>>>>>> >>>>>>>>> >>>>>>>>>> > Phone Number: 617-724-2358 Fax: 617-726-7422 >>>>>>>> > >>>>>>>> > In order to help us help you, please follow the steps in: >>>>>>>> > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>>>>>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> >>>>>>>> -- >>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>> MGH-NMR Center >>>>>>>> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>>>>>>> Phone Number: 617-724-2358 >>>>>>>> Fax: 617-726-7422 >>>>>>>> >>>>>>>> In order to help us help you, please follow the steps in: >>>>>>>> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> >>>>>>> Douglas N. Greve, Ph.D. >>>>>>> MGH-NMR Center >>>>>>> greve(a)nmr.mgh.harvard.edu >>>>>>> Phone Number: 617-724-2358 Fax: 617-726-7422 >>>>>>> >>>>>>> In order to help us help you, please follow the steps in: >>>>>>> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve(a)nmr.mgh.harvard.edu >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> >>>> In order to help us help you, please follow the steps in: >>>> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> >>>> >>>> >>> >

2 1

fsaverage Talairach Coordinates
by Matt Leonard 24 Aug '09

24 Aug '09

Hi, I've been asked to report Talairach coordinates in a paper, but I've been told that the coordinates that are listed on the fsaverage brain (in the talairach.xfm file) are not accurate. Does anyone have a way to get the true Talairach coordinates on the fsaverage brain? Thanks, Matt

2 3

mri_surfcluster with qdecs sig.mgh file
by Rosa Steimke 24 Aug '09

24 Aug '09

dear freesurfer experts. i have another problem in generating output useing mr_surfcluster command. i was wondering how to generate an output with the significant clusters from my qdec analysis i learnd that i have to use the mri_surfcluster command and use the sig.mgh file from my qdec. however i am very uncertain about how to apply the explanation (from freesurfer wiki) of the mri_surfcluster commands to the sig.mgh. i got the error message that the --sum command cannot be used for the sig.mgh file and i dont understand whether i have to apply more commands (besids thresholding, subjects and such) to generate the and output that gives me the size, significant values and coordinates of each of the clusters i can see in qdec. thanks for your help. rosa -- Jetzt kostenlos herunterladen: Internet Explorer 8 und Mozilla Firefox 3 - sicherer, schneller und einfacher! http://portal.gmx.net/de/go/atbrowser

2 1

Re: [Freesurfer] Freesurfer Digest, Vol 66, Issue 9
by Sebastian Moeller 24 Aug '09

24 Aug '09

Hi Guang, if I recall correctly "the sliver problem" stems from the use of an incompatible libGL. I did the following that a colleague found out: add the following line to ${FREESURFER_HOME}/bin/tksurfer (that is the script that calls tksurfer.bin): setenv LD_PRELOAD ${FREESURFER_HOME}bin/libGL.so.1 Also unpack the following to reside in your ${FREESURFER_HOME}/bin directory: (Those are GL libraries from a redhat 4 / centos 4 system that seem to work with tksurfer). Nick, do you think it would be possible to make this change for the distribution (it was inspired by your inclusion of libGlut to begin with). ahoi & good luck Sebastian On Aug 5, 2009, at 7:22 AM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Date: Wed, 5 Aug 2009 08:49:15 -0500 > From: Guang Zeng <freesurfer_zg(a)hotmail.com> > Subject: [Freesurfer] "redraw failed: no gl window open" problem > To: <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <SNT112-W300BF5F653E2F82B84CEA29C0D0(a)phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > > Hi, there, > > I am running the tksurfer command to view the cortical surface data > as tksurfer bert lh inflated. But I met a problem. > I only can view a sliver part of the brain. This sliver portion can > rotate and do everything that tksurfer is supposed to do, > but I can't view any more of the brain than a tiny piece. Tkmedit > works fine. > > When I run the command, it gave me something like this: > > surfer: current subjects dir: /home/m047599/freesurfer-install/ > freesurfer/subjects > surfer: not in "scripts" dir ==> using cwd for session root > surfer: session root data dir ($session) set to: > surfer: /home/m047599/freesurfer-install/freesurfer > surfer: Reading header info from /home/m047599/freesurfer-install/ > freesurfer/subjects/bert/mri/T1.mgz > surfer: vertices=131369, faces=262734 > Loading /home/m047599/freesurfer-install/freesurfer/surface_labels.txt > surfer: ### redraw failed: no gl window open > surfer: single buffered window > surfer: tkoInitWindow(bert) > surfer: using interface /home/m047599/freesurfer-install/freesurfer/ > lib/tcl/tksurfer.tcl > Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/ > tkm_common.tcl > Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/ > tkm_wrappers.tcl > Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/ > fsgdfPlot.tcl > Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/ > tkUtils.tcl > Successfully parsed tksurfer.tcl > reading white matter vertex locations... > > > I searched the previous posts, it looks like somebody have the same > problem. > There is no NVidia and native Linux system on my computer. I run > tksurfer on a virtual Linux machine using NX 3. 3. 0. 6. > I ran the xdpyinfo | grep GL, it shows that I have GLX and SGI-GLX. > I ran the glxgrears, it works, although very slow. > > So, how can I solve this problem, any suggestions are highly > appreciated. > > Thanks a lot!

3 3

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