Freesurfer

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30097 discussions

Converting fsaveraged EPI to volume
by Marcel Falkiewicz 03 Sep '13

03 Sep '13

Hello, I would like to perform some Bayesian analyses implemented in SPM, but with the data normalized with FreeSurfer. I would like to merge together surface and subcortal normalized timeseries into a single 4d timeseries in volumetric space, which could be used as an input to spm. I tried using vlrmerge, but it produces only a single volume. One method would be splitting the timeseries for each space into single volumes, using vlrmerge on each triplet and then merging the results. However, this would take enourmous ammout of time. Do you know any quicker workarounds? Thanks in advance, Marcel

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mri_vol2surf projection of white matter results
by Robert Schulz 03 Sep '13

03 Sep '13

Dear Freesurfers, I transferred the white matter binary mask (derived from aseg, volume) to FSL and performed probabilistic tractography in it. Now I'd like to project the 'outer' white matter results (vol) onto the white surface. To test for the acuracy of this approach, I tried to project the white matter mask (binarized, volume) itself on the surface, proper projection should give only 1s (ones) on the surface, which holds true for the majority of vertices. I used the following command: mri_vol2surf --mov whitevolume.mgz --reg struct2freesurfer.dat --projdist-max 0 3 0.1 --interp nearest --hemi rh --out ... Is there a way to optimize this? The binarized white matter data (volume) is just below the white matter surface in most cases, sometimes, voxels are also above the surface. If I try trilinear I get values far away from 1 (hence values which are not included in the primary data (=binarized mask). Looking forward to your suggestions. Thank you very much, Best Robert -- Besuchen Sie uns auf: www.uke.de _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING

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mri_vol2surf projection of white matter results
by Robert Schulz 03 Sep '13

03 Sep '13

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mri_surf2surf to fsaverageX introduces offset
by Franz Liem 03 Sep '13

03 Sep '13

Dear Freesurfers, I tried to map a single subject surface to fsaverageX (for the sake of demonstration lets take fsaverage6). I did the following: mri_surf2surf --hemi lh --srcsubject $s --sval-xyz white --trgsubject fsaverage6 --tval-xyz --tval ./lh.white.ico6 This produces a surface that seems systematically shifted (see figure). Also the newly generated surface does not contain valid geomery information (see mris_info print of lh.white and lh.white.ico6). Is there a way to fix this? Another question: is there a reason why mris_decimate is not included in the freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 build Any help is very much appreciated. Best, Franz mris_info $s/surf/lh.white > SURFACE INFO ======================================== > type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE > num vertices: 118611 > num faces : 237218 > num strips : 0 > surface area: 77595.6 > AvgVtxArea 0.654202 > AvgVtxDist 0.885026 > StdVtxDist 0.251941 > ctr : (-33.3535, -11.9536, 42.7693) > vertex locs : surfaceRAS > talairch.xfm: > 1.045 -0.093 -0.014 1.081; > 0.099 1.095 0.070 -4.263; > 0.010 -0.083 1.290 -41.092; > 0.000 0.000 0.000 1.000; > surfaceRAS to talaraiched surfaceRAS: > 1.045 -0.093 -0.014 1.177; > 0.099 1.095 0.070 13.377; > 0.010 -0.083 1.290 -49.756; > 0.000 0.000 0.000 1.000; > talairached surfaceRAS to surfaceRAS: > 0.949 0.081 0.006 -1.900; > -0.085 0.902 -0.050 -14.449; > -0.013 0.058 0.772 37.650; > 0.000 0.000 0.000 1.000; > volume geometry: > extent : (256, 256, 256) > voxel : ( 1.0000, 1.0000, 1.0000) > x_(ras) : (-1.0000, -0.0000, 0.0000) > y_(ras) : (-0.0000, 0.0000, -1.0000) > z_(ras) : ( 0.0000, 1.0000, -0.0000) > c_(ras) : ( 0.0989, 0.9660, 0.9027) > ... mris_info lh.white.ico6 > SURFACE INFO ======================================== > type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE > num vertices: 40962 > num faces : 81920 > num strips : 0 > surface area: 75477.4 > AvgVtxArea 1.842620 > AvgVtxDist 1.573724 > StdVtxDist 0.523314 > ctr : (-33.3983, -12.0872, 42.7743) > vertex locs : surfaceRAS > volume geometry info is either not contained or not valid. > ...

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Re: [Freesurfer] apply fnirt transformation on a surface
by Bruce Fischl 03 Sep '13

03 Sep '13

thanks Matt Bruce On Mon, 2 Sep 2013, Glasser, Matthew wrote: > Hi Bruce, > > Connectome Workbench commandline utilities can do this with FSL warp > fields: > > wb_command -surface-apply-warpfield > > One needs to use the inverse warp as the <warpfield> argument and the > forward warp as the -fnirt <forward-warp>. > > Peace, > > Matt. > > On 9/2/13 11:19 AM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: > >> A veritable game of telephone! Thanks Jesper. Matt? >> >> On Mon, 2 Sep 2013, Jesper Andersson wrote: >> >>> Hi guys, >>> I didn't think we had any tools for doing that, and said so much on the >>> FSL >>> mailbase. But apparently the WashU people has something that does just >>> that >>> for you. I think the best person to contact about the details is Matt >>> Glasser. >>> >>> J >>> >>> On 2 Sep 2013, at 15:58, Saad Jbabdi <saad(a)FMRIB.OX.AC.UK> >>> wrote: >>> >>> Hi In Probtrackx, this is done internally. >>> If you just want to transform the vertex coordinates, then I think >>> you'll need to play with the FNIRT source code - I've CC'd Jesper who >>> knows better. >>> >>> Cheers, >>> Saad >>> >>> >>> >>> On 2 Sep 2013, at 15:56, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>> wrote: >>> >>> you might check on the FSL list. I think I've seen some >>> traffic indicating that there are some tools for doing >>> this. I'l cc Saad as he might know >>> >>> cheers >>> Bruce >>> >>> >>> On Mon, 2 Sep 2013, Douglas Greve wrote: >>> >>> Hi Shani, I don't think you can apply a FNIRT >>> transform to a surface. >>> doug >>> On 9/2/13 8:20 AM, Shani Ben Amitay wrote: >>> Dear freesurfer people, >>> Any idea whether I can apply transformation >>> that was calculated by fsl >>> fnirt on the white/pial surfaces calculated >>> using the freesurfer >>> stream? >>> Thanks! >>> Shani >>> _______________________________________________ >>> 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. >>> >>> >>> >>> -- >>> Saad Jbabdi >>> University of Oxford, FMRIB Centre >>> >>> JR Hospital, Headington, OX3 9DU, UK >>> (+44)1865-222466 (fax 717) >>> www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi >>> >>> >>> > > > ________________________________ > 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. > > >

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FW: apply fnirt transformation on a surface
by Matt Glasser 02 Sep '13

02 Sep '13

On 9/2/13 12:02 PM, "Glasser, Matthew" <glasserm(a)wusm.wustl.edu> wrote: >Hi Bruce, > >Connectome Workbench commandline utilities can do this with FSL warp >fields: > >wb_command -surface-apply-warpfield > >One needs to use the inverse warp as the <warpfield> argument and the >forward warp as the -fnirt <forward-warp>. > >Peace, > >Matt. > >On 9/2/13 11:19 AM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: > >>A veritable game of telephone! Thanks Jesper. Matt? >> >>On Mon, 2 Sep 2013, Jesper Andersson wrote: >> >>> Hi guys, >>> I didn't think we had any tools for doing that, and said so much on the >>>FSL >>> mailbase. But apparently the WashU people has something that does just >>>that >>> for you. I think the best person to contact about the details is Matt >>> Glasser. >>> >>> J >>> >>> On 2 Sep 2013, at 15:58, Saad Jbabdi <saad(a)FMRIB.OX.AC.UK> >>> wrote: >>> >>> Hi In Probtrackx, this is done internally. >>> If you just want to transform the vertex coordinates, then I think >>> you'll need to play with the FNIRT source code - I've CC'd Jesper who >>> knows better. >>> >>> Cheers, >>> Saad >>> >>> >>> >>> On 2 Sep 2013, at 15:56, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>> wrote: >>> >>> you might check on the FSL list. I think I've seen some >>> traffic indicating that there are some tools for doing >>> this. I'l cc Saad as he might know >>> >>> cheers >>> Bruce >>> >>> >>> On Mon, 2 Sep 2013, Douglas Greve wrote: >>> >>> Hi Shani, I don't think you can apply a FNIRT >>> transform to a surface. >>> doug >>> On 9/2/13 8:20 AM, Shani Ben Amitay wrote: >>> Dear freesurfer people, >>> Any idea whether I can apply transformation >>> that was calculated by fsl >>> fnirt on the white/pial surfaces calculated >>> using the freesurfer >>> stream? >>> Thanks! >>> Shani >>> _______________________________________________ >>> 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. >>> >>> >>> >>> -- >>> Saad Jbabdi >>> University of Oxford, FMRIB Centre >>> >>> JR Hospital, Headington, OX3 9DU, UK >>> (+44)1865-222466 (fax 717) >>> www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi >>> >>> >>> >

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apply fnirt transformation on a surface
by Shani Ben Amitay 02 Sep '13

02 Sep '13

Dear freesurfer people, Any idea whether I can apply transformation that was calculated by fsl fnirt on the white/pial surfaces calculated using the freesurfer stream? Thanks! Shani

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Re: [Freesurfer] apply fnirt transformation on a surface
by Bruce Fischl 02 Sep '13

02 Sep '13

A veritable game of telephone! Thanks Jesper. Matt? On Mon, 2 Sep 2013, Jesper Andersson wrote: > Hi guys, > I didn't think we had any tools for doing that, and said so much on the FSL > mailbase. But apparently the WashU people has something that does just that > for you. I think the best person to contact about the details is Matt > Glasser. > > J > > On 2 Sep 2013, at 15:58, Saad Jbabdi <saad(a)FMRIB.OX.AC.UK> > wrote: > > Hi In Probtrackx, this is done internally. > If you just want to transform the vertex coordinates, then I think > you'll need to play with the FNIRT source code - I've CC'd Jesper who > knows better. > > Cheers, > Saad > > > > On 2 Sep 2013, at 15:56, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > > you might check on the FSL list. I think I've seen some > traffic indicating that there are some tools for doing > this. I'l cc Saad as he might know > > cheers > Bruce > > > On Mon, 2 Sep 2013, Douglas Greve wrote: > > Hi Shani, I don't think you can apply a FNIRT > transform to a surface. > doug > On 9/2/13 8:20 AM, Shani Ben Amitay wrote: > Dear freesurfer people, > Any idea whether I can apply transformation > that was calculated by fsl > fnirt on the white/pial surfaces calculated > using the freesurfer > stream? > Thanks! > Shani > _______________________________________________ > 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. > > > > -- > Saad Jbabdi > University of Oxford, FMRIB Centre > > JR Hospital, Headington, OX3 9DU, UK > (+44)1865-222466 (fax 717) > www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi > > > >

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problems with aparcstats2table
by pietro de rossi 02 Sep '13

02 Sep '13

Dear FreeSurfers, I am extracting thickness values through the aparcstats2table command line. Everything works just fine for --hemi lh using the --skip flag. However, when it comes to the right hemisphere I get SUBJECTS_DIR : /usr/local/freesurfer/subjects Parsing the .stats files Traceback (most recent call last): File "/usr/local/freesurfer/bin/aparcstats2table", line 321, in <module> parc_measure_map = parsed.parse(options.meas) File "/usr/local/freesurfer/bin/fsutils.py", line 194, in parse parcid = strlist[0] IndexError: list index out of range I find it weird given that I am extracting thickness values for the same subjects. Can anybody help me find out what the problem is? Thank you in advance, Pietro -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA

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Using edited ribbon.mgz in make_average_subject
by Miggy Chuapoco 30 Aug '13

30 Aug '13

Hi all, I've used itksnap to make edits to the ribbon.mgz (which was first converted to a nifti) file to fix the segmentations of several subjects and I now want to use this file to recreate the surface and curvature files for each subject so that I can make an average subject that uses these fixed segmentations. I am essentially trying to use a segmentation that I have fixed in itkgray to make an average subject, however looking at the processing stream in order to recreate the surface and curvature files I need to have a wm.mgz file. I've tried to find a way to maybe extract a wm.mgz file from the edited ribbon file and run -autorecon2-wm in order to recreate the surface and curvature files with the fixed segmentation, but I have yet to find a way to do this. Does anyone know if this is possible of if there is a way around this? Thanks, Miggy Chuapoco

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