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30096 discussions

mris_divide_parcellation color table error
by Tina Jeon 29 May '13

29 May '13

Hello freesurfers, I am trying to create a figure similar to the Hagmann et al 2008 paper with 998 rois overlaid onto the surface, however, I am finding that there is no random, unique color for each parcellation unit like described in the help file for mris_divide_parcellation. I have attached a snapshot of my annotation file overlaid onto the surface, as you can see, the color iterates the same/similar color for a particular label. Can you tell me what I am doing wrong? Is there a pre-existing atlas as described in the Hagmann paper? My input: mris_ca_label -t ./FreeSurferColorLUT.txt subject_name lh ./lh.sphere.reg $FREESURFER_HOME/average/lh.curvature.buckner40.filled.desikan_killany.2010-03-25.gcs ./lh.aparc.998rois.annot mris_divide_parcellation subject_name lh ./lh.aparc.998rois.annot ./splittable.txt ./lh.annotation.998rois_26.annot Many thanks, Tina Jeon, MS UT Southwestern Medical Center '14 ________________________________ UT Southwestern Medical Center The future of medicine, today.

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R: Re: very slow analysis with recon-all
by stdp82＠virgilio.it 29 May '13

29 May '13

Bruce and Sebastian thank you very much. I have checked the files but they are all wrong. These are the image info: data_type FLOAT32dim1 280dim2 240dim3 240dim4 1datatype 16pixdim1 0.5999984741pixdim2 1.0416666269pixdim3 1.0416666269pixdim4 0.0000000000cal_max 0.0000cal_min 0.0000file_type NIFTI-1+ Waiting for your feedback. Thank you very much. Stefano ----Messaggio originale---- Da: sebastian.moeller1(a)rwth-aachen.de Data: 26-mag-2013 21.31 A: "Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu> Cc: <stdp82(a)virgilio.it>, <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] very slow analysis with recon-all Hi Stefano, hi Bruce, sorry to partly high-jack your thread Stafano. In my experience with NHPs I often encounter problems like included cerebellum, so I routinely check the filled.mgz before actually running the surface recon, to confirm that the cerebellum (or other non-white matter) is NOT part of either hemisphere. (In my cases typically I then have to either edit the wm.mgz, the brain mask, or the pons cutting plane, but I guess that is NHP specific). Now wouldn't that filled.mgz check not also work for human recons? best Sebastian On May 26, 2013, at 21:13 , Bruce Fischl wrote: > Hi Stefano > > a defect with over 60K vertices is more than 1/2 the size of a typical hemisphere, so something has gone badly wrong. Have you checked the skull stripping? The aseg? The talairach? There shouldn't be a defect that big - you will need to figure out why > > cheers > Bruce > On Sun, 26 May 2013, stdp82(a)virgilio.it wrote: > >> Hi list, >> I'm running recon-all on two T1 but the command is for two days >> on CORRECTING DEFECT 11 (vertices=55538, convex hull=7811). >> Is it ok? What's happen? >> Thanks, >> Stefano >> > _______________________________________________ > 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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no hippocampal stats despite running FS 5.3 with -hippo-subfields
by Salil Soman 29 May '13

29 May '13

Dear Freesurfer Experts, I have been running freesurfer 5.3 without any reported errors using the following command: recon-all -i SPGR/*.gz -s SUBJECTIDENTIFIER -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -all However, when I look for any of the hippocampal subfield stats (as described on http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation) I do not find any of them. Any suggestions on what I am doing incorrectly? Best wishes, Salil Soman, MD, MS

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R: R: Re: very slow analysis with recon-all
by stdp82＠virgilio.it 29 May '13

29 May '13

I apologize. This is the correct info:data_type INT16dim1 280dim2 240dim3 240dim4 1datatype 4pixdim1 0.5999984741pixdim2 1.0416666269pixdim3 1.0416666269pixdim4 0.0000000000cal_max 0.0000cal_min 0.0000file_type NIFTI-1+ ----Messaggio originale---- Da: stdp82(a)virgilio.it Data: 30-mag-2013 0.30 A: <sebastian.moeller1(a)rwth-aachen.de>, "Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: [Freesurfer] R: Re: very slow analysis with recon-all Bruce and Sebastian thank you very much. I have checked the files but they are all wrong. These are the image info: data_type FLOAT32dim1 280dim2 240dim3 240dim4 1datatype 16pixdim1 0.5999984741pixdim2 1.0416666269pixdim3 1.0416666269pixdim4 0.0000000000cal_max 0.0000cal_min 0.0000file_type NIFTI-1+ Waiting for your feedback. Thank you very much. Stefano ----Messaggio originale---- Da: sebastian.moeller1(a)rwth-aachen.de Data: 26-mag-2013 21.31 A: "Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu> Cc: <stdp82(a)virgilio.it>, <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] very slow analysis with recon-all Hi Stefano, hi Bruce, sorry to partly high-jack your thread Stafano. In my experience with NHPs I often encounter problems like included cerebellum, so I routinely check the filled.mgz before actually running the surface recon, to confirm that the cerebellum (or other non-white matter) is NOT part of either hemisphere. (In my cases typically I then have to either edit the wm.mgz, the brain mask, or the pons cutting plane, but I guess that is NHP specific). Now wouldn't that filled.mgz check not also work for human recons? best Sebastian On May 26, 2013, at 21:13 , Bruce Fischl wrote: > Hi Stefano > > a defect with over 60K vertices is more than 1/2 the size of a typical hemisphere, so something has gone badly wrong. Have you checked the skull stripping? The aseg? The talairach? There shouldn't be a defect that big - you will need to figure out why > > cheers > Bruce > On Sun, 26 May 2013, stdp82(a)virgilio.it wrote: > >> Hi list, >> I'm running recon-all on two T1 but the command is for two days >> on CORRECTING DEFECT 11 (vertices=55538, convex hull=7811). >> Is it ok? What's happen? >> Thanks, >> Stefano >> > _______________________________________________ > 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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Reposition Surface
by Derin J Cobia 29 May '13

29 May '13

Just a question about the Tools --> Reposition Surface... feature in Freeview. Is that up and running? Is there any accompanying documentation? Thanks. -Derin

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Re: [Freesurfer] SUMA and FSFAST
by Douglas N Greve 29 May '13

29 May '13

Thanks Ziad, looks like it is similar to FSFAST. doug On 05/29/2013 11:50 AM, Ziad Saad wrote: > Hi Joe, > > As Doug guessed, I never used FSFAST so I can't really tell you much > about how they differ. > > SUMA will require you use FreeSurfer to create the surfaces and warp > them to standard spherical space. For the analysis stream, the one > difference that comes to mind is that we recreate standard-mesh > versions of FreeSurfer's surfaces (via sphere.reg) to make all > surfaces isotopic across all the subjects. After that, and aside from > the surface-specific procedures such as smoothing or clustering, all > level-I and level-II voxel-wise computations can be carried out on > surface-based data. > A recent description of the analysis stream is in this paper > http://afni.nimh.nih.gov/pub/dist/papers/Saad_SUMA_2011.pdf . > > cheers, > z > > > On May 29, 2013, at 09:44 AM, Douglas Greve wrote: > >> >> sorry, I've never used SUMA. Maybe Ziad can chime in (though he's >> probably never used FSFAST!) >> doug >> >> >> On 5/28/13 8:57 PM, Joseph Dien wrote: >>> I was wondering if someone could give me a summary as to how SUMA >>> and FSFAST differ? In other words, user interface aside, what would >>> be reasons to use one or the other? >>> >>> Joe >>> >>> >>> -------------------------------------------------------------------------------- >>> >>> Joseph Dien, >>> Senior Research Scientist >>> University of Maryland >>> >>> E-mail: jdien07(a)mac.com <mailto:jdien07@mac.com> >>> Phone: 301-226-8848 >>> Fax: 301-226-8811 >>> http://joedien.com// >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> 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. >> > -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Contrast of three groups
by Jacobs H (NP) 29 May '13

29 May '13

Hi FreeSurfers, I have a more statistical question: I have three groups of subjects and I want to examine the effect of a continuous variable (cognition). Is it possible to examine three groups? Or should I do pairwise comparisons? What would the contrast than look like? Something like this: 0 0 0 0 0 0 0.33 0.33 0.33 (first three zeros for the three groups; three zeros for age-correction; three weights for cognition scores)?? Thanks! Heidi ================================================ Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jacobs(a)maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ================================================

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error loading volume brainmask.gcut.mgz
by Claudia Dacquino 29 May '13

29 May '13

Hi Freesurfers, I'm trying to remove some dura which affect my surfaces with the command recon-all -skullstrip -clean-bm -gcut -subjid but then I can't use tkmedit to check that. The message I get is: Error: Loading volume brainmask.gcut.mgz Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. Actually I did check in brainmask.gcut.mgz directory properties, and I saw the size of image is something like 150 KB, instead of 1 MB like is brainmask.mgz. What is the problem? Thanks, Claudia

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Re: [Freesurfer] head motion values
by Joseph Dien 29 May '13

29 May '13

I have a follow-up question for this thread. I'm currently assessing whether to switch from SPM8 to FSFAST. As part of this process, I did a comparison between the SPM8 and the preproc-sess motion correction outputs but found they were quite different for the example data I looked at. Furthermore, I found that the fmcpr.mcdat output and the mcprextreg output are quite different even though they are both generated by fsfast. The following three charts are for mcprextreg, fmcpr.mcdat, and SPM8 respectively. Finally, I'm including a correlation matrix (I don't see any correspondences). The data are actually two separate sessions with a rest break, resulting in a discontinuity at the midpoint. The SPM realignment was run separately on each and as usual the first volume was the reference volume while FSFAST was run on both sessions as a merged set and I think used the middle volume as its reference volume. This shouldn't have resulted in such a large difference between SPM8 and FSFAST though (Ardekani et al 2001 reported they didn't differ that much in accuracy for SPM99 and AFNI98 versions and my understanding is that FSFAST uses AFNI's routine) and certainly not between the two FSFAST outputs. On the other hand, the magnitude of movement in this example is small so I guess my main concern is the discrepancy between mcprextreg and fmcpr.mcdat. I want to make sure I know what I'm looking at and therefore how to use it properly. I looked up the documentation on AFNI's 3dvolreg (http://afni.nimh.nih.gov/pub/dist/doc/program_help/3dvolreg.html) Would I be correct in thinking that mcprextreg results from the -1Dfile option and fmcpr.mcdat results from the -dfile option? I can take this to the AFNI message board once I'm sure where these files came from. Respectfully, Joe > Either fmcpr.mcdat or fmc.mcdat > > On 09/13/2012 02:07 PM, New Fei Ho wrote: > > Hi Doug, > > > > Can you point out the name of file that I should be looking at? > > > > I assumed they were either the mcextreg and mcprextreg output files, but > > these only have 6 columns. > > > > Thanks, > > New Fei > > > >> Hi New Fei, I did some digging and found the docs for the output (pasted > >> below). Translations (displacement) are in mm, rotations are in degrees > >> doug > >> > >> 1. n : time point > >> 2. roll : rotation about the I-S axis (degrees CCW) > >> 3. pitch : rotation about the R-L axis (degrees CCW) > >> 4. yaw : rotation about the A-P axis (degrees CCW) > >> 5. dS : displacement in the Superior direction (mm) > >> 6. dL : displacement in the Left direction (mm) > >> 7. dP : displacement in the Posterior direction (mm) > >> 8. rmsold : RMS difference between input frame and reference frame > >> 9. rmsnew : RMS difference between output frame and reference frame > >> 10. trans : translation (mm) = sqrt(dS^2 + dL^2 + dP^2) > >> > >> > >> On 09/13/2012 11:21 AM, New Fei Ho wrote: > >>> Hi Doug, > >>> > >>> To explicitly clarify, does this mean > >>> X: L-R > >>> Y: Anterior-Posterior > >>> Z: Inferior-Superior > >>> > >>> And are the values of translation/rotation in millimetres? > >>> > >>> Thanks, > >>> New Fei > >>> > >>> > >>>> If by XYZ you mean column, row, slice, then yes. The values are with > >>>> respect to the middle time point (or whatever you used as the > >>>> template), > >>>> it is not the relative difference. > >>>> doug > >>>> > >>>> On 09/12/2012 05:37 PM, New Fei Ho wrote: > >>>>> Hi, > >>>>> > >>>>> I would like to compare the mean head motion between two groups. > >>>>> > >>>>> Just to clarify the values found in the mcprextreg file: > >>>>> 1. Do the six columns represent translationX, translationY, > >>>>> translationZ > >>>>> and rotationX, rotationY, rotationZ? > >>>>> > >>>>> 2. Are the values found in each time-point (i) absolute, i.e. the > >>>>> absolute > >>>>> difference in displacement between this time-point and the middle > >>>>> time-point, or (ii) relative i.e. difference between consecutive > >>>>> time-points? > >>>>> > >>>>> Thanks, > >>>>> Newfei > >>>>> _______________________________________________ > >>>>> Freesurfer mailing list > >>>>> Freesurfer(a)nmr.mgh.harvard.edu > >>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>>>> > >>>>> > >>>> -- > >>>> Douglas N. Greve, Ph.D. > >>>> MGH-NMR Center > >>>> gr...(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 > >>>> > >>>> _______________________________________________ > >>>> Freesurfer mailing list > >>>> Freesurfer(a)nmr.mgh.harvard.edu > >>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >>>> > >>>> > >>>> > >> -- > >> Douglas N. Greve, Ph.D. > >> MGH-NMR Center > >> gr...(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 > >> > >> > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...(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 _______________________________________________ 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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SUMA and FSFAST
by Joseph Dien 29 May '13

29 May '13

I was wondering if someone could give me a summary as to how SUMA and FSFAST differ? In other words, user interface aside, what would be reasons to use one or the other? Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07(a)mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com//

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