Freesurfer October 2008

freesurfer@nmr.mgh.harvard.edu

71 participants
110 discussions

LGI error in make_outer_surface at 31
by Juranek, Jenifer 07 Apr '11

07 Apr '11

Hi, Encountering some difficulties with LGI on a RHEL4 box (64bit) with MATLAB v7.6.0.324 (R2008a) installed. Subject was processed under fsv405. Specific error is pasted below: Any suggestions to correct my error? Thanks, Jenifer >> reading filled volume... closing volume... ??? Undefined function or method 'fspecial' for input arguments of type 'char'. Error in ==> make_outer_surface at 31 Gaussian = fspecial('gaussian',[2 2],1); >> ERROR: make_outer_surface did not create output file 'tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Sep 24 11:51:01 CDT 2008 [jjuranek@localhost jjuranek_fsv405]$

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mri_volcluster --ERROR: you must specify a pos or neg sign with --fwhm
by PKUNWAR＠nmr.mgh.harvard.edu 26 Aug '09

26 Aug '09

Hi all, I was going through the FSFAST TUTORIAL from wiki( https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial?action=highlight&v…) I got the follwoing error during mri_volcluster, "NOT Adjusting threshold for 1-tailed test ERROR: you must specify a pos or neg sign with --fwhm" I have fwhm.dat file with 4. something vlaue. Command used, [galen:odd-v-0] (nmr-std-env) mri_volcluster --in tal.rfx.osgm/osgm/sig.nii --thmin 2 --fwhmdat tal.rfx.osgm/fwhm.dat --cwpvalthresh 0.1 --mask tal.rfx.osgm/mask.nii --fsaverage --sum tal.rfx.osgm/osgm/cluster.sum --cwsig tal.rfx.osgm/osgm/cwsig.cluster.nii --out tal.rfx.osgm/osgm/sig.cluster.nii --ocn tal.rfx.osgm/osgm/ocn.cluster.nii without --fwhmdat flag, it gave me another error "ERROR: need csd with --cwsig" will appreciate for help thanks pratap ----------------------------------- FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.1-20070927 RedHat release: CentOS release 4.4 (Final) Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64 NMR Center info (/space/freesurfer exists): machine: galen SUBJECTS_DIR: /autofs/space/galen_003/users/carl/Tutorial/buckner_data/FsFastTutorialData/FSFTUTDIR/subjects PWD: /space/galen/3/users/carl/Tutorial/buckner_data/FsFastTutorialData/FSFTUTDIR/fb1-preproc-study/group-analysis-tut/sm-gamma-fwhm5/odd-v-0

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4.1.0 on Ubuntu 8.04
by hashiryu 17 Dec '08

17 Dec '08

Dear all, I have installed the version 4.1.0 (centos x86_64) on Ubuntu 8.04 and tried the test commands for tkmedit and tksurfer as in "Testing your FreeSurfer installation. However, the graphics "flashed" when I typed the command and then disappeared. There was no error message on the terminal. The graphics showed up very briefly when I cricked on some places on the screen where the graphics flashed before. I also tried the centos4 32 bit version and the red hat 9 version, but ended up with the same problem. Is anyone having the similar problem? Thank you, Ryu Hashimoto

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design matrix : inter-run effetcs
by Andersson Frederic 02 Dec '08

02 Dec '08

Hi, Computing individual fMRI analysis (several runs) and looking at the design matrix (X.mat), I saw that only one regressor represents each condition. I was expecting that the number of regressors concerning a condition would be the number of runs (as SPM). There are "inter-run effect" regressors but is this better if I affect a different value for each of run and each condition (see examples below). Other question concerning design matrix : only 3 movement parameters included in the design matrix. Why 3 rather than the 6 computed during movement correction? Concerning inter-run effects and movement parameters, is there any advantage of reducing the number of regressors but having a less ideal model? >>> 1 condition = 1regressor 0 = rest 1=conditionA 2=conditionB Pardagim files : RUN#1 RUN#2 RUN#3 0 0 0 0 0 0 3 0 3 0 3 0 6 0 6 0 6 0 9 0 9 0 9 0 12 0 12 0 12 0 15 1 15 1 15 1 18 1 18 1 18 1 21 1 21 1 21 1 24 1 24 1 24 1 27 1 27 1 27 1 30 0 30 0 30 0 33 0 33 0 33 0 36 0 36 0 36 0 39 0 39 0 39 0 42 2 42 2 42 2 45 2 45 2 45 2 48 2 48 2 48 2 51 2 51 2 51 2 54 2 54 2 54 2 57 0 57 0 57 0 >>> 1 condition = 1regressor / run 0=rest 1=conditionA run#1 2=conditionB run#1 3=conditionA run#2 4=conditionB run#2 5=conditionA run#3 6=conditionB run#3 Pardagim files : RUN#1 RUN#2 RUN#3 0 0 0 0 0 0 3 0 3 0 3 0 6 0 6 0 6 0 9 0 9 0 9 0 12 0 12 0 12 0 15 1 15 3 15 5 18 1 18 3 18 5 21 1 21 3 21 5 24 1 24 3 24 5 27 1 27 3 27 5 30 0 30 0 30 0 33 0 33 0 33 0 36 0 36 0 36 0 39 0 39 0 39 0 42 2 42 4 42 6 45 2 45 4 45 6 48 2 48 4 48 6 51 2 51 4 51 6 54 2 54 4 54 6 57 0 57 0 57 0 Frédéric ANDERSSON.

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6 direction mgh gradient sequence
by Victoria Williams 12 Nov '08

12 Nov '08

Hello, Can anyone point me to where I could find a mgh gradient file for dti processing with 6 directions? I am trying to rerun some old data through dt_recon and the gradient_mgh_dti sequence packs start at 13. Any suggestions? Thanks, Tori

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Re: [Freesurfer] volumes in wmparc.stats vs. aparc.stats
by Kathy Zhang 11 Nov '08

11 Nov '08

Hello, I've recently started a project that involves measuring the volume of the hippocampus and other subcortical structures, so I was also wondering whether aseg.stats was more accurate or wmparc.stats. So far the difference between them appears to be approximately a hundred voxels for each right/left hippocampus. Thank you, Kathy Zhang '09 On Wed, Oct 8, 2008 at 12:08 PM, Nurunisa Neyzi <nneyzi(a)gmail.com> wrote: Hi, for subcortical segmentations, is it then better to use the volumes in wmparc.stats than those in aseg.stats? On Tue, Jul 22, 2008 at 2:54 PM, Doug Greve <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Actually, the construction of aparc+aseg and wmparc do use info about where > the surface is to refine the aseg cortical boundaries. This information is > stored in ribbon.mgz (and it overrides the aseg definition). At some point, > we will use the surfaces to directly refine the aseg boundaries. > > doug > > > > > Michael Harms wrote: > > Hi Chris, > Doug, please correct me if I'm wrong, but the original gm/wm > segmentation contained in aseg.mgz is based on the 3D volume-based > tissue segmentation. This original segmentation then forms the basis > for all subsequent additional segmentations of either GM or WM in the 3D > volume. That is, aparc+aseg.mgz and wmparc.mgz make "use" of the > surface based parcellation, but only to decide the most appropriate > label to assign to GM/WM as defined in the already existing volume-based > segmentation that is contained in aseg.mgz. > > Thus, since the GM/WM in aparc+aseg.mgz and wmparc.mgz is still based on > the 3D volume segmentation, there is no apriori reason that their > spatial extent will correspond precisely to the more accurate gray and > white mattes surfaces that come out of the surface-based processing > stream. (Although certainly we would hope that the discrepancies don't > become too large). > > cheers, > Mike H. > > On Thu, 2008-07-17 at 12:00 -0500, bell0368(a)umn.edu <mailto:bell0368@umn.edu> wrote: > > > I have sent two images created with the following commands. > > tkmedit $subjid brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white > -segmentation (aparc+aseg.mgz and wmparc.mgz) > $FREESURFER_HOME/FreesurferColorLUT.txt > > The wm segmenations go through the "main surface" and the "orig surface" > into the gray matter, for example in the rh-supramarginal and > rh-postcentral. From your last response I am unsure as to which pipeline > creates the wm parcellations, the volume-based pipeline (.i.e aseg.mgz) or > the surface-based pipeline (i.e. ribbon.mgz) or some combination of the > two. It seems to me that the gm/wm parcellations are created using the > surface pipeline and then transferred to the closest class-matched voxels > from Left-Cerebral-Cortex and Left-Cerebral-White-Matter aseg > segmentations. I guess the question is how are we getting from the surface > parcellations back to volume space; is there a binary? > In a related vein, the value from aseg.stats "surface-based-volume mm3 > lh-cerebral-white-matter" seems to be created with mri_segstats or is it > from mris_wm_volume? Thanks for all your help! > > Chris Bell > > > > > > On Jul 17 2008, Doug Greve wrote: > > > > When the volume is created, a decision has to be made at each voxel as > to what to classify it as. This is used when the aseg.mgz and > ribbon.mgz are created. aparc+aseg.mgz inherit these decisions from > these files. When using mri_segstats with --pv, it will take the > volume of a 1mm3 voxel and divide it up so that it can contribute to > more than one region. But there's not a way to put the partial volume > information into the segmentation itself. Not sure why that do not > appear alingned, but we've been recently looking into this for other > reasons. Can you send a pic.? > > doug > > > > On Wed, 16 Jul 2008, bell0368(a)umn.edu <mailto:bell0368@umn.edu> wrote: > > > > I was wondering how the calculations of the wm volume were performed as > well. The six values below are volume values from aseg I believe. I > assume mris_wm_volume does more than sub-divide these regions into the > wm parcellations, but probably also includes partial volume estimations > along the wm/gm surface, is this correct? I basically have the same > question for the gm volume values in aparc.stats; do they include > partial volume calculations from the gm/pial and gm/white borders? Which > binary is used to create these values for gm in aparc.stats... is it > mri_segstats (with --pv)? I was assuming it would be an mris (surface) > calculation as well. I am asking because if you use tkmedit to view the > ?h.surface files and load the aparc+aseg or wmparc segmentation volumes > in also, the surfaces and the segmentations don't seem to line up. Is > there a way to create a segmentation volume that includes > partial-volumed voxels at the gray/white and gray/pial boundries? Thanks > for your help. > > Chris Bell > > > > > the interior voxels are only included in the volume if they are one of > the following in the aseg.mgz: > > case Left_Cerebral_Cortex: > case Right_Cerebral_Cortex: > case Left_Cerebral_White_Matter: > case Right_Cerebral_White_Matter: > case Left_WM_hypointensities: > case Right_WM_hypointensities: > > cheers, > Bruce > > > > On Tue, 15 Jul 2008, Marin Richardson wrote: > > OK, so aparc.stats is better for cortical gray matter. I want to look > at the > parcellated white matter volumes as well - is the only/best option to > use the > wm volumes from wmparc.stats? > > Also, when using mris_wm_volume to calculate total white matter, I > saw the > result defined as the volume within the white matter surface minus > non-WM > structures? Can you tell me which regions are and are not included? > > Marin > > > > > Doug Greve <[EMAIL PROTECTED]> 7/15/2008 12:02 PM >>> > > It is better to use the aparc as it is derived from surface > measurements, which have sub-voxel resolution. The wmparc.stats are > generated by counting 1mm^3 voxels. > > doug > > Marin Richardson wrote: > > > Hi all, > > I noticed that the gray volumes for parcellated cortical regions > in > wmparc.stats are different from those for the same region in > aparc.stats (e.g. > ctx-lh-middletemporal = 8419 in wmparc.stats, middletemporal = > 9466 in > lh.aparc.stats). Why are the values different and which one is a > better > measure to use? > > Thanks, > Marin > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > > > > _______________________________________________ Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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> > 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> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>

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Extraction mean curvature values
by Carl Schultz 02 Nov '08

02 Nov '08

Dear all, I compared the mean curvature between two groups using the mri_glmfit command and the Monte carlo simulation. Is there a possibility to extract the smoothed average curvature values of the significant clusters for all subjects? Thank you in advance Best regards Christoph Schultz University of Jena Department of Psychiatry Germany ____________________ Universitätsklinikum Jena Körperschaft des öffentlichen Rechts und Teilkörperschaft der Friedrich-Schiller-Universität Jena Bachstraße 18, 07743 Jena Verwaltungsratsvorsitzender: Prof. Dr. Walter Bauer-Wabnegg; Medizinischer Vorstand: Prof. Dr. Klaus Höffken; Wissenschaftlicher Vorstand: Prof. Dr. Klaus Benndorf; Kaufmännischer Vorstand und Sprecher des Klinikumsvorstandes Rudolf Kruse Bankverbindung: Sparkasse Jena; BLZ: 830 530 30; Kto.: 221; Gerichtsstand Jena Steuernummer: 161/144/02978; USt.-IdNr. : DE 150545777

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Re: [Freesurfer] Group Thickness Maps/Looking at outputs from mri_preproc
by Bramen, Jennifer E. 29 Oct '08

29 Oct '08

When I look in the contrast folder, there is only one gamma.mgh image, but I have two groups. I am assuming this is the mean thickness, or the mean difference in thickness between groups. How do I get it to save out one file for each group? Where is there a good explanation of the output files from qdec? Thanks Jen On Oct 28, 2008, at 4:30 PM, Doug Greve wrote: If you go into the qdec output directory, you will find a contrast for each group (class). In the contrast directory, you will find a file called gamma.mgh. This will be the average thickness for the group. You can load it into tksurfer, something like: tksurfer fsaverage lh inflated -overlay gamma.mgh doug Bramen, Jennifer E. wrote: Dear Freesurfer List I want to look at the average thickness maps for each of my groups, not just the statistical maps displayed by qdec. I think I found a tool that can do this. I used mri_preproc and a list of subjects instead of a single subject, and now have the output. I do not know to view this output though (<group descriptor>_thickness_fsavg.mgh). Can someone explain what this output is and how I can use it? The other alternative is make_average_surface for each of my groups. Is that what I need to be doing? It takes a ong time to run, so I was hoping there was another way to go. Thank you Best regards, Jennifer Bramen, Ph.D. Postdoc David Geffen School of Medicine at UCLA Developmental Cognitive Neuroimaging 635 Charles Young Drive South Los Angeles, CA 90095-7332 Phone: (310)267-5116 Fax: (310)206-5518 Email: jbramen(a)mednet.ucla.edu Campus Mail Code 176919 IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. _______________________________________________ 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 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 Best regards, Jennifer Bramen, Ph.D. Postdoc David Geffen School of Medicine at UCLA Developmental Cognitive Neuroimaging 635 Charles Young Drive South Los Angeles, CA 90095-7332 Phone: (310)267-5116 Fax: (310)206-5518 Email: jbramen(a)mednet.ucla.edu Campus Mail Code 176919 IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

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Viewing atlas?
by Ryan Scotton 29 Oct '08

29 Oct '08

Hi Freesurfers, Some associates of mine are working on a pipeline that generates cortical parcellations and we are looking to compare its measurements to some measurements generated by the freesurfer pipeline. However, our pipeline parcellates broader regions which include several labels generated by the FS cortical parcellation process within each of our labels. What we need is to get a general idea of where every label generated by FS fits within the context of our broader labeling scheme. SO, this may be an obvious question, but how might i be able to view an atlas image volume with the FS parcellation/labeling scheme applied to it in order to get a general idea of how the separate labeling schemes match up? Thanks! Ryan

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Group Thickness Maps/Looking at outputs from mri_preproc
by Bramen, Jennifer E. 28 Oct '08

28 Oct '08

Dear Freesurfer List I want to look at the average thickness maps for each of my groups, not just the statistical maps displayed by qdec. I think I found a tool that can do this. I used mri_preproc and a list of subjects instead of a single subject, and now have the output. I do not know to view this output though (<group descriptor>_thickness_fsavg.mgh). Can someone explain what this output is and how I can use it? The other alternative is make_average_surface for each of my groups. Is that what I need to be doing? It takes a ong time to run, so I was hoping there was another way to go. Thank you Best regards, Jennifer Bramen, Ph.D. Postdoc David Geffen School of Medicine at UCLA Developmental Cognitive Neuroimaging 635 Charles Young Drive South Los Angeles, CA 90095-7332 Phone: (310)267-5116 Fax: (310)206-5518 Email: jbramen(a)mednet.ucla.edu Campus Mail Code 176919 IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

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Freesurfer October 2008