Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

ROI label Error
by Barnali Basu 05 Mar '09

05 Mar '09

HI I have an ROI from BrainVoyager (text file, attached) which I am trying to load in Freesurfer. I have edited the text file according to Freesurfer label format, still it shows error as ERROR: cannot find or read t.roi.label the Freesurfer label file with first 100 voxel coordinates is also attached. Any help on how to load this label will be appreciated -- Barnali Basu

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Qdec Outputs - Looking For Statistical Maps To Overlay In SurfStat
by Jennifer Bramen 05 Mar '09

05 Mar '09

Dear Freesurfer List I am trying to use SurfStat to create figures based on my qdec results. However, I cannot figure out what outputs form qdec are what, or what their iunits are. I cannot find a description of qdec's outputs on the Freesurfer Wiki. 1) I want to find the statistic overlay for my contrast of interest. Qdec creates a folder for each possible test I could make based on the design. For exasmple, I would like to overlay the results from the folder lh-Avg-thickness-TESSF-Cor. I think I want to use the gamma.mgh file as my overlay. Is that the true? I have some questions about the units of the gamma.mgh files though. When I use SurfStat, it automatically scales this at -0.2 - 0.2. I assumed this was the Anti- Long P scale used by qdec, so I tried to rescale my display to match the colorscale I use to display results in qdec. However, when I tried to change the scale to -3 - > 3, I get nothing. In qdec, I do see effects using this exact scale( min 1.3, max 3, min -1.3, max -3). So This suggests to me that the gamma.mgh is not in the same units (not anti-log(-p)). What are the units? 2) I was told that qdec saves a mean thickness file. I was also told it was one of the gamma.mgh files. Qdec creates a folder for each hemisphere called, for example, lh-Avg-Intercept-thickness. I assumed this was the correct overlay, but it looked to be demeaned as it had both negative a positive values. Is it demeaned? Is there a file that qdec saves that is just thickness? Or is there a way to manipulate the files so that they are not demeaned? Thank you for your assistance Best regards, Jennifer Bramen, Ph.D. Assistant Research Neuroscientist 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

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partial volume correction in mri_segstats
by Anthony 04 Mar '09

04 Mar '09

Hi all, In recon-all pipeline , mri_segstats runs with -pv mri/norm.mgz option ,as written from http://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats , it is used to compensate partial voluming. I wonder what exactly does this do, as the volumes given by aseg.stats are different from aseg.mgz and why is it more accurate ? I will appreciate if anyone could help to clarify this . Thanks Get your new Email address! Grab the Email name you've always wanted before someone else does! http://mail.promotions.yahoo.com/newdomains/aa/

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performance: bert -autorecon1
by Stephen Towler 04 Mar '09

04 Mar '09

Hi all. Documentation estimates 30 minutes for -autorecon1 on the sample data provided with the most recent freesurfer release. Our 2008 iMac with 4GB of RAM takes about 90 minutes. Throughout the job CPU utilization was high but there was plenty of free RAM. Is 90 minutes common for similarly equipped leopard systems? Thanks, Stephen -- Stephen Towler Graduate Student, Neuropsychology Dept. Clinical and Health Psychology stowler(a)phhp.ufl.edu calendar: http://cli.gs/9nvvDL 352-273-8715 lab (Shands G078) 352-273-6015 lab (HPNP) 352-682-5231 mobile 352-273-6156 fax Price Lab PO Box 100165 101 S. Newell Drive University of Florida Gainesville, FL 32610

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qdec error in analyze
by Prapti Gautam 04 Mar '09

04 Mar '09

Dear all, I've come across a similar problem to the one described before in qdec, but cannot find a solution for it, I've previously visualised my data using qdec, but when I tried to run it again I get the following error. I've checked to make sure my subject is named correctly and I am in the correct subject directory. Any help will be great appreciated, gdfReadHeader: reading /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/qde c.fsgd ERROR: gdfRead: /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/qde c.fsgd is not formatted properly. The first string is 'q&@', should be 'GroupDescriptorFile' Error in Analyze: command failed: mri_glmfit --y /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/y.m gh --fsgd /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/qde c.fsgd --glmdir /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled --surf fsaverage lh --C /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/con trasts/Avg-Intercept.mat --C /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/con trasts/Avg-thickness-dig_back-Cor.mat --C /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/qdec/Untitled/con trasts/Avg-thickness-educ-Cor.mat Thanks, Prapti ---------- Message: 7 Date: Mon, 08 Dec 2008 11:43:28 -0500 From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] qdec message To: juliaaltenburg(a)yahoo.de Cc: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <1228754609.6864.17.camel(a)minerva.nmr.mgh.harvard.edu> Content-Type: text/plain Julia, Does it give any further details in the error message? It would be in the terminal output (the popup box would not have the full message). Do all of those files in the command line exist and are readable? You can also try copy-and-pasting that command directly to the terminal (outside of qdec) to see what error message it displays. Nick On Mon, 2008-12-08 at 10:57 +0000, Julia Altenburg wrote: > Hey all, > > I'm getting the following message while using qdec > > Error in Analyze: command failed: mri_glmfit --y /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/y.mgh --fsgd /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/qdec. fsgd dods --glmdir /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled --surf fsaverage lh --C /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr asts/lh-Avg-Intercept-thickness.mat --C /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr asts/lh-Avg-thickness-alter-Cor.mat --C /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr asts/lh-Diff-BPD-KG-Intercept-thickness.mat --C /Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/contr asts/lh-Diff-BPD-KG-Cor-thickness-alter.mat > > I've a qdec.table and a fsgd.file included in my subject folder. > Do I have to type a command to get the fsgd. file connected? > I'm not really sure what causes the error. While using an older freesurfer version on a different mac this (but some other) error doesn't show up. > > > FREESURFER_HOME: /Applications/freesurfer > > Build stamp: freesurfer-Darwin-tiger-i686-stable-pub-v4.1.0 > > Kernel info: Darwin 8.11.1 i386 > > > Thank you in advance > Cheers Julia > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ------------------------------ Message: 8 Date: Mon, 08 Dec 2008 12:51:32 -0500 From: Doug Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Statistic analysing for a mask To: Alexandru Hanganu <hanganu.alexandru(a)yahoo.de> Cc: FS Mailing List <Freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <493D5EA4.5050905(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Try adding --noreshape to both mri_vol2surf and mri_surf2surf cmd lines. doug Alexandru Hanganu wrote: > Dear Freesurfer users, > > We have an MNI mask and we want to apply this mask on a group of > subjects for small volume correction. > so we did the following steps: > > 1. cd $SUBJECTS_DIR/fsaverage/surf > fslregister --s fsaverage --mov /path/to/TT_avg152T1.nii --reg > TT_avg152T1_to_fsaverage.dat > > 2. cd $SUBJECTS_DIR/fsaverage/surf > mri_vol2surf --mov /path/to/ROI5.nii --reg > TT_avg152T1_to_fsaverage.dat --projdist-max 0 1 0.1 --interp nearest > --hemi lh --out lh.fsaverage.ROI5.mgh > > 3. cd $SUBJECTS_DIR/subjid/surf > mri_surf2surf --s subjid --trgsubject fsaverage --hemi lh --sval > lh.thickness --tval lh.thickness.fsaverage.mgh > . > . > . > Surf2Surf: Dividing by number of hits (163842) > INFO: nSrcLost = 0 > nTrg121 = 147410, nTrgMulti = 16432, MnTrgMultiHits = 2.25237 > nSrc121 = 86069, nSrcLost = 0, nSrcMulti = 42416, MnSrcMultiHits = > 2.31875 > Saving target data > > > > 4. Next step was just for verifying, but we received an error (maybe > it's not so important): > cd $SUBJECTS_DIR/subjid/surf > mri_segstats --seg $SUBJECTS_DIR/fsaverage/surf/lh.fsaverage.ROI5.mgh > --in lh.thickness.fsaverage.mgh --sum segstats-ROI5.txt > > Loading > /usr/local/freesurfer/subjects/fsaverage/surf/lh.fsaverage.ROI5.mgh > Loading lh.thickness.fsaverage.mgh > ERROR: dimension mismatch between input volume and seg > > We want to determine the statistics only for this mask for the whole > group of subjects (qdec, or mri_glmfit). > If the mapping of our subjects thickness data was good, what should we > do next in order to achieve our goal ? > > Thank you. > > Best regards, > Dr. Alexandru Hanganu > ___________________________________ > Department of Neurology, > Schleswig-Holstein University Hospital, Kiel Campus > Arnold-Heller-Str. 3, building no. 41 > D-24105 Kiel, Germany. > >----------------------------------------------------------------------- - > >_______________________________________________ >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

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wm edits
by Nasim Maleki 04 Mar '09

04 Mar '09

Dear Freesurfers, I have a question on manual white matter edits: I have cases where a considerable amount of gray matter is classified as white in my wm.mgz and therefore the original surface (green) is not accurate but then that is fixed in the next steps and the wm surface (yellow) is accurate in 90% of the areas but not accurate in other 10% . Now my questions are: 1-Will I get accurate results if I do the edits (erasing misclassified white matter in wm.mgz) to my white matter mask only in those 10% areas that the wm surface is not accurate or should I correct the wm.mgz 'every where' no matter what? 2- Will you necessarily get more accurate results by editing your wm.mgz where pixels are classified as white by mistake BUT your final white matter surface is accurate? 3-How much on average takes you to do the manual white matter edits for each of your subjects?! Thank you, Nasim

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Y axis values in time course in relation to percent signal change
by Dave Brohawn 04 Mar '09

04 Mar '09

Hello, I am not sure what y-axis values are in a time course plot. Here is my bugr information: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4-stable-v4.2.0d-20090227 RedHat release: CentOS release 5.2 (Final) Kernel info: Linux 2.6.18-92.el5 i686 NMR Center info (/space/freesurfer exists): machine: seymour SUBJECTS_DIR: /autofs/space/ventzl_016/users/ PWD: /autofs/space/ventzl_016/users I entered tksurfer fsaverage lh inflated When it came up, I loaded this time course data for a group of 8 subjects: /autofs/space/ventzl_016/users/CC-n8/newEMerror-tpx/lh.h.nii I then plugged in a vertex of interest (124608) and the time course plot came up. It is correct is showing the me the time course for 4 different contrasts included in this analysis, though I am not sure what the y-axis is. Its values are incremented by whole 1's (1 2 3). We are looking for percent signal change values. Can you tell me what these y-axis values are, and if there is a way to calculate percent signal change from them if I write these time course values to file? Thank you very much, Dave Brohawn

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Version differences
by Martin Ystad 03 Mar '09

03 Mar '09

Hello, I'm re-running some of my volumes previously processed through an older version of FreeSurfer (in 2004/2005 - version 3.01 I think). At the time they were processed through autorecon2 and 3, and problems that appeared were addressed by manual editing. However, when I re-process the volumes on version 4.2.0 in freesurfer, new segmentation errors appear, although I have kept my old manual edits from last time (see pictures). At the same time, we experience more than usual segmentation errors on new volumes that we process. Actually, many of these errors appeared after we updated from version 4.1 to 4.2. Is there any settings that I can tweak to make the segmentation algorithms behave more like they did before, or do I have to roll back to a previous version? Thanks Martin Ystad

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Problem while fixing the Surface Topology
by Pradeep Reddy Ramana 03 Mar '09

03 Mar '09

Hello FS Team, I had a question recently regarding an error encountered in the freesurfer recon-all. I believe error is the result of: mris_fix_topology -mgz -sphere qsphere.nofix -ga FirstOrderPoly lh CORRECTING DEFECT 3 (vertices=10731, convex hull=2557) normal vector of length zero at vertex 90051 with 0 faces vertex 90051 has 0 face No such file or directory recon-all exited with ERRORS I will appreciate very much if you can suggest a possible fix or a rerun with some set of flags etc. The partial log and a previous post by somebody else is here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg09492.html Thanks, Pradeep -- Pradeep Kumar Reddy. Raamana PhD Student - Biomedical Engg. Medical Image Analysis Lab, Simon Fraser University, Burnaby BC - V5A1S6 - Canada. Work : +1 778 782 5509 "What is written without effort is, in general, read without pleasure." - Samuel Johnson

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Configure Overlay Display for >2 Colors
by Jeff Sadino 02 Mar '09

02 Mar '09

Hello Surfers, I have an overlay file with values ranging from -4.63 (n=138477) to 1.34 (n=25365). I would like to display this data with more than the two colors of the Green/Red, Heat, Blue/Red, or complex Color Scales in the Configure Overlay dialog. So far, no luck, even with toying with the min, max, mid, and piecewise options every way I can think of. Is there some way to get a fuller color spectrum on my overlay? Thank you, Jeff Sadino _________________________________________________________________ Hotmail® is up to 70% faster. Now good news travels really fast. http://windowslive.com/online/hotmail?ocid=TXT_TAGLM_WL_HM_70faster_032009

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