Freesurfer

freesurfer@nmr.mgh.harvard.edu

2 participants
30134 discussions

interpretation of a 3-way interaction
by Yang, Daniel 21 Feb '14

21 Feb '14

Dear FreeSurfers, I have two discrete and binary factors (Dx: patients vs. controls; Sex: female vs. male), one continuous variable (Age), one nuisance factor (IQ). If there is a 3-way interaction of Dx x Sex x Age, regressing out IQ, is the following interpretation correct? Red/yellow: In females (vs. males), the Age effect of cortical thickening is stronger in patients (vs. controls). Blue/cyan: In females (vs. males), the Age effect of cortical thinning is stronger in patients (vs. controls). Note. by stronger, I mean greater magnitude without sign. Thanks, Daniel

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continusous x continuous interaction?
by Yang, Daniel 21 Feb '14

21 Feb '14

Dear FreeSurfer Experts, In the example here: http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V, it describes the testing of the main effects of two continuous variables. In order to test the interaction effect, I think we can form an interaction term like age x weight as the third covariate, that is, Regressor1: All ones. Codes intercept/mean for Main Regressor2: age for each subject. Codes age slope for Main Regressor3: weight for each subject. Codes weight slope for Main Regressor4: age x weight for each subject. Codes age x weight interaction effect and then specify a contrast [0 0 0 1]? Is that the way to go? Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.yang(a)yale.edu

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Segmentation process
by Saurabh Thakur 21 Feb '14

21 Feb '14

Hi Freesurfer expert, Thanks for all your help, I have explored the tkmedit ,tksurfer and freeview. How to move ahead with segmentation task. I looking forward to create my own .aseg file for sub cortical region. Is it possible...? And if possible,please share major breakpoint of the process. Thanks in advance. cheers Saurabh Thakur,

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viewing corrected result error
by charujing123 20 Feb '14

20 Feb '14

Hi all, I try to see the cluster wised result by typing "freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=./Diff-CON-IA-Intercept-thickness/mc-z.neg.sig.cluster.mgh:overlay_threshold=2,5:annot=./Diff-CON-IA-Intercept-thickness/mc-z.neg.sig.ocn.annot",but it feedback some error infomation as below: Did not find any volume geometry information in the surface ԥhreading colortable from annotation file... colortable with 1 entries read (originally none) colortable with 1 entries read (originally none) Thanks. All the best 2014-02-20 charujing123

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questions of clusters defined and sign of the threshold in simulation
by charujing123 20 Feb '14

20 Feb '14

Hi FS experts and users, May I ask some questions about clusterwise correction for multiple comparisons? 1,In mri_glmfit-sim command, there is a --sim(--sim nulltype nsim threshold csdbase) option. Choose the voxel/vertex-wise threshhold used to define clusters. This will be -log10(p), where p is the p-value. Eg, to use all voxels/vertices with p < .01, then set the threshhold = 2.I want to know what is meaning of "using all voxels with p < 0.01". Does it mean that considering all voxels whose p value below 0.01 in every iterations. Then it generates some clusters in every iteration. Is it right? 2,Also there is a --sim-sign option in this command. I want to know meaning of the sign: abs,pos,neg.Does it represent one- and two-tailed tests? Thanks. All the best. Rujing Zha 2014-02-20 charujing123

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mris_convert
by Karen Marie Sandø Ambrosen 20 Feb '14

20 Feb '14

Hi Freesurfer experts, I am trying to run tracktography from freesurfer labels using probtrackx2 in fsl. To convert the labels to surfaces I use the label2surf command as recommended on the fslwiki. To use the label2surf command I need to convert the surface, e.g. lh.white into a fsl-compatible format using mris_convert: mris_convert lh.white lh.white.gii When I load lh.white and the created lh.white.gii into freeview the two are not aligned. Aren't they suppose to be similar when lh.white.gii is use in the label2surf command? Do I need additional arguments in the mris_convert command? Best, Karen

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Fwd: recon-all trouble
by will brown 20 Feb '14

20 Feb '14

Hi all, I'm having a recon-all error that I haven't encountered before with one particular run of scans. I'm a bit too much of a newby to be able to see which stage the error is occurring so any help would be appreciated. I have attached error log. Thanks, Will

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Topological defect
by Ray, Siddharth 20 Feb '14

20 Feb '14

Hi all, I am having an topological defect error while running few of subjects. I have gone through the freesurfer correcting topological defects wikipage. But I was trying understand the log file. For an example, I got the following error for one subject: Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 13 iterations marking ambiguous vertices... 70557 ambiguous faces found in tessellation segmenting defects... 78 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 19 into 0 -merging segment 22 into 0 -merging segment 68 into 49 -merging segment 61 into 55 74 defects to be corrected 0 vertices coincident reading input surface /work/02510/sray2/Free_Sub/DATA/50011/50011/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.4264 (-4.2132) -vertex loglikelihood: -5.7733 (-2.8866) -normal dot loglikelihood: -3.6047 (-3.6047) -quad curv loglikelihood: -6.1117 (-3.0559) Total Loglikelihood : -23.9161 CORRECTING DEFECT 0 (vertices=27967, convex hull=5893) Segmentation fault mris_euler_number ../surf/lh.orig mris_fix_topology failed! (euler number != 2) Trying mris_topo_fixer... cp ../surf/lh.orig.nofix ../surf/lh.orig euler # = v-e+f = 2g-2: 116732 - 351516 + 234344 = -440 --> 221 holes F =2V-4: 234344 != 233464-4 (-884) 2E=3F: 703032 = 703032 (0) total defect index = 442 cp ../surf/lh.qsphere.nofix ../surf/lh.qsphere cp ../surf/lh.smoothwm.nofix ../surf/lh.smoothwm /work/02510/sray2/Free_Sub/DATA/50011/50011/scripts mris_topo_fixer -mgz -warnings -seed 1234 50011 lh verbose mode on (medium mode): printing warnings setting seed for random number genererator to 1234 Before topology correction, eno=-440 (nv=116732, nf=234344, ne=351516, g=221) Surface Diagnostics: eno=-440 (nv=116732, nf=234344, ne=351516) # of border vertices [ #v ~ #f ] 0 # of edges with single face 0 # of edges with more than 2 faces 0 # of corner configurations 0 The original surface is a valid manifold Counting the number of connected components The original surface has one component The original surface does not self-intersect The surface has 221 loops (X=-440) Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations identify defects... marking ambiguous vertices... 68425 ambiguous faces found in tessellation segmenting defects... analyzing defects for overlaps... INFO: assuming .mgz format reading input surface /work/02510/sray2/Free_Sub/DATA/50011/50011/surf/lh.orig... reading brain volume from brain... reading wm segmentation from wm... Detecting contrast direction: right direction [ GM (86.66) < WM (96.03) ] Computing Initial Surface Statistics -face loglikelihood: -5.8578 (-2.9289) -vertex loglikelihood: -5.7524 (-2.8762) -normal dot loglikelihood: -3.6033 (-3.6033) -quad curv loglikelihood: -5.8101 (-2.9050) Total Loglikelihood : -21.0236 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX Correcting Topology of defect 1 with euler number -257 (129 loops) computing statistics for defect 1: 33364 vertices location: [ (156,125,84) - average intensity = 92.126 ] -gray ( 86.57 , 6.29 ) -white ( 95.91 , 6.08 ) -gray ( 89.98 , 24.95 ) -white ( 98.58 , 24.03 ) -intensity (86.574921 [log = -2.404119 ]- 95.914825 [log = -2.517448 ]) -curv (k1=-0.162 (0.730) , r1 = 6.179 | k2=-0.060 (0.191), r2 = 16.806 ) -curv (k1=-0.124 (0.768) , r1 = 8.076 | k2=-0.032 (0.282), r2 = 31.306 ) MRISalloc(8654176, 520): could not allocate vertices Cannot allocate memory And In some of my subjects the log file stop writing after: "CORRECTING DEFECT 0 (vertices=53786, convex hull=13985)" My question is what exactly these highlighted number means? Do I have an estimation of number of slices that are to be treated manually? Thanks, -Siddharth

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Re: [Freesurfer] Dilated PV spaces
by Douglas N Greve 20 Feb '14

20 Feb '14

It is not the dicom file but the rawavg.mgz that is the immediate problem. As for the subject you sent, it is hard to say what is going wrong. It looks like there might be a lot of WM pathology. Is that right? That might be difficult for our intensity normalization. You can try placing control points in voxels that you are sure are WM (and not equal to 110 on the T1.mgz) doug On 02/20/2014 01:06 PM, Victor Kovac wrote: > Hi Doug, > > I will would double-check the dcm files and re-run recon-all on that scan. > > Attached are an image of the segmentation and the recon-all.log file > from another timepoint of this subject. As you can see, a great deal > of cortical gray and white matter is missed. > > Thank you for your help! > Victor > > > On Wed, Feb 19, 2014 at 4:26 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > It looks like that file is corrupted. Is this disk full? > > > On 02/19/2014 05:21 PM, Victor Kovac wrote: > > Hi Doug. > > This is the output: > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from > /lustre/kovacv/FS/post_analysis/MPS2005-2/mri/rawavg.mgz... > mghRead(/lustre/kovacv/FS/post_analysis/MPS2005-2/mri/rawavg.mgz): > could not read 131072 bytes at slice 150 > > I was wondering if it might be that the dicom file > corresponding to slice 150 was corrupted, so I checked slice > 150 in the sagittal plane, but I see no error. > > Please advise. > > Thanks! > Victor > > > On Wed, Feb 19, 2014 at 3:48 PM, 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>>> wrote: > > The log file you sent shows recon-all failing at a very early > point before the issue with the PV spaces could become a > problem. > It appears to fail at this command-line. > > mri_convert > /lustre/kovacv/FS/post_analysis/MPS2005-2/mri/rawavg.mgz > /lustre/kovacv/FS/post_analysis/MPS2005-2/mri/orig.mgz > --conform > > Can you run this and post the terminal output to the list > > > > On 02/19/2014 12:08 PM, Victor Kovac wrote: > > Hello FreeSurfer experts, > > > > I have four scans from a subject who has ubiquitous, dilated > > perivascular spaces (image attached) that seem to be > preventing > > recon-all from finishing. I have attached the > recon-all.log from one > > of the scans. > > > > Any advice on what I could try to get these scans > analyzed would be > > greatly appreciated. > > > > Thank you! > > Victor > > > > > > _______________________________________________ > > 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>> > > > 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@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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>> > > 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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > -- 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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Error in qdec: load data file
by Miranka Wirth 20 Feb '14

20 Feb '14

Hi FreeSurfers, I have trouble loading the .dat file into qdec, receiving the following error message: Verifying subject data.sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject 'DEM001.freesurfer' in > SUBJECTS_DIR My SUBJECTS_DIR is set correctly and the particular subject exists in this directory. Also, loading one subject works (even though the error message appears) Loading two subjects, is not working. I am thankful for any information what I could check. I have also read earlier comments in the mailing list but could not solve the problem. Cheers Miranka

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