Freesurfer

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30088 discussions

Hippocampal subfields script.
by Alan Francis 03 Feb '14

03 Feb '14

Hi Eugenio: I have HSF data on 60 Asperger brains. Is there a script that will allow me to extract the volumes into a single location? thanks so much, Alan Francis Martinos Center

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Cortical parcellation: what are the black spots?
by Qingyang Li 03 Feb '14

03 Feb '14

Dear Freesurfer experts, I was looking at the results of my data when I found that there were some black spots in my parcellation results (Please see the attached screenshot, the black spots were indicated by arrows). I did not see any hole or other errors in the surfaces generated for this subject. I hope you can help me with why the black spots were there? is it a big deal or something that I can ignore? If they need to be fixed, what should I do? Thanks! I am sorry if this question has been posted here. I really tried to find the answer by myself but I did not find anything. Thanks, Yang ------ Qingyang Li Balance and focus.

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Fwd: Difficulties with including hypo-intense areas (MS-lesions) as white matter without additionally transforming the lesion into "normal white matter".
by Linn Christin Bonaventure Norbom 03 Feb '14

03 Feb '14

---------- Forwarded message ---------- From: Linn Christin Bonaventure Norbom <linnnorbom(a)gmail.com> Date: Mon, Feb 3, 2014 at 5:44 PM Subject: Re: [Freesurfer] Difficulties with including hypo-intense areas (MS-lesions) as white matter without additionally transforming the lesion into "normal white matter". To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Hi again, Sorry for being unclear. Here is a picture of the lesion. If I understand correctly it is now NOT included as white matter. All I want to do is include it as white matter, so that it will be registered as a hypo-intense area in aseg.stats. So the way to do this is to edit the aseg.mgz and not the wm.mgz? Cheers Linn Norbom On Mon, Feb 3, 2014 at 5:30 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Linn > I'm not sure I understand, but if you can paste them into the aseg.mgz as > hypointensities I think things should work properly > > cheers > Bruce > > On Mon, 3 Feb 2014, Linn Christin Bonaventure Norbom wrote: > > Hi, >> >> I would like to include unregistered hypo-intense lesions into white >> matter >> (as now they are excluded from cortex, and not registered as anything) >> without transforming the lesion from hypo-intense to normal (110). Is it >> possible to include these areas in white matter and additionally keep the >> statistic volume of these areas as hypo-intense-wm in the aseg.stats? >> >> >> Thank you in advance, >> Regards Linn Norbom >> >> >> > > 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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Difficulties with including hypo-intense areas (MS-lesions) as white matter without additionally transforming the lesion into "normal white matter".
by Linn Christin Bonaventure Norbom 03 Feb '14

03 Feb '14

Hi, I would like to include unregistered hypo-intense lesions into white matter (as now they are excluded from cortex, and not registered as anything) without transforming the lesion from hypo-intense to normal (110). Is it possible to include these areas in white matter and additionally keep the statistic volume of these areas as hypo-intense-wm in the aseg.stats? Thank you in advance, Regards Linn Norbom

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Destrieux Atlas with Kid brains
by Mher Alaverdyan 03 Feb '14

03 Feb '14

Hi all, I just wanted to know if it is acceptable to use the Destrieux atlas in FS for parcellation of brain images of pre-adolescents. If not this atlas, then which would be a recommended atlas to use for this population. Thanks

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calculating spc on lobes annotation in longitudinal structural analysis
by Jeremy Young 03 Feb '14

03 Feb '14

Dear all, I'm trying to get thickness spc stats for the individual lobe labels (specifically the frontal lobe) I created per subject per time point (in subject's longitudinal analysis template space) using: mri_annotation2label --subject $i --hemi ?h --lobesStrict ?h.lobes I've run mris_anatomical_stats to get out the stats and put them in each subject and time point's stats folder: mris_anatomical_stats -a lobes.annot -f $i/stats/lh.lobes.stats $i ?h Now I'm trying to calculate the spc using: long_stats_slopes --qdec long.qdec.table.dat --stats lh.lobes --meas thickness --do-spc --time years --out-spc lh.spc.lobes.txt but I'm getting an error (it works when I use the regular aparc and aseg stats files though). Here's my output: --- Parsing the qdec table: long.qdec.table.dat Working in SUBJECTS_DIR: /home/j/jy/jy72/scratch/AE/FSstruct/ Subject-Template: CISC4962plate INFO: 2 TPs in CISC4962plate , mean age: 0.565 aparcstats2table --common-parcs --hemi lh --parc lobes --subjects CISC4962.long.CISC4962plate CISC4962-2.long.CISC4962plate --meas thickness --tablefile ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat -d space SUBJECTS_DIR : /home/j/jy/jy72/scratch/AE/FSstruct/ Parsing the .stats files Building the table.. Writing the table to ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat Writing ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat ... mri_glmfit --table ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat --X ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat --allow-zero-dof --no-contrasts-ok --glmdir ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /mnt/lustre/scratch/jeremy/AE/FSstruct/qdec cmdline mri_glmfit --table ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat --X ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat --allow-zero-dof --no-contrasts-ok --glmdir ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm sysname Linux hostname apollo-login machine x86_64 user jy72 FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /mnt/lustre/scratch/jeremy/AE/FSstruct/qdec/tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat logyflag 0 X ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat usedti 0 glmdir ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm Loading y from /mnt/lustre/scratch/jeremy/AE/FSstruct/qdec/tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat Found 6 data colums Found 2 data rows Saving design matrix to ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/Xg.dat Normalized matrix condition is 1 Matrix condition is 1.76991 search space = 6.000000 DOF = 0 Starting fit and test Fit completed in 0 minutes Writing results lh.lobes.thickness lh_frontal_thickness lh_cingulate_thickness lh_occipital_thickness lh_temporal_thickness lh_parietal_thickness lh_insula_thickness mri_glmfit done mri_convert --frame 0 ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh mri_convert --frame 0 ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) keeping frame 0 writing to ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh... mri_convert --frame 1 ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh mri_convert --frame 1 ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) keeping frame 1 writing to ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh... mris_calc -o ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-spc.dat.mgh ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh div ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh ERROR: mris_calc compute sym. pct. change (spc) problem? --- Am I missing a step somewhere when trying to do this? Please help. Thanks! Jeremy -- Jeremy Young PhD Researcher Behavioural and Clinical Neuroscience School of Psychology University of Sussex Brighton BN1 9QH 01273 872776 J.Young(a)sussex.ac.uk

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tkmedit.bin: Command not found
by Saurabh Thakur 03 Feb '14

03 Feb '14

Hello, I have just installed freesurfer in my linux ubuntu12.04 machine. I am getting error such as : *tkmedit.bin: Command not found* but the recon-all --help is working perfectly. My environment variable is working. Please help me where i m going wrong asap. Saurabh T.

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A question regarding DODS or DOSS
by KimMJ 02 Feb '14

02 Feb '14

Dear Doug and experts My question is about the choice of DODS or DOSS.I want to compare cortical thickness between 2 groups (disease group and control group), while controlling for the effect of age (nuisance covariate).I've already read through the mailing list about the issue of DODS and DOSS designs. If I understand correctly, I have to first use DODS (QDEC) in order to find areas of significant group*age interaction by using the contrast (0 0 1 -1).Given there is no area of interaction that survived multiple comparisons correction, I can go with DOSS (1 -1 0) using mri_glmfit (command line) to test between-group differences in cortical thickness, controlling for the effect of age. Am I right? My another question is that 'MUST' I rerun DOSS model after confirming no group*age interaction in DODS ? Or can I directly use the results of DODS to look for between-group differences controlling for age (1 -1 0 0), since there is no group*age interaction ?Is there much difference in results between the above-mentioned two approaches?I've found a reply by Doug from the mailing list: If there is no interaction, then either DODS or DOSS is appropriate. DOSS will be more powerful and a little more interpretable (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg33418.html) From this context, what does the 'powerful' mean? Does DOSS yield higher statistical values than DODS? Apology for the beginner's questions.Thank you in advance for your help. MJ

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LGI ERROR: make_roi_paths did not complete successfully!
by Wanda Truong 31 Jan '14

31 Jan '14

Hello Marie, I am trying to conduct a local gyrification index analysis, however I am getting this error ERROR: make_roi_paths did not complete successfully! Which is the same as the one posted earlier by someone else: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032203.html I added the "patch": function [verticeslist]=SearchProjectionOnPial(mesh_total,mesh_outer,perim, step) % step is typically set between 5 and 10. Default is 7, increasing it will % limit redundancies in the resulting path file. verticeslist=[]; si=max(size(perim)); for t=1:step:si [nearestIndexMT,nearestValuesMT]=mesh_vertex_nearest(mesh_total.vertices,mesh_outer.vertices(perim(t),:)); verticeslist= [verticeslist nearestIndexMT]; end verticeslist=unique(verticeslist); to my $freesurfer_home/matlab directly as a .m file. However, I'm still getting the same error: Error in dsearchn (line 80) [d(i),t(i)] = min(sum((x-yi).^2,2)); Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(vertices,points); Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); >> ERROR: make_roi_paths did not complete successfully! Darwin Vinas-iMac.local 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 recon-all -s SFS026 exited with ERRORS at Thu Jan 30 14:26:16 MST 2014 Thanks, Wanda -- Wanda Truong, MSc

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ERROR: dimension mismatch between y and X.
by Wanda Truong 31 Jan '14

31 Jan '14

Hi everyone, I get this error when running surface area analysis in QDEC: Vinas-iMac:~/Documents/Wanda/Wanda_SFS] vinagoghari% mri_glmfit --y /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh --fsgd /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd dods --glmdir /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled --surf fsaverage lh --label /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label --C /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Avg-Intercept-area.mat --C /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Diff-Control-Relative-Intercept-area.mat gdfReadHeader: reading /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 40.6327 13.0176 1 IntraCranialVol 1.50352e+06 187456 Class Means of each Continuous Variable 1 GroupControl 38.8261 1480505.5707 2 GroupRelative 42.2308 1523881.3029 INFO: gd2mtx_method is dods Reading source surface /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /Users/vinagoghari/Documents/Wanda/Wanda_SFS cmdline mri_glmfit --y /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh --fsgd /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd dods --glmdir /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled --surf fsaverage lh --label /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label --C /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Avg-Intercept-area.mat --C /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Diff-Control-Relative-Intercept-area.mat sysname Darwin hostname Vinas-iMac.local machine x86_64 user vinagoghari FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh logyflag 0 usedti 0 FSGD /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd labelmask /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label maskinv 0 glmdir /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled Loading y from /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh INFO: gd2mtx_method is dods Saving design matrix to /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/Xg.dat Normalized matrix condition is 400.101 Matrix condition is 1e+08 Found 148151 points in label. Pruning voxels by thr: 0.000000 Found 148025 voxels in mask Saving mask to /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/mask.mgh Reshaping mriglm->mask... search space = 73649.347769 ERROR: dimension mismatch between y and X. y has 3528 inputs, X has 49 rows. My QDEC table has 49 subjects,2 groups, and 4 variables. Many thanks, Wanda -- Wanda Truong, MSc

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