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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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Recon-all error
by Emad Ahmadi 31 Jan '14

31 Jan '14

Hello, I am using recon-all, and it gives me error and exits and I cannot understand why. I would appreciate it if you give me a clue why it's not working. I've written a piece of script (recon.bash attached) to be copied to the subject's folder, and when run it should automatically go through the analysis pipeline, but it gives me the error and exits. Thank you very much, Emad Emad Ahmadi, MD ------------------------------------------------ Postdoc Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: emad(a)nmr.mgh.harvard.edu

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adding color scale to freeview
by Fred Lado 31 Jan '14

31 Jan '14

Dear Freesurfer Experts, Is there a way to create custom color scale - like “Heat”, “Jet”, etc - for use in Freeview? Thanks, Fred Lado Montefiore Medical Center

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mri_convert - Scaling of Values
by Daniel Carey 31 Jan '14

31 Jan '14

Dear All, We have been using mri_convert to convert .nii format quantitative scans (specifically R1 volumes) into .mgz (float) format, so they can be used as input to mri_vol2surf. Inputting the .nii files to mri_vol2surf has produced an error in values in the output paint file, whereas this issue appears not to occur with the .mgz input. In running mri_convert, we are encountering an issue with the scaling of image values. Optimally, we would like to preserve the values within the quantitative volume, such that mri_convert does not change these when we output to .mgz. In some cases, we have noted non-linear differences in the output .mgz values, compared to the input volume. We have been using the -ns flag, and still see these issues. Is there a way to set the output .mgz scale factor to preserve the existing values exactly as per the quantitative input volume? Any advice would be greatly appreciated. Many thanks in advance. Best wishes, Dan --- Daniel Carey Marie Curie Ph.D. Fellow, Centre for Brain and Cognitive Development, 32 Torrington Sq., London WC1E 7HX UK email: d.carey(a)bbk.ac.uk web: http://www.cbcd.bbk.ac.uk/people/students/daniel_carey

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bbregister and AFNI
by Ajay Kurani 31 Jan '14

31 Jan '14

Hi all, I used freesurfer to process my anatomical scans, followed by BBregister to align my resting state scan to the anatomical and finally afni to process the resting state fmri scans. After recon-all I used bbregister: *bbregister -s ${sub}_FS --mov ${sub}.RS.nii --reg $sub_RS_register.dat --init-header --bold --frame $LAST --nearest --template-out $sub.RS.template.nii* I used the following for manual adjustments (although none were needed!) *tkregister2 --mov $sub.RS.template.nii --reg $sub_RS_register.dat --surf* The plan is to apply the reg file to the entire resting state timeseries ($sub.RS.nii). My question is the following: 1) Does bbregister already move the last timepoint in $sub.RS.nii as well as $sub.RS.template.nii or does it just store the rigid transformation in the reg file (this is what I assume)? This is the reason I assume we supply reg into tkregister2 as I assume the transform is not applied to the nifti file header itself. 2) Assuming the transformations are not applied to the file itself, how would I go about doing this? I used the following based on previous posts: *mri_vol2vol --mov $sub.RS.nii --reg $sub_RS_register.dat --fstarg --interp nearest --o $sub.RS.align.nii --precision short --no-resample * I used no-resample as I do not want to put the data into orig space. The plan is to align all of my timepoints to the last time point (same as $sub.RS.template.nii). ----Is --fstarg the best option (default orig.mgz vs --fstarg rawavg.mgz)? ----Is the transform stored in the header of $sub.RS.align.nii and not in the $sub.RS.template.nii file or $sub.RS.nii? 3) Using @SUMA_Make_Spec_FS did not correctly convert brain.mgz and aseg.mgz correctly when overlaid with the original $sub.SPGR.FS.mgz as well as $sub.RS.align.nii or $sub.RS.nii so I just used the following instead /mri directory: *mri_convert -ot nii brain.mgz brain.nii* *mri_convert -ot nii aseg.mgz aseg.nii* *4) Following relates to viewing images created in AFNI correctly if anyone knows: * When I tried to use AFNI to view the original anatomical scan $sub.SPGR.FS.mgz and $sub.RS.align.nii it was not aligned (assume anatomical is similar to rawavg.mgz). When I load brain.nii and $sub.RS.align.nii into afni they are not overlapped perfectly as in tkregister2. Additionally I get an error about deobliquing the $sub.RS.align.nii file. Interestingly enough I do not get this error with the $sub.RS.template.nii so I am not sure if there is an error in applying the transform or if the template file has no transform info stored while the aligned file does. How would I apply the reg file to all timepoints without getting the oblique error or should I use the following command and is this correct: *3dWarp -deoblique -gridset $sub.RS.nii -prefix $sub.RS.align.deobl.nii $sub.RS.align.nii* Would i deoblique using the gridset of the original $sub.RS.nii, the aligned file $sub.RS.align.nii or just the template file (or does it not matter since the voxel dimensions are the same even though centers are different). Sorry for the long email but thanks in advance for any advice / explanations. Sincerely, Ajay

2 1

brainmask VS wm correction
by elisa veronese 31 Jan '14

31 Jan '14

Dear all, I am trying to manually correct the segmentation result in one subject. My problem is that I am not sure if in the area highlighted with the green circle (see attached file) the volume I should correct is the brainmask.mgz or the wm.mgz. The pial boundary looks uncorrect, so I'd correct the brainmask. But those voxels seem to belong to the wm.mgz volume, as well... Thank you. Best, Elisa -- Elisa Veronese - PhD *Research Unit on Brain Imaging and Neuropsychology (RUBIN)* *Inter-University Center for Behavioral Neurosciences (ICBN)University of Udine and University of Verona, ItalyICBN Website: http://icbn.uniud.it/tiki-index.php <http://icbn.uniud.it/tiki-index.php>*

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