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30097 discussions

Checking segmentations with aseg.mgz
by Reema Jayakar 18 Jul '16

18 Jul '16

Hello FS Listserv members, With regard to checking amygdala segmentation, is it appropriate to overlay the aseg.mgz file on the brainmask.mgz? Or should I be overlaying aseg.mgz on norm.mgz? I am aware of the general rule of thumb that editing the subcortical segmentations generally is not recommended. Also, where can I find documentation on the Freeview options "Resample to standard RAS space" and "Apply registration file". I am trying to understand whether or not it is necessary for me to use any of these options for what I am doing with the subcortical segmentations. Thanks in advance for your help! Reema -- *Reema Jayakar, M.A.* Doctoral Candidate - Clinical Neuropsychology Health Resources and Services Administration (HRSA) Fellow Department of Psychology Georgia State University Email: rjayakar1(a)student.gsu.edu

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FSGD error: class Input not defined
by Jarek Rokicki 18 Jul '16

18 Jul '16

Dear Freesurfer experts, I am trying to perform the resting state fMRI analysis as in: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkth… I got stuck with the STEP8, when I tried to use my own fsgd file. I tried to test for two group difference, no covariance as in: https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G0V But I am getting this error: mri_glmfit --y fc.lpccseed.surf.lh/L_PCC/ces.nii.gz --wls fc.lpccseed.surf.lh/L_PCC/cesvar.nii.gz --fsgd ../glm_file.fsgd --C ../group.diff.mtx --surface fsaverage lh --glmdir my-glm.wls --nii.gz gdfRead(): reading ../glm_file.fsgd Input line 1, subjid = HM-HR10-002Rest Group1, class Input not defined FSGDF Format Error: file = ../glm_file.fsgd, tag=Input I am testing the pipeline so just 8 subjects so far. I've checked the ces.nii.gz and cesvar.nii.gz and both of them have correct dimensions of 163842 x 1 x 1 x 8. Thank you for your help in advance. *fsdg_file is:* GroupDescriptorFile 1 Title OSGM Class Group1 Class Group2 Input HM-HR10-002Rest Group1 Input HM-HR10-005Rest Group1 Input HM-HR10-007Rest Group1 Input HM-HR10-010Rest Group1 Input PD0001Rest Group2 Input PD0002Rest Group2 Input PD0004Rest Group2 Input PD0005Rest Group2 *mtx file is:* 1 -1 宜しくお願い致します。 Sincerely, Jarek Rokicki, Ph.D. Integrative Brain Imaging Center (IBIC) National Center of Neurology and Psychiatry (NCNP) *4-1-1 Ogawahigashi-chyo, Kodaira, Tokyo 187-8551 Japan* TEL: +81-80-6628-5709 国立精神・神経医療研究センター脳病態統合イメージングセンター(IBIC) 臨床脳画像研究部画像情報解析研究室 *〒187-8551 東京都小平市小川東町4-1-1*

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FS-FAST "If: Expression Syntax" Error
by Hibert, Matthew Louis 18 Jul '16

18 Jul '16

Hi All, I'm running into an error analyzing some fMRI data with FS-FAST in Freesurfer version 5.3. The analysis runs fine until it gets to the register-sess part, which quits before actually starting to do any registration. The last line of the log file, attached, is "if: Expression syntax", but there are no other errors prior to that. The command I'm using, analysis, and contrasts have all worked on several other similar data sets. Has anyone encountered this problem before, or know what's causing it? Thanks, Matt Clinical Research Coordinator Stufflebeam Lab Athinoula A. Martinos Center Massachusetts General Hospital 149 13th Street, Room 1115S Charlestown, MA 02129

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Question about NULL event with Optseq2
by Feng Zhou 18 Jul '16

18 Jul '16

Dear experts, I'd like to use optseq2 to optimize the order of events as well as inter stimulus intervals. My experiment contains 3 runs and each run contains 3 events, say Cp, Cn and Pobe events Each stimulu will be presented 4, 4 and 1 sec and the numbers of times that each event type will be presented during the course of the run are 12 12 and 4 respectively, and interstimulus interval ranges from 8–12 sec. So each run would last around 380 sec. I used the following code: optseq2 --ntp 380 --tr 1 --psdwin 0 20 1 --ev Cp 4 12 --ev Cn 4 12 --ev Prob 1 3 --evc 1 -1 0 --tnullmin 8 --tnullmax 12 --nkeep 3 --o IAPS --nsearch 10000 However, the durations of some NULL events were more than 12 sec and the last NULL events were more than 30 sec. Did I use optseq2 in the right way? How could I fix it? Thanks in advance & Best regards, Feng Zhou

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Inquiries about thickness and lgi group analysis
by Mahtab Farahbakhsh 18 Jul '16

18 Jul '16

Dear FreeSurfer, I am doing group analysis for thickness and LGI values. I have just got the output and the output of both analyses (sig.mgh file view in Freeview) are exactly the same. Would you please guide me with this? Best Regards, Mahtab.

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mri_glmfit error
by Chatzi, Vasiliki 18 Jul '16

18 Jul '16

Dear Developers, I am trying to run the mri_glmfit command and I get two different errors for two different subjects. Please find details below. I would be really grateful if you could provide any advice. Error1 setenv SUBJECTS_DIR ./ mri_glmfit --glmdir ./ --y lh.10.lgi.mgh --fsgd fsgd_test2.txt --no-contrasts-ok --surf subject1 lh gdfReadHeader: reading fsgd_test2.txt INFO: gd2mtx_method is dods Reading source surface .//subject1/surf/lh.white Number of vertices 167703 Number of faces 335402 Total area 108706.031250 AvgVtxArea 0.648206 AvgVtxDist 0.881642 StdVtxDist 0.250483 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /home/test cmdline mri_glmfit --glmdir ./ --y lh.10.lgi.mgh --fsgd fsgd_test2.txt --no-contrasts-ok --surf subject1 lh sysname Linux hostname machine x86_64 user FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/test/lh.10.lgi.mgh logyflag 0 usedti 0 FSGD fsgd_test2.txt labelmask .//subject1ii/label/lh.cortex.label maskinv 0 glmdir ./ IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory ./ Loading y from /home/test/lh.10.lgi.mgh INFO: gd2mtx_method is dods Saving design matrix to .//Xg.dat Normalized matrix condition is 1 Matrix condition is 1 Found 158404 points in label. ERROR: mri_reshape: number of elements cannot change nv1 = 167703, nv1 = 163842 Pruning voxels by thr: 0.000000 Found 163842 voxels in mask Saving mask to .//mask.mgh Reshaping mriglm->mask... ERROR: mri_reshape: number of elements cannot change nv1 = 163842, nv1 = 167703 search space = 108705.102552 DOF = 0 ERROR: DOF = 0 Error 2 setenv SUBJECTS_DIR ./ mri_glmfit --glmdir ./ --y lh.10.lgi.mgh --fsgd fsgd_test2.txt --no-contrasts-ok --surf subject2 lh gdfReadHeader: reading fsgd_test2.txt INFO: gd2mtx_method is dods Reading source surface .//subject2/surf/lh.white Number of vertices 129318 Number of faces 258632 Total area 86174.742188 AvgVtxArea 0.666379 AvgVtxDist 0.893985 StdVtxDist 0.260921 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /home/test cmdline mri_glmfit --glmdir ./ --y lh.10.lgi.mgh --fsgd fsgd_test2.txt --no-contrasts-ok --surf subject2 lh sysname Linux hostname machine x86_64 user FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/test/lh.10.lgi.mgh logyflag 0 usedti 0 FSGD fsgd_test2.txt labelmask .//subject2/label/lh.cortex.label maskinv 0 glmdir ./ IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory ./ Loading y from /home/test/lh.10.lgi.mgh INFO: gd2mtx_method is dods Saving design matrix to .//Xg.dat Normalized matrix condition is 1 Matrix condition is 1 Found 121215 points in label. ERROR: mri_reshape: number of elements cannot change nv1 = 129318, nv1 = 163842 Pruning voxels by thr: 0.000000 Segmentation fault Bets wishes, Vasiliki

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Comparing between a group of subject
by Aman Montazeri 18 Jul '16

18 Jul '16

Hi Freesurferes, Sorry for my simple and rookie question, I'm a new user and couldn't find my answer after a bit googling. I have a group of subjects and want to compare their thickness with a baseline (average of my subjects). I thought to use the mri_avarage to make the baseline (Average of all of my subjects), but don't know how to compare them with the baseline after making the baseline. Any help would be highly appreciated Thanks, Aman Ps. I have looked into GLM and longitudinal processing tutorials; GLM doesn't work for me as I don't have any variable to regress against; longitudinal processing is also for comparing different time shots of the same subject (my case are 40 different subjects).

2 1

BrainSegVolNotVent
by Eryilmaz, H. Hamdi 18 Jul '16

18 Jul '16

Hello Doug and Freesurfers, I am trying to compute a structural measure called 'BrainSegVolNotVent' as an approximate value of total brain volume. 'BrainSegVolNotVent' is now present in aseg.stats files but the dataset I'm working on was preprocessed using FS 5.0, which did not produce this variable. Per your advice I found in a previous email, I reran mri_segstats adding the flags --brainmask mri/brainmask.mgz --brain-vol-from-seg. The new aseg.stats file contains the following lines that were added after running this command: # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1667093, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1667093.000000, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 232145.000000, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1410666, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1410666.000000, mm^3 The numbers look a bit odd. BrainSegVol and BrainSegVolNotVent should normally be close to each other, right? Also unitless values such as BrainSegNVox and BrainMaskNVox seem to be equal to their corresponding volumetric values. Do you have any idea what might have gone wrong? Here's the command I ran: mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /usr/local/freesurfer/stable5_0_0/ASegStatsLUT.txt --subject SUBJECT_ID --brainmask mri/brainmask.mgz --brain-vol-from-seg Thanks very much for your help! Best, Hamdi

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mri_glmfit error: Matrix is ill-conditioned or badly scaled
by Jennifer Legault 18 Jul '16

18 Jul '16

Hi Freesurfer Experts, I am trying to run mri_glmfit and while 90% of my files work, some of them display the error below. I have tried demeaning, and then tried multiplying this value by 100, and I still get the same error. Any feedback would be greatly appreciated. mris_preproc done srcsubject = fsaverage srcval = rh.mono_EnglishParityRT_age_gender_TIV.volume.00.mgh srctype = trgsubject = fsaverage trgval = rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /gpfs/scratch/jtl190/Math_reconstruction/fsaverage/surf/rh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh gdfReadHeader: reading /gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 19.5833 1.32025 1 eTIV 1.61645e+06 145343 2 EnglishParityRT 0.00012207 25139.1 Class Means of each Continuous Variable 1 Monolingual_male 19.7143 1678946.5893 -4197.2796 2 Monolingual_female 19.4000 1528966.6750 5876.1917 INFO: gd2mtx_method is dods Reading source surface /gpfs/scratch/jtl190/Math_reconstruction/fsaverage/surf/rh.white Number of vertices 163842 Number of faces 327680 Total area 65020.765625 AvgVtxArea 0.396850 AvgVtxDist 0.717994 StdVtxDist 0.193566 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /gpfs/scratch/jtl190/Math_reconstruction cmdline mri_glmfit --y rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh --fsgd /gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd --C /gpfs/scratch/jtl190/Contrast_files/Contrast_math_monly_EnglishParityRT_a_g_TIV.txt --surf fsaverage rh --cortex --glmdir rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir sysname Linux hostname cyberstar129.hpc.rcc.psu.edu machine x86_64 user jtl190 FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /gpfs/scratch/jtl190/Math_reconstruction/rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh logyflag 0 usedti 0 FSGD /gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd labelmask /gpfs/scratch/jtl190/Math_reconstruction/fsaverage/label/rh.cortex.label maskinv 0 glmdir rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir Loading y from /gpfs/scratch/jtl190/Math_reconstruction/rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh INFO: gd2mtx_method is dods Saving design matrix to rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir/Xg.dat Normalized matrix condition is 22568.9 Design matrix ------------------ 1.000 0.000 18.000 0.000 1865790.250 0.000 -8952.208 0.000; 0.000 1.000 0.000 19.000 0.000 1520429.625 0.000 -4605.208; 1.000 0.000 19.000 0.000 1749716.750 0.000 -39407.207 0.000; 0.000 1.000 0.000 18.000 0.000 1589109.250 0.000 -17967.209; 1.000 0.000 21.000 0.000 1472295.125 0.000 19531.791 0.000; 1.000 0.000 18.000 0.000 1580381.375 0.000 -17027.209 0.000; 1.000 0.000 20.000 0.000 1813373.500 0.000 16152.792 0.000; 1.000 0.000 21.000 0.000 1638616.500 0.000 -9074.208 0.000; 0.000 1.000 0.000 21.000 0.000 1297920.500 0.000 61860.793; 0.000 1.000 0.000 18.000 0.000 1634762.625 0.000 -22671.209; 0.000 1.000 0.000 21.000 0.000 1602611.375 0.000 12763.792; 1.000 0.000 21.000 0.000 1632452.625 0.000 9395.292 0.000; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 22568.9 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh --fsgd /gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd --C /gpfs/scratch/jtl190/Contrast_files/Contrast_math_monly_EnglishParityRT_a_g_TIV.txt --surf fsaverage rh --cortex --glmdir rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir 2. The FSGD file (if using one) 3. And the design matrix above I am also attaching the FSGD file. Best, Jennifer Legault

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registering to fsaverage
by Trisanna Sprung-Much 18 Jul '16

18 Jul '16

Hi there So I have sulcal labels from another software (.mnc format) from which I am trying to generate some probability maps. I was able to convert the .mnc to .mgz surface overlay using mri_vol2surf for my MRIs after running all MRIs in recon-all. So, now I have all my painted voxels as surface overlays, as I was instructed to do a few months ago. I was told that the next step would be to use mri_surf2surf to resample the overlays to fsaverage. I am a bit confused as I would think that the next step would be to take the surface overlays and inflate them before I register them to fsaverage. I see that when recon-all runs, it computes the registration of the MRI surface to fsaverage and saves it as sphere.reg. *Is there a way I can inflate my surface overlays in a similar manner and then apply this same registration to my surface overlays?* Or am I missing something? thanks very much! Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

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