Freesurfer July 2016

freesurfer@nmr.mgh.harvard.edu

143 participants
252 discussions

Assessing local correlations across 2 modalities
by Elijah Mak 10 Aug '16

10 Aug '16

Dear Freesurfer Community, I am currently trying to investigate the local correlations across 2 modalities (i.e. Tau-PET and cortical thinning). I understand that this sort of questions has been conventionally addressed using the Biological Parametric Mapping (BPM) toolbox in MATLAB. Is there a way in Freesurfer to properly address this? My PET data have already been registered and projected to the surfaces for each individual. Thanks a lot. Best Wishes, Elijah -- Elijah Mak PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ

2 1

Error with qdec
by Mahtab Farahbakhsh 10 Aug '16

10 Aug '16

Dear FreeSurfer, I am trying to compare my subjects to the healthy group, but when I put the matrix into qdec, I get the following error: Normalized matrix condition is 1e+08 Design matrix ------------------ 1.000 0.000 0.000 0.000 68.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 66.000 0.000; 1.000 0.000 0.000 0.000 40.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 35.000 0.000; 1.000 0.000 0.000 0.000 72.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 71.000 0.000; 1.000 0.000 0.000 0.000 22.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 22.000 0.000; 0.000 1.000 0.000 0.000 0.000 20.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 20.000; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 1. Your command line: mri_glmfit --y /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/y.mgh --fsgd /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/qdec.fsgd dods --glmdir /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled --surf fsaverage lh --label /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/fsaverage/label/lh.aparc.label --C /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-Avg-thickness-age-Cor.mat --C /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-Diff-Male-Female-Intercept-thickness.mat --C /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-Diff-Male-Female-Cor-thickness-age.mat --C /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-Diff-spelling-healthy-Intercept-thickness.mat --C /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-Diff-spelling-healthy-Cor-thickness-age.mat --C /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-X-gender2-diagnosis_spelling-Intercept-thickness.mat --C /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-X-gender2-diagnosis_spelling-Cor-thickness-age.mat the table file is also attached to the mail. Would you please kindly guide me with this? Best Regards, Mahtab.

2 1

bbregister problem in FS5.1
by Fred Sampedro 10 Aug '16

10 Aug '16

Dear FS experts, I've installed freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 and I'm trying to run bbregister to register a AV45-PET image to its corresponding FS processed T1 image. For that, I'm trying to run: bbregister --s SUBJ_ID --mov SUBJ_PET --reg register.dat --init-fsl --t1 And I keep getting segfaults: Log file is register.dat.log dom jul 24 16:44:19 CEST 2016 $Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $ Linux fredlab 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15 17:43:14 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz ./tmp.bbregister.5353/template.nii mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz ./tmp.bbregister.5353/template.nii Segmentation fault (core dumped) I have tried the same installation and command in two different computers and obtained the same segfault. I have also tried the same pipeline using instead the FS version freesurfer-Linux-centos4-stable-pub-v5.1.0.tar.gz and get the same result. I didn't have this issue using freesurfer 5.3, but I need to use 5.1 for an ongoing project. I'm in an Ubuntu 14.04 LTS with 3.6GB of Memory, Processor Intel Core 2 Duo 3.0GHz, Graphics Intel Q45/Q43 OS type 64 bits. Any help would be much appreciated, Thanks a lot in advance, Fred Sampedro

3 5

Qdec Generate Stats Data Table Error
by Limachia, Gaurang (NIH/NINDS) [F] 10 Aug '16

10 Aug '16

Hello All, My table.dat file loaded fine. However, I came across the following error when I was running the Qdec generate stats data table. If you can let me know what I can do to fix the following error I would greatly appreciate it. Uncaught exception: command failed: asegstats2table --common-segs --meas volume --tablefile /local/limachiagv/freesurfer/subjects/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects CON_201 CON_202 CON_203 CON_204 CON_205 CON_206 CON_207 CON_209 CON_211 CON_212 CON_213 CON_214 CON_215 CON_216 CON_217 CON_218 CON_219 CON_220 CON_221 CON_222 CON_223 CON_225 CON_226 CON_227 CON_228 CON_230 CON_231 CON_232 CON_233 CON_234 CON_235 CON_236 CON_237 CON_239 CON_240 CON_241 CON_242 CON_244 CON_245 CON_246 CON_247 CON_248 CON_249 CON_250 CON_251 CON_252 CON_253 CON_254 CON_255 CON_256 CON_257 CON_258 CON_259 CON_260 PAT_402 PAT_403 PAT_407 PAT_409 PAT_410 PAT_411 PAT_412 PAT_413 PAT_414 PAT_415 PAT_416 PAT_417 PAT_418 PAT_419 PAT_421 PAT_422 PAT_424 PAT_425 PAT_426 PAT_427 PAT_428 PAT_429 PAT_430 PAT_431 PAT_432 PAT_433 PAT_437 PAT_439 PAT_440 SUBJECTS_DIR : /local/limachiagv/freesurfer/subjects Parsing the .stats files ERROR: The stats file /local/limachiagv/freesurfer/subjects/CON_201/stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files Thanks, Gaurang

2 1

group analysis/ region of interest (ROI) approach
by miracle ozzoude 10 Aug '16

10 Aug '16

Hey FreeSurfer experts, Does anyone know the steps i have to perform if I want to conduct surface based thickness analysis using GLM but with ROI approach. Thank you very much. Best, Paul

4 5

ROIs defined in MNI space and vol2surf
by Funk, Quentin 04 Aug '16

04 Aug '16

All, I have a question regarding the required registration file in mri_vol2surf. I have some spherical ROI's in MNI space produced via 3dUndump--they're volume files that show up in the correct places when loaded in with an MNI standard subject such as fsaverage. I also have some patients scans. I'd really like to compute cortical thickness for these ROI's on my patient scans, so I attempt to follow the instructions at ( https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness ), but these instructions assume that the ROI is in the native space--which produces no problems until the step : 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 \ --reshape My question is then three parts: (1) Why does vol2surf require a registration file? Shouldn't it be possible to do it as a straight conversion of data types if I know that my surface is registered to the file that I want? Perhaps naive, my first intuition was to construct a TT.dat that was the identity matrix, but this fails, with the response listed in (2). (2) How can I do this without shifting my data? If I follow the instructions, when the surface is overlayed on fsaverage's lh.pial, the entire surface is included in the overlay. (3) What exactly do the numbers mean in the registration file TT.dat (as in the instructions on the website)? The 4x4 matrix is clear, and the first two numbers appear to have something to do with Voxel resolution, but I'm unable to find documentation that explains the notation in the output. Any help anyone can offer would be tremendously appreciated. -qf Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list 10 years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

5 7

Coordinates in TRACULA group analysis
by Anri WATANABE 03 Aug '16

03 Aug '16

Dear experts, I use TRACULA to examine a measure (FA) at each voxel in one pathway. pathstats.byvoxel.txt files show coordinates in native space and after converting those the new files don't show any coordinates which are in MNI space. Could you tell me how can I know MNI coordinate values? Thank you! Regards, Anri ********************************************************************** 京都府立医科大学附属病院精神科・心療内科渡辺杏里 ********************************************************************** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine **********************************************************************

2 21

mri_normalize, 110 is too dark
by tvg[fs] 03 Aug '16

03 Aug '16

Dear community and developers, I am experiencing issues during the normalization step, converting NU.mgz to T1.mgz. Gray matter is falsely recognized as white matter and high intensity WM is ignored. The resulting T1.mgz collapses the wrong voxels into the 110 bin. It seems that what mri_normalize assumes a peak in the WM intensity distribution that is too low. In NU.mgz WM seems centered around 140 not 110. Note that this is not due to RF-field inhomogeneities. It is likely of physiological origin - Is there a way to explicitly tell mri_normalize to use a different intensity peak? I realize that correction can be done with control points, however I understand that does not compute a new intensity distribution, but merely adds voxels around CPs. This is undesirable since I have >20 scans to process. Also this will not correct the falsely tagged GM voxels. I've tried to trick mri_normalize by adjusting NU.mgz intensity by -30 (140-30 = 110). This did not give me the wished-for effect. - Is it possible to bypass preprocessing steps of mri_normalize before collapsing? - In general it would help if there is some elaboration on the options: -no1d, -nosnr, -gentle, -f vs -fonly, -prune, -g, -monkey - is [-monkey] just shorthand for [-no1d -n 1]? Thanks, Tom System: Mac OS X 10.10.5 freesurfer-Darwin-lion-stable-pub-v5.3.0 > mri_normalize --version stable5

2 2

Where are time series from adjusted (post selxavg3) ROIs
by ERIK JAHNER 01 Aug '16

01 Aug '16

Dear Freesurfer experts I have been going through the documentation trying to figure out how to extract the time series for an ROI (Posteriorcingulate) after removing the regressors that I put in my mkanalysis-sess. I have run the selxavg3. 1. Is this time course what is in the meanfunc.nii.gz? 2. If it is, how do I pull this out in matrix format (.mat) out of the where I basically get one mean adjusted value for the ROI at each timepoint? (e.g. For the Posteriorcingulate, I want 210 values representing the mean activation after removing the effect of my covariates wm and css for each of the 210 timepoints). 3. Is this information in the X.mat file? If so, what is its location? Thanks Erik Jahner

2 1

Running Retinotopy in FSFAST, Design Matrix has Empty Regressors
by Taylor, Johnmark 01 Aug '16

01 Aug '16

Hello, I am trying to run a retinotopy analysis in fsfast, using only polar angle. However, when I try to run it, I am getting the error "Input to SVD must not contain NaN or Inf." I have traced this error and it looks like the design matrix X has 12 regressors (the first 12) that consist solely of zeros. I am using the following commands: mkanalysis-sess -analysis retinotopy -fsd bold -runlistfile runlist.txt -native -funcstem fmc -nuisreg mcextreg 3 -retinotopy 36.4 -per-session -paradigm retino.par -inorm -spmhrf 0 -TR .650 -polyfit 2 -nskip 19 selxavg3-sess -analysis retinotopy -sf sublist.txt -df sessdir Any idea what the first 12 regressors in the design matrix might correspond to in retinotopy analyses and why they'd be empty? I have looked at the documentation and there doesn't seem to be a clear labeling of the retinotopy design matrix anywhere, although perhaps I'm missing something. Thank you very much, JohnMark

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Freesurfer July 2016