Freesurfer December 2016

freesurfer@nmr.mgh.harvard.edu

95 participants
146 discussions

Edits to White Matter
by Gundel, Tristan J 30 Jan '17

30 Jan '17

Hello, I work in a lab that is currently using the Freesurfer algorithm to collect data from MRI images of individuals with Multiple Sclerosis. In order to increase the precision of our white matter masks we have combined your algorithm with ANTS, hoping to achieve more accurate surface volumes and aparc+aseg masks. Unfortunately we have had some issues when we edit our ANTS white matter mask (using value of 255) and then put it through freesurfer again, re-running recon-all (recon-all -autorecon2 -wm -autorecon3 -w <subID>). Our wm_surface and aparc+aseg mask do not change based on the edits we have made, and do not follow the white matter volume surface volume. How can we be sure that our white matter mask, and the edits we make to it, are considered in the creation of wm_surface and aparc+aseg mask? Please let me know if any of this is unclear and I will explain it in more detail. Thank you, Tristan

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Neighborhood of a vertex
by Onur Uğurlu 24 Jan '17

24 Jan '17

Hi all, I have a 'lh.thickness.asc' file which contains thickness values of each vertex. The format of the file is following; <vertex index> <x> <y> <z> <thickness> However, x,y,z are not integer. What is the unit of the x,y,z values in the file? I am trying to find all the neighborhood of any given vertex as x,y,z -> x+1,y,z etc, can you suggest a method for this problem. Sincerely yours, Onur

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Problem with freeview
by Jennifer Szeto 04 Jan '17

04 Jan '17

Hi Freesurfer Experts, I have installed Freesurfer5.3 and it seems to be working fine. However when i tried to load up the GLM analysis (after doing mris_preproc and mri_glmfit) results on freeview, i got the following message: "OpenGL warning: No pincher, please call crStateSetCurrentPointers () in your SPU Did not find any volume geometry information in the surface" Just wondering if anyone knows the solution to this? Thanks for your help! Jen

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minor edits to aseg lead to exist with errors in about 25% of my scans
by Lucette Cysique 04 Jan '17

04 Jan '17

Dear FS Wiki I run my scan in FS without any problem example: #@#%# recon-all-run-time-hours 8.342 recon-all -s 877 finished without error then I do some edits to the aseg in freeview edits include: relabelling correctly lateral ventricles voxels mostly in the posterior horn of the lateral ventricles; white matter hyperintensities around those voxels which are erroneously considered as cortex also more often in the posterior horn of the lateral ventricles; and correcting erroneous allocation of choroid plexus also typically in the posterior horn of the lateral ventricles Once done, I re-run using recon-all -s $i -autorecon2-noaseg example: /mridata/workingdata/HIV/subjects/877 /usr/local/FREESURFER/freesurfer5.3.0/bin/recon-all -s 877 -autorecon2-noaseg in 25% of cases, I get the following error message and the process exists example: #-------------------------------------------- #@# Intensity Normalization2 Wed Dec 14 12:33:54 AEDT 2016 /mridata/workingdata/HIV/subjects/011/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz mri_normalize: aseg volume aseg.mgz must be conformed using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.mgz Linux katana.neura.edu.au 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 011 exited with ERRORS at Wed Dec 14 12:33:56 AEDT 2016 in the other no problem example: #@#%# recon-all-run-time-hours 1.116 recon-all -s 877 finished without error at Thu Dec 1 14:42:27 AEDT 2016

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Structural analysis
by Silas 04 Jan '17

04 Jan '17

Dear FreeSurfer team, I'm currently doing a structural FS analysis with 50 Multiple Sclerosis (MS) patients and 25 Healthy Controls (HC). FLAIR-lesions were drawn onto the aseg.mgz as White Matter Hypointensities (=77). I've finished the analysis, but have some questions regarding my results. Results: HC (n=25) MS (n=50) p-value Mean TIV (SD) [ml] 1594.9 (154.7) 1559.5 (140.1) > 0.05 Mean WMV (SD) [ml] 503.6 (57.3) 485.2 (59.5) > 0.05 Mean GMV (SD) [ml] 657.2 (69.9) 635.1 (47.9) > 0.05 Mean WMHV (SD) [ml] 1.12 (0.4) 5.97 (5.7) 0.0000677 1) Does these results look correct? WMV < GMV? 2) What is the difference between WMV+GMV and TIV? CSF? Ventricles? 3) I find no atrophy in the MS patients; are there reported any problems with FS and MS patients? 4) What is White Matter Hypointensities comprised of in HC? Best, Silas

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Error from trac-all prep: data and bvals/bvecs do not contain the same number of entries
by Hao wen 04 Jan '17

04 Jan '17

Hello: I followed the tutorial for tracula, because of the tutorial data that you give dont have the T1 image, so I use on of my own diffision data and the reconall-ed T1 image, and I always get the same errors: data and bvals/bvecs do not contain the same number of entries , So I guessed that it is the problem from the data(dwi.nii, T1.nii, .bvec, bval), but I tried to figure out the data dimension differences between my data and the tutorial data(tutorial_data/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm), Here is the output: 1) FS tutorial data(dicom format): This is the bval info and i guess the bvec dimension is the same bValue = 700 nB0 = 10 nDir = 60 this is the dwi.dicom information: dimensions: 128 x 128 x 60 x 70 So the nFrames is equal to the bvel and bval columns(70), which makes sense. 2) My data information(which is .nii.gz format): The bvec and bval info: number of columns for bval and bvec is 136 The dwi.nii.gz dimensions: dimensions: 96 x 96 x 59 x 137 So for my data, the number of columns(or transpose the files, the same spirit) is nFrames-1, I guess that is the problem, but my data can be run for Mrtrix and Dipy, even in the dipy tutorial, the data that they offer, the number of columns is the number of frames(volumes) minus 1, So for TRACULA, is it a mandatory that the number of columns in bvec and bval is equal to the number of volumes in dwi image??? I know sometime people dont write the first 0 in bvec and bval, so if I just add it, and run it for TRACULA, it will work??? I will try it tomorrow!!! Really need your help, I stuck for this in a while:) the log file is attached. Thanks in advance

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Tracula Set: No Match
by Katherine Damme 03 Jan '17

03 Jan '17

Hello! I have been getting a "set: No match." error. I haven't been able to sort out what is causing it. Attached you will find the configuration file, command, and log files associated with this error. "mv -f /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot xfmrot /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.ecclog /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs set: No match."

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flirt: command not found
by michal heker 03 Jan '17

03 Jan '17

Hello freesurfer developers, I am trying to use TRACULA reconstruction with *Virtual Box* on my data (I have my own nii files). I have followed all the stages in the freesurfer tutorial. I get the following problem: INFO: SUBJECTS_DIR is /media/sf_share/diffusion_recons INFO: Diffusion root is media/sf_share/diffusion_ourbrains Actual FREESURFER_HOME /usr/local/freesurfer flirt: Command not found. dcmlist: Subscript out of range. What am i doing wrong? find attached is a copy of my dmrirc file Thanks for your help, Michal

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mri_glmfit-sim
by stdp82＠virgilio.it 31 Dec '16

31 Dec '16

Hi list, which is the correct option, please? 1- mri_glmfit-sim --glmdir my-glm.wls --cache 1.3 abs --cwpvalthresh .0166 --3spaces 2- mri_glmfit-sim --glmdir my-glm.wls --cache 1.3 abs --cwpvalthresh .05 --3spaces Thanks Best regards Stefano

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Revisiting GM ROI list
by P Taylor 30 Dec '16

30 Dec '16

Hi, Doug- I've looked more into my earlier question of identifying FS-returned regions, in particular: 1) which regions of the whole FreeSurferColorLUT.txt seem to get returned by default recon-all calls (for either the 2000- or 2009-parc+segs); and 2) which of those regions are GM and non-GM (WM/CSF/other), based both on the mri_binarize list you had posted earlier in this thread and on the names given in the LUT. I'd like to pick your brain on this. A) The main questions I have relate to the regions labeled from [0, 256], which seem have the same labelling in both the 2000 and 2009 parc+segs. >From a few different FreeSurfer recon-alls on healthy adults, below is a list of the ROIs that seem to be consistently returned by recon-all (a much sparser subset than all 256). For each, I have included the number and label, as well as put arrows by the numbers that, according to the MatchValues list in mri_binarize, should be in either the WM or Vent masks, (and hence non-arrowed regions should be GM, by how that function returns "--gm"). My main questions arise about #30, 62, 80 and 85, as they don't appear to be GM-- therefore, am I correct that I should also *exclude* those four regions from a list of GM regions? (Here, "FS_nongm*" means that it was in the list of non-GM regions in mri_binarize, as either unknown, WM, CSF or ventricle.) ------------------------------------------------------------ ----------------------------------------- 0 Unknown -> FS_nongm 2 Left-Cerebral-White-Matter -> FS_nongm_wm 4 Left-Lateral-Ventricle -> FS_nongm_vent 5 Left-Inf-Lat-Vent -> FS_nongm_vent 7 Left-Cerebellum-White-Matter -> FS_nongm_wm 8 Left-Cerebellum-Cortex 10 Left-Thalamus-Proper 11 Left-Caudate 12 Left-Putamen 13 Left-Pallidum 14 3rd-Ventricle -> FS_nongm_vent 15 4th-Ventricle -> FS_nongm_vent 16 Brain-Stem 17 Left-Hippocampus 18 Left-Amygdala 24 CSF -> FS_nongm_csf 26 Left-Accumbens-area 28 Left-VentralDC 30 Left-vessel -------> *should be in list of FS_nongm? 31 Left-choroid-plexus -> FS_nongm_vent 41 Right-Cerebral-White-Matter -> FS_nongm_wm 43 Right-Lateral-Ventricle -> FS_nongm_vent 44 Right-Inf-Lat-Vent -> FS_nongm_vent 46 Right-Cerebellum-White-Matter -> FS_nongm_wm 47 Right-Cerebellum-Cortex 49 Right-Thalamus-Proper 50 Right-Caudate 52 Right-Pallidum 53 Right-Hippocampus 54 Right-Amygdala 58 Right-Accumbens-area 60 Right-VentralDC 62 Right-vessel -------> *should be in list of FS_nongm? 63 Right-choroid-plexus -> FS_nongm_vent 72 5th-Ventricle -> FS_nongm_vent 77 WM-hypointensities -> FS_nongm_wm 80 non-WM-hypointensities -------> *should be in list of FS_nongm_wm? 85 Optic-Chiasm -------> *should be in list of FS_nongm? 251 CC_Posterior -> FS_nongm_wm 252 CC_Mid_Posterior -> FS_nongm_wm 253 CC_Central -> FS_nongm_wm 254 CC_Mid_Anterior -> FS_nongm_wm 255 CC_Anterior -> FS_nongm_wm ------------------------------------------------------------ -------------------- It seem that the new version of mri_binarize that you had sent me might still include those four flagged regions in the 'mri_binarize --gm' output. B) For the ROIs specific to the 2000aparc+aseg, I think it also seems pretty clear: + 1000 and 2000 are returned as "ctx_*_unknown"; + All ROIs in the intervals [1001, 1003] and [1005, 1035] can be returned, and these are all LH GM; + All ROIs in the intervals [2001, 2003] and [2005, 2035] can be returned, and these are all RH GM; + ROIs '1004' and '2004' are the "ctx-?h-corpuscallosum", which would be WM, but they don't seem to be returned. C) For the ROIs specific to 2009aparc+aseg, I think it also seems pretty clear: + 11100 and 12100 are returned as "ctx_*_Unknown"; + All ROIs in the intervals [11101, 11141] and [11143, 11175] can be returned, and these are all LH GM; + All ROIs in the intervals [12101, 12141] and [12143, 12175] can be returned, and these are all RH GM; + ROIs '11142' and '12142' are the "ctx_?h_Medial_wall", which would be non-GM, but they don't seem to be returned. D) And you mentioned that the regions in the interval [3000, 4035] are WM parcellations. So, in total, does that seem like a complete categorization of regions that are typically returned, as well as their classification as either GM or non-GM? And in particular, I would be happy to know your thoughts on the flagged ROIs in the interval [0, 256]. Thanks, pt

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Freesurfer December 2016