Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

Running recon-all with T1 and FLAIR
by Silas 21 Aug '16

21 Aug '16

Dear FreeSurfer team, I'm doing a structural analysis with 50 MS patients and 50 healthy controls (T1, T2 and FLAIR). The MS patients have multiple lesions mainly in white matter. My co-worker did manual editing (bullet points) in the FLAIR images, and i would like to use these edits when running recon-all in order to avoid further manual editing. The data i'm working with is already resliced to 1 mm and co-registered in MNI-space. 1) Can i use this data or would it be preferable to use the original T1's? My thought was to run the following command: recon-all -subject subjectname -i /path/to/input_volume -FLAIR /path/to/FLAIR_volume_with_edits -FLAIRpial -all 2) Does this look correct? Is there anything i should be aware of? 3) Does it make a difference running recon-all -all with the FLAIR image - compared to running recon-all -autorecon3 with the FLAIR after running recon-all -all with only the T1? 4) I've also thought about using the lesion segmentation toolbox for SPM and completely avoid manual editing - is this preferable to using the FLAIR with manual editing? 5) How is the general strength of analysing corpus callosum structurally in MS patients using FreeSurfer? Best, Silas

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Question re extracting average thickness values per subject based on cache.th13.abs.y.ocn.dat
by Gold, Andrea (NIH/NIMH) [F] 20 Aug '16

20 Aug '16

Hi, I’m trying to extract the average thickness per subject in significant clusters from a Qdec analysis, and hope to clarify 2 things re: the “cache.th13.abs.y.ocn.dat“ output from this command: mri_glmfit-sim --glmdir (dir) --cache 1.3 abs --cwp 0.05 —2spaces I’ve attached all relevant output files. This analysis has 2 clusters, and I understand the 2 clusters match the order of the clusters in the cache.th13.abs.sig.cluster.summary file (left=cluster 1, right=cluster 2). 1) Would you please confirm whether the rows of the cache.th13.abs.y.ocn.dat“ match the order of subjects listed in the qdec.fsgd file? 2) Also, I noticed the cache.th13.abs.sig.cluster.summary file lists MNI coordinates – is there a way to get this to print Talairach coordinates from the mri_glmfit-sim command? If not, that’s fine – I can get them from qdec but just curious. Thanks! Andrea -- Andrea Gold, Ph.D. Section on Development and Affective Neuroscience National Institute of Mental Health Room 201, Bldg. 15K, MSC 2670 Bethesda, MD 20892-2670 Phone: 301-827-9804 Fax: 301-402-2010 Email: andrea.gold(a)nih.gov<applewebdata://D38F487B-BA2B-4BF6-A9C4-96248AB2BE51/andrea.gold@nih.gov>

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Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS
by Elijah Mak 19 Aug '16

19 Aug '16

Hi Anastasia, Thanks, it works, but only for MNI reg option. For the CVS stream, there was an error message during -prior. ERROR: fio_pushd: /Users/MacPro/Documents/22995_EM/dmri/xfms/cvs/final_CVSmorph_tocvs_avg35/mri This error message did not halt the process though. Could this be a clue? Thanks for your patience :) Best Wishes, Elijah -- Elijah Mak, Gates Scholar PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ

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Freeview quits unexpectedly
by Corriveau-Lecavalier Nick 19 Aug '16

19 Aug '16

Hello FreeSurfer developers, I am trying to load a thickness file (ex: lh.long.thickness-avg.fwhm10.mgh) in freeview, but as soon as I click the file or press enter after the command line, the program quits unexpectedly. I can load T1, orig.mgz, .pial files, etc. without problem. But when it comes to files that came out of the long_mris_slopes command, freeview quits inevitably. Is it a problem with freesurfer or my computer (ex: graphic card not good enough)? Do you have any idea why it keeps crashing? I am running a Macbook Air mid 2013 with OS X El Captain, 1.3 GHz Intel Core i5, 4 GB 1600 Mhz DDR3, Graphics: Intel HD Graphics 5000 1536 MB. Regards, Nick

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Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS
by Elijah Mak 19 Aug '16

19 Aug '16

Hi Anastasia, Thank you for looking into that subject. I have tried reinitiliasation a few times and in all cases, it just could not find a satisfactory control point fit during the -prior stage. Therefore, the -prior stage has been running for more than 10 hours now. This occurs in other a small number of other subjects as well. WARN: Could not find satisfactory control point fit - try 596 How can I resolve this? And what type of problem could be reflected by this? Bad aparc+aseg.mgz / registration to template? If all else fails, I will exclude subjects using the criteria that you set in the Neuroimage paper: where a subject was excluded if there were failures of reconstruction in 2 or more WM tracts. Thank you for your help! Best Wishes, Elijah -- Elijah Mak, Gates Scholar PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ

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Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS
by Elijah Mak 19 Aug '16

19 Aug '16

Dear Anastasia, I have also uploaded the file with the problem (22995_EM.zip), and this is how my config file looks like after modifications: set subjlist = (22995) set pathlist = (fmajor_PP) set ncpts = (7) set reinit = (1) Thanks again! Best Wishes, Elijah -- Elijah Mak PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ

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Projecting FA map onto fsaverge surface
by Taha Abdullah 19 Aug '16

19 Aug '16

Hello All, I am trying to project FA map (dtifit_FA.nii.gz) and the endpt[1/2].pd.nii.gz from TRACULA onto fsaverage surface space. I was following instructions on http://web.mit.edu/fsl_v5.0.8/fsl/doc/wiki/FDT(2f)UserGuide.html, under FreeSurfer Registration, to create the various xfms files. Next, I registered the FA map to subject conformed space using flirt - flirt -in dtifit_FA.nii.gz -ref ../../mri/orig.nii.gz -applyxfm -init ./xfms_taha/fa2freesurfer.mat -out fa2FS.nii.gz Then, I used mri_vol2surf to project the registered FA map onto fsaverage surface with the following command. - mri_vol2surf --mov fa2FS.nii.gz --projdist-max 6 6 1 --cortex --hemi rh --trgsubject fsaverage --regheader taha_brain --reg ./xfms_taha/fa2freesurfer.mat --o FA_2fsavg_surf.mgh Upon viewing in freeview the fsavg rh.white surface and fa2FS.nii.gz (FA map in FreeSurfer space) did not allign properly. I have tried some variations wtihout any luck. I used the following command line for freeview. - freeview -f /usr/local/freesurfer/subjects/fsaverage/surf/rh.white:overlay=FA_2fsavg_surf.mgh -v fa2FS.nii.gz - Attached are some pics of the FA confomred map and fsaverage.rh.white surface Do I need a xfm file for taliarch allignment? Any advice or insight would be greatly appreciated. Thanks in advance, Taha *Terminal output: from mri_vol2surf* srcvol = fa2FS.nii.gz srcreg = ./xfms_taha/fa2freesurfer.mat srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = fsaverage surfreg = sphere.reg ProjDist = 0.5 reshape = 0 interp = nearest float2int = round GetProjMax = 1 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /usr/local/freesurfer/subjects/taha_brain/mri/orig.mgz as target reference. Loading label /usr/local/freesurfer/subjects/fsaverage/label/rh.cortex.label Reading surface /usr/local/freesurfer/subjects/taha_brain/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 6 6 6 using old Done mapping volume to surface Number of source voxels hit = 81606 Reading source surface registration /usr/local/freesurfer/subjects/taha_brain/surf/rh.sphere.reg Done loading source registration surface Reading target registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Done loading target registration surface Mapping Surfaces (taha_brain -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (143161) Reverse Loop had 26084 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 107182, nSrcLost = 0, nSrcMulti = 35979, MnSrcMultiHits = 2.29979 nTrg121 = 142955, nTrgMulti = 20887, MnTrgMultiHits = 2.24882 Masking with /usr/local/freesurfer/subjects/fsaverage/label/rh.cortex.label Writing to FA_2fsavg_surf.mgh Dim: 163842 1 1 -- Taha Abdullah Department of Physiology Northwestern University Feinberg School of Medicine Masters of Science Physiology and Biophysics, Georgetown University 2015 Work: (312)-503-0413

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Re: [Freesurfer] error in manual edit by freeview
by 3110103623＠zju.edu.cn 19 Aug '16

19 Aug '16

Hi Doug and Ruopeng Can you receive pictures and brainmask.mgz file in attachment? I don't know why this slice mismatch with other slices, other files such as T1 and wm.mgz and other subjects works well. Thank you very much. Regards Cong > Date: Wed, 17 Aug 2016 10:49:35 -0400 > From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] error in manual edit by freeview > > I'm not sure what you are describing. Can you send a picture? > > > On 8/17/16 8:42 AM, ?? wrote: > > Hi dear all > > I am using freeview to edit segmentation, I found one slice in coronal view in brainmask.mgz mismatch with other slice, this slice obviously move down. WM and T1.mgz are normal, I don?t know how to move this wrong slice back. Any advice will be appreciated. > > > > thanks very much. > > CONG

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red and blue gradient color map for freeview
by Eun Young Choi 19 Aug '16

19 Aug '16

Hi all, I'd like to have a freeview color map that has both a red-yellow gradient and a blue-light blue gradient (the typical colors for positive and negative fcMRI correlations) and ideally no color for 0... None of the standard color maps in freeview work well and I can't seem to find one online. Has anyone created one? Or know where I can view the text file for the standard color maps that come with freeview, so I can create one myself? Thank you! Eun Young

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LME contrast 3 groups
by Sarah Hirsiger 19 Aug '16

19 Aug '16

Dear FreeSurfer experts, I would appreciate a confirmation regarding correctness of my approach. I am trying to run an LME model for three groups (group1=controls, group2 and group3) and two time points. I followed the tutorial on https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels <https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels> and adapted the four group example. However, I am not 100% sure if my adaption is correct and would appreciate your input. The design matrix for the model contains the following columns: 1) Intercept 2) time (tij) 3) one for Group2 and zero otherwise 4) column 3) .* time 5) one for Group3 and zero otherwise 6) column 5) .* time To test the null hypothesis of no group differences in the rate of change over time among the three groups I applied the following contrast: 0 0 0 1 0 0 0 0 0 -1 0 1 Is this contrast correct? In a second step, I would use the additional three contrasts to identify which groups were different: 0 0 0 1 0 0 and 0 0 0 0 0 1 and 0 0 0 -1 0 0 1 I really appreciate your help! Best wishes Sarah

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