Freesurfer August 2016

freesurfer@nmr.mgh.harvard.edu

127 participants
198 discussions

Recon-all error using Freesurfer 6.0
by Elpiniki Andrew 22 Aug '16

22 Aug '16

Hello Freesurfer experts, I'm having a bit of difficulty running the recon-all command. I recently downloaded Freesurfer version 6.0. The command that I'm running is: recon-all -all -s $name -hippocampal-subfields-T1 However I keep receiving this error: If: Expression Syntax I've attached the output using the -debug flag. I'm using Linux ( centos6.3). Not sure if this is related but I initially had an issue with recon-all stopped with an error when I first ran the same dataset. There was an error in the log file " too many levels of symbolic links". So, I created a new subjects directory and created a symlink to the fsaverage dir as per the instructions on the freesurfer wiki page. Thankyou very much in advance for your time and efforts! Kind regards, Elpiniki

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$SUBJECTS_DIR
by Adil Javed 22 Aug '16

22 Aug '16

HI,1-I'm working with FreeSurfer that is on a server. I don't have permission to create files under the $SUBJECTS_DIR. Is there any way I can specify -subject to be in a directory for which I do have permission? for example: recon-all -subject /location of the file or my own subject_dir location -all 2-Also, Is there a way to segment the cortices as a whole, like left and right frontal cx, parietal cx, temporal cx, occipital cx? Thanks, AJ

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Structural group analysis
by Silas 22 Aug '16

22 Aug '16

Dear FreeSurfer team, I'm doing a structural analysis with around 20 subjects and I'm specifically interested in the areas premotor cortex and primary motor cortex. By matlab analysis I've found a very strong statistical significant difference in the cortical thickness when comparing these two areas with all subjects (data extracted from FreeSurfer recon-all pipeline). I would like to visualize these results on the surface of fsaverage, and I'm familiar with the FreeSurfer group analysis pipeline. So far I've simply made a OSGM group analysis and visualized these results on the fsaverage in a premade label of premotor cortex and primary motor cortex and correlated for multiple comparisons using your precomputed monte carlo simulation - but this doesn't make it. Do you guys have a clever way to visualize these results in FreeSurfer? I have one group and would like to visualize the difference between two areas. I've thought about presenting each subject two times in the FSGD-file (primary motor cortex and premotor cortex), but this isn't possible and seems as a clumsy way to solve this problem. Please let me know if my problem is incomprehensible! Best, Silas

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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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Freesurfer August 2016