Freesurfer

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30080 discussions

voxel values in destrieux file
by pierre deman 23 Aug '16

23 Aug '16

Hello, I am looking at the destrieux atlas generated by recon-all (I use the freesurfer dev version), the file aparc.a2009+aseg.mgz), and sometimes the value of a voxel doesn't exist in the FreesurferColorLut. I have quite a lot of values between 2036 and 2100 (2038, 2074, 2075 for example) and I don't find these values in the FreeSurferColorLut. Is that normal ? What do they correspond at ? Regards, Pierre -- DEMAN Pierre Mobile : +33 7 82 57 80 94

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Support for surface data on NeuroVault.org
by Chris Filo Gorgolewski 22 Aug '16

22 Aug '16

Dear FreeSurfer community, I am one of the developers of NeuroVault.org - an open repository for vizualizing, analyzing, and sharing of statistical and parcellation maps of the human brain. So far NeuroVault was limited only to volumetric data in the MNI space since this is the most common way of reporting MRI results. Now I would like to start working on adding support for surface data beginning with outputs of FreeSurfer. Since I'm not a FreeSurfer expert I would like to ask the community a few questions: 1. In NeuroVault users are asked to upload their statistical maps in form of files. I'm planning to target outputs of mri_glmfit: preferably Z.mgh but also sig.mgh. Is this the most sensible thing to do? 2. I want to be able to tell if a given map is in fsaverage space. Is there any place in the .mgh header that specifies which space the map is in? 3. fsaverage has different subsampling flavours - how often are they used? Is support for them an important feature? 4. Results come in two files - one per each hemisphere. Is there any way (from the headers) to check if two files provided by a user match? 5. As with the volumetric data I want to provide a 3D interactive viewer. I had some initial success with Brain Browser. Are you aware of any other javascript based viewers that work well with FreeSurfer data? 6. Which surface should be the default view: inflated, pial, or white? 7. Finally NeuroVault gives users ability to compare maps and even search through the whole repository to find statistical maps with similar patterns. This is currently implemented for volumetric data, but could be extended to surface data. The problem arises when one wants to compare MNI volumetric data with fsaverage surface data. So far I have been using mri_vol2surf with target subject being fsaverage (with a supplied affine correction matrix), but this solution is far from optimal since fsaverage folding patterns are quite different from MNI. I was thinking that maybe a more accurate way of dealing with this would be to reconstruct MNI152 cortical surface model, do surface registration of it to fsaverage, and use that to sample statistical maps in MNI space. What do you think? Thank you for any help feedback you can provide! Best, Chris Gorgolewski

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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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