Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

permutation/monte carlo
by maaike rive 23 Aug '16

23 Aug '16

Dear Douglas, Sorry to bother you with this, but after reading the thread about the Eklund papers I'm getting confused about what I actually did when correcting for multiple comparisons and I'd also like to know whether I'm on the safe side. I used pre-cashed Monte Carlo simulation with a cluster finding threshold of 0.05 (at least so I thought): mri_glmfit -sim - -glmdir - -cache 1.3 abs - - cache-dir - - cwpvalthresh 0.01 Am I correct? And am I also correct that the FDR may be about 13% instead of 5% when doing this? (I smoothed thickness and surface area data with FWMH 10mm, but not the lGI data, because they were already very smooth and pre-cashed simulation didn't work after additional smoothing). Thanks, Maaike

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Recon-all Correcting Defect 0
by Heidi Foo 23 Aug '16

23 Aug '16

Dear FreeSurfer team, I apologize for sending this email again. I am currently running recon-all for my subjects but for 2 of them, it stops at XL correcting defect. Do you have any ideas how I can deal with this problem? Attached the log file for your reference. Thanks. Regards, Heidi

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qcache for qdec longitudinal analysis
by Nick Corriveau Lecavalier 23 Aug '16

23 Aug '16

Hi Freesurfer team, I am planning on following this page for my longitudinal group analysis using QDEC: http://www.freesurfer.net/fswiki/FsTutorial/QdecGroupAnalysis_freeview. However, it tells me to run -qcache for all of my subjects. Since I already ran the -long stream for all my subjects, do I need to rerun them all adding the -qcache command? Also, I have also run the long_mris_slopes on all of my subjects, which produced smoothed thickness files for all of my subjects (which are all in the ''base'' files). Does these files are okay for my QDEC analysis, or I really need to run all of my subjects all over again adding -qcache? Thank you very much, Nick Corriveau-Lecavalier, B.Sc. (Hons.) Étudiant au Ph.D. recherche/intervention, option neuropsychologie clinique Coordonateur à la recherche, Association étudiante des cycles supérieurs en psychologie de l'Université de Montréal (AÉCSPUM) Université de Montréal Centre de recherche de l'Institut universitaire de gériatrie de Montréal, bureau M7819

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Re: [Freesurfer] [Martinos-faculty] Open position as MRI physicist at Copenhagen University Hospital, Denmark (fwd)
by Bruce Fischl 23 Aug '16

23 Aug '16

FYI The Neurobiology Research Unit (NRU) at Copenhagen University Hospital, Rigshospitalet has an opening for a MRI physicist position. The position entails design, development, implementation and evaluation of novel multimodal MRI acquisition protocols and image analysis techniques in relation to our many exciting brain research projects which employ Siemens 3 Tesla MRI. Also, ample opportunities will be given to conduct own research projects. This is a fully funded 2-year full time position with potential for on-going renewal. Employment will start October 1st, 2016, or as soon as possible thereafter. Salary will be according to the current agreement and hence an annual gross salary of minimum DDK 460,000 (~USD 70,000) can be expected. A special reduced tax scheme is offered for researchers recruited abroad, see https://www.workindenmark.dk/Working-in-DK/Tax. Primary work place will be Neurobiology Research Unit, Rigshospitalet. Close collaboration will take place with our national collaborators at the Department of Clinical Physiology and the Department of Diagnostic Radiology at Rigshospitalet as well as with our international collaborators. For further information and application, see: https://candidate.hr-manager.net/ApplicationInit.aspx?cid=342&ProjectId=201… _______________________________________________ Martinos-faculty mailing list Martinos-faculty(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/martinos-faculty

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Visualising path.mean.txt in MNI space after trac-all -stat
by Elijah Mak 23 Aug '16

23 Aug '16

Hi Anastasia and others, I am trying to visualise the *.path.mean.txt on MNI template after running trac-all -stat. I used this command: freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w stats/*.path.mean.txt However, it looks like something has gone wrong with the labelling and position of the tracts (note the CST highlighted in green). Everything was fine and correctly labelled when I checked the merged tracks. Thanks again for your help! Best Wishes, Elijah P.S. On another note, the reinit=1 trick works very well and I was able to reconstruct the tracts in almost all cases. Thanks! -- Elijah Mak PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ

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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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