Freesurfer May 2021

freesurfer@nmr.mgh.harvard.edu

97 participants
125 discussions

Cerebellum Segmentation
by A.R. Sekar 15 May '21

15 May '21

External Email - Use Caution Hello Experts! This is the first time I am doing tractography and my aim is to do it specifically for the cerebellum. I saw online that FreeSurfurer can segment the cerebellum, to create the ROI but I’m not entirely sure how to go about this. So far I have done the pre-processing, co-registration onto diffusion space and created FOD. I have also ran recon all on my structural data. It would be great if you could give me advice and any feedback about the pipeline. Thanks for your help! Regards, Akila

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FreeSurfer Error: xx: Subscript out of range
by Shanika Jayakody 14 May '21

14 May '21

External Email - Use Caution Dear FreeSurfer team I have been trying to run trac pre-processing on some subjects but keep getting the error "xx: Subscript out of range." The number of data entries in bvecs/bval files are similar to the .nii file and I have used configuration files similar to the ones I have been using Attached here are my configuration file and trac-log file. Any suggestion/advice is really appriciated Thank you Regards Oshadi

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Re NEUROIMAGINGPOSITION IN EPILEPSY Available
by Xiaozhen You 13 May '21

13 May '21

External Email - Use Caution *NEUROIMAGING POSITION IN EPILEPSY* *AT CHILDREN’S NATIONAL HOSPITAL AND THE GEORGE WASHINGTON UNIVERSITY* A position is available starting *Spring/Summer 2021* in the Comprehensive Pediatric Epilepsy Program at Children’s National Hospital affiliated with George Washington University in Washington DC (Polerlab.org <http://secure-web.cisco.com/1Y4lk4CR_HLS6scGFa1DcCuY-aG2PbH_t2oHL0ieCABcIRd…>). This position involves the application of state-of-the-art functional and structural MRI imaging methods applied in clinical research. The candidate will apply methods previously developed but not used in epilepsy as well as develop novel computational imaging methods. Our aim is to apply sophisticated approaches to answer clinical questions (e.g, identify seizure focus; develop sensitive MRI metrics of cognitive reorganization; examine pre- and post-surgical changes structurally and functionally to build sensitive predictive models). The candidate will have the opportunity to initiate his/her own research projects, mine existing data, and collaborate with a multidisciplinary team including neurologists, neurosurgeon, neuropsychologists, fellows, graduate students, and undergraduate research assistants. Candidate qualifications and educational background are flexible and the position will be tailored accordingly. We prefer a postdoctoral level; however, will consider an advanced graduate student. An early career faculty position is an option as well. Appointments are for two years minimum, renewable upon mutual agreement. Candidates should have graduate school training in engineering, neuroscience, computational, or other biological sciences. Experience with computer programming and image processing is essential. Familiarity with fMRI analysis software including SPM, FSL, AFNI, and Freesurfer, as well as programming environments such as MATLAB or Python is highly desirable. Children’s National Hospital is an equal opportunity employer. Full-time employees receive full benefits, competitive salaries, and excellent resources for career development. To apply, please send a letter describing research interests and experience, curriculum vita, and names and contact information of three references to William Gaillard, MD at wgaillar(a)childrensnational.org and Madison Berl, PhD at mberl(a)childrensnational.org.

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Infant Freesurfer exiting without error
by COLLEEN PLETCHER 13 May '21

13 May '21

External Email - Use Caution Hi, I am trying to run infant freesurfer using the --segfile and --masked options. When I attempt to run it, it runs for a bit and then I get this: USAGE: mri_or <options> fname1 fname2 .. After this, the program exits. I am not getting any error, so I am confused about why it is exiting suddenly? Thank you very much! -Colleen

2 9

Sulcal probability maps
by Kristi Drudik 12 May '21

12 May '21

External Email - Use Caution Good afternoon, I hope this email finds you well. I am in the process of "painting" MRI surfaces from the Human connectome project in FreeSurfer, meaning creating labels on the surfaces to analyze sulcal morphology. We are interested in the spatial variability of the sulcus and thus, want to create surface spatial probability maps using FreeSurfer (please see attachment for an example of such surface probability maps). These maps would represent the likelihood of each vertex on the FreeSurfer fsaverage surface belonging to the sulcus of interest (from 0% to 100%). To obtain these probability maps, I: * Painted the sulcus of interest on the surface by creating a .label file. * Registered this .label file to fsaverage (mri_label2label) * Converted the .label file to vol (mri_label2vol) * Converted it to a surface file (mri_vol2surf) * Concatenated the data to create an average (mri_concat --mean) * Blurred the data and loaded the blurred average as an overlay onto the fsaverage pial (mris_fwhm) Because this seems very convoluted, my question becomes: Is there a more direct way to generate these maps from the labels themselves, rather than going from label to vol, then back to surf? Finally, I would like these maps to represent a 0-100% range of each vertex in fsaverage belonging to the sulcus of interest. However, this method creates a 0-1 range (please see colour bar in attachment). Is there a way to change this to a percentage? Thank you very much for your time and help. Please let me know if you have any questions. Best, Kristi Kristi Drudik Ph.D. Student, Clinical Psychology Montreal Neurological Institute McGill University Montreal, Canada

3 20

Cluster correction at subject level using -log10(p) values
by Leonardo Tozzi 12 May '21

12 May '21

External Email - Use Caution Dear Experts, I am running an analysis where I have -log10(p) values on the cortical surface of some subjects stored as a MGH file. I would now like to run a cluster level correction on these data at the level of each individual subject using mri_mcsim followed by mri_surfcluster and I would like to constrain my inference to a ROI. I have a few questions. First of all, is it correct that I should to a -log10(p) transform on my p values before entering them in mri_surfcluster? Second, will the csd generated by mcsim be valid to feed in mri_surfcluster since the values are a -log10(p) transformed? Does mcsim -log transform the gaussian noise it uses at some point or is this not necessary? My calls to the two methods are as follows (for one hemisphere): First the mcsim: mri_mcsim --o “${subject}_mcsim_lh_${roi}" --base mc-z --surface ${subject} lh --nreps 10000 --label $roi Then the mri_surfcluster: mri_surfcluster --in "/${subject}_lh_${roi}_neglog10p_signed.mgh" \ --csd "${subject}_mcsim_lh_${roi}/fwhm05/abs/th30/mc-z.csd" \ --clabel "${subject}/label/lh.${roi}.label" \ --cwsig "${subject}_lh_${roi}_neglog10p_abs_clu05.mgh" \ --vwsig "${subject}_lh_${roi}_neglog10p_abs_vox05.mgh" \ --sum "${subject}_lh_${roi}_neglog10p_abs_summary.txt" \ --thmin 3 \ --surf white \ --subject ${subject } \ --hemi lh \ --ocn “${subject}_lh_${roi}_neglog10p_abs_clu05_clunum.mgh" \ --cwpvalthresh 0.05 In the call of mri_surfcluster, I want a cluster forming threshold of p=0.001, which would correspond to -logp(0.001)=3. Is it correct that the argument --thmin should be expressed as -log10(p) but the parameter cwpvalthresh should be p? The reason why I think I did something wrong is that I get a lot of clusters from this analysis, sometimes >15 per individual. This makes me think that the correction might not be as stringent as I would like to. Thank you, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Researcher Stanford University | 401 Quarry Rd ltozzi(a)stanford.edu<mailto:ltozzi@stanford.edu> | (650) 5615738 Connect with us! [signature_1075933358]<https://secure-web.cisco.com/154LqJFzFLISeYtGLsUgwToWD-mN0G4thIfubhtThzJ6F9…> [signature_1282923475] <http://secure-web.cisco.com/11JA0cps0LSyc_YKkvLkjj53ioS8G144vcOsjQghqMz-F2M…> [signature_911042299] <https://secure-web.cisco.com/1Mkao1uevqs0RL-8o0FG2efSSKGQAOwrHeahbv3dcsTbir…>

2 6

volume ROI to surface for cortical thickness
by M Pope 12 May '21

12 May '21

External Email - Use Caution Dear Freesurfer experts, I have created volumetric ROIs of entorhinal cortex regions and have registered them to subjects’ native space (T1). I now wish to register them to the subject surface in order to get information such as cortical thickness- using mri_vol2surf and mri_segstats I believe. I was looking at your tutorial regarding this VolumeRoiCorticalThickness - Free Surfer Wiki (harvard.edu)<https://secure-web.cisco.com/1NhD55JOKQjBEatrGH8aFF1vX2Pc2cSmUgIdVJu201vnm4…> and had a few questions. First of all- could you explain why you are going through fsaverage. Is there some kind of advantage to doing this procedure of registration, mri_vol2surf and then mri_surf2surf rather than just using mri_vol2surf with the subject space as the regheader?? When I tried through fsaverage as explained in the tutorial (following the exact same commands) the ROI appeared wrong in the surface and the thickness stats were incorrect. Secondly, when doing the procedure as per the tutorial, do you mean that we have to register each subject's mask to the fsaverage- or only one, e.g a ROI derived from the subject-specific group template (we have one produced through ANTs). Lastly- some explanation about how projfrac and projdist work would be very helpful. What numbers are considered best practice? Thankyou, Marianna Pope

2 4

Registering preop and postop MRI scans
by Peled, Noam 11 May '21

11 May '21

Dear group, I have preop and postop MRI scans of an epileptic patient. I ran recon-all on the preop, and bbregister on the postop to register it to the preop. I'm not sure why, but the results weren't really good. Maybe I should try using the longitudinal pipeline? Thanks, Noam

2 2

About segmentation of hippocampal subfields and nuclei of the amygdala
by 笹林大樹 11 May '21

11 May '21

External Email - Use Caution Dear Freesurfer experts, I am trying to assess volumes of hippocampal subfields and amygdala nuclei using Freesurfer (ver7.0). However, after following the URL below and using Matlab R2014b runtime, I am unable to proceed any further with the analysis because Matlab quits in the middle of the runtime due to an error. https://secure-web.cisco.com/1DH7AiF5RJ4wYplilcwV6vMLR0ziT4UWVek6O3a6IVZCy9… <https://secure-web.cisco.com/1DH7AiF5RJ4wYplilcwV6vMLR0ziT4UWVek6O3a6IVZCy9…> I contacted Mathworks and they instructed me to contact someone who is familiar with the operation of FreeSurfer. Therefore, could you please let us know how to solve this problem? I also attached the log. Thank you very much, Daiki Sasabayashi

2 2

Capture multiple images using freeview
by Xiaojiang Yang 11 May '21

11 May '21

External Email - Use Caution Dear FS developers, I know how to use freeview to capture one static image and save it to a file. For example, I can capture coronal view's slice 100 using this command: freeview \ -v $SUBJECTS_DIR/$subjectid/mri/orig.mgz \ -f $SUBJECTS_DIR/$ subjectid /surf/lh.white:edgecolor='255,255,255' \ -f $SUBJECTS_DIR/$ subjectid /surf/lh.pial:edgecolor='0,0,255' \ -f $SUBJECTS_DIR/$ subjectid /surf/rh.white:edgecolor='255,255,255' \ -f $SUBJECTS_DIR/$ subjectid /surf/rh.pial:edgecolor='0,0,255' \ -viewsize 1024 1024 -viewport coronal --nocursor -zoom 1.5 \ -slice 127 127 *100 *-ss tmp/captued My first question is: how can I capture all 256 coronal slices using one freeview command? If I use a loop to run that above freeview command, it would be very very slow, because it needs to load the volume and all surfaces 256 times. Do you have a method that allows me to load the volume and surfaces only once and capture many images and save them? My 2nd question is: do you have a method to capture images in the background without needing to open the freeview GUI? Thanks John

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Freesurfer May 2021