Freesurfer May 2018

freesurfer@nmr.mgh.harvard.edu

117 participants
167 discussions

FS-FAST error:
by 高寒 29 May '18

29 May '18

External Email - Use Caution FS-FAST error: analysis language.sm05.lh does not exist, see mkanalysis-sess Hello FreeSurfer Developers, I'm attempting to run FS-FAST on my own data, as described on the FS-FAST tutorial (http://www.freesurfer.net/fswiki/FsFastTutorialV5.1/FsFastFirstLevel) but I get the following error when I run the selxavg3-sess command: ERROR: analysis language.sm05.lh does not exist, see mkanalysis-sess I assume there is something wrong with my mkanalysis-sess command because I can finish the whole process with the fsfast-functional data without an error. My research paradigm is like this: Task-fMRI*, 􏰕􏰗Picture Naming􏰞, Block-design with 30s On - 30s Off. 3 Trials. TR = 3000 ms; TE = 30 ms; flip angle = 90 degrees; matrix size = 96 􏰝 96; FOV = 240 􏰝 240 mm; 46 contiguous transversal slices; voxel size = 2.5 􏰝 2.5 􏰝 3 mm3; 3 dummy scans􏰘Scanning time = 3 min 09s. The first 3 TR have already been removed before I got the data. So I got 60 TR. And this the paradigm file<http://www.freesurfer.net/fswiki/FsFastTutorialV5.1/FsFastDirStruct> I set up: 0.000 1 30.000 1.000 recited 30.000 2 30.000 1.000 null 60.000 1 30.000 1.000 recited 90.000 2 30.000 1.000 null 120.000 1 30.000 1.000 recited 150.000 2 30.000 1.000 null This is the mkanalysis-sess command I set up: mkanalysis-sess \ -fsd bold -stc up -surface fsaverage lh -fwhm 5 \ -event-related -paradigm language.par -nconditions 2 \ -spmhrf 0 -TR 3 -refeventdur 30 -nskip 0 -polyfit 2 \ -analysis my-language.sm05.lh -per-run -force \ Thank you for help. Sincerely yours. Gao Han

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mri_label2label: Empty label file
by Emmanuel Nwosu 29 May '18

29 May '18

External Email - Use Caution Dear FreeSurfer users, I want to extract the thickness value of a significant cluster from all the subjects used for a comparison for further statistical analyses. I ran the mri_surfcluster first to create the ROI label with fsaverage and then used mri_label2label to map this label to all the subjects but the label generated for some of the subjects are empty (i.e the label file size is 0kb). Does anyone know the reason for this? and how it can be resolved? I need the label for all the subjects before running the mris_anatomical_stats and aparcstats2table. Any help on this will be appreciated. Kind regards Emmanuel

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FW: Number of iterations with --cache flag
by Backhausen, Lea 29 May '18

29 May '18

External Email - Use Caution Sorry, found it! It’s 10000 as indicated in the sig.cluster.summary file. Best, Lea Backhausen ------------------------------ Lea Backhausen Research Assistant Department of Child and Adolescent Psychiatry, Faculty of Medicine of the TU Dresden, Germany http://www.uniklinikum-dresden.de<http://www.uniklinikum-dresden.de/> From: Backhausen, Lea Sent: Tuesday, May 29, 2018 4:53 PM To: 'freesurfer(a)nmr.mgh.harvard.edu' Subject: Number of iterations with --cache flag Dear FreeSurfer Experts, I am wondering how many iterations are run in the precomputed Z Monte Carlo simulation when using the --cache flag with mri_glmfit –sim. Sorry if this has been documented somewhere, I cannot find it – can anyone direct me to the right page? Thank you for your help! Best Lea Backhausen ------------------------------ Lea Backhausen Research Assistant Department of Child and Adolescent Psychiatry, Faculty of Medicine of the TU Dresden, Germany http://www.uniklinikum-dresden.de<http://www.uniklinikum-dresden.de/>

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Command to export hippocampal subfields segmentations
by Miguel Ángel Rivas Fernández 29 May '18

29 May '18

External Email - Use Caution Hi Freesurfer developers, I was looking for the freesurfer command to export hippocampal sufields segmentations but I did not found. What is the command to export this measures and in what folder are exported the file? Thanks a lot. Best, -- *Miguel Ángel Rivas Fernández*

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Number of iterations with --cache flag
by Backhausen, Lea 29 May '18

29 May '18

External Email - Use Caution Dear FreeSurfer Experts, I am wondering how many iterations are run in the precomputed Z Monte Carlo simulation when using the --cache flag with mri_glmfit –sim. Sorry if this has been documented somewhere, I cannot find it – can anyone direct me to the right page? Thank you for your help! Best Lea Backhausen ------------------------------ Lea Backhausen Research Assistant Department of Child and Adolescent Psychiatry, Faculty of Medicine of the TU Dresden, Germany http://www.uniklinikum-dresden.de<http://www.uniklinikum-dresden.de/>

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hippo subfields and amygdala
by Erik O'Hanlon 29 May '18

29 May '18

External Email - Use Caution Hi FS experts, I have run my analysis using the dev version and have all the necessary volume.txt files. As a secondary step, I want to use some of the subfields as seed volumes for tractography (using ExploreDTI). I have may diffusion data in the same space as the FS brain.mgz but am wondering how I should make the subfield masks so that they will be in the same coordinate space when exported as a nii file. If I use Freeview and load the brain.mgz and then the subfield volumes, is it simply a case of reducing the LUT to the specific subfield and then save that as a volume/mask ? Will that mask be in the same coordinate space and regsitered the brain.nii too. Is it just a matter of doing this process numerous times in Freeview and each time simply changing the LUT corresponding to the specific ROI needed to get the masks I want to use for each subject. Thanks for any information you can offer Best regards Erik Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon(a)rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> RCSI LEADING THE WORLD TO BETTER HEALTH [cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]

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Cerebellar Parcellation Viewing and Corrections
by Rockhill, Alexander P. 25 May '18

25 May '18

Hi all, I apologize if it is well documented and I am just not seeing it but is there a way to view and edit cerebellar parcellations? Thanks, Alex Rockhill Translational Neuroengineering Laboratory Department of Psychiatry Massachusetts General Hospital, Martinos Center 149 13th St Charlestown #2301, Boston, MA 02129

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Lookup table to surface overlay
by Funk, Quentin 25 May '18

25 May '18

External Email - Use Caution Freesurfer experts, I have some lookup table volume files in MNI space that I'd like to overlay on a surface (say, fsaverage's lh.pial). Currently I'm using this command: mri_vol2surf --mov look_up_table.nii --regheader fsaverage --interp nearest --hemi lh --surf pial --o lh_lookup_overlay.mgh Then I choose "color wheel" as the overlay option in freeview. This works OK, but it's a bit imperfect. There are voxels that somehow don't get a value (and show up in the configuration window as 0's (even though the entire MNI brain is covered by the LUT), and it's a bit 'edgy' and not smooth. Are there any better ways to do this? Thanks for any help! Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003<tel:713-363-9003> Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Re: [Freesurfer] RAS coordinates for inflated surface
by Giulia Liberati 25 May '18

25 May '18

External Email - Use Caution Hi Bruce, You are right. There was a silly bug in my plotting script which I managed to fix. So now everything is at its place! Thank you very much for your patience and support! Giulia 2018-05-25 15:52 GMT+02:00 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: > Hi Giulia, > > no, that shouldn't be the case. You don't care about the RAS coordinates > of the inflated vertex - only its index. Use the index to look up the > corresponding vertex on another surface like white, then use its RAS > coords. Should work for any spot in the brain. > > cheers > Bruce > On Fri, 25 May 2018, Giulia > Liberati wrote: > > > > > External Email - Use Caution > > > > Thank you Bruce, > > > > Yes, this is what I did. > > > > Because the insular contacts are not in the insula anymore after I use > the vertex to find the RAS > > coordinates for the inflated surface, my conclusion is that this only > works with surface electrodes, > > not depth electrodes. > > > > Best wishes, > > > > Giulia > > > > On Thu, 24 May 2018 at 23:22, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > > Hi Giulia > > > > find the vertex index of the vertex you are interested in, then > read the > > surface whose RAS coordinates you want (e.g. the white or pial) and > > lookup the RAS coords of the vertex at that index. > > > > cheers > > Bruce > > On Thu, 24 May 2018, > > Giulia Liberati wrote: > > > > > > > > External Email - Use Caution > > > > > > Dear FreeSurfer experts, > > > How can you obtain RAS coordinates for an inflated surface when > you have vertex #? > > > > > > I am using the function read_surf('lh.inflated') to find the > coordinates of some > > electrode contacts > > > located in the left insula. However, when I plot the coordinates > using plotPialSurf > > (iElVis), these > > > locations are completely off (i.e., far outside from the insula). > > > > > > I don't understand what is going wrong. > > > > > > Any possible explanation? > > > > > > Thanks in advance! > > > > > > Giulia > > > > > > > > > > > > > > > -- > > > Giulia Liberati, PhD > > > > > > Institute of Neuroscience (IoNS) > > > Université catholique de Louvain > > > Avenue Mounier 53 bte B1.53.02 à 1200 Woluwe-Saint-Lambert > > > Claude Bernard; Etage 02; Local 0826; Site Bruxelles Woluwe > > > Brussels, Belgium > > > > > > > > > > -- > > Giulia Liberati, PhD > > > > Institute of Neuroscience (IoNS) > > Université catholique de Louvain > > Avenue Mounier 53 bte B1.53.02 à 1200 Woluwe-Saint-Lambert > > Claude Bernard; Etage 02; Local 0826; Site Bruxelles Woluwe > > Brussels, Belgium > > > > > -- Giulia Liberati, PhD Institute of Neuroscience (IoNS) Université catholique de Louvain Avenue Mounier 53 bte B1.53.02 à 1200 Woluwe-Saint-Lambert Claude Bernard; Etage 02; Local 0826; Site Bruxelles Woluwe Brussels, Belgium

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Re: [Freesurfer] RAS coordinates for inflated surface
by Giulia Liberati 25 May '18

25 May '18

External Email - Use Caution Thank you Bruce, Yes, this is what I did. Because the insular contacts are not in the insula anymore after I use the vertex to find the RAS coordinates for the inflated surface, my conclusion is that this only works with surface electrodes, not depth electrodes. Best wishes, Giulia On Thu, 24 May 2018 at 23:22, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Giulia > > find the vertex index of the vertex you are interested in, then read the > surface whose RAS coordinates you want (e.g. the white or pial) and > lookup the RAS coords of the vertex at that index. > > cheers > Bruce > On Thu, 24 May 2018, > Giulia Liberati wrote: > > > > > External Email - Use Caution > > > > Dear FreeSurfer experts, > > How can you obtain RAS coordinates for an inflated surface when you have > vertex #? > > > > I am using the function read_surf('lh.inflated') to find the coordinates > of some electrode contacts > > located in the left insula. However, when I plot the coordinates using > plotPialSurf (iElVis), these > > locations are completely off (i.e., far outside from the insula). > > > > I don't understand what is going wrong. > > > > Any possible explanation? > > > > Thanks in advance! > > > > Giulia > > > > > > > > > > -- > > Giulia Liberati, PhD > > > > Institute of Neuroscience (IoNS) > > Université catholique de Louvain > > Avenue Mounier 53 bte B1.53.02 à 1200 Woluwe-Saint-Lambert > > Claude Bernard; Etage 02; Local 0826; Site Bruxelles Woluwe > > Brussels, Belgium > > > > -- Giulia Liberati, PhD Institute of Neuroscience (IoNS) Université catholique de Louvain Avenue Mounier 53 bte B1.53.02 à 1200 Woluwe-Saint-Lambert Claude Bernard; Etage 02; Local 0826; Site Bruxelles Woluwe Brussels, Belgium

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Freesurfer May 2018