Freesurfer November 2016

freesurfer@nmr.mgh.harvard.edu

120 participants
214 discussions

Re: [Freesurfer] Extracting structural measures from trend-level PET clusters
by Elijah Mak 14 Nov '16

14 Nov '16

Hi, A bit more info: the stack of thickness maps consists of lh.thickness.fwhm15.fsaverage.mghs that were created after -qcache. I used mri_concat --f --o to create the stack of mghs. I also noticed that the vertex values are in the range of 20-30, whereas those in the lh.thickness.fsvaerage mghs are in the expected range. Should I be using this for the calculation of the thickness in the clusters instead? Best Wishes, Elijah On Sat, Nov 12, 2016 at 12:15 AM, Elijah Mak <fkm24(a)medschl.cam.ac.uk> wrote: > Thanks, Doug. > > It works but I am not sure if the values I'm getting are correct. Is this > supposed to be reporting the mean cortical thickness of each cluster? I > have pasted the output below from the avgwf below. The names of the > clusters correspond to the regions from the "summary" text, am I right? > > > Group lh_fusiform lh_precentral lh_insular lh_precuneus lh_parsorbitalis > 1 24.29454 29.53935 14.24736 28.97924 31.54577 > 1 25.68872 28.26156 17.47828 28.20604 30.38902 > 2 25.46281 30.75879 19.34943 29.59019 32.0404 > 2 25.55514 27.23871 17.27937 29.14274 29.75657 > > Another related question: Is it possible to simply take the mean cortical > thickness across the voxels exceeding p<0.001 from the uncorrected sig.mgh? > > Thanks again! > > Best Wishes, > Elijah > > -- Elijah Mak, Gates Scholar PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ

2 1

Invalid FreeSurfer license key problem
by Xiangzhen Kong 14 Nov '16

14 Nov '16

Hi, Anyone has solved a similar problem with 'Invalid FreeSurfer license key'? I have just got a license though email, and put the four-line code in a file named license.txt. Now the file is in the folder where I installed freesurfer. It should work well but it didn't. When I used tksurfer, something was printed out. "ERROR: Invalid FreeSurfer license key found in license file xxxxx/freesurfer/license.txt" Please help. Thanks, Xiangzhen -- ----------------------------------------------------------------------------------------- Kong Xiangzhen State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China, 100875.

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Voxel time series after nuisance regressors removal using fsfast
by Ladan Shahshahani 13 Nov '16

13 Nov '16

Dear fsfast users, I've just started to use fsfast for resting state fMRI data processing. I wonder if I could have a 4-D nifti file after nuisance regressors are removed. I do not want to perform any functional connectivity analysis. I just need each voxel time series after nuisance regressors are removed. Any ideas? Thanks in advance. Ladan

2 1

dtrecon
by John Anderson 13 Nov '16

13 Nov '16

2 1

images of 0.25 tesla
by merlinverdecia＠infomed.sld.cu 12 Nov '16

12 Nov '16

Ok, thank you ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. -- Este mensaje le ha llegado mediante el servicio de correo electronico que ofrece Infomed para respaldar el cumplimiento de las misiones del Sistema Nacional de Salud. La persona que envia este correo asume el compromiso de usar el servicio a tales fines y cumplir con las regulaciones establecidas Infomed: http://www.sld.cu/

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images of 0.25 tesla
by merlinverdecia＠infomed.sld.cu 12 Nov '16

12 Nov '16

Hi, The images to which I have access are those generated by a mri with a power of 0.25 tesla. Would it be possible to process images generated by an mri that has a power of 0.25 tesla? What previous processing would I have to do? What options do I have to process these images? I would be very grateful if you would help me. Thank you in advance regards, Merlin ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. -- Este mensaje le ha llegado mediante el servicio de correo electronico que ofrece Infomed para respaldar el cumplimiento de las misiones del Sistema Nacional de Salud. La persona que envia este correo asume el compromiso de usar el servicio a tales fines y cumplir con las regulaciones establecidas Infomed: http://www.sld.cu/

2 1

Support for fsaverage surface maps in NeuroVault
by Chris Filo Gorgolewski 11 Nov '16

11 Nov '16

Dear all, I'm very happy to announce a preliminary support for uploading, visualizing and sharing surface maps in fsaverage space in NeuroVault.org. The following features are currently supported: 1. Uploading .mgh, .curv, and .gii scalar maps: 2. Visualization of the surface map projected into the MNI volume (using MNI template surface reconstruction instead of fsaverage) 3. Downloading of the maps in GIFTI format (with metadata correction making viewing of the files in both Freeview and Connectome Workbench easy). Example map: http://neurovault.org/images/31996/ Thanks to the projection to the MNI volume space all of the extra analysis features of NeuroVault (cognitive decoding using neurosynth, gene expression decoding using Allen Brain Atlas data, searching for maps with similar activation patterns) will work seamlessly. TODO (aka help needed): 1. Improve the surface reconstruction of the MNI atlas (the cortex is too thin in some areas) 2. Provide 3D visualization using brainbrowser 3. Add Connectome workbench scene files and include fsaverage GIFTI surfaces in download packages. 4. Make volume projection asynchronous to improve response time (it takes several seconds to process one map right now leaving the user with no feedback). Please let me know what do you think! Don't forget to share your maps! Best, Chris

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Re: [Freesurfer] Extracting structural measures from trend-level PET clusters
by Elijah Mak 11 Nov '16

11 Nov '16

Thanks, Doug. It works but I am not sure if the values I'm getting are correct. Is this supposed to be reporting the mean cortical thickness of each cluster? I have pasted the output below from the avgwf below. The names of the clusters correspond to the regions from the "summary" text, am I right? Group lh_fusiform lh_precentral lh_insular lh_precuneus lh_parsorbitalis 1 24.29454 29.53935 14.24736 28.97924 31.54577 1 25.68872 28.26156 17.47828 28.20604 30.38902 2 25.46281 30.75879 19.34943 29.59019 32.0404 2 25.55514 27.23871 17.27937 29.14274 29.75657 Another related question: Is it possible to simply take the mean cortical thickness across the voxels exceeding p<0.001 from the uncorrected sig.mgh? Thanks again! Best Wishes, Elijah

1 0

recon all
by John Anderson 11 Nov '16

11 Nov '16

3 7

How to view overlapping voxels across multiple sig.mgh files?
by Elijah Mak 11 Nov '16

11 Nov '16

Hi Freesurfer Team, I am just wondering if there is a neat way to derive .mgh files containing cluster information about spatially overlapping voxels across various sig.mgh? Thank you. Best Wishes, Elijah

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Freesurfer November 2016