Freesurfer February 2018

freesurfer@nmr.mgh.harvard.edu

119 participants
170 discussions

Question of fs-fast
by stdp82＠virgilio.it 28 Feb '18

28 Feb '18

Hi list, I wonder to know whether the FS-FAST tool is applicable on High Res Hippo fMRI images (175x60x175mm; 0.39x2x0.39mm). In particular do you think that it could be possible to map the FC of a subfiled with the rest of the hippocampus? If yes, have you particular advises on this issue. Thanks Stefano

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demean age in CT analysis in QDEC?
by C.P.E. Rollins 28 Feb '18

28 Feb '18

Dear Freesurfer developers, I'm running a standard cortical thickness analysis between 2 patient groups (patients with schizophrenia with hallucinations (H) vs. patients with schizophrenia without hallucinations (NH)). I'm looking at the main effect of group (H vs. NH), while controlling for sex and age. I'm using default QDEC parameters (DODS, fwhm 10). I'm wondering whether I should demean age (ie., demeaned = age - mean age), as this has been recommended by FSL for VBM. I'm asking because whether or not I demean changes my results in QDEC. Moreover, I'm wondering whether it makes any difference to include age (demeaned or not) as a nuisance factor or a covariate. I've attached my qdec table (I'm not including both age and demeaned age in my model, I've just put them both in for viewing purposes. Age_MC is demeaned age). Thanks in advance, I hugely appreciate your insight. Kindest regards, Colleen -- Colleen Rollins, PhD Candidate Department of Psychiatry University of Cambridge Herchel Smith Building, Robinson Way, Cambridge CB2 0SZ

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Re: [Freesurfer] Extraction of cortical thickness in native space
by Albrecht, Daniel S. 28 Feb '18

28 Feb '18

Hi Doug, Sorry for the lack of information. We aren’t getting any specific error message or failure, it’s more so that we’re unable to get a good registration of the native space T1 to fsaverage. We tried several registration tools/commands, but an example of one of the best is below: mri_coreg –s fsaverage –mov /path_to_T1.nii.gz –reg T1_lin_fsaverage.lta –regdat T1_lin_fsaverage.dat We then visualized with the suggested tkregisterfv command: tkregisterfv –mov /path_to_T1.nii.gz –targ /path_to_fsaverage/mri/brainmask.mgz –reg T1_lin_fsaverage.dat See the relatively poor registration in the screenshot attached here. I tried to overlay this ROI using tkmedit with the registration from the step above as suggested by the “VolumeRoiCorticalThickness” page, and get the suboptimal overlay in the second attached image. Any suggestions for improving this registration? Thanks, Dan

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1st International Workshop on Predictive Processing (WoPP)
by Sanjeev Nara 28 Feb '18

28 Feb '18

Dear All, We invite you to the " 1st International Workshop on Predictive Processing (WoPP) " organized by Basque Center on Cognition, Brain and Language (BCBL) that will be held in one of most beautiful cities in europe, San Sebastian, Spain from 20 - 22 June 2018 , at Palacio Miramar in Donostia - San Sebastián. The aim of the workshop is to discuss predictive coding and its underlying mechanisms from behaviour to neuroscience. We aim at calling together researchers and students from various domains such as vision, audition and language, to build bridges between various research fields and share this common and exciting interest on prediction. Please visit http://www.bcbl.eu/events/prediction-2018/en/ for details about abstract submission and registration. Dear Researcher, We are happy to announce the new discussion arena fully centred on predictive processing. The Workshop on Predictive Processing (WoPP) will take place in San Sebastian (Spain) on June 20-22, 2018. The goal of the workshop is to address the role of predictive processing in cognition. Some of the crucial issues in this timely research topic are the extent to which prediction is a fundamental mechanism of brain function, the role of prediction in learning, and, how predictive processing is expressed across distinct cognitive domains. This workshop will gather experts from different fields in cognitive neuroscience including sensory processing, attention and memory, to work alongside the community of language processing, with the aim of furthering our understanding of the role of predictive processing in cognition. The conference will include keynote speakers, regular talks, symposiums and poster sessions. Keynote speakers will be the main sources of discussion: Sophie Scott , University College London Moshe Bar , Bar-Ilan University Pascal Fries, Ernst Strüngmann Institute (ESI) Each keynote will be followed by a symposium on a related topic. Each symposium will be co-organized by two experts in the field, and will last 2 hours. Symposium organizers are Gina Kuperberg, Matt Davis, Craig Richter, Julien Vezoli, Lucia Amoruso and Ruth De Diego Balaguer. For further information please visit: http://www.bcbl.eu/events/prediction-2018/en/ We look forward to seeing you at the conference. Yours sincerely, The Organizing Committee Manuel Carreiras, Clara Martin, Nicola Molinaro & David Soto IMPORTANT DATES TO REMEMBER: Abstract submission and Registration OPEN Abstract deadline: April, 6th, 2018. Notification of abstract acceptance : April 24th, 2018. Early registration deadline: May 11th, 2018. Online registration deadline: May 30th, 2018. Conference dates: June 20-22, 2018.

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thickness measure in basal ganglia
by Giovanni de Marco 27 Feb '18

27 Feb '18

Hello, In stats-table, I did'n t find the thickness of basal ganglia. Please, c an we get thickness in basal ganglia? ( Ma ybe freesurfer measures only the cortical thickness) Many thanks for your response. Giovanni -- Tel: +33 (0) 6 74 61 01 65 demarco.giovanni(a)gmail.com

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Invalid MEX file - FS dev-version error?
by Reetta-Liina Armio 27 Feb '18

27 Feb '18

Dear Freesurfer developers, I have run basic segmentation (and hippocampal segmentation) with Freesurfer 6.0. I have now tried to run amygdala segmentation with dev-version (downloaded from the FS-site today). I have run the same amygdalasegmentation with same platform etc in October 2017 and was able to get the volumes. I’m now trying to repeat the run with newer dev-version. I get this Error ”invalid MEX file.” So there is something wrong with the path? Could you kindly help me with this? Thank you in advance! See log-file and Matlab-version attached. Best, Reetta-Liina Armio Lähetetty iPhonesta >

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Freeview update on Mac
by Sarah Cole 27 Feb '18

27 Feb '18

Hi Doug/Zeke, Could you please update the page for freeview update on Mac- if it is available. https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview Thanks, S

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Re: [Freesurfer] Freesurfer Digest, Vol 168, Issue 54
by AKUDJEDU, THEOPHILUS 27 Feb '18

27 Feb '18

Hi Eugenio, The folder scripts/ does not contain T1.log for hippocampal subfields. It only has the log files I sent earlier. Thanks Theo ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: 27 February 2018 17:00:01 To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 168, Issue 54 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Hippocampal Subfield Error (Iglesias Gonzalez, Eugenio) 2. Re: Invalid MEX file - FS dev-version error? (Hoopes, Andrew) 3. Re: Creating ROI on the functional map (Sarah Cole) 4. Freeview update on Mac (Sarah Cole) 5. Re: Invalid MEX file - FS dev-version error? (Fereshte) 6. Re: Antwort: Re: Quality issues when running recon-all (Bruce Fischl) ---------------------------------------------------------------------- Message: 1 Date: Tue, 27 Feb 2018 16:13:30 +0000 From: "Iglesias Gonzalez, Eugenio" <e.iglesias(a)ucl.ac.uk> Subject: Re: [Freesurfer] Hippocampal Subfield Error To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CD18A07C-5FC8-4EC4-BE83-D282314FF98F(a)ucl.ac.uk> Content-Type: text/plain; charset="utf-8" Hi Theo, Sorry for not being more clear; I meant hippocampal-subfields-T1.log, which should be in the directory ?scripts?. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "AKUDJEDU, THEOPHILUS" <T.AKUDJEDU1(a)nuigalway.ie> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, 27 February 2018 at 15:31 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Hippocampal Subfield Error Dear Eugenio, Attached as requested. Thanks Theo

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Quality issues when running recon-all
by adriancarl.steiner＠uzh.ch 27 Feb '18

27 Feb '18

Dear Freesurfer community, I am at my first experience with Freesurfer. Following the tutorial, I ran Freesurfer on MR images for my Master Thesis. When running Freesurfer's 'recon-all' command on a Mac Pro to process a .nii MRI file, I was able to complete all calculations in approximately 10 hours as estimated, and obtained a message that all operations were completed without Errors or bugs. However, the image I was able to retrieve from the lh.pial file seems to be of greatly inferior quality compared to the ones we obtained from a test run using tutorial data. Attached to this mail, you will find screenshots of the MR and the lh.pial output from Freesurfer. This is the code I entered into Terminal to set up recon-all: export FREESURFER_HOME=/Volumes/LaCie/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh mri_convert -c -oc 0 0 0 /Volumes/LACIE-SHARE/Adrian/Patient data .nii/IA/IA_MRpre .nii/T1_3D_TFE_DBS.nii /Volumes/LaCie/freesurfer/buckner_data/tutorial_subjs/multimodal/fmri/fbirn-101/template.nii S_NAME=IA DATA_PATH=/Volumes/LaCie/freesurfer/buckner_data/tutorial_subjs/multimodal/fmri/fbirn-101/template.nii recon-all -i $DATA_PATH -subject $S_NAME -all Given the good quality of the MR, I expected a better quality in the Freesurfer Output. Could you please help me understand how I can improve my results? Thank you in advance for your Support Adrian Steiner

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Re: [Freesurfer] Hippocampal Subfield Error
by Iglesias Gonzalez, Eugenio 27 Feb '18

27 Feb '18

Hi Theo, Sorry for not being more clear; I meant hippocampal-subfields-T1.log, which should be in the directory “scripts”. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "AKUDJEDU, THEOPHILUS" <T.AKUDJEDU1(a)nuigalway.ie> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, 27 February 2018 at 15:31 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Hippocampal Subfield Error Dear Eugenio, Attached as requested. Thanks Theo

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Freesurfer February 2018