Freesurfer

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30089 discussions

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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Hippocampal Subfield Error
by AKUDJEDU, THEOPHILUS 27 Feb '18

27 Feb '18

Dear Eugenio, Attached as requested. Thanks Theo

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Hippocampal Subfield Error
by AKUDJEDU, THEOPHILUS 27 Feb '18

27 Feb '18

Dear Eugenio, Attached are all the log files as requested. Thanks Theo ________________________________ From: AKUDJEDU, THEOPHILUS Sent: 27 February 2018 15:22 To: freesurfer(a)nmr.mgh.harvard.edu Subject: Hippocampal Subfield Error Dear Eugenio, Attached are all the log files as requested. Thanks Theo

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

27 Feb '18

Dear Theo, Would you mind sending up the log of the hippocampal subfields as well? 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 11:13 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Hippocampal Subfield Error Dear Eugenio, I executed the command below and it exited with errors (log files attached. Thanks Theo recon-all -all -s CHRM2001 -hippocampal-subfields-T1

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Hippocampal Subfield Error
by AKUDJEDU, THEOPHILUS 27 Feb '18

27 Feb '18

Dear Eugenio, I executed the command below and it exited with errors (log files attached. Thanks Theo recon-all -all -s CHRM2001 -hippocampal-subfields-T1

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