Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30065 discussions

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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Re: [Freesurfer] MRI protocol for hippocampal subfield segmentation
by Gabor Perlaki 27 Feb '18

27 Feb '18

According to Bruce's request I repost the rest of thread: We set up our our hippocampal subfield T2 protocol based on the ADNI protocol (with some minor differences) as suggested by Iglesias. However, we see an artefact similar to the image found in ADNI2 training manual (page 28): http://adni.loni.usc.edu/wp-content/uploads/2012/10/ ADNI2MRITrainingManual_2014.pdf Please see the hyperintense artefact in the anterior part of the sagittal and axial images. Do you also see this artefact in your images? Do you have any idea about the cause of the artefact or do you have any suggestion on how to get rid of it?

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KWWidgets
by Melvin Robinson 27 Feb '18

27 Feb '18

A FreeSurfer build from source requires KWWidgets, but it has been deprecated for 10 years. What does Freesurfer use this code for?

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aseg and aparcstats2table on longitudinal data
by Lisa Delalande 26 Feb '18

26 Feb '18

Hi FreeSurfer experts, I would like to use the asegstats2table and the aparcstats2table commands on my longitudinal data, that have been processing following the longitudinal pipeline (recon-all -cross, - base and finally -long). And I have two questions : 1) Am I obliged to do the long_stats_slopes --qdec ./qdec/longi_presentacio.qdec.table.dat --stats aseg.stats --meas volume --do-avg --do-rate --do-pc1 --time months command before using the aseg/aparc commands ? 2) And I would like to know which subjectsID I have to choose for the command line, example : asegstats2table --subjects *001_tp1 002_tp1*...etc. (cross)? OR *template_001 template_002*...etc (base)? OR *001_tp1.long.template_001 002_tp1.long.template_002*...etc (long)? Knowing that it's for a comparison test-retest (microlongitudinal : 1 month). Thanks you for your precious help, Best regards, Lisa

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questions about the segamentation volume
by Ting Li 26 Feb '18

26 Feb '18

Hi FreeSurfer Expert, I followed the Anatomical ROI analysis tutorial and make a aseg.vol.table for the 40 subjects. However, the segment volume can various a lot in different subjects, such as Left-Lateral-Ventricle, Left-Inf-Lat-Vent. I attached a screenshot. Thanks for your response. Best wishes, Ting

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