Freesurfer March 2021

freesurfer@nmr.mgh.harvard.edu

106 participants
144 discussions

Error flag i <file path> unrecognized
by Timothy Brackins 19 Mar '21

19 Mar '21

External Email - Use Caution Hello FreeSurfer Developers, I am brand new to using freesurfer, just learning for the first time. I have freesurfer installed and sourced on linux Ubuntu 18.04.5 LTS. My NfTI files are stored on a windows share drive which I mount to the linux machine. Upon entering the recon-all command I receive the Error flag i <file path> unrecognized. I searched the archives but did not see a similar issue.Thank you in advance for your time and help with this. -- Timothy Brackins Doctoral Student, Cognitive Sciences Cognitive Aging and Memory (CAM) Lab Stony Brook University Email: timothy.brackins(a)stonybrook.edu <julia.kearle(a)stonybrook.edu> Lab Website: https://secure-web.cisco.com/1Ry_JC145aM8XwIFAq-LQSD7fYGd_v5PVnOcPMnS80qPgG…

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Prevent segmentHA_T1_long.sh from creating several LWPs
by Micael Andersson UMU 19 Mar '21

19 Mar '21

External Email - Use Caution Dear FreeSurfer users I have been running the longitudinal pipeline with hippocampus segmentation in FreeSurfer 7.1.1 on a computer cluster with a batch-system that regulates number of cores to use. There is though a problem when running /segmentHA_T1.sh/ and /segmentHA_T1_long.sh/ since they creates several LWPs. Setting /export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1/ does lock a process to one core at a time, but NLWP is not 1, which is a problem on the cluster system. Does anyone know how to solve this problem? Best regards Micael -- Micael Andersson Forskningsingenjör / Research engineer Umeå centre for Functional Brain Imaging (UFBI), http://secure-web.cisco.com/1FVOAhfwsPjDydJp65dw8Jr7D6RjBpT0ekDZTL4Olv87Usm… IMB, http://secure-web.cisco.com/1b9zLIOnP6D3n8IxdAvOLEP45ia7eb0r2jLKePKBOD0wuU7… Umeå universitet / University of Umeå När du skickar e-post till Umeå universitet innebär det att universitetet behandlar dina personuppgifter. Läs mer här: http://secure-web.cisco.com/127kZD8iFGMg4-p6Kat01Bm5EnfhpuTO0YX-PZEricNYuxx… By sending an email to Umeå University, the University will need to process your personal data. For more information, please read: http://secure-web.cisco.com/1Navs0amoVnm_DMw_6OVnHiV5Dl_vreYGzeu71n23GmQT5a…

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Cortical thickness on version 6 vs 7
by Xiaojiang Yang 18 Mar '21

18 Mar '21

External Email - Use Caution Dear Freesurfer developers, I have a cohort of subjects that are already run under FS 6. I recently upgraded Freesurfer from 6.0 to 7.1.1, and now I also have run these subjects under FS 7. When comparing the cortical thickness results obtained from FS6 and FS7, I found that FS 7 results are much smaller than the FS6 ones. On average, about 13%-21% decrease in the subject's average cortical thickness. Specifically, on a cohort of images from GE scanners, the average cortical thickness from FS6 is 2.5mm, but from FS7 is less than 2.0mm. According to some published papers, I think 2.5mm as the average cortical thickness is more accurate than 2.0mm. Have you encountered this issue or question before? Do you think I should keep using FS6? Please give me your advice. Thank you! John.

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Samseg longitudinal processing
by Jayachandra Raghava 18 Mar '21

18 Mar '21

External Email - Use Caution Hello Freesurfer Experts, I am using Freesurfer version 7.1.1 to perform longitudinal Samseg processing (using run_samseg_long) on my T1 longitudinal data. 1) First, I run the mri_robust_template to generate the mean.mgz using T1.mgz from the cross sectional recon-all pipeline. Would it be better to use T1.mgz from the longitudinally processed data? 2) There are few subjects who do not have followup data. How do I process these subjects to avoid the bias introduced by the longitudinal Samseg pipeline? 3) For the same subject, I see that the subcortical volumes from longitudinal recon-all pipeline from aseg.stats (e.g Left-Hippocampus volume is 3321.5mm3) are different to the subcortical volumes from longitudinal samseg pipeline from samseg.stats (e.g Left-Hippocampus volume is 3899.628686mm3). Which of these measures would be recommended? Thank you very much for your support! Best wishes Jay

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Putamen and claustrum
by Donatas Sederevicius 18 Mar '21

18 Mar '21

External Email - Use Caution Dear FreeSurfers, I had a look at the RB_all_2020-01-02.gca atlas and there was no probabilistic information regarding the claustrum. However, in the mailing archive I have found the following: "On 2 May 2017, at 17:57, Douglas Greve wrote: […] Putamen should be smaller because we now try to remove claustrum." Could you give a brief description of how you try to achieve it (if it is still the case)? Thank you. -Donatas

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7.1.1 recon-all steps verification
by Jaiashre Sridhar 18 Mar '21

18 Mar '21

External Email - Use Caution Hello, I am using FreeSurfer version v7.1.1. For few subjects who have already been through the complete recon-all pipeline, I would like to re-run the recon steps downstream of “-fill”. I am using the following commands to do so. Can an expert check and let me know if this encompasses all the downstream steps accurately for v7.1.1? ### Recon commands begin ### recon-all -s [subjid] -tessellate -smooth1 -inflate1 -qsphere -fix cd [subdir]/mri #-------------------------------------------- #@# AutoDetGWStats lh mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh #-------------------------------------------- #@# AutoDetGWStats rh mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh #-------------------------------------------- #@# WhitePreAparc lh mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 #-------------------------------------------- #@# WhitePreAparc rh mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 #-------------------------------------------- #@# CortexLabel lh mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 0 ../label/lh.cortex.label #-------------------------------------------- #@# CortexLabel+HipAmyg lh mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 1 ../label/lh.cortex+hipamyg.label #-------------------------------------------- #@# CortexLabel rh mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 0 ../label/rh.cortex.label #-------------------------------------------- #@# CortexLabel+HipAmyg rh mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 1 ../label/rh.cortex+hipamyg.label recon-all -s [subjid] -smooth2 -inflate2 -curvHK -autorecon3 ### Recon commands end ### Additional question – Is there an individual flag that replaces the hardcoded commands above for AutoDetGWStats, CortexLabel, WhitePreAparc and CortexLabel+HipAmyg? According to the [subjid]/scripts/recon-all.cmd file, I see that these additional commands are added to v7.1.1 but are not present in the recon steps listed here for stable 7.1.1 release https://secure-web.cisco.com/1mh5NrCnQZwjol6BqUWZ3zVU1wUDX0ceM5QaWcfAsgmEUH…. Thank you in advance for your response. Sincerely, Jaiashre.

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FreeSurfer brainmask.mgz: B-1 corrected?
by Arman Avesta 18 Mar '21

18 Mar '21

External Email - Use Caution Hi FreeSurfer gang, I'm using ADNI's pre-processed data to train a neural network. Specifically, for each included subject I'm using FreeSurfer Cross-Sectional brainmask.mgz (as input). My question is: are these ADNI pre-processed brainmask.mgz volumes already B1-corrected? (All ADNI subjects that I'm including in my project have B1 acquisition). If not, is there a simple way to perform B1 correction on brainmask.mgz? Thank you so much,Arman Arman Avesta, MD Radiology Resident & PhD Student Yale School of Medicine & Yale Graduate School of Arts and Sciences Email: arman.avesta(a)yale.edu Phone: 617-763-6632

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TRACULA error: missing output volume name
by Shanika Jayakody 18 Mar '21

18 Mar '21

External Email - Use Caution Dear FreeSurfer team I have been running TRACULA for some time now but recently, I come across a message "missing output volume name" and I cannot do preprocessing in new or old subjects (even subjects who completed preprocessing without error) I have not made any change to the configuration files. It is the same format that I have been using. Any advice on this is appreciated. I have attached one of the configuration files. Thanks, Shanika

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Phase encoding direction in Philips
by Benxamin varela lópez 18 Mar '21

18 Mar '21

External Email - Use Caution Hello dear experts. I am conducting a TBSS analysis. My MRI data was acquired by using a Philips Achieva. Since my data is derived from a Philips I am having problems accessing the acquisition parameters. Specifically I am interested in knowing the phase encoded direction. In the DICOM header it is specified "Phase encoding direction" = col, but there is no information about the direction (Anterior-Posterior/Posterior-Anterior). Based on the appearance of my data I assume this is a P-A acquisition but I would like to be sure (attached is a screenshot of my images). Thank you very much in advance. Benxa.

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Longitudinal Registration
by Suzan Maleki 18 Mar '21

18 Mar '21

External Email - Use Caution Hi FS experts, I appreciate it if you help me with a question on your longitudinal processing pipeline. If I use FreeSurfer to generate an unbiased T1 image template from N time points (non-linear registration), then how can I apply the within subject transformation matrix (Jacobian matrix) to that subject's DTI maps. Does FreeSurfer save the transformation matrix from N.Time-Points toward Template image? and if so, in which folder directory it will be saved? Also, given that FS uses vertices, should I first convert that transformation matrix to voxel space (eg. using surf2voxels ?) and then multiply that into different time-points of one's DTI images. Hope my questions are clear and looking forward to hearing from you:-) Best Suzan -- *Suzan Maleki* PhD Student *Brain, Mind and Society Research Hub* *Turner Institute for Brain and Mental Health* School of Psychological Sciences Monash University 770 Blackburn Road Clayton VIC 3800 Australia E: *suzan.maleki(a)monash.edu <suzan.maleki(a)monash.edu>* W: http://secure-web.cisco.com/11rJxuhHbcEcZqCYP3vJeG9D1pvF71PV1NgM7qYlH-yg7b7…

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Freesurfer March 2021