Freesurfer August 2020

freesurfer@nmr.mgh.harvard.edu

101 participants
152 discussions

Re: [Freesurfer] Cannot disable the topology correction
by k3ops＠free.fr 01 Sep '20

01 Sep '20

External Email - Use Caution Hi Douglas, thanks for your answer. I agree that desabling the topology correction is not recommended but I am dealing with subjects having many lacunar infarcts that impact this step (running for more than 2 days sometimes and leading to segmentation errors like removing gyri from cerebral cortex). Is there a way to configure the behavior of the topology correction (like number of iterations, ...) from the "recon-all" command line? Thanks, Florent On 8/25/2020 11:24 AM, dgreve(a)mgh.harvard.edu wrote: > Date: Tue, 25 Aug 2020 11:24:28 -0400 > From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] Cannot disable the topology correction > To: <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <5284d1e1-011c-2e25-9d22-e222bd9e5989(a)mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8"; format=flowed > > If the topology correction has not been done, then the stream cannot > proceed. If you really want to skip the topofix, then just copy > lh.orig.nofix to lh.orig and run with -nofix, but this is not recommeneded > > On 8/25/2020 11:04 AM, k3ops(a)free.fr wrote: > > External Email - Use Caution > > > > Hi FS team, > > > > I am having an error when disabling (-nofix) the topology correction with the recon-all command. > > The "-nofix" option is skipping the topology correction as expected but then the next step is failing because "?h.orig" file does not exist. > > > > When reading the recon-all table here: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0 > > it looks like "-fix" step (topology correction) is first copying the following file: "cp ?h.orig.nofix ?h.orig" > > So if this step is ignored with the "-nofix" option then "?h.orig" files are not created, which is causing a failure with next step (cannot read ?h.orig). > > > > Do you have any solution to that? > > My goal is to run FreeSurfer without topology correction because for some cases it is running in an infinite loop (more than 2 days of processing). > > > > Thanks, > > Florent > > > > FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 > > Platform: Ubuntu 18.04 > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mris_anatomical_stats
by Palin, Tara 01 Sep '20

01 Sep '20

External Email - Use Caution When using the following command line: mris_anatomical_stats -th3 -mgz- cortex ../label/?h.cortex.label -f ../stats/?h.aparc.pial.stats -b -a ../label/?h.aparc.annot -c ../label/aparc.annot.ctab subject ?h pial do we generate a pial surface area (for each hemisphere) that excludes the medial wall? Thank you, Tara ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Schwartz atlas reference in recon-all 3T flag
by Hye Min Shin 01 Sep '20

01 Sep '20

External Email - Use Caution Hello, I understand that from a previous FreeSurfer question the Schwartz atlas used in the 3T flag during recon-all is not published yet ( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47175.html) Since this question was asked back in 2016 I wanted to double-check if the reference atlas for the Schwartz atlas is still not published yet. Best, Julia Shin

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One hemisphere recon-all and aparc+aseg.mgz
by Alina Rojas 01 Sep '20

01 Sep '20

External Email - Use Caution Hello Freesurfer experts, i’m attempting to run recon-all on only one hemisphere for further processing steps. For these I need wmparc.mgz, aparc.a2009s+aseg.mgz, aparc+aseg.mgz. recon-all -sd ${TARGET_FOLDER} -subjid $SUBJECTID -i $T1 -qcache -openmp ${OMP_NUM_THREADS} -all -hemi lh -no-isrunning It crashes before the files are made. How can I get these files? I attached the recon-all.log file. Thank you, Alina Rojas

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Petsurfer - negative values after RBV partial volume correction
by Albrecht, Daniel S. 01 Sep '20

01 Sep '20

Hello, I’ve been running RBV partial volume correction on some amyloid PET data recently using mri_gtmpvc, and for ~90% of subjects the resulting rbv.nii.gz looks as expected with the exception of negative values in the bilateral accumbens (see attached image, thresholded from 0-4000 in scanner units). Any ideas why this might be happening? This is the command I’ve been using: mri_gtmpvc --i $PETimg \ --reg $identity_mtrx \ --seg $FSdir/${subject}/mri/gtmseg.mgz \ --psf 6 --default-seg-merge --auto-mask PSF .01 --rbv \ --no-rescale --threads 8 \ --o $outname Thanks very much, Dan

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group level analysis
by Zeng, Qi 31 Aug '20

31 Aug '20

External Email - Use Caution Hi, When conducting group-level analysis, for example comparing volumetric differences or tractography FA across subjects between groups. How we correct for the size of the brain when comparing volumetric differences or correct for the whole brain FA? Thank you so much! Best, Qi

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Re: [Freesurfer] VirtualBox Ubuntu Password Request
by fsbuild 31 Aug '20

31 Aug '20

External Email - Use Caution Hello Eileen, I will send the password to your email shortly. - R. On Aug 31, 2020, at 11:46, XU Eileen <s1659680(a)sms.ed.ac.uk> wrote:        External Email - Use Caution        Dear FreeSurfer Developers, I’m attempting to login to the Ubuntu VM disk image downloaded through the VirtualBox setup page, however I could not find the password for the “developer” account in the documentation or set up a personal account through the VM. I’m quite new to Linux, so apologies if this is a simple fix that I’ve failed to find. Many thanks,Eileen The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr..mgh.harvard.edu/mailman/listinfo/freesurfer

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VirtualBox Ubuntu Password Request
by XU Eileen 31 Aug '20

31 Aug '20

External Email - Use Caution Dear FreeSurfer Developers, I'm attempting to login to the Ubuntu VM disk image downloaded through the VirtualBox setup page, however I could not find the password for the "developer" account in the documentation or set up a personal account through the VM. I'm quite new to Linux, so apologies if this is a simple fix that I've failed to find. Many thanks, Eileen The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Postdoc Opportunity in Montréal
by Lussier,Desiree 31 Aug '20

31 Aug '20

External Email - Use Caution Seeking Postdoctoral Fellow for Multiomics Investigations in Neurodegenerative Diseases The Multiomics Investigation of Neurodegenerative Diseases Lab, directed by Dr. AmanPreet Badhwar, is looking for a postdoctoral fellow. The successful candidate will leverage extensive datasets (neuroimaging, molecular ‘omics’ and clinical/neuropsychological data) to test hypotheses linking multiomics changes to age-related dementias, with an initial focus on Alzheimer’s disease and Vascular Cognitive Impairment and Dementia (VCID). The desired candidate is a motivated individual willing to work in a highly collaborative and multidisciplinary environment. The candidate is also expected to work closely with research teams with expertise in machine learning and AI, and she/he will have opportunities to build on, and/or develop these skills. Education and experience requirements * Prior training in Neuroscience (age-related dementias a plus) or Biomedical Engineering * Experience in structural MRI, resting-state functional MRI, brain connectivity * Knowledge of Matlab and/or Python programing * Expertise in statistics (SPSS, R, Nilearn/Nistats, or other) * Team-oriented; excellent organizational, interpersonal and communication skills * Experience in multivariate pattern analysis, computational modeling, and/or machine learning are all assets Start duration and salary The position is available beginning 2021 in the laboratory of Dr. AmanPreet Badhwar, located at the Centre de Recherche de l’Institut Universitaire de Gériatrie de Montréal (CRIUGM), University of Montreal, Montreal, Canada. Funding is available for 1 year, renewable, but selected candidates are expected to apply for external fellowships. Candidates must be a Canadian citizen/permanent resident or be eligible to work in Canada (after obtaining an appropriate visa). Contact Applicants should submit a cover letter stating their research interests and experience, together with a CV, transcripts, and contact information for two reference writers. Please send as a single PDF via email with the subject heading “ApplicantName_Postdoctoral_Applicant” to Dr. AmanPreet Badhwar at amanpreet.badhwar(a)criugm.qc.ca<mailto:amanpreet.badhwar@criugm.qc.ca>. Applications will be accepted until the position is filled.

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How to re-run recon-all
by Camargo, Aldo 29 Aug '20

29 Aug '20

External Email - Use Caution Hi Freeserufer experts: By mistake I cancel the recon-all when it was about 3 hours of processing. There is a way to re-run the recon-all and that continues where it was stopped ? Thanks a lot, Aldo

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Freesurfer August 2020