Freesurfer

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19 participants
30132 discussions

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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quality of hippocampal subfields with freesurfer 7 or 6
by Annelies Vant Westeinde 01 Sep '20

01 Sep '20

External Email - Use Caution Hello, I have processed (recon-all) my data both with the latest Freesurfer 7.1.1 version, and with the older Freesurfer 6.0 on Mac. I am interested in the hippocampal subfields and processed those using the segmentHA_T1.sh command on the 7.1.1 data. I am wondering though if it matters for the hippocampal subfields volume accuracy which version you ran the recon-all with. Do you recommend creating the subfields on the 7.1.1 version, or does it not matter? I am unsure which to use, because for our data, the surfaces on the cortex seem a bit more accurate with FS 6, while the subcortical regions seem more accurate with FS 7 (we want to use both in our analyses and I want to do as little editing as possible). In addition, are there any instructions on how to do quality control for the hippocampal subfields? As we can't "see" the subfields, how could we best judge which ones to discard and which not? Thank you! Annelies Annelies van't Westeinde | PHD Candidate Department of Women's and Children's Health | Karolinska Institutet 171 77 Solna | Karolinskavägen 37A +46 760967499 annelies.vant.westeinde(a)ki.se | ki.se<http://ki.se/en/startpage> ______________________________________ Karolinska Institutet – a medical university När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>.

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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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How can I get only aparc+aseg.mgz
by Camargo, Aldo 28 Aug '20

28 Aug '20

External Email - Use Caution Hi Freesurfer experts: I would like to get the aparc+aseg.mgz file, which options of recon-all should I use to get only that file. Because recon-all takes several hours. Have a nice day, Aldo

2 1

Question about LGI stats file
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 28 Aug '20

28 Aug '20

External Email - Use Caution Dear FreeSurfer experts, Hope this email finds you well. I was wondering if someone could please help clarify some components of the LGI pipeline. So the wiki tells us the following command needs to be done to obtain a stats file with the LGI info for one subject: mri_segstats --annot my_subject_id lh aparc --i $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats Should I perform this for each subject and then join them all into one file? I was hoping that you guys could direct me to some stats2table command that could do all of this automatically and thus be less time consuming. Thank you and stay safe All the best, Alex

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