Freesurfer September 2020

freesurfer@nmr.mgh.harvard.edu

111 participants
165 discussions

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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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>.

1 0

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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Freesurfer September 2020