Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Hippocampus Subfield analysis error
by Hannah's USC Email 24 Jan '18

24 Jan '18

Hi Freesurfer experts, I tried to do hippocampus subfield analysis but failed. I got this error message: #@# Hippocampal Subfields processing (T1 only) left Fri Jan 19 15:27:36 PST 2018 dirname: Command not found. pwd: Command not found. pwd: Command not found. /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found. #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Fri Jan 19 15:27:36 PST 2018 dirname: Command not found. pwd: Command not found. pwd: Command not found. /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found. Your help would be greatly appreciated. Thanks!

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Which Dev Version is Best?
by Maksimovskiy, Arkadiy 24 Jan '18

24 Jan '18

Dear Experts, I was wondering if the OSX-ElCapitan Dev version of freesurfer is only for ElCapital? It has a later date of modification than the “dev” version, so I wanted to check, in case it has new patches. I am running OSX-Sierra, and would love to hear which one would be best. Thank you, Arkadiy

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White Matter Edits: Removing White Matter from the WM Surface
by Maksimovskiy, Arkadiy 24 Jan '18

24 Jan '18

Dear Experts, I came across white matter that has been included in the WM surface, but should not be there. Screenshots included; this is a little WM surface circle in the anterior prefrontal/parietal brain region. There doesn’t seem to be anything to remove from the WM volume (as screen shots shows). I was wondering if someone might be able to suggest a way to edit this. Thank you for your time, Arkadiy[cid:image001.png@01D3952B.46606090][cid:image002.png@01D3952B.46606090][cid:image003.png@01D3952B.46606090][cid:image004.png@01D3952B.46606090][cid:image005.png@01D3952B.46606090]

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mri_convert trying to find DWI parameters from Philips scans
by Rockers, Elijah D. 24 Jan '18

24 Jan '18

Hello, I am using mri_convert to convert my standard T1-weighted structural images into nifti format. The conversion works, but it might be somewhat delayed due to spamming the console with the following message ERROR: don't know how to get DWI parameters from --Philips Healthcare-- ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 DICOM File: sd_withholder/withholder_MRI/scans/1201_T1W_TFE/DICOM/1.3.46.670589.11.42034.5.0.10936.2017012009011821006-1201-95-sktipi.dcm break DICOMRead.c:5228 As far as I can tell, it spams this message once for each dicom file in the directory, and there being hundreds or even thousands of dicom files for a single subject, this can get old pretty quick. I think this might be new behavior in freesurfer 6, because I don't recall seeing this with 5.3 (although I could be wrong) Is there anyway to disable this? Thanks, - Eli Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

2 1

Question about annotation of surface volume in freeview
by Josh Gray 24 Jan '18

24 Jan '18

Hello, I am looking to highlight specific regions from desikan atlas (i.e., ?h.apart.annot; https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation) rather than all of the regions in freeview. For example, I would like to highlight middle frontal gyrus and superior frontal gyrus on the surface lh_inflated only. Is there a way to easily do this? Thank you, Josh

2 1

segmentations binair or probabilistic
by Dijkshoorn, A.B.C. (Aicha) 24 Jan '18

24 Jan '18

Dear free surfer developers, I have a method-related question. That is whether the output of the segmentations (i.e. white matter or gray matter) is binair (yes/no) or probabilistic (eg. >0.35 =gray matter and <0.35 white matter etc.) Kind regards, Aicha Dijkshoorn

2 1

Question about compare left and right hemi of longitudinal data
by lanbo Wang 24 Jan '18

24 Jan '18

Hi, all experts. I want to compare changes rate between left and right hemisphere of longitudinal data, How should I do that, how to combine xhemi with two stage or LME? Best, Lanbo

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Freesurfer longitudinal templates failed - time points from different scanners
by Ambrosino di Bruttopilo-3, S. 24 Jan '18

24 Jan '18

Dear experts, I run FreeSurfer 6.0 longitudinal pipeline on a set of scans acquired with identical protocol (ADNI) but 2 different Philips 3T scanners (all time 1 with Achieva, all time 2 with Ingenia). Unfortunately ~ 50% of the within-subjects templates completely failed. Is there anything I could try to fix this, or should just accept that is not possible to run FS longitudinal with this data? Thanks a lot! Sara ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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external WM and GM masks as input to recon-all?
by MIKHAEL Shadia 23 Jan '18

23 Jan '18

Dear FreeSurfer experts, Could you please advise on whether it would be possible to run recon-all in FreeSurfer 6.0 using externally-derived probabilistic white matter and grey matter masks, both of which include the cerebellum but not the ventricles, and if so, how? Would the flag -autorecon2-pial suffice? Thank you in advance. Shadia -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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recon-all exited with error
by Trisanna Sprung-Much 23 Jan '18

23 Jan '18

Hi there I ran Freesurfer 6.0 on a subject last night and it took about 12 hours (seemed to get to the very end) and then exited with errors. I can open my surfaces so I think it ended roughly with the atlas labelling. I attach the recon-all log file here. best wishes Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

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