Freesurfer

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30089 discussions

TRACULA registration
by Gabriela Longo 28 Feb '18

28 Feb '18

Hi, I processed some subjects in TRACULA for a longitudinal evaluation. I registered all of them in the MNI template (set doregmni = 1 set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz). I checked the registration of my dtifit_FA.bbr.nii.gz with the MNI of all subjects. However, when I performed the group analysis, I got more NaN than expected and I checked the images and the results are outside the MNI template (I am sending a picture). I went back and checked the registration of the paths. Despite the dtifit_FA.bbr.nii.gz is correctly registered in the MNI, the paths aren't. I am struggling here to find solutions. I really appreciate any insight to help me to solve this issue. Thanks in advance, Gabriela Longo [image: Imagem inline 2]

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mri_segstats - CTABWriteFileASCII; could not open file for writing
by Yash Patel 28 Feb '18

28 Feb '18

Hello FreeSurfer experts, I am attempting to run "mri_segstats --annot [subjectid] lh aparc --sum [outputpath] --i [inputfile] --id 1001 --id 1002 ... --id 1035" Whenever I try, I receive the following error (in error.log file); CTABwriteFileASCII(/tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab): could not open for writing CTABreadASCII(/tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab): could not open file The output in the command prompt is below: cmdline mri_segstats --annot brno/661A.long.024ns lh aparc --i vol2surf/661A.v2s.0.5pf.mgh --sum stats/661A.05pf.sum --id 1001 --id 1002 --id 1003 --id 1005 --id 1006 --id 1007 --id 1008 --id 1009 --id 1010 --id 1011 --id 1012 --id 1013 --id 1014 --id 1015 --id 1016 --id 1017 --id 1018 --id 1019 --id 1020 --id 1021 --id 1022 --id 1023 --id 1024 --id 1025 --id 1026 --id 1027 --id 1028 --id 1029 --id 1030 --id 1031 --id 1032 --id 1033 --id 1034 --id 1035 --ctab-default sysname Darwin hostname ypatel-BYOD.local machine x86_64 user ypatel UseRobust 0 Constructing seg from annotation Reading annotation /Users/ypatel/Documents/brno/661A.long.024ns/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 1000 CTABwriteFileASCII(/tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab): could not open for writing No such file or directory CTABreadASCII(/tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab): could not open file No such file or directory ERROR: reading /tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab Interestingly, I ran the SAME code a few weeks ago, and everything worked fine. Somehow something has changed. I also made sure I have permission to /tmp Please let me know if you guys have a suggestion, Thank you Yash

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Fwd: Freeview update on Mac
by Sarah Cole 28 Feb '18

28 Feb '18

Great! Thank you so much, Andrew. I downloaded the updated Freeview. I am still wondering how to draw an ROI on the surface in Freeview. I don't have the options. Could you please let me know what command you are running to get the Freeview? I am having the updated version Jan 2018. Thanks, Sarah On Tue, Feb 27, 2018 at 11:40 AM, Hoopes, Andrew <AHOOPES(a)mgh.harvard.edu> wrote: > Hi Sarah, I updated the wiki page. We actually just put up a standalone, > dev freeview app today. > > best > Andrew > > > On February 27, 2018 at 11:38:57 AM, Sarah Cole (coleashley00(a)gmail.com) > wrote: > > Hi Doug/Zeke, > > Could you please update the page for freeview update on Mac- if it is > available. > > https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview > > > Thanks, > > S > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. >

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Resolution limits of FLAIR/T2w for effective pial refinement
by Christopher Markiewicz 28 Feb '18

28 Feb '18

Hi all, I wonder if people have any data (or anecdotes - I'm not picky) with regard to how high of resolution T2w or FLAIR images need to be in order to be useful for FreeSurfer's pial refinement. I've seen a couple threads suggesting the optimal is ~1mm isotropic, and that thick slice (1x1x5 mm^3) FLAIR images could be tried, but might hurt more than help, and I'm wondering if there's a suboptimal-but-still-useful range somewhere in between. For the record, this isn't a question of what scan parameters are recommended, but rather is in the context of data that's already been collected, which I would like to preprocess as well as possible. So, at what resolutions would you recommend (a) completely ignoring T2w/FLAIR images; (b) including T2w/FLAIR images that pass QC; (c) trying and seeing? Do these answers change at all with T1w resolution? -- Chris Markiewicz Center for Reproducible Neuroscience Stanford University

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Images fail to convert
by Cheryl McCreary 28 Feb '18

28 Feb '18

Dear Experts, I am trying to process a some T1 data through FreeSurfer 5.3.0, but it seems to fail during the first format conversion step. This data is from a multicenter study so I am not familiar with the acquisition details although the images visually look ok. Any suggestions? Thanks, Cheryl -- Cheryl McCreary, PhD MR Research Manager University of Calgary Ph: 403 944 8781 or 403 210 6258

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missing '*h.pial*' files, cannot find fseverage folder.
by shilin18 28 Feb '18

28 Feb '18

Hi all, very nice to find a place to ask all the fs giants a question. I run recon-all …-all -localGI, which always return this at the end. Can anyone help me find out what I need to do to evade this error? Every time I delete the shortcut folder created during the process and copy the fsaverage folder to the SUBJECT_DIR folder and run recon-all … -qcache it will go through. But I think something is missing because in the surf folder, there are no *h.pial.outer_smoothed files created. I really need the files to go forward. Also, are there ways to manually generate *h.pial-outer-smoothed and other related files, so as to accomplish the final step for iElvis if the *h.pial-outer-smoothed files and a bunch of *h.pial* files are missing? Thanks. Reporting on 70 segmentations Using PrintSegStat mri_segstats done /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/SHICEP_S15_84_KG/label INFO: fsaverage subject does not have uptodate *rhinal labels! \n cd /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR; rm -Rf fsaverage; cd - \n INFO: Creating symlink to fsaverage subject... \n cd /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR; ln -s /Applications/freesurfer/subjects/fsaverage; cd - \n #-------------------------------------------- #@# BA_exvivo Labels lh Tue Feb 27 02:44:34 PST 2018 \n mri_label2label --srcsubject fsaverage --srclabel /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/fsaverage/label/lh.BA1_exvivo.label --trgsubject SHICEP_S15_84_KG --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface \n No such file or directory mri_label2label.bin: could not open label file /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/fsaverage/label/lh.BA1_exvivo.label srclabel = /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = SHICEP_S15_84_KG trglabel = ./lh.BA1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR FREESURFER_HOME /Applications/freesurfer Loading source label. No such file or directory ERROR reading /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/fsaverage/label/lh.BA1_exvivo.label Darwin Lin.local 17.4.0 Darwin Kernel Version 17.4.0: Sun Dec 17 09:19:54 PST 2017; root:xnu-4570.41.2~1/RELEASE_X86_64 x86_64 recon-all -s SHICEP_S15_84_KG exited with ERRORS at Tue Feb 27 02:44:34 PST 2018 For more details, see the log file /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/SHICEP_S15_84_KG/scripts/recon-all.log To report a problem, seehttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Question of fs-fast
by stdp82＠virgilio.it 28 Feb '18

28 Feb '18

Hi list, I wonder to know whether the FS-FAST tool is applicable on High Res Hippo fMRI images (175x60x175mm; 0.39x2x0.39mm). In particular do you think that it could be possible to map the FC of a subfiled with the rest of the hippocampus? If yes, have you particular advises on this issue. Thanks Stefano

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demean age in CT analysis in QDEC?
by C.P.E. Rollins 28 Feb '18

28 Feb '18

Dear Freesurfer developers, I'm running a standard cortical thickness analysis between 2 patient groups (patients with schizophrenia with hallucinations (H) vs. patients with schizophrenia without hallucinations (NH)). I'm looking at the main effect of group (H vs. NH), while controlling for sex and age. I'm using default QDEC parameters (DODS, fwhm 10). I'm wondering whether I should demean age (ie., demeaned = age - mean age), as this has been recommended by FSL for VBM. I'm asking because whether or not I demean changes my results in QDEC. Moreover, I'm wondering whether it makes any difference to include age (demeaned or not) as a nuisance factor or a covariate. I've attached my qdec table (I'm not including both age and demeaned age in my model, I've just put them both in for viewing purposes. Age_MC is demeaned age). Thanks in advance, I hugely appreciate your insight. Kindest regards, Colleen -- Colleen Rollins, PhD Candidate Department of Psychiatry University of Cambridge Herchel Smith Building, Robinson Way, Cambridge CB2 0SZ

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Re: [Freesurfer] Extraction of cortical thickness in native space
by Albrecht, Daniel S. 28 Feb '18

28 Feb '18

Hi Doug, Sorry for the lack of information. We aren’t getting any specific error message or failure, it’s more so that we’re unable to get a good registration of the native space T1 to fsaverage. We tried several registration tools/commands, but an example of one of the best is below: mri_coreg –s fsaverage –mov /path_to_T1.nii.gz –reg T1_lin_fsaverage.lta –regdat T1_lin_fsaverage.dat We then visualized with the suggested tkregisterfv command: tkregisterfv –mov /path_to_T1.nii.gz –targ /path_to_fsaverage/mri/brainmask.mgz –reg T1_lin_fsaverage.dat See the relatively poor registration in the screenshot attached here. I tried to overlay this ROI using tkmedit with the registration from the step above as suggested by the “VolumeRoiCorticalThickness” page, and get the suboptimal overlay in the second attached image. Any suggestions for improving this registration? Thanks, Dan

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1st International Workshop on Predictive Processing (WoPP)
by Sanjeev Nara 28 Feb '18

28 Feb '18

Dear All, We invite you to the " 1st International Workshop on Predictive Processing (WoPP) " organized by Basque Center on Cognition, Brain and Language (BCBL) that will be held in one of most beautiful cities in europe, San Sebastian, Spain from 20 - 22 June 2018 , at Palacio Miramar in Donostia - San Sebastián. The aim of the workshop is to discuss predictive coding and its underlying mechanisms from behaviour to neuroscience. We aim at calling together researchers and students from various domains such as vision, audition and language, to build bridges between various research fields and share this common and exciting interest on prediction. Please visit http://www.bcbl.eu/events/prediction-2018/en/ for details about abstract submission and registration. Dear Researcher, We are happy to announce the new discussion arena fully centred on predictive processing. The Workshop on Predictive Processing (WoPP) will take place in San Sebastian (Spain) on June 20-22, 2018. The goal of the workshop is to address the role of predictive processing in cognition. Some of the crucial issues in this timely research topic are the extent to which prediction is a fundamental mechanism of brain function, the role of prediction in learning, and, how predictive processing is expressed across distinct cognitive domains. This workshop will gather experts from different fields in cognitive neuroscience including sensory processing, attention and memory, to work alongside the community of language processing, with the aim of furthering our understanding of the role of predictive processing in cognition. The conference will include keynote speakers, regular talks, symposiums and poster sessions. Keynote speakers will be the main sources of discussion: Sophie Scott , University College London Moshe Bar , Bar-Ilan University Pascal Fries, Ernst Strüngmann Institute (ESI) Each keynote will be followed by a symposium on a related topic. Each symposium will be co-organized by two experts in the field, and will last 2 hours. Symposium organizers are Gina Kuperberg, Matt Davis, Craig Richter, Julien Vezoli, Lucia Amoruso and Ruth De Diego Balaguer. For further information please visit: http://www.bcbl.eu/events/prediction-2018/en/ We look forward to seeing you at the conference. Yours sincerely, The Organizing Committee Manuel Carreiras, Clara Martin, Nicola Molinaro & David Soto IMPORTANT DATES TO REMEMBER: Abstract submission and Registration OPEN Abstract deadline: April, 6th, 2018. Notification of abstract acceptance : April 24th, 2018. Early registration deadline: May 11th, 2018. Online registration deadline: May 30th, 2018. Conference dates: June 20-22, 2018.

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