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Re: [Freesurfer] Converting labels drew by freeview to volumeError: coordinate mismatch
by ZORO 04 Dec '19

04 Dec '19

External Email - Use Caution Thank you so much! It works.

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TRACULA QUESTION:CONFIGURATION FILE ISSUE
by Benxamin varela lópez 04 Dec '19

04 Dec '19

External Email - Use Caution Dear Freesurfers experts, I'm a beginner in the diffusion imaging preprocessing. I was following the freesurfer/dti tutorial with my own data when i get stuck in the trac-all step. I have created the configuration files trying to follow the tutorial instructions and when I tried to run the trac-all command I get the following error: pcpb3846:4220 lab1-rmn$ trac-all -prep -c $TUTORIAL_DATA/outputs/dmrirc.tutorial set: Variable name must contain alphanumeric characters. ERROR: must specify either one number of control points ERROR: or as many numbers as pathways You can find my configuration file in attached. Any help would be very appreciated. Thank in advance. Best regards,

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hippocampal subfields as masks for mri_segstats
by Marcel Heers 04 Dec '19

04 Dec '19

External Email - Use Caution Dear all, (dear Eugenio), I would like to use hippocampal subfields as masks for mri_segstats to retrieve intensity values. I am having problems loading the subfields file although it works fine with aseg.mgz. Does anyone know the cause? Thank you in advance! Best regards Marcel mri_segstats --seg $SUBJECTS_DIR/test/mri/aseg.mgz --ctab-default --sum output.txt --in $SUBJECTS_DIR/test/mri/T1.mgz mri_segstats --seg $SUBJECTS_DIR/test/mri/lh.hippoAymgLabels-T1.v21.HBT.mgz --sum output.txt --in $SUBJECTS_DIR/test/mri/T1.mgz ERROR: loading $SUBJECTS_DIR/test/mri/lh.hippoAymgLabels-T1.v21.HBT.mgz

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MRI label 2 label issue
by Rellick, Stephanie 04 Dec '19

04 Dec '19

External Email - Use Caution Hello, I am having an issue with the mri_label2label command. What I did was mri merge of the BA4 a and p labels for each hemisphere from the fsaverage files, ending up with a lh.BA4.label and a rh.BA4.label. I am wanting to now map the fsaverage lh.BA4.label and rh.BA4.label onto the individual subjects into my study, and was told that to do this, I needed to create those same labels using the BA4 a & p labels in the individual subject label file, and then run the command mri_label2label. This is the command that I am running: mri_label2label --srcsubject fsaverage --srclabel lh.BA4.label --trgsubject SRMC01_1.long.SRMC01 --trglabel lh.BA4.label --regmethod surface --hemi lh And it keeps giving me this error message: srclabel = lh.BA4.label srcsubject = fsaverage trgsubject = SRMC01_1.long.SRMC01 trglabel = lh.BA4.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 ./ FREESURFER_HOME /Applications/freesurfer Loading source label. Found 7403 points in source label. Starting surface-based mapping Reading source registration .//fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface .//SRMC01_1.long.SRMC01/surf/lh.white MRISread(.//SRMC01_1.long.SRMC01/surf/lh.white): could not open file No such file or directory ERROR: could not read .//SRMC01_1.long.SRMC01/surf/lh.white The lh.white file is definitely in the surface folder under that subject so I'm not sure why is says there is no such file or directory. Any help would be greatly appreciated!! Stephanie

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3 positions at Barcelonabeta Brain Research Center
by Juan Domingo Gispert López 04 Dec '19

04 Dec '19

External Email - Use Caution The Neuroimaging Research Group of the Alzheimer's Prevention Program of the Barcelonabeta Brain Research center is seeking a Post-Doctoral researcher (open to Ph.D. students), a Neuroimaging Data Analyst and a Scientific Project Manager. For further information on the positions and instructions on how to apply, please visit the following links: Post-Doctoral or PhD position: https://www.barcelonabeta.org/sites/default/files/2019-11/Predoc_postdoc_AM… Neuroimaging Data Analyst: https://www.barcelonabeta.org/sites/default/files/2019-11/MRI%20Analyst-AD%… Scientific Project Manager: https://www.barcelonabeta.org/sites/default/files/2019-11/1906%20Scientific… -- *Juan Domingo Gispert*Group Leader - Neuroimaging *BarcelonaBeta* * Brain Research Center (BBRC) *jdgispert(a)barcelonabeta.org T. (+34) 93 326 31 67 C/ Wellington, 30 <https://maps.google.com/?q=C/+Wellington,+30+08005+Barcelona&entry=gmail&so…> 08005 Barcelona <https://maps.google.com/?q=C/+Wellington,+30+08005+Barcelona&entry=gmail&so…> www.barcelonabeta.org www.fpmaragall.org ------------------------------ Confidencialitat correu electrònic BBRC <https://www.barcelonabeta.org/ca/politica-privacitat-web>. Confidencialidad correo electrónico BBRC <https://www.barcelonabeta.org/es/politica-privacidad-web>. E-mail confidentiality BBRC <https://www.barcelonabeta.org/en/privacy-policy-web>. Gràcies per estalviar paper. *Gracias por ahorrar papel. *Thanks for saving paper.

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Trouble running Freeview from Mac Terminal
by Stockmann, Jason 04 Dec '19

04 Dec '19

Hi, I have been having trouble running freeview from the Mac OS terminal via XQuartz on my laptop. I have seen the problem with both Mac OS 10.15.1 (Catalina) and the previous version of Mac OS. I get the error copied below. I am however able to run other GUIs such as fslview. The problem seems to be unique to freeview as best I can tell. Has anyone else ever experienced this error? --- Jason > [deepbrain:~] (nmr-stable60-env) freeview > X Error: BadValue (integer parameter out of range for operation) 2 > Extension: 149 (Uknown extension) > Minor opcode: 3 (Unknown request) > Resource id: 0x0 > Abort (core dumped) > [deepbrain:~] (nmr-stable60-env) > ---- Jason Stockmann Assistant Professor in Radiology A. A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Charlestown, MA 02129 jstockmann(a)mgh.harvard.edu<mailto:jstockmann@mgh.harvard.edu> +1 315 450 3309

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Converting labels drew by freeview to volume Error: coordinate mismatch
by zorothustra 04 Dec '19

04 Dec '19

External Email - Use Caution Hello Freesurfer Developers, I'm trying to get superior colliculus' ROI mannually by freeview. I load "orig.mgz" as volumes and set the "orig.mgz" as the ROI's template then draw the ROI and save it as a label file. After that I use "mri_label2vol --label sc.label --temp T1.nii --reg register.dat --o sc.nii", "T1.nii" is my initial structure image, "register.dat" got from the code:" tkregister2 --mov T1.nii --s SUB --regheader --noedit --reg register.dat", and it worked, but the coordinate mismatch, much different from the SC's position in the T1 space( Load T1.nii as volume and SC.label as ROI in freeview, and they are matched). Can anyone help me? Thank you! 1)FreeSurfer version: freesurfer-local-build-dev-20191104 2)platform: Ubuntu 18.04

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LME Contrast Question
by Hua, Jessica 04 Dec '19

04 Dec '19

External Email - Use Caution Hi FreeSurfer Experts, I had a question regarding contrasts for univariate LME models. I am interested in looking at the interaction of alcohol with change in volume across two time-points. Included in my model are covariates Gender, ICV, and Previous Drinking History. My X matrix includes 7 columns: Column 1 = 1s Column 2 = time Column 3 = alcohol Column 4 = time*alcohol Column 5 = Gender Column 6 = ICV Column 7 = Previous Drinking History My contrast is C = [0 0 0 1 0 0 0 ]. I have 4 different previous drinking history variables. However, when I change column 7 with my different previous drinking history variables, the F and P values for the interaction are the same. Am I setting up my contrasts incorrectly? Best, Jessica Hua

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Re: [Freesurfer] [External] Freesurfer Digest, Vol 190, Issue 3
by Ferraro, Pilar 04 Dec '19

04 Dec '19

External Email - Use Caution Yes, absolutely, this should work! Many Thanks! I have just one last question concerning the colors in FreeView. I have a fsgd file with class 1 (patients) coming first and then class 0 (hc) after. The contrast matrix is 1 -1 0. Among the results I see blue and red regions in Freeview. Am I correct assuming that blue regions are the ones where cortical thickness is reduced in patients relative to HC (correcting for disease duration)? I just wanted to ask for a confirmation. Many thanks, Pilar > > Message: 2 > Date: Mon, 2 Dec 2019 16:06:54 +0000 > From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] Fw: Regression Analysis accounting for one > variable > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <c8973136-8b3d-801a-9e88-2d6b8fd396be(a)mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > It sounds like it would be a one-group, two-variable situation, like this > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V > Is that not correct? > > > On 11/28/2019 5:24 AM, Ferraro, Pilar wrote: > > External Email - Use Caution > > Hi, > > I apologize if I did not explain my issue properly. > I'm interested in looking at age-related thickness reductions in 1 group (patients), but I'd like to also account for the effect of disease duration. > We can say that in my case disease duration is the nuisance factor. > Briefly, I have the same issue reported in here (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32860.html) but with only one group. > How would you recommend to proceed? > > Many thanks, > > Pilar > > ________________________________ > Message: 2 > Date: Wed, 27 Nov 2019 16:56:20 +0000 > From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu><mailto:DGREVE@mgh.harvard.edu> > Subject: Re: [Freesurfer] [External] Freesurfer Digest, Vol 189, Issue > 36 > To: "freesurfer(a)nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> > Message-ID: <fbb77a97-61b5-fac5-e2b3-0ee327e29ce3(a)mgh.harvard.edu><mailto:fbb77a97-61b5-fac5-e2b3-0ee327e29ce3@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > what is the difference between and independent variable and a covariate? > > On 11/27/2019 6:57 AM, Ferraro, Pilar wrote: >> External Email - Use Caution >> >> Yes, I did. >> But in this case I have two factors, not only one. In particular, I have an independent variable X and a covariate I?d like to include in the model. >> How would you suggest to proceed? >> >> >> Thanks, >> >> Pilar > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Re: [Freesurfer] freeview parallelized binary
by Hoopes, Andrew 04 Dec '19

04 Dec '19

Hi Dustin, The freeview binaries that we ship are the same binaries installed on the cluster. You should try specifying the number of threads available to openmp by setting the OMP_NUM_THREADS env variable to something like 4 or 8 on your local machine to see if this makes a difference. Best, Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Clark, Dustin Christopher" <clarkdc(a)bu.edu> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, November 26, 2019 at 9:43 AM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] freeview parallelized binary External Email - Use Caution Hello, We recently noticed freeview on the MGH cluster was using multiple cores when loading niftis, however, our local installation only uses one core when loading the same nifiti. Is it possible to get access to this freeview binary or the source code to build it for parallelization on our system? Thank you, Dustin Clark

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