Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30079 discussions

Course in Advanced Neuroimaging (Barcelona)
by Erick Canales 19 Sep '16

19 Sep '16

Dear colleagues, I am pleased to announce our upcoming Course in Advanced Neuroimaging held annually in Barcelona. It takes a practical approach and does not require qualifications or previous experience in neuroimaging. It will be taught in Spanish. The multidisciplinary programme provides thorough training in the analysis of brain images from different MRI modalities and data modeling techniques, including voxel-based morphometry, cortical thickness, diffusion tensor imaging and fibre tracking, functional MRI and brain connectivity, as well as the statistical methods behind these techniques including elements of meta-analysis, and more. The course consists of a four-month online theoretical module (starting on October 17th) and a period of practical face-to-face training (split between two days in November and two weeks at the end of April) held in Barcelona. For further information, please visit the website: www.cursoneuroimagen.com Best regards, Erick J. Canales-Rodríguez, Joaquim Radua and Raymond Salvador FIDMAG Research Foundation and Sociedad Española de Neuroimagen *www.fidmag.com <http://www.fidmag.com/>*

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Unpacking DWI Data
by Emily Louise Belleau 18 Sep '16

18 Sep '16

Hello Freesurfer Experts, Our research team has recently collected data from Martinos Center. The entire scanning protocol (including anatomical, functional runs, DWI) is in one directory. Therefore I have been using unpacksdcmdir to tell me what runs go with each scanning sequence. I have had no trouble unpacking the functional and anatomical runs. I have had difficulties unpacking the DWI data. I have been recently warned that unpackdcmdir does not correctly unpack DWI data. Is there a work around or another tool I could use? It seems that most tools are for unpacking per run (dcmtonii), and would not work in my situation where all scans are in one folder? The runs that say "err" which typically indicated something is missing in the scan appear to be unpacking. However, it does say on the terminal that there is an error but attempting to unpack anyway. Some of the runs that say "ok" in the scan log are not unpacking properly. Additionally, we are finding that when we unpack on of the DWI sequences we used, we get bvec and bval files. However, we do not when we unpack a different DWI sequence we also ran we do not get the corresponding bvec and bval files. The command I am using, where I put related runs into related folders: unpacksdcmdir -src dicomdir -targ targetdir -fsfast \ -run 2 bold nii f.nii \ -run 3 bold nii f.nii \ -run 4 bold nii f.nii \ -run 5 bold nii f.nii \ -run 6 bold nii f.nii \ -run 8 3danat mgz 001.mgz \ -run 9 3danat mgz 001.mgz Any help would be great appreciated! Thanks! Rmily

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optseq2 downloading pb
by Alexandre Obert 18 Sep '16

18 Sep '16

Dear all, I would like to download optseq2 from https://surfer.nmr.mgh.harvard.edu/optseq/ it remains unavailable for several days. Is there any other way to obtain it ? Regards, Alexandre Obert -- Alexandre OBERT Doctorant en Psychologie Cognitive Université de Reims Champagne-Ardenne Laboratoire C2S : Cognition, Santé, Socialisation (EA6291) 57, rue Pierre Taittinger - 51096 Reims Cedex - France http://www.univ-reims.fr/C2S

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Any binaries while Martinos disks being repaired / FTP server is down?
by DT 17 Sep '16

17 Sep '16

I tried to download the current freesurfer release from the FTP site, and got a 550 error. After searching, I found the mailing list discussion of the disk problems / server outage with no ETA for its return. (here https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-June/046338.html and here https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-September/04766… ) Unfortunately, the source code repo, library repo seem unreachable as well. I found an unofficial copy of the source code on github ( https://github.com/neurodebian/freesurfer) but can't compile with the standard ubuntu 14.04 minc library (getting "cannot find miopen: No such file or directory" right now) and my skills at troubleshooting the compilation are... not great. Any chance that - someone can provide the linux distribution file? (i know it's huge) - someone can give me pointers with the library dependencies? - someone knows when the ftp server might be back up? If the packages exist somewhere and the server will be down for a bit, I would be happy to host the FTP site. Please let me know if I can help. Dave

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area and smoothing
by Seung Gul Kang 17 Sep '16

17 Sep '16

Dear Freesurfer experts, 1. I want to compare the area and/or areapial between two groups in qdec menu. I think that the eTIV or total surface area should be used as a covariate. Which is more appropriate between eTIV and total surface area? 2. Is there any guideline or rule for the smoothing in the thickness, area, and volume comparison? How about the smoothing=5? Thank you. Best, Seung-Gul --- *Seung Gul Kang, M.D., Ph.D. * *Psychiatrist, Associate Professor*; Department of Psychiatry, Gil Medical Center, Gachon University, School of Medicine, 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea *Research scholar*; Sleep Disorders Clinical Research Program, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, 1 Bowdoin Square, 9th floor, Boston, MA 02114, USA *Collaboration researcher*; Division of Sleep & Circadian Disorders, Brigham & Women's Hospital, Harvard Medical School, 221 Longwood Ave, Boston MA 02115 ᐧ

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Paired analysis - mismatch between matrix and contrast
by Nick Corriveau Lecavalier 16 Sep '16

16 Sep '16

Hi Freesurfer team, I'm trying to run a longitudinal group analysis (2 groups, 2 time points) using the paired analysis procedure: https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis. I have followed all the instructions but when it comes to the mri_glmfit, it says that my contrast files has 2 columns, while the matrix has 44. What did I go wrong? I join with this message the log, fsgd and contrasts files. Thank you! Nick Corriveau-Lecavalier, B.Sc. (Hons.) Étudiant au Ph.D. recherche/intervention, option neuropsychologie clinique Coordonateur à la recherche, Association étudiante des cycles supérieurs en psychologie de l'Université de Montréal (AÉCSPUM) Université de Montréal Centre de recherche de l'Institut universitaire de gériatrie de Montréal, bureau M7819

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longitudinal spc over an ROI
by Rachel Romeo 16 Sep '16

16 Sep '16

Hi, I have 3 participant groups in my data set, all with 2 longitudinal time points approximately evenly spaced. I've run everyone through the longitudinal pipeline, and used the Monte Carlo simulation to find a cluster that differs in SPC between groups 1 and 2. Now I want to calculate the average SPC in that cluster for group 3, simply for qualitative reference. I've extracted the cluster to a label using mri_surfcluster, mapped that label to each of the participants' surfaces using mri_label2label, and used mris_anatomical_stats to extract the average thickness in the ROI, and then I manually calculated SPC per subject. But, no matter whether I use participants' CROSS or LONG surfaces, I can't replicate the average SPC values in the "y.ocn.dat" file generated by the simulation. My guess is that the difference arises because of the averaging -- I'm averaging over thickness, and then calculating SPC, whereas I'm guessing that the GLM calculates SPC per voxel, and then averages over the cluster. Is there a way I can extract the average SPC for group 3 over this ROI? Thanks, Rachel

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Dev builds not found
by Leila Reddy 16 Sep '16

16 Sep '16

Hi,I get an error with mri_nu_correct.mni. I've seen on the FS wiki that this is because I have a new version of perl and that I should download the development version. However, I cannot access this page ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/ (nothing happens on a linux machine, and I get a 550 Failed to change directory error on a Mac). Is there another place I can download the fixed version from? Thanks,Leila

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Z-stat - z.mgh
by Robby De Pauw 16 Sep '16

16 Sep '16

Dear FreeSurfer users I am not able to extract the Z-values as they are not present in my output: z.mgh -- z-stat that corresponds to the significance Are these Z-values always produced (or only in case of two group comparison)? Is there a way to produce this map myself? This is my output after fitting the model (mri_glmfit) and after clusterwise correction for MC: C.dat cache.th13.abs.sig.voxel.mgh F.asc cache.th13.abs.y.ocn.dat F.csv cnr.mgh F.mgh gamma.mgh cache.th13.abs.pdf.dat gammavar.mgh cache.th13.abs.sig.cluster.mgh maxvox.dat cache.th13.abs.sig.cluster.summary sig.asc cache.th13.abs.sig.masked.mgh sig.csv cache.th13.abs.sig.ocn.annot sig.mgh cache.th13.abs.sig.ocn.mgh I am currently working on the latest version of FreeSurfer: freesurfer-Darwin-lion-stable-pub-v5.3.0 Thank you for your response, Greetings Robby Robby De Pauw, PT, MT, drs. T +32 09 332 12 19 | Email Robby.DePauw(a)Ugent.be<mailto:Robby.DePauw@ugent.be> Ghent University | Rehabilitation Sciences and Physiotherapy Campus Heymans 3B3 (022) De Pintelaan 185 BE-9000 Ghent Route to my office<https://soleway.ugent.be/routes/1090>

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hide colored slices in 3d view?
by j.oschwald＠psychologie.uzh.ch 16 Sep '16

16 Sep '16

Hi Freesurfer users, I wrote a script to automatize taking screenshots in Freeview. Unfortunately, in the 3d view the colored slices are automatically included in the picture. Is there a way to hide them? I am using the current 5.3 version of Freesurfer. I know that the development build includes this option (-hide-3d-slices), but I cannot access the FTP server right now to download it. Is there probably also a command in the version I am currently using? Best Jessica

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