Freesurfer June 2017

freesurfer@nmr.mgh.harvard.edu

116 participants
186 discussions

No keyboard input accepted in freeview and tkmedit
by Caspar M. Schwiedrzik 20 Jun '17

20 Jun '17

Hi! I have a weird issue where tkmedit and freeview both do not accept any keyboard input. This is Freesurfer v5.3 running on Centos 7, connecting via RDP. I saw a couple of posts by other users having this problem, but I could not find any solutions/replies on the mailing list. Does anyone know how to fix this? Thanks, Caspar

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seed to seed replica of fsfast
by Lee, Erik Gordon 20 Jun '17

20 Jun '17

Hi All, I am trying to do some seed to seed functional connectivity calculations that replicate my analysis design in fsfast. I know FreeSurfer 6 has the fcseedcor function, but it appears that this requires a low pass filter, which is not a part of our processing stream. Also I don't think the fcseedcor function has any detrending which is a part of our analysis. I am putting together a Matlab script to do this for me, and want to be sure that the steps are equivalent. This is my normal mkanalysis-sess command: mkanalysis-sess -analysis targ.2cm.rh -surface fsaverage rh -fwhm 6 -notask -taskreg target_2cm.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -fsd rest -TR 3 -per-run -hpf .01 -tpexclude tpe_file -nuisreg global.waveform.dat 1 This is what I am doing in Matlab: -First, I apply a polynomial detrending to all the seeds and nuisance regressors (first five components from vcsf and wm, first three from mcextreg, and one component of global signal), while ignoring any bad timepoints. -Second, I make all signals evenly sampled again by applying a linear interpolation over missing timepoints for both the seeds and nuisance regressors. -Third, I apply a high order high pass filter. -Fourth, I get rid of all the timepoints that were generated from the linear interpolation (now post filtering). -Fifth, I use a glm to regress all the nuisance variables from the ROI signals. -Sixth compute the correlation coefficients between seeds using the residuals from the previous step. How similar is that to what is done in fsfast? Any tips on what to change? Thanks! Erik

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Cropping of slices during recon-all
by Jerry Jeyachandra 20 Jun '17

20 Jun '17

Hi Freesurfer team, I have a compressed nifti file converted from DICOM that I am running through recon-all. From my understanding first mri_convert is run on the original nifti file in order to generate 001.mgz which is then averaged across multiple runs to make rawavg.mgz. Since I'm only using 1 run, rawavg.mgz should be equivalent to 001.mgz. Now I've noticed that compared to simply loading in the original NIFTI image, loading in rawavg.mgz produces a cropped version of the image where the bottom section (neck region and below) is cropped out. In addition the SI axis which used to be 255 voxels in height, is now shorter (different across individuals run through recon-all). With a set of voxel indices in the original NIFTI image, I'd like to find a corresponding set of voxel indices in the cropped rawavg.mgz. Does FreeSurfer store any information related to the cropping that is done, I expect that there is only a translational shift in the SI axis but I'd like to automatically extract this value for each individual I've run through recon-all. Thanks, Jerrold Jeyachandra

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volume, thickness and surface area analyses
by Lim, Lena 20 Jun '17

20 Jun '17

Dear Freesurfer Experts, A review questioned the validity of examining volume in addition to cortical thickness and surface area within the same study. In particular, he commented that "The volume is the product of the thickness and area ...As the product of two Gaussian-distributed variables is not Gaussian-distributed, the volume is likely to violate assumptions of the statistical methods." Could you please kindly advice on this? Many thanks, Lena

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Left Cerebellum Exterior and Right Cerebellum Exterior mean value generation
by M Janani 20 Jun '17

20 Jun '17

Hi freesurfer team, I apologize, I am new to freesurfer. I'm doing analysis on PiB. I have successfully got my .stats files by running the recon-all command. When I checked for Left Cerebellum Exterior and Right Cerebellum Exterior value in the aseg.stats file, they are not exist. May I know the reason for it? Also is there any command to get the above mentioned segmentations mean value. Any guidance would be much appreciated! Regards, Janani ::DISCLAIMER:: ---------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. ----------------------------------------------------------------------------------------------------------------------------------------------------

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QModeling: a multiplatform, easy-to-use and open-source toolbox for the pharmacokinetic analysis of PET studies
by José Paredes Pacheco 20 Jun '17

20 Jun '17

Dear Freesurfer users, We have created QModeling: a multiplatform, easy-to-use and open-source toolbox for the pharmacokinetic analysis of PET studies. We think this will be useful to many of you if you use SPM. The relevance of this kind of analyses for the study of normal and pathologic brain physiology suggests the need to link kinetic modeling with the established neuroimaging pipelines for preprocessing and statistics. For this reason, QModeling has been developed as a free extension of Statistical Parametric Mapping (SPM). Currently, this new toolbox allows applying SRTM, SRTM2 and Patlak reference models to dynamic PET data. Also, preliminary testing shows reliable results and good computation times. For more details please see: - Post in Spanish: http://uimcimes.es/contenidos/general.action?idsupersection=5&idselectedsec… To download: - Post in English: http://www.uimcimes.es/contenidos/golink?p=1 The toolbox will continue to be developed, so we would be happy to have users feedback. Any question or suggestion can be sent to nroe(a)fguma.es We hope it will be of use to some of you. Best regards, José Neuroimaging technician CIMES Molecular Imaging Unit, Bioengineering department C/ Marques de Beccaria, 3 29010, Málaga Spain Contact email: j.paredes(a)fguma.es Website URL: www.uimcimes.es

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qdec FindClustersAndGotoMax Plot ERROR
by Hossein Rejali 20 Jun '17

20 Jun '17

Hello, I'm fairly new to freesurfer, I've been going through the tutorials to get my hands dirty. Currently on the Surface Group Analysis with Qdec tutorial, when applying the FindClustersAndGotoMax, the command line generates the cluster stats but underneath prints: invalid command name "FsgdfPlot_SetPoint" invalid command name "FsgdfPlot_SetInfo" There is no plot that is generated. I'm running the freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c freesurfer version. Any guidance would be much appreciated! Thank you in advance. Kinds Regards, Hossein Rejali

2 1

Libnetcdf.so.6 error during mris_make_surfaces
by Lisa Kramarenko 20 Jun '17

20 Jun '17

Hi, I am getting the following error when my HCP pipelines come to the mris_make surfaces step: mris_make_surfaces: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory I saw this response: https://www.mail-archive.com/hcp-users@humanconnectome.org/msg02418.html but the files are not available anymore and I cannot find where to download it. I have Ubuntu 14.04 (64-bit). Do you have any idea about what causes this problem and how to solve it? Thanks a lot! Lisa

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Re: [Freesurfer] LME correction in longitudinal analysis
by Livia Liu 19 Jun '17

19 Jun '17

Dear Martin, Thank you so much for all the help that you had given me. Kind regards, Livia

1 0

WM Volume
by Michael Davies 19 Jun '17

19 Jun '17

Hello, i am currently looking at the WM Volume in heat mode and am curious as to if i need to fill in all the small missing voxels located within the boundary as well as the bigger holes? Kind regards, Michael

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Freesurfer June 2017