Freesurfer

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30088 discussions

Correcting defect problem after checking skull stripped and editing wm.mgz
by Jiun Wei Chen 10 Sep '19

10 Sep '19

External Email - Use Caution Dear freesurfer experts, When executing recon-all in two subjects with brain lesions, the recon-all process stopped at CORRECTING DEFECT 13 (vertices=49319, convex hull=12973, v0=65403) and CORRECTING DEFECT 6 (vertices=23529, convex hull=6740, v0=16029), respectively. After reading the relevant problem from freesufer mailing list, I had checked the skull and cerebellum not attached to the surface, two hemispheres are separated using freeview. In addition, I also load the brain.mgz, wm.mgz, ?h.orig.nofix and ?h.inflated.nofix and separately overlap the ?h.defect_label onto ?h.orig.nofix , ?h.inflated.nofix to edit wm.mgz to solve this problem. However, after editing wm.mgz in two subjects, the recon-all process still stopped at CORRECTING DEFECT 0 (vertices=32853, convex hull=7926) and CORRECTING DEFECT 6 (vertices=16533, convex hull= 4510) , respectively. Although I try to erase the non-white matter and label voxels as white matter as much as possible, there are too many voxels I think I need to label, which may cause the failure. I can't figure out how to continue to solve this problem. I use freesurfer version 6.0.0. I really appreciate your help. Thanks a lot. Best regards, Jiun-Wei

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Re: [Freesurfer] Issue downloading FS-FAST fMRI tutorial data {Disarmed}
by fsbuild 09 Sep '19

09 Sep '19

External Email - Use Caution OK, give it another try. - R. I have the same issue for the following command:wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-tutorial.subjects.tar.gzIf you could add that file too, that would be great.RamiOn Mon, Sep 9, 2019 at 4:04 PM fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution        There should be a file there now, so please try it again.- robOn Sep 9, 2019, at 14:26, Rami Hamati <rhama036(a)uottawa.ca> wrote:        External Email - Use Caution        Hello there,When attempting to get the analysed functional data using the below command:wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gzI get the following OUTPUT error:--2019-09-09 14:21:20--  ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz           => ‘fsfast-functional.tar.gz’Resolving surfer.nmr.mgh.harvard.edu (surfer.nmr.mgh.harvard.edu)... 132.183.240.105Connecting to surfer.nmr.mgh.harvard.edu (surfer.nmr.mgh.harvard.edu)|132.183.240.105|:21... connected.Logging in as anonymous ... Logged in!==> SYST ... done.    ==> PWD ... done..==> TYPE I ... done.  ==> CWD (1) /pub/data ... done..==> SIZE fsfast-functional.tar.gz ... done.==> PASV ... done.    ==> RETR fsfast-functional.tar.gz ... No such file ‘fsfast-functional.tar.gz’.Could you please advise.Thank you,Rami_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Rami Hamati, MSc. Nsc (Candidate)Royal's Institute of Mental Health ResearchMood Disorders Research Unit1145 Carling Ave, Ottawa, ON K1Z 7K4T: 613-722-6521 ext. 6838rhama036@uottawa.ca_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Issue downloading FS-FAST fMRI tutorial data
by fsbuild 09 Sep '19

09 Sep '19

External Email - Use Caution There should be a file there now, so please try it again. - rob On Sep 9, 2019, at 14:26, Rami Hamati <rhama036(a)uottawa.ca> wrote:        External Email - Use Caution        Hello there,When attempting to get the analysed functional data using the below command:wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gzI get the following OUTPUT error:--2019-09-09 14:21:20--  ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz           => ‘fsfast-functional.tar.gz’Resolving surfer.nmr.mgh.harvard.edu (surfer.nmr.mgh.harvard.edu)... 132.183.240.105Connecting to surfer.nmr.mgh..harvard.edu (surfer.nmr.mgh.harvard.edu)|132.183.240.105|:21... connected.Logging in as anonymous ... Logged in!==> SYST ... done.    ==> PWD ... done.==> TYPE I ... done.  ==> CWD (1) /pub/data ... done.==> SIZE fsfast-functional.tar.gz ... done.==> PASV ... done.    ==> RETR fsfast-functional.tar.gz ... No such file ‘fsfast-functional.tar.gz’.Could you please advise.Thank you,Rami_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Extracting contrast data from mri_glmfit to graph
by cody samth 09 Sep '19

09 Sep '19

External Email - Use Caution Hello, I have a question regarding how to graph results that came from a vertex wise analysis using the command mri_glmfit and mri_glmfit-sim. I was interested in investigating an interaction effect between groups and my variable of interest (continuous) while co-varying for three nuisance variables. After running mri_glmfit and mri_glmfit-sim to correct for multiple comparisons. I visualized the results and found significant clusters. I'm interested in graphing these results. Based on archived questions to this mailing list the individual values for each cluster can be found within the ocn.dat file and the cluster information can be found in the summary file. My analysis looked at volume, thickness and surface area. Since mean volume and area is difficult to interpret I want to convert the values to a total measure. It has been suggested in the past this can be done by multiplying each individuals values within the ocn.dat file by the number of vertices the cluster has. However, from my understanding this could be done by altering the mri_segstats command (that mri_glmfit-sim automatically runs) to include the --accumulate option. When I do these methods to convert mean area and volume to total area and volume the results are different. My first question is 1) Shouldn't these values be identical? The values from multiplying mean volume by number of vertices are roughly around 3500. Whereas using the --accumulate in mri_segstats are around 2500. What could be causing this discrepancy? 2) If my cluster has a size of 1500 mm^2 (in a model for area) does it make sense that every individual's values after extraction and conversion to total area are larger than the cluster size? 3) ocn.dat files are the input values meaning they're raw and would need to be corrected in a statistically (in a similar way that I modeled it in freesurfer) before graphing right?

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freesurfer 6.0 hires fix
by Aaron Tanenbaum 09 Sep '19

09 Sep '19

External Email - Use Caution I noticed that you guys released a fix to improve the -hires option. I have been processing some of our data using the hires flag. if i use this fix do i need to run recon-all from the beginning or can I run over the old folders?

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Issue downloading FS-FAST fMRI tutorial data
by Rami Hamati 09 Sep '19

09 Sep '19

External Email - Use Caution Hello there, When attempting to get the analysed functional data using the below command: wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz I get the following OUTPUT error: --2019-09-09 14:21:20-- ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz => ‘fsfast-functional.tar.gz’ Resolving surfer.nmr.mgh.harvard.edu (surfer.nmr.mgh.harvard.edu) 132.183.240.105 Connecting to surfer.nmr.mgh.harvard.edu (surfer.nmr.mgh.harvard.edu)|132.183.240.105|:21... connected. Logging in as anonymous ... Logged in! ==> SYST ... done. ==> PWD ... done. ==> TYPE I ... done. ==> CWD (1) /pub/data ... done. ==> SIZE fsfast-functional.tar.gz ... done. ==> PASV ... done. ==> RETR fsfast-functional.tar.gz ... *No such file ‘fsfast-functional.tar.gz’.* Could you please advise. Thank you, Rami

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fspalm error
by Barbour, Tracy,M.D. 09 Sep '19

09 Sep '19

Hello Freesurfer community! I am trying to run fspalm on surface based data. I have installed PALM, fspalm, mri_surfcluster, and mri_volcluster. This is my fspalm command: fspalm --glmdir TEPSC.glmdir --cft 1.3 --twotail --name palm-twotail-1.3 --iters 1000 --2spaces --cwp .05 When I run the fspalm command I get the error: "for surface based analysis, input cannot be nii or nii.gz" I thought that fspalm was supposed to convert ces.nii.gz files into something that PALM could use. Please let me know if there is another step I need to run or if I need to change the script. Best, Tracy

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Re: [Freesurfer] Morphological Features, Description & References
by Loske, Philipp 09 Sep '19

09 Sep '19

External Email - Use Caution Hi you two, thank you very much for your quick reply! Just two short followup questions: @Bruce: Is this published in any paper or documentation so I can cite it? @Doug: Has this method been implemented with the last release of FS in 6.0.0 or already before in 5.3.0 (I'm still using this version)? Cheers Philipp For cortical volume we compute vertex-wise volume based on dividing each obliquely truncated trilateral pyramid into three tetrahedra. Based on Anderson M. Winkler's srf2vol matlab script. On 9/6/2019 10:22 AM, Bruce Fischl wrote: Hi Philipp I'll leave the volume question to Doug. The curvatures are estimated by fitting a second order polynomial to the local height function in the tangent bundle then computing the Hessian using the white (gray/white boundary) surface. We also have some discrete measures of curvature that uses the Gauss-Bonnet theorem, but those aren't run by default. cheers Bruce On Fri, 6 Sep 2019, Loske, Philipp wrote: External Email - Use Caution Hello FreeSurfer Developers, I have a question about references and descriptions to all the morphological features available in aparc.stats, extracted from structural MRI. I am using all the different features (SurfArea, GrayVol, ThickAvg, ThickStd, MeanCurv, GausCurv, FoldInd, CurvInd) for the 68 cortical regions available from the Desikan Kiliany atlas. I have been trying to find references to how these features are measured or derived, but couldn't find a proper list of references to each of the features. I a lot of references here https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation, with detailed descriptions on surface reconstruction and how cortical thickness is measured, but couldn't find a detailed explanation on the other features, especially curvature values. I think I have been able to find out what each of the measurements mean and how they are calculated in principle, through searching the internet a lot, but with no direct link to FreeSurfer. For instance, I know you can calculate the curvature values from the principle curvatures, but how does FS estimate those form the reconstructed Surface? And which one of the two surfaces does it use? White-pial or pial-csf surface? I found https://brainder.org/ really helpful, but it says for example that a new way of measuring cortical volume was implemented in FS 6.0.0, so does that mean for previous versions FS uses the Thickness x SurfaceArea method? Would be great if you can help me with this, or point me to the correct website I might just have missed during my search. Best wishes Philipp The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683.

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error while running "-hippocampal-subfields-T1" with Freesurfer 6.0
by shahrzad kharabian 09 Sep '19

09 Sep '19

External Email - Use Caution Hi, I have already run recon-all with default options on a large set of T1-weighted images, using Freesurfer v 6.0. Now we want to extract the hippocmpal subfields from these already processed images. Apparently our installation was missing Matlab Compiler Runtime (MCR) for Matlab 2012b.We followed the instructions and downloaded it and placed it in the $FREESURFER_HOME. Yet now when running the "recon-all -s subj_id -hippocampal-subfields-T1" command, I get the following error: $FREESURFER_HOME/bin: Permission denied. and the error occurs in the step: $FREESURFER_HOME/bin/segmentSF_T1.sh --- I am using a bash shell. But also temporarily changing the shell to tcsh and adding the Freesurfer to the path, did not solve the problem. How can the error be avoided? Thanks a lot for your help in advance, Shahrazd

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multiple T2s
by Aaron Tanenbaum 08 Sep '19

08 Sep '19

External Email - Use Caution Does freesurfer 6.0 have the ability to use multiple T2s in recon-all. If so how does one get it to work. It only seems to use the last T2 in the call to recon-all.

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