Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30081 discussions

qdec load error missing BLT
by Joshua Lee 23 Jun '16

23 Jun '16

When loading qdec I get can't find package BLT FsgdfPlot::InitFsgdf: Couldn't find fsgdfPlot.tcl on Ubuntu with FreeSurfer5.3

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patch error
by S.V.Shepherd [work] 23 Jun '16

23 Jun '16

Hello all, I'm trying to make a patch and have run into the 'bad vertex' error. It's come up a few times on the listserv, but I never saw a public resolution. One possible source of errors is that I had to do a manual correction in FreeView, including a 'remove intersections' in FreeView. However, tksurfer had no trouble mapping the curvature to the finished surface, so I assume this was not likely to be the source of the error. Details below: $ mris_flatten -w 0 -distances 20 7 lh.cort.patch.3d lh.cort.patch.flat using write iterations = 0 sampling 7 neighbors out to a distance of 20 mm reading patch lh.cort.patch.3d with 1919246708 vertices (2846533.5% of total) MRISreadPatch: bad vertex # (1701060705) found in patch file No such file or directory stephen *stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7699

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Qdec
by j.anderson＠publicist.com 23 Jun '16

23 Jun '16

Dear Freesurfer experts, I wanted to run cortical thickness analysis between two groups to check the diffetence in thickness between the groups. I used Qdec My question is regarding correcting for multiple comparisons. There are two options FDR and montecarlo. Which option do you recommend? Are there any role that can force the analysis to be corrected with any of them Thanks John

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recon-all warnings
by Rockers, Elijah D. 23 Jun '16

23 Jun '16

Hello, Doing a recon-all -all yields some deprecation warnings. defined(@array) is deprecated at /freesurfer/mni/bin/nu_estimate_np_and_em line 165. Use of ?PATTERN? without explicit operator is deprecated at /freesurfer/mni/bin/sharpen_volume line 153. I think my results should still be OK because it's a warning, but I just wanted to make sure. Thanks, Eli Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list 10 years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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doubts
by Elias Vergílio Da Cás 23 Jun '16

23 Jun '16

Hi, *After the command: * asegstats2table --subjects AntonioMagnani -- meas volume --tablefile TESTE.txt This message: [image: Imagem inline 1] Thanks. elias. -- Atte. Elias Vergílio Da Cás - Físico UFES/HUCAM/EBSERH

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Converting fsaverage to MNI space
by Skyler Gabriel Shollenbarger 23 Jun '16

23 Jun '16

Hi FS community, I am trying to convert fsaverage to MNI space. The command did not produce computation errors, however the output file is upside down (not L-R reversed). Any thoughts on how to orient the output correctly (see attached pictures for output file)? mri_vol2vol --mov fsaverage.DKT40+aseg.nii --targ /usr/local/fsl/data/standard/MNI152_T1_2mm.nii.gz --o fsaverage_MNI_DKT40+aseg.nii --interp nearest --reg /Applications/freesurfer/average/mni152.register.dat Thank you for your time, Skyler

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matrix is ill-conditioned or badly scaled, condno = 1e+08
by Arkadiy Maksimovskiy 23 Jun '16

23 Jun '16

Hello, Hello, I am getting the following error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Command line: mri_glmfit --y lh.BD_SD.thickness.10B.mgh --fsgd FSGD_Collapsed_Across_Smokers_demeaned.fsgd dods --C BDvsSD1.mtx --surf fsaverage lh --cortex --glmdir lh.BD_SD.glmdir The FSGD file (if using one) Design matrix: Design matrix ------------------ 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 9.340 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 -2.660 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.849 0.000 0.000 0.000 0.000 0.000 -31.660 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 -37.660 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 26.340 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -0.151 0.000 0.000 0.000 0.000 0.000 -20.660; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -1.151 0.000 0.000 0.000 0.000 0.000 -22.660 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 3.849 0.000 0.000 0.000 0.000 0.000 -16.660 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -1.151 0.000 0.000 0.000 0.000 0.000 14.340 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 2.849 0.000 0.000 0.000 0.000 0.000 -27.660 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.849 0.000 0.000 0.000 0.000 0.000 4.340 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -0.151 0.000 0.000 0.000 0.000 0.000 -30.660 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.849 0.000 0.000 0.000 0.000 0.000 -28.660 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.849 0.000 0.000 0.000 0.000 0.000 -23.660 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 -27.660 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 2.849 0.000 0.000 0.000 0.000 0.000 13.340 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 5.340 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 36.340 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -1.151 0.000 0.000 0.000 0.000 0.000 -0.660 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 54.340 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -1.151 0.000 0.000 0.000 0.000 0.000 45.340 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 22.340 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 1.849 0.000 0.000 0.000 0.000 0.000 38.340 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -1.151 0.000 0.000 0.000 0.000 0.000 -12.660 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 0.849 0.000 0.000 0.000 0.000 0.000 -12.660 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -0.151 0.000 0.000 0.000 0.000 0.000 16.340 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -0.151 0.000 0.000 0.000 0.000 0.000 50.340 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 -35.660 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -1.151 0.000 0.000 0.000 0.000 0.000 59.340 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -0.151 0.000 0.000 0.000 0.000 0.000 25.340 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -1.151 0.000 0.000 0.000 0.000 0.000 32.340 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 14.340 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -0.151 0.000 0.000 0.000 0.000 0.000 -23.660 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 3.849 0.000 0.000 0.000 0.000 0.000 -22.660 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 2.849 0.000 0.000 0.000 0.000 0.000 -1.660 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 -22.660 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -0.151 0.000 0.000 0.000 0.000 0.000 3.340 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -1.151 0.000 0.000 0.000 0.000 0.000 35.340 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.849 0.000 0.000 0.000 0.000 0.000 -36.660 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.849 0.000 0.000 0.000 0.000 0.000 -39.660 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 -25.660 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -0.151 0.000 0.000 0.000 0.000 0.000 -18.660 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 -37.660 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.849 0.000 0.000 0.000 0.000 0.000 -14.660 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 4.849 0.000 0.000 0.000 0.000 0.000 -2.660 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.849 0.000 0.000 0.000 0.000 0.000 -26.660 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 19.340 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.849 0.000 0.000 0.000 0.000 0.000 23.340 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 2.849 0.000 0.000 0.000 0.000 0.000 2.340 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.849 0.000 0.000 0.000 0.000 0.000 33.340 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -2.151 0.000 0.000 0.000 0.000 0.000 29.340 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -0.151 0.000 0.000 0.000 0.000 0.000 -31.660 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 3.849 0.000 0.000 0.000 0.000 0.000 22.340 0.000 0.000 0.000; -------------------------------- FSGD File: GroupDescriptorFile 1 Title Title Class HDMale Class HDFemale Class SDMale Class SDFemale Class BDMale Class BDFemale SomeTag Variables BG_Proc BD_Clock Input 0286_recon BDMale -2.150943396 9.339622642 Input 0174_recon BDMale -2.150943396 -2.660377358 Input 0259_recon BDMale 1.849056604 -31.66037736 Input 0119_recon BDMale -2.150943396 -37.66037736 Input 0037_recon BDMale -2.150943396 26.33962264 Input 0027_recon BDFemale -0.150943396 -20.66037736 Input 0312_recon BDMale -1.150943396 -22.66037736 Input 0173_recon BDMale 3.849056604 -16.66037736 Input 0213_recon BDMale -1.150943396 14.33962264 Input 0371_recon BDMale 2.849056604 -27.66037736 Input 0109_recon BDMale 1.849056604 4.339622642 Input 0144_recon BDMale -0.150943396 -30.66037736 Input 0236_recon BDMale 0.849056604 -28.66037736 Input 0028_recon BDMale 0.849056604 -23.66037736 Input 0006_recon BDMale -2.150943396 -27.66037736 Input 0218_recon BDMale 2.849056604 13.33962264 Input 0361_recon BDMale -2.150943396 5.339622642 Input 0026_recon HDMale -2.150943396 36.33962264 Input 0098_recon HDMale -1.150943396 -0.660377358 Input 0273_recon HDMale -2.150943396 54.33962264 Input 0011_recon HDMale -1.150943396 45.33962264 Input 0304_recon HDMale -2.150943396 22.33962264 Input 0147_recon HDMale 1.849056604 38.33962264 Input 0166_recon HDMale -1.150943396 -12.66037736 Input 0170_recon HDMale 0.849056604 -12.66037736 Input 0275_recon HDMale -0.150943396 16.33962264 Input 0133_recon HDMale -0.150943396 50.33962264 Input 0021_recon HDMale -2.150943396 -35.66037736 Input 0013_recon HDMale -1.150943396 59.33962264 Input 0381_recon HDMale -0.150943396 25.33962264 Input 0380_recon HDMale -1.150943396 32.33962264 Input 0139_recon HDMale -2.150943396 14.33962264 Input 0252_recon SDMale -0.150943396 -23.66037736 Input 0209_recon SDFemale 3.849056604 -22.66037736 Input 0262_recon SDMale 2.849056604 -1.660377358 Input 0370_recon SDMale -2.150943396 -22.66037736 Input 0315_recon SDMale -0.150943396 3.339622642 Input 0244_recon SDMale -1.150943396 35.33962264 Input 0104_recon SDMale 1.849056604 -36.66037736 Input 0189_recon SDMale 0.849056604 -39.66037736 Input 0131_recon SDMale -2.150943396 -25.66037736 Input 0292_recon SDFemale -0.150943396 -18.66037736 Input 0266_recon SDMale -2.150943396 -37.66037736 Input 0069_recon SDFemale 1.849056604 -14.66037736 Input 0177_recon SDMale 4.849056604 -2.660377358 Input 0016_recon SDFemale 0.849056604 -26.66037736 Input 0372_recon SDMale -2.150943396 19.33962264 Input 0095_recon SDFemale 1.849056604 23.33962264 Input 0368_recon SDFemale 2.849056604 2.339622642 Input 0015_recon SDMale 1.849056604 33.33962264 Input 0321_recon SDMale -2.150943396 29.33962264 Input 0151_recon SDMale -0.150943396 -31.66037736 Input 0323_recon SDMale 3.849056604 22.33962264 DefaultVariable BD_Clock Note: In attempt to trouble-shoot, I demeaned this file, and am still getting the same error. My contrasts are: 0 0 0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 Thank you for your help, Arkadiy

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Re: [Freesurfer] Freesurfer Digest, Vol 148, Issue 28
by Arkadiy Maksimovskiy 23 Jun '16

23 Jun '16

Hi Doug, Still no luck getting the script- the site does not load for some reason. Any chance you might be able to paste it into the message body? Thanks, - Arkadiy On Sun, Jun 19, 2016 at 12:00 PM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: GLM_Fit Question (Douglas Greve) > 2. Using Freesurfer commands in matlab (HARI GURAGAIN) > 3. change the algorithm (N Saf) > 4. Re: change the algorithm (Bruce Fischl) > 5. Re: registering to fsaverage (Trisanna Sprung-Much) > 6. Re: registering to fsaverage (Bruce Fischl) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 18 Jun 2016 23:54:18 +0200 > From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] GLM_Fit Question > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <5765C30A.5080604(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > try now > > On 6/16/16 11:50 PM, Arkadiy Maksimovskiy wrote: > > Hi Freesurfers, > > > > I am having a similar problem with the FSGD file as the user indicated > > at this thread: > > > > > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40599.html > > > > I am trying to access the script that Doug wrote in order to fix it, > > however, the link to download the script does not seem to be working. > > I was wondering if someone might be able to upload it again. > > > > Thank you in advance for your help, > > > > Arkadiy > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Recon-all error at Talaraich transform
by Cook, Bernie 23 Jun '16

23 Jun '16

Hi all, In attempting to run a recon-all of the included subject "bert" on Mac OS X Yosemite and accompanying download, I'm receiving an error at the Talaraich transform step. However, it does not seem to be outputting a description of what is happening. With the computer I'm using, I often have to input an administrator password for something as simple as moving a file or running a "sudo" command. Would this potentially be failing because a certain permission is needed that is incapable of prompting the user for a password? If this could be the case, where might I move the file/how might I change permissions to access this? See below for the requested information. Thanks in advance. FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 14.3.-0 x86_64 1) subject name: bert 2) command line: recon-all -s bert -all 3) error message: "recon-all -s bert exited with ERRORS at Thu Jun 23 09:48:07 EDT 2016" (during Talaraich transform) 4) script/recon-all.log: see attached [1455168447449_PastedImage] Bernard L. Cook Biomedical Engineering | Class of 2017 BMES at Ohio State | Professional Development Chair '16-'17 IBRC | Undergraduate Research Assistant 440-623-4710 cook.1327(a)osu.edu<mailto:cook.1327@osu.edu>

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RA position available
by Bruce Fischl 23 Jun '16

23 Jun '16

The UCSF Department of Radiology and Biomedical Imaging is looking for a researcher with strong interests in neuroimaging interested in a Specialist position at UCSF. We are a neurodevelopment and neuroimaging lab. Specialists (research assistant) appointed at the junior rank must possess a baccalaureate degree (or equivalent degree) or four years of equivalent research experience (e.g., with instrumentation and research equipment, social science research methods, or creative activities). Specialists appointed at the Assistant or Associate rank must possess a master’s degree (or equivalent degree) or at least five years of experience demonstrating expertise in the relevant specialization. Specialists appointed at the full rank must possess a PhD degree or ten or more years of experience demonstrating expertise in the relevant specialization. The ideal candidate will have 1+ years of lab experience (beyond coursework lab experience) and familiarity with one or more of the following: Matlab, R, Linux/Unix, C+ or other statistical or MRI image analysis software such as Freesurfer or FSL. We are seeking candidates with a strong background in neurosciences or biomedical engineering who have the ability to perform independent research in addition to supporting the lab. Candidates interested in working in the lab for at least 2 years are preferred. Combining neuroimaging, genetics and computational methods, we are primarily interested in elucidating mechanisms underlying neurodevelopment. Working in close collaboration with local collaborators at UCSF and investigators at UCSD, University of Oslo, and Harvard University/Martinos Center, the specialist will assist in a) developing a novel automated MRI atlas of the human brainstem and cerebellum, b) validating this hindbrain atlas on neuroimaging pediatric datasets with brain malformations, and c) organize and analyze our large database of pediatric neuroimaging and genetics datasets that we have in-house. UC San Francisco seeks candidates whose experience, teaching, research, or community service has prepared them to contribute to our commitment to diversity and excellence. The University of California is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age or protected veteran status. To apply, please provide the following materials to Dr. Rahul Desikan (rahul.desikan(a)ucsf.edu) 1) CV (must contain previous research experience) 2) Cover Letter - Short statement on why you are interested in this position and how this position will help you achieve your career goals 3) Three references

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