Freesurfer September 2018

freesurfer@nmr.mgh.harvard.edu

109 participants
160 discussions

Re: [Freesurfer] tksurfer-sess frame time course question
by ylab 29 Sep '18

29 Sep '18

External Email - Use Caution Dear Doug, Thank you very much for your response. >> (1) why did I get Frame (0-8) for my data that should have 12 frames? > When you use -rmprestim, it subtracts the mean of the prestim baseline > AND removes the prestim time points (-4 -2 and 0) so you only end up > with 9 frames. I see. This makes perfect sense. >> (2) how can I visualize contrasts created with -setwdelay? > Your visualization command is correct. I don’t understand why you are > seeing the same image for each frame. Can you load them separately and > see if they are different? I tried to load them separately, but still got the same images. tksurfer-sess -df sessdirfile -s YY03 -analysis YY.sm5.lh -contrast w1_all_null -map sig tksurfer-sess -df sessdirfile -s YY03 -analysis YY.sm5.lh -contrast w5_all_null -map sig I also loaded /YY03/bold/YY.sm5.lh/w1_all_null/sig.nii.gz, and /YY03/bold/YY.sm5.lh/w5_all_null/sig.nii.gz, using GUI on FreeView, still got the same images. Then, I created new contrasts without -rmprestim mkcontrast-sess -analysis YY.sm5.lh -contrast w1b_all_null -a 1 -a 2 -a 3 -a 4 -a 5 -a 6 -a 7 -a 8 -c 0 -setwdelay [1 0 0 0 0 0 0 0 0 0 0 0] mkcontrast-sess -analysis YY.sm5.lh -contrast w5b_all_null -a 1 -a 2 -a 3 -a 4 -a 5 -a 6 -a 7 -a 8 -c 0 -setwdelay [0 0 0 0 1 0 0 0 0 0 0 0] Without -rmprestim, I was able to see different maps. So it looks like when I used -rmprestim, I failed to create different sig.nii.gz files for the different contrasts. Now, I can continue my analyses without -rmprestim. But I have one follow up question. (3) when I used -rmprestim with mkcontrast-sess, is it correct to assume that the statistical results produced by selxavg3-sess were based on the data with the prestimulus activation subtracted? With -rmprestim, sig.nii.gz had 9 frames. I am confused because, the data I visualized with freesurfer version 5 by clicking the activated areas had 12 frames. I am wondering where did the first three frames came from in those plots. Thank you in advance. Shogo

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Re recon -all
by Miguel Ángel Rivas Fernández 28 Sep '18

28 Sep '18

External Email - Use Caution Hi Freesurfer devs, I tried to re run the recon -all after put some control points in the brainmask and I get the following error: pcpb3846:~ lab1-rmn$ recon -all -autorecon2-cp -autorecon3 -4025 cp_before -bash: recon: command not found What could be the problem? The Freesurfer version that I am using at this moment is freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Thanks in advance, Best, -- *Miguel Ángel Rivas Fernández*

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Clarification about .annot file format
by paul mccarthy 28 Sep '18

28 Sep '18

External Email - Use Caution Howdy, There is a discussion regarding the .annot file format over at the nibabel github repository, regarding the interpretation of the flag/alpha value: https://github.com/nipy/nibabel/issues/649 If one wishes to create an .annot file with colours that have a transparency value, how should it be stored in the file? By piecing together the information from the freesurfer code [1,2], and Graham Wideman's helpful notes [3], I came to the conclusion that alpha values should be stored as 1-the actual value. But it would be great to get some clarification on this from somebody who knows more than me Thanks very much, Paul McCarthy [1] https://github.com/freesurfer/freesurfer/blob/dev/matlab/read_annotation.m [2] https://github.com/freesurfer/freesurfer/blob/dev/matlab/write_annotation.m [3] https://surfer.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles#Annota…

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longitudinal TRACULA -prep error
by Carissa Nicole Weis 27 Sep '18

27 Sep '18

External Email - Use Caution Hello, I'm running into an error in the longitudinal TRACULA pipeline that I'm not sure how to resolve. I saw this error in the message board but there was no resolution to the problem so I thought I'd ask again. I've successfully run the recon-all longitudinal pipeline and am trying to run the trac-all -prep step with a longitudinal configuration file. Here's the error, it happens for both time points listed in my configuration file: #@# Image corrections Thu Sep 27 12:59:31 CDT 2018 mri_convert /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1 /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz mri_convert /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1 /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ reading from /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1... crypt_gkey = *CyXds2s6sOqQ Starting DICOMRead2() dcmfile = /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1 dcmdir = /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI Ref Series No = 6 Found 2666 files, checking for dicoms Found 2660 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 2 Vs: 0 0 1 Second Sorting Counting frames nframes = 38 nslices = 70 ndcmfiles = 2660 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=10000.00, TE=57.70, TI=0.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (-0, -0, 1) writing to /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz... crypt_gkey = *CyXds2s6sOqQ mri_probedicom --i /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1 > /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dcminfo.dat cp /bigraid-03/LS/Scripts/iStar/DTI_CWEIS_MS/istar_bvecs.txt /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvecs cp /bigraid-03/LS/Scripts/iStar/DTI_CWEIS_MS/istar_bvals.txt /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvals mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs.tmp /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvecs mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvals.tmp /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvals flip4fsl /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 2 fslswapdim /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz x -y z /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz INFO: found /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.mghdti.bvecs /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.mghdti.bvals /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvals eddy_correct /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi.nii.gz 0 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0000 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0001 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0002 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0003 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0004 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0005 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0006 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0007 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0008 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0009 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0010 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0011 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0012 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0013 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0014 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0015 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0016 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0017 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0018 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0019 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0020 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0021 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0022 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0023 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0024 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0025 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0026 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0027 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0028 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0029 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0030 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0031 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0032 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0033 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0034 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0035 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0036 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0037 mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs.norot xfmrot /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi.ecclog /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs.norot /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi.nii.gz /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_eddy.nii.gz mri_convert / /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/b0mag.nii.gz mri_convert / /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/b0mag.nii.gz corRead(): can't open file /COR-.info $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ reading from /... crypt_gkey = *CyXds2s6sOqQ Linux vis-1.mortimer 2.6.32-754.3.5.el6.x86_64 #1 SMP Tue Aug 14 20:46:41 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Thu Sep 27 13:41:04 CDT 2018 #------------------------------------- /sharedapps/LS/psych_imaging/freesurfer/5.3.0_9.19.18/bin/trac-preproc #------------------------------------- #@# Inter-subject registration (base template) Thu Sep 27 13:41:05 CDT 2018 cp /bigraid-03/LS/Data/istar/freesurfer/106_day2.fs.long.106/dmri/xfms/mni2anatorig.mat /bigraid-03/LS/Data/istar/freesurfer/106_day2.fs.long.106/dmri/xfms/anatorig2mni.mat /bigraid-03/LS/Data/istar/freesurfer/106/dmri/xfms cp: cannot stat `/bigraid-03/LS/Data/istar/freesurfer/106_day2.fs.long.106/dmri/xfms/mni2anatorig.mat': No such file or directory cp: cannot stat `/bigraid-03/LS/Data/istar/freesurfer/106_day2.fs.long.106/dmri/xfms/anatorig2mni.mat': No such file or directory Linux vis-1.mortimer 2.6.32-754.3.5.el6.x86_64 #1 SMP Tue Aug 14 20:46:41 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Thu Sep 27 13:41:05 CDT 2018 Here's the contents of my configuration file: setenv SUBJECTS_DIR /bigraid-03/LS/Data/istar/Freesurfer setsubjlist= ( 106_day2.fs 106_6mo.fs ) set baselist = ( 106 106 ) set runlist = (1 2) set dcmlist = ( /bigraid-03/LS/RawData/iSTAR/106_day2/106_day2/p*/e*/DTI_all/DTI/*.1 /bigraid-03/LS/RawData/iSTAR/106_6mo /106_6mo/p*/e*/DTI_all/DTI/*.1 ) set bvecfile = /bigraid-03/LS/Scripts/iStar/DTI_CWEIS_MS/istar_bvecs.txt set bvalfile = /bigraid-03/LS/Scripts/iStar/DTI_CWEIS_MS/istar_bvals.txt set dob0 = 1 set b0mlist = None set b0plist = None set echospacing=None set doeddy =1 set dorotbvecs =1 set thrbet = 0.5 set doregflt =0 set doregbbr =1 set doregmni =1 set mnitemp= $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz set dogregcvs = 0 set cvstemp =cvs_avg35 set cvstempdir = $FREESURFER_HOME/subjects set usemaskanat =1 set pathlist = (lh.unc_AS rh.unc_AS fmajor_PP fminor_PP lh.ccg_PP rh.ccg_PP lh.cab_PP rh.cab_PP ) set ncpts = (5 5 7 5 5 5 4 4) set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt set nstick =2 set nburnin =200 set nsample = 7500 set nkeep = 5 set reinit =0 Thanks so much for your help! Carissa Carissa N. Weis, B.S. Graduate Student Affective Neuroscience Laboratory University of Wisconsin-Milwaukee cnweis(a)uwm.edu

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Re: [Freesurfer] Reporting Cohen's D for a significant cluster
by Maksimovskiy, Arkadiy 27 Sep '18

27 Sep '18

Hi Bruce, I am including the previous correspondence below, but here is a quick summary: My goal is to get the Cohen’s D value for a max vertex of a significant cluster. I entered the max vertex number in the bottom left of the freeview window (cursor window), where it says vertex. When I hit enter, RAS coordinates change, but the vertex # goes back to what it was previously and Cohen’s D (loaded as an overlay) does not change. The cohen’s D only changes when I move the mouse and click manually. I am attaching two screenshots of the before, during entry, and after to illustrate the process. * arkadiy [cid:image001.png@01D455A5.FF5396E0][cid:image002.png@01D455A5.FF5396E0][cid:image003.png@01D455A5.FF5396E0] Previous Correspondence: Hi Arkadiy can you include the previous correspondance so we have context? And what window did you enter numbers? Was it the left hand side of the info window (under "cursor")? cheers Bruce On Wed, 26 Sep 2018, Maksimovskiy, Arkadiy wrote: Hi Bruce, I wanted to follow up on this as I was unsuccessful in doing what you suggested using Freeview (2.0)- entering numbers into the window does not change anything. Might there be another way to find out the Cohen’s D? Thank you for your help, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School Re: [Freesurfer] Reporting Cohen's D for a significant cluster<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg59519.html> 2018-09-20<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…> Thread<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…> Maksimovskiy, Arkadiy<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> Hi Bruce, Thank you so much for the tip and the quick response. For some reason, the position and Cohen’s D value do not change when I input the vertex and I think this might be due to an outdated Freeview version (2.0) that I am using. I attempted to load the new one from this link: https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview But I am getting an error: The requested URL /pub/dist/freesurfer/freeview/freeview_osx.tar.gz was not found on this server. I was wondering if you have this file available at another location? Thanks again, arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School ___ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Re: [Freesurfer] Reporting Cohen's D for a significant cluster<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg59515.html> 2018-09-20<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…> Thread<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…> Bruce Fischl<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> Hi Arkadiy if you have the surface loaded you can always type a vertex number into the info field (that shows the current selected vertex) at the bottom of the freeview window. It will then jump to that vertex, and adjust the views accordingly cheers Bruce On Thu, 20 Sep 2018, Maksimovskiy, Arkadiy wrote: Update: It occurred to me that reporting it for the max verted might be the best idea. In this case, might anyone know what is the best way to navigate the Freeview to a specific vertex number (is there a place where I can input that number). Thanks again. From: "Maksimovskiy, Arkadiy" Date: Thursday, September 20, 2018 at 10:56 AM To: "freesurfer(a)nmr.mgh.harvard.edu" Subject: Reporting Cohen's D for a significant cluster Dear Experts, I was requested to report the Cohen’s D value for a significant cluster, which resulted from a cortical thickness analysis. I was able to calculate it and open the resulting Cohen’s D mgh file in Freeview, together with the file, indicating a significant cluster. As expected, when I move the cursor within the significant cluster, Cohen’s D value changes with every vertex. I was wondering if you might have any recommendations for which of the Cohen’s D values to report, and how best to obtain that value? Thank you for your help, arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School ___ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Re: [Freesurfer] Reporting Cohen's D for a significant cluster<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg59514.html> 2018-09-20<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…> Thread<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…> Maksimovskiy, Arkadiy<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> Update: It occurred to me that reporting it for the max verted might be the best idea. In this case, might anyone know what is the best way to navigate the Freeview to a specific vertex number (is there a place where I can input that number). Thanks again. From: "Maksimovskiy, Arkadiy" Date: Thursday, September 20, 2018 at 10:56 AM To: "freesurfer(a)nmr.mgh.harvard.edu" Subject: Reporting Cohen's D for a significant cluster Dear Experts, I was requested to report the Cohen’s D value for a significant cluster, which resulted from a cortical thickness analysis. I was able to calculate it and open the resulting Cohen’s D mgh file in Freeview, together with the file, indicating a significant cluster. As expected, when I move the cursor within the significant cluster, Cohen’s D value changes with every vertex. I was wondering if you might have any recommendations for which of the Cohen’s D values to report, and how best to obtain that value? Thank you for your help, arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School ___ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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Research Specialist Position at the Center for Healthy Minds
by Center for Healthy Minds Recruiting 27 Sep '18

27 Sep '18

External Email - Use Caution Hello! The Center for Healthy Minds (CHM) at the University of Wisconsin-Madison is currently seeking a Research Specialist! The Research Specialist will be responsible for scientific integrity of data collection, data processing, and participant recruitment, screening, and scheduling for research at CHM. This individual may work on several research projects examining the import of individual differences in the time course of emotional responses for varied domains including cognition, health, and well-being, while elucidating the critical functional and structural brain substrates underlying these relationships. Please see the attached position description for more information. Warmly, Audrey Jacobsen Administrative Assistant The Center for Healthy Minds University of Wisconsin-Madison Pronouns: she/hers

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tksurfer-sess frame time course question
by 伊藤匠吾 27 Sep '18

27 Sep '18

External Email - Use Caution Hello, I am new to FreeSurfer. I conducted an experiment with event-related design. There were eight non-fixation conditions. In every trial, a simple stimulus was presented for about 1.5 sec, and the subject made a button press. I did the following analyses: preproc-sess -df sessdirfile -s YY03 -per-run -fwhm 5 -sliceorder siemens -surface fsaverage lhrh -mni305 -fsd bold mkanalysis-sess -a YY.sm5.lh -surface fsaverage lh -TR 2 -p OWN.par -event-related -fsd bold -per-run -fwhm 5 -nconditions 8 -mcextreg -fir 4 24 -polyfit 2 -force mkcontrast-sess -analysis YY.sm5.lh -contrast all_null -a 1 -a 2 -a 3 -a 4 -a 5 -a 6 -a 7 -a 8 -c 0 -rmprestim selxavg3-sess -df sessdirfile -sf sessid -analysis YY.sm5.lh then, I checked the data with tksurfer-sess (tksurfer-sess -df sessdirfile -s YY03 -analysis YY.sm5.lh -contrast all_null). When clicked Overlay/Configure, I see Frame (0-8). Frame #1 shows clear task-related activations (visual, auditory, motor areas). Because I used -fir 4 24, I think I should have 12 time points, not 9. I am currently using version 6, but I also checked the data with version 5, confirmed the same outcome. raw plots by tksurfer-sess (version 5) showed hemodynamic responses for -4 sec to 20 sec. So the data seem to have correct length. Then, I created several contrasts with -setwdelay for all_null weigting different time points like this w1_all_null : 1 0 0 0 0 0 0 0 0 0 0 0 w3_all_null : 0 0 1 0 0 0 0 0 0 0 0 0 w5_all_null : 0 0 0 0 1 0 0 0 0 0 0 0 w7_all_null : 0 0 0 0 0 0 1 0 0 0 0 0 with the following command, I see 4 frames, which probably correspond to each contrast. tksurfer-sess -df sessdirfile -s YY03 -analysis YY.sm5.lh -contrast w1_all_null -contrast w3_all_null -contrast w5_all_null -contrast w7_all_null However, when changing "frame" gives exactly the same image. (1) why did I get Frame (0-8) for my data that should have 12 frames? (2) how can I visualize contrasts created with -setwdelay? I would appreciate for any comments/suggestions. Here is my environment: -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Users/guest/Documents/FreeSurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl ------------------------------------------------------------------ Thank you! Shoo

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Freeview error
by Md. Mamun Al-Amin 27 Sep '18

27 Sep '18

External Email - Use Caution Dear Experts I have been encountered a problem opening Freeview window in Mac Terminal. Could you please help me troubleshooting this problem? Here is the screenshot. Thanks in advance. -- Kind regards Md. Mamun Al-Amin ------------------------------ *PhD Candidate, Queensland Brain Institute* *The University of Queensland* *Building 79, St Lucia QLD 4072* *https://qbi.uq.edu.au/profile/877/md-mamun-al-amin <https://qbi.uq.edu.au/profile/877/md-mamun-al-amin>*

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Re: [Freesurfer] Best way to update Freeview
by Maksimovskiy, Arkadiy 27 Sep '18

27 Sep '18

Hi everyone, I was able to download Freeview- the link now works. However I am having an issue with starting this version. bash-3.2$ export FREESURFER_HOME=/Applications/freesurfer_6.0/ bash-3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer_6.0/ FSFAST_HOME /Applications/freesurfer_6.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Volumes/DrEmetBrown/ MNI_DIR /Applications/freesurfer_6.0/mni bash-3.2$ freeview dyld: Library not loaded: @rpath/QtWidgets.framework/Versions/5/QtWidgets Referenced from: /Applications/freesurfer_6.0//Freeview.app/Contents/MacOS/Freeview Reason: image not found Abort I am running a Mac OS HighSierra (10.13.6). It seems that people had similar issues in the past, but not quiet like this one. I would love to hear any tips on how to fix it. Thanks, arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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ERROR: dimension mismatch between X and contrast
by Backhausen, Lea 27 Sep '18

27 Sep '18

External Email - Use Caution Dear FreeSurfer experts, I get this error message when running group analysis on cortical thickness using glmfit: ERROR: dimension mismatch between X and contrast Contrasts/ADHD_COM_TD_age_IQ.mtx X has 9 cols, C has 10 cols Please find attached the FSGD file, the contrast file and the terminal output below. I want to do ANCOVA with three groups (ADHD, COM and TD) controlling for the effects of age and IQ. So I assume the regressors would be ADHD COM TD age IQ and my contras matrix 1 -1 0 0 0 1 0 -1 0 0 according to information from these two tutorials: https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V and https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V. Can anybody help me out? Where am I wrong? Why does glmfit assume X has 9 cols? Any help would be much appreciated, thank you in advance! Best Lea Terminal Output: mri_glmfit --y rh.thickness.ADHD_COM_TD_orig.15.mgh --fsgd FSGD/ADHD_COM_TD_orig_age_IQ.fsgd --C Contrasts/ADHD_COM_TD_age_IQ.mtx --surf fsaverage rh --cortex --glmdir rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir gdfRead(): reading FSGD/ADHD_COM_TD_orig_age_IQ.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 13.6015 1.73148 1 IQ 107.288 11.1649 Class Means of each Continuous Variable 1 ADHD 13.7193 104.3478 2 COM 12.8657 105.3929 3 TD 14.0119 112.3784 INFO: gd2mtx_method is dods Reading source surface /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/SUBJECTS/fsaverage/surf/rh.white Number of vertices 163842 Number of faces 327680 Total area 65020.839844 AvgVtxArea 0.396851 AvgVtxDist 0.717994 StdVtxDist 0.193566 $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/SUBJECTS cmdline mri_glmfit.bin --y rh.thickness.ADHD_COM_TD_orig.15.mgh --fsgd FSGD/ADHD_COM_TD_orig_age_IQ.fsgd --C Contrasts/ADHD_COM_TD_age_IQ.mtx --surf fsaverage rh --cortex --glmdir rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir sysname Darwin hostname edr06188.dip.tu-dresden.de machine x86_64 user Lea FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/SUBJECTS/rh.thickness.ADHD_COM_TD_orig.15.mgh logyflag 0 usedti 0 FSGD FSGD/ADHD_COM_TD_orig_age_IQ.fsgd labelmask /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/SUBJECTS/fsaverage/label/rh.cortex.label maskinv 0 glmdir rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir Loading y from /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/SUBJECTS/rh.thickness.ADHD_COM_TD_orig.15.mgh ... done reading. INFO: gd2mtx_method is dods Saving design matrix to rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir/Xg.dat Computing normalized matrix Normalized matrix condition is 1027 Matrix condition is 4.07619e+06 Found 149926 points in label. Pruning voxels by thr: 1.175494e-38 Found 149926 voxels in mask Saving mask to rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir/mask.mgh Reshaping mriglm->mask... search space = 74490.844410 ERROR: dimension mismatch between X and contrast Contrasts/ADHD_COM_TD_age_IQ.mtx X has 9 cols, C has 10 cols

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Freesurfer September 2018