Freesurfer

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30088 discussions

Fwd: fcseedcor output
by Sara Jafakesh 11 Dec '18

11 Dec '18

External Email - Use Caution -----Original Message----- From: "Sara Jafakesh" <S.Jafakesh(a)sutech.ac.ir> To: freesurfer(a)nmr.mgh.harvard.edu Cc: DGREVE(a)mgh.harvard.edu Date: Sat, 08 Dec 2018 22:25:20 +0330 Subject: Fwd: fcseedcor output -----Original Message----- From: "Sara Jafakesh" <S.Jafakesh(a)sutech.ac.ir> To: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> Date: Sat, 08 Dec 2018 12:21:06 +0330 Subject: Re: fcseedcor output Dear Greve I send the entire email chain: I think some thing wrong with my matlab setting, It is not compatible with my freesurfer I guess, but I dont know how can I compatible matlab with freesurfer. best.. Can? you send the full terminal output? On 12/05/2018 01:25 AM, Sara Jafakesh wrote: > > ????????External Email - Use Caution > > > Dear freesurfer experts, > I want to calculate corrolation between two seeds with > freesurfer-linux-centos6_x86_64_stable_pub-v6 .after using > fcseed-config and fcseed-sess, I used fcseedcor. the command > that I trying to run is as follow: > fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed > lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg mcprextreg > 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat > but the output of fcseedcor is not dat file ( the > connectivity matrix for my result 2*2 matrix) as it has been > explained in the fcssedcor help. the output is just the log > file named seedcor2.dat.log. although it has been done > without error. > I really dont know what is the problem. > I would be grateful if you could help me. > best regards, > sara hi sara, can you include the entire email chain so that I can see the context? On 12/7/18 4:19 PM, Sara Jafakesh wrote: External Email - Use Caution Dear Dr.GREVE , thank you for your reply my full terminal output is: [user at localhost subjects]$ fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg mcprextreg 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat Sat Dec 1 18:05:11 IRST 2018 setenv SUBJECTS_DIR /home/user/freesurfer/subjects cd /home/user/freesurfer/subjects /home/user/freesurfer/fsfast/bin/fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg mcprextreg 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c $Id: fcseedcor,v 1.3 2015/12/10 22:51:29 zkaufman Exp $ Linux localhost.localdomain 2.6.32-642.el6.x86_64 #1 SMP Tue May 10 17:27:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux ------- matlab output -------------------- matlab: Command not found. Started at Sat Dec 1 18:05:11 IRST 2018 Ended at Sat Dec 1 18:05:12 IRST 2018 Fcseedcor-Run-Time-Sec 1 Fcseedcor-Run-Time-Hours 0.00 fcseedcor Done best, sara -----Original Message----- From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> To: Sara Jafakesh <S.Jafakesh(a)sutech.ac.ir>, "87fc6eef-18d0-2f7d-99f5-eb8a79707c5c(a)mgh.harvard.edu" <87fc6eef-18d0-2f7d-99f5-eb8a79707c5c(a)mgh.harvard.edu> Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Date: Fri, 7 Dec 2018 22:33:49 +0000 Subject: Re: fcseedcor output hi sara, can you include the entire email chain so that I can see the context? On 12/7/18 4:19 PM, Sara Jafakesh wrote: External Email - Use Caution Dear Dr.GREVE , thank you for your reply my full terminal outpou is : [user@localhost subjects]$ fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg mcprextreg 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat Sat Dec 1 18:05:11 IRST 2018 setenv SUBJECTS_DIR /home/user/freesurfer/subjects cd /home/user/freesurfer/subjects /home/user/freesurfer/fsfast/bin/fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg mcprextreg 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c $Id: fcseedcor,v 1.3 2015/12/10 22:51:29 zkaufman Exp $ Linux localhost.localdomain 2.6.32-642.el6.x86_64 #1 SMP Tue May 10 17:27:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux ------- matlab output -------------------- matlab: Command not found. Started at Sat Dec 1 18:05:11 IRST 2018 Ended at Sat Dec 1 18:05:12 IRST 2018 Fcseedcor-Run-Time-Sec 1 Fcseedcor-Run-Time-Hours 0.00 fcseedcor Done best, sara 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.

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Conversion of registration files
by Jane Tseng 11 Dec '18

11 Dec '18

External Email - Use Caution Dear Freesurfer experts, I was wondering if there is any way to convert the .dat file output from spmregister (generated using Freesurfer version 5.3) to a .lta file? Thank you! Best wishes, Jane

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segmentHA_T2 newbie questions
by Freesurfer 11 Dec '18

11 Dec '18

External Email - Use Caution Hi, Trying to run the HippoAmig segmentation with T1-w and T2-w files for the first time and I have a few basic questions I could not resolve looking on the FS wiki: 1. Does the T2-w image need to be first recon-all processed like the T1-w? On the wiki the command line is: segmentHA_T2.sh bert FILE_ADDITIONAL_SCAN ANALYSIS_ID USE_T1 2. Does “bert” correspond to the directory for recon-all subject “bert” after been processed? 3. Does the FILE_ADDITIONAL_SCAN need to be a nit scan or should it point to the freesurfer directory post recon-all (this is kind of related to question #1 I realize). 4. In ANALYSIS_IS can I type just “T2”? Thanks! K

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Freeview Scrolling through slices on a Mac
by Chris Petty 11 Dec '18

11 Dec '18

External Email - Use Caution Maybe I am missing something, but how can I scroll through slices with keyboard or mouse in Freeview on a Mac? Nothing I’ve tried works thus far. Any typical key ( cmd, ctrl, shift ) with scroll just zooms. Up/down moves the image up and down … shift / option / cmd with up / down either zooms or moves up / down. I’m just trying to add control points and definitely need to scroll through slices without clicking on the image. Thanks, -Chris

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Version 6.0.0 or 6.0.1?
by Kirstie Whitaker 11 Dec '18

11 Dec '18

External Email - Use Caution Hi Freesurfer team, On the download website version 6.0.0 is linked: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall But on this list there has been discussion of version 6.0.1 which can be downloaded from https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1 What's the recommended version to use? I've been using 6.0.0 but with an updated make file following the instructions in this email: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-April/056644.ht… Is the makefile updated in 6.0.1? Are there any other differences? I'm having a lot of difficulty getting recon-all to run reliably with 6.0.0 (some subjects are fine, others not!) and I'm wondering if that's because I'm supposed to be using 6.0.1? Thank you for your help! Kirstie -- Kirstie Whitaker, PhD Research Fellow, Alan Turing Institute Research Associate, University of Cambridge *Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB *Phone: *+44 7583 535 307 *Website:* https://whitakerlab.github.io *Twitter:* @kirstie_j <https://twitter.com/kirstie_j>

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Re: [Freesurfer] Recon command with T1 and T2
by Maksimovskiy, Arkadiy 11 Dec '18

11 Dec '18

Thank you Doug. Much appreciated. -arkadiy

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Recon command with T1 and T2
by Maksimovskiy, Arkadiy 11 Dec '18

11 Dec '18

Dear Experts, I am planning to run "recon" using T1 and T2 images, and was wondering if you wouldn't mind confirming whether this is the right command with recon: recon-all -s ${subject} -i T1.nii -T2 T2.nii -all I have seen a slightly different variation in the mailing archives, but this was years ago, and I believe that mine is consistent with the Wiki. Additionally, should the -T2pial flag be included? Thank you for your help, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. <https://www.researchgate.net/profile/Arkadiy_Maksimovskiy2> Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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Command to convert subcortical values into subcortical segmentation
by Conchy PF 11 Dec '18

11 Dec '18

External Email - Use Caution Hello FS experts, I was wondering if there is a command similar to annotval2surfoverlay.m that allows converting subcortical values into aseg.annot subcortical segmentation. Thank you in advance and kind regards, Lisbeth

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Re: [Freesurfer] Increasing the Number of a non-FreeSurfer Parcellation
by Maedeh Khalilian 11 Dec '18

11 Dec '18

External Email - Use Caution Dear Bruce The parcellation I have is not on surface, it is volumetric. I wanna increase the number of its ROIs, I thought maybe I can change it into an annotation file and then use "mris_divide_parcellation". Hope it is clear enough now. Best Maedeh

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GLM multiple comparison correction
by Barletta, Valeria 11 Dec '18

11 Dec '18

Good morning! We are running a GLM with two groups (patients versus controls) and one variable (age). We are using the following option to correct for multiple comparisons: mri_glmfit-sim --glmdir ${glm_dir}/${hemi}_contrast-${contrast}_${surfname_t1} --cache 1.3 pos If we change the option "pos" with "neg" or "abs", we obtain exactly the same cluster (attached). Is this normal? What is the option "pos" staying for exactly? Thanks, Valeria

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