[Freesurfer] Reliability of Optic Chiasm Volume Measurements in FreeSurfer

External Email - Use Caution Dear FreeSurfer experts, I am examining the optic chiasm segmentation in FreeSurfer. How reliable is the volume measurement of the optic chiasm when using FreeSurfer? Best regards Knut Jørgen Bjuland ___

Re: [Freesurfer] question about infantfreesurfer

External Email - Use Caution What I mean is that it's a beta version, so I just wanted to make sure that I can use these results in a publication. Knut Jørgen Bjuland ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://ma

[Freesurfer] question about infantfreesurfer

External Email - Use Caution Dear freesufer experts, Does anyone know whether infantFreesurfer is ready to use for publication purposes? Thank you! Knut Jørgen Bjuland, PhD Telemark Hospital ___ Freesurfer mailing list Freesurfer@nmr.mg

[Freesurfer] Evaluating the Reliability of Optic Chiasma Analysis in Freesurfer

External Email - Use Caution Dear FreeSurfer experte I am currently engaged in a detailed volume analysis project where I am utilizing the optic chiasma as a key focal point. In this context, I'm specifically interested in understanding how reliable the optic chiasma measuremen

[Freesurfer] problem with infantfreesurfer

External Email - Use Caution Dear Freesurfer expert I have found this problem when I am running infant freesurfer on newborn mri image. Best regards Knut Jørgen Bjuland mri_convert --conform /home/knutjb/subjects/EPOP510_fs/work/mprage.nu.conf.nii.gz /home/knutjb/subjects/E

[Freesurfer] Freesurfer binary for Centos 9

External Email - Use Caution Dear Freesurfer surfer experts, Will Freesurfer surfer be built for Centos 9 as the cluster I am using has now been upgraded to Centos 9? Is there a source package for Freesurfer 7.4.1? Best regards, Knut Jørgen Bjuland __

Re: [Freesurfer] infant freesurfer crash

External Email - Use Caution I made it work by using fsl 5.0.11 witouth python. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Knut J Bjuland Sent: Friday, July 1, 2022 9:44 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer

[Freesurfer] infant freesurfer crash

External Email - Use Caution I am able to run infant freesurfer on my local pc but when I run on a cluster I get segmentation error when running sscn_skullstrip. Segment error in $ sscnn_skullstrip -i /cluster/projects/nn9208k/007_fs/work/mprage.nu.conf.nii.gz -o /cluster/proj

[Freesurfer] Monte Carlo for lme

External Email - Use Caution Dear Freesurfer experts, I am looking into Monte Carlo simulation to control for multiple comparisons for lme in Matlab. Are there any good library that has implemented this in Matlab? Best regards Knut Jørgen Bjuland PhD _

Re: [Freesurfer] Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames!

Sent: Friday, February 25, 2022 7:46 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! I'm not sure what question you are asking On 2/25/2022 1:17 PM, Knut J Bjuland wrote: Ext

Re: [Freesurfer] Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames!

External Email - Use Caution What do you recommend should I use dcm2nixx or use mri_concat in order to deal with multi frame t1 mri? Knut j Bjuland Sent from my iPad On 25 Feb 2022, at 19:47, Douglas N. Greve wrote: I'm not sure what question you are asking On 2/25/2

[Freesurfer] Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames!

External Email - Use Caution Dear Freesurfer experts, I get this error when I am running FreeSurfer. Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /home/knutjb/subjects/test/mri/orig/001.mgz has 4 frames If this is a multi-frame

Re: [Freesurfer] In the Desikan-Killiani parcellatino scheme, which parcellations contain the extrastriate cortex?

u! Knut On 19/01/2022 16:20, Fischl, Bruce wrote: Hi Knut Can you be more specific about what you mean by extrastriate cortex? Do you mean all visual cortex that is not V1? Bruce *From:* Knut J Bjuland *Sent:* Wednesday, January 19, 2022 8:43 AM *To:* Fischl, Bruce ; Freesurfer Mailing

Re: [Freesurfer] In the Desikan-Killiani parcellatino scheme, which parcellations contain the extrastriate cortex?

2/01/2022 16:58, Fischl, Bruce wrote: Hi Knut Including Ron in the conversation. Of course outside striate cortex the mapping between folding and function isn’t so straightforward. And Happy New Year to all! Bruce *From:* freesurfer-boun...@nmr.mgh.harvard.edu *On Behalf Of *Knut J Bjuland *Se

[Freesurfer] In the Desikan-Killiani parcellatino scheme, which parcellations contain the extrastriate cortex?

External Email - Use Caution Dear freesurfer experts In the Desikan-Killiani parcellatino scheme, which parcellations contain the extrastriate cortex? Knut Jørgen Bjuland ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu htt

[Freesurfer] mri_preproc with ico < 7?

External Email - Use Caution Dear Freesurfer experts, Is it possible to run mri_preproc with ico with lower than 7, for instance with ico equal to 4 or 5 in order to downsample the surface? (Since the surface is smoothed, it should be possible to downsample to save processing t

[Freesurfer] lme_mass_fit_Rgw will only fit 20 % and then it quits using Matlab 2020b

External Email - Use Caution Dear freesurfer experts When I run lme_mass_fit_Rgw it stop fitting after i have runed 20 % as seen below. I have listed freesurfer matlab toolbox first in the Matlab 2020b path list. I am running on Fedora 33 and the mgh files work when I am runnin

[Freesurfer] strange error in lme_mass_RgGrow

External Email - Use Caution When I run lme_mass_RgGrow on mgh using lme it wil fit 20 % before it quite. Is there a problem with my system? Region 4450: Convergence at iteration 3. Initial and final likelihoods: 473.1215, 473.7587. Aproximate percentage of fitted locations: 20

Re: [Freesurfer] error in longitudinal stream fs7.1 ERROR: Number of filenames for --iscalein should agree with number of init LTAs (--ixforms)! worked in fs6

, I just found that error yesterday. I put a new longmc script in that same location with another fix -- but I have not fully tested it yet:) On 7/21/2020 1:12 AM, Knut J Bjuland wrote: External Email - Use Caution Thanks it worked for subjects with more than one timepoint but when I

Re: [Freesurfer] error in longitudinal stream fs7.1 ERROR: Number of filenames for --iscalein should agree with number of init LTAs (--ixforms)! worked in fs6

External Email - Use Caution Thanks Sure, Here is the log file. Knut Jørgen On 16/07/2020 16:12, Douglas N. Greve wrote: Can you send the log file? On 7/15/2020 1:51 PM, Knut J Bjuland wrote: External Email - Use Caution Dear freesurfer experts I was able to run

Re: [Freesurfer] error in longitudinal stream fs7.1 ERROR: Number of filenames for --iscalein should agree with number of init LTAs (--ixforms)! worked in fs6

External Email - Use Caution It ran on a computer with CentOS Linux release 7.8.2003 (Core) and Freesurfer was build using easybuild by the cluster support staff. Knut Jørgen On 15/07/2020 19:51, Knut J Bjuland wrote: External Email - Use Caution Dear freesurfer

[Freesurfer] error in longitudinal stream fs7.1 ERROR: Number of filenames for --iscalein should agree with number of init LTAs (--ixforms)! worked in fs6

External Email - Use Caution Dear freesurfer experts I was able to run the same subects on the longitudinal stream using FS 6 , but when I use FS7.1 I got this error RROR: Number of filenames for --iscalein should agree with number of init LTAs (--ixforms)! ERROR: @#@FSTIME 20

[Freesurfer] freevieer This application failed to start because no Qt platform plugin could be initialized.

External Email - Use Caution Dear FreeSurfer experts I have used this script to start Freeview from within Matlab fs=getenv('FREESURFER_HOME'); setenv('FS_QT_HOME',fullfile(fs,'lib','qt')); setenv('QTLIBPATH',fullfile(fs,'lib','qt','lib')) setenv('qtplugin',fullfile(fs,'lib','qt'

[Freesurfer] unable to start freevie from within matlab

External Email - Use Caution Dear FreeSurfer experts I have used this script to start Freeview from within Matlab fs=getenv('FREESURFER_HOME'); setenv('FS_QT_HOME',fullfile(fs,'lib','qt')); setenv('QTLIBPATH',fullfile(fs,'lib','qt','lib')) setenv('qtplugin',fullfile(fs,'lib','qt'

[Freesurfer] mean for a bash script from mris_calc.

External Email - Use Caution Dear Freesurfer experts, I have tried to use mris_calc to calculate mean and std and export the variable to bash with this command, mean=$(mris_calc mghfile std), but the array is not stored in mean. Is there any other way to calculate, mean and

[Freesurfer] lme models time or time^2

External Email - Use Caution Dear FreeSurfer expert I have a lme model with 3 timelines where one timeline is baseline. I two models y = intercept + time + group + sex + time_at_baseline and y = intercept +time +time² + group + sex +time_at_baseline Both time² and time is

[Freesurfer] low snr with t1_mp2rage compared to MPRAGE

External Email - Use Caution Dear freesurfer experts, I have some image that are in t1_mp2rage_sag. Are there anything I should be aware of when importing them into freesurfer from nifit? How can I detect what sequence that is used in the MRI dicoms? When I compare these imag

[Freesurfer] bug repport freeview crash with symbol _ZN17QAbstractItemView11eventFilterEP7QObjectP6QEvent version Qt_5 not defined in file libQt5Widgets.so.5 with link time reference

External Email - Use Caution I have update to the latest freeview, when I start I got this error message. Copyright (C) 2018 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later This is free software: you are free to change a

Re: [Freesurfer] lack of convergence when analyzing tbss-data with FreeSurfer's lme code

there any guidelines on what algorithm is best suited for DTI- data ? Also: Are there any other tweaks that can be applied to achieve better convergence? Best regards Knut J Bjuland PhD > On 25 Nov 2018, at 09:21, Knut J Bjuland wrote: > >External Email - Use Caution

[Freesurfer] lack of convergence when analyzing tbss-data with FreeSurfer's lme code

e the number of iterations, is that possible and would that help? Best regards Knut J Bjuland PhD ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] freeview crash when launch in ubuntu 18.04

External Email - Use Caution Dear Freesurfer exports, I am unable to launch freeview. I have uncommented qt_setup to be able to start freeview but now it does not start at all. I am sending output from a session where I started it using gdb. Please look below. I am using the late

[Freesurfer] Is longitudinal lme analysis invalid when it doesn't converge?

External Email - Use Caution Dear FreeSurfer experts I ran the lme scripts in FreeSurfer on FA-data (dMRI). The script doesn't crash but 70% of the models yield this message: "Algorithm does not converge after 50 iterations!!!" Does that mean the results (pvalues) are invalid? I

[Freesurfer] I ran the linear mixed model matlab code on DTI-data (FA) from tbss (700 subjects and ca. 130 000 voxels) but converges only on 30 %

External Email - Use Caution Dear FreeSurfer experts, I ran the linear mixed model matlab code on DTI-data (FA) from tbss (700 subjects and ca. 130 000 voxels). I adapted the code a little bit to accommodate the data format. I have a longitudinal design with 3 time points and

Re: [Freesurfer] freeview. crash with undefined symbol: _ZN6QMutex12lockInternalEv when I choose colormap lookup table

1 (0x7f78aeca2000) libXau.so.6 => /lib64/libXau.so.6 (0x7f78aea9e000) I have Fedora 27. Knut Jørgen From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Knut J Bjuland Sent: Tuesday, March 6, 2018 10:21 PM To: Freesurfer support list Subject:

[Freesurfer] freeview. crash with undefined symbol: _ZN6QMutex12lockInternalEv when I choose colormap lookup table

Dear Freesurfer export, When I chose colormap to lookup table with bert/mri/aseg.mgz freeview crash with the following message. [New Thread 0x7fffce7f4700 (LWP 78012)] /usr/local/freesurfer60/bin/freeview.bin: symbol lookup error: /usr/local/freesurfer60/bin/freeview.bin: undefined symbol

[Freesurfer] AnatomiCuts in tracula

Dear Freesurfer expert I have used Tracula and I read that AnatomiCuts could improve Tracula performance. Can I use AnatomiCuts with Tracula in Freesurfer 6.0 or developer version. If this is not the case, will it be released in Freesurfer 6.1 Best regards Knut Jørgen Bjuland PhD __

Re: [Freesurfer] Differences in aseg volumes between FreeSurfer 5.3.0 and FreeSurfer 6.0

to:fis...@nmr.mgh.harvard.edu>> wrote: Hi Knut the best would be if you can just tar and gzip the entire subject dir and upload it according to these dirs: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange cheers Bruce On Sat, 6 May 2017, Knut J Bjuland wrote: Hi Bruce Where sho

Re: [Freesurfer] Differences in aseg volumes between FreeSurfer 5.3.0 and FreeSurfer 6.0

] Differences in aseg volumes between FreeSurfer 5.3.0 and FreeSurfer 6.0 Include the orig.mgz and voxel cords and I'll see if I have already fixed it On May 5, 2017, at 10:11 AM, Knut J Bjuland mailto:knutjor...@outlook.com>> wrote: Hi Bruce I found some filled-in occipital horn and some in t

Re: [Freesurfer] Differences in aseg volumes between FreeSurfer 5.3.0 and FreeSurfer 6.0

is it being filled? If it is the occipital horn we may soon have a patch for it cheers Bruce On Thu, 4 May 2017, Knut J Bjuland wrote: Hi Are there any options that I can use in Freesurfer 6.0 that can prevent lef t lateral ventricle from being filled with WM? Should I send the MPRAGE seq uence infor

[Freesurfer] Differences in aseg volumes between FreeSurfer 5.3.0 and FreeSurfer 6.0

Dear FreeSurfer expert, I have compared the aseg volume between FreeSurfer 5.3 and FreeSurfer 6.0 with asegstatsdiff from FreeSurfer 6.0 for each subject in my data set. I have enclosed the range for some of the volume. I found the largest differences in subcortical structures, especially in

[Freesurfer] Topup before trac-all

uld I reorganise my bvec and bvals? Thank you! Knut J Bjuland ___ Freesurfer mailing list Freesurfer@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

Re: [Freesurfer] obtain fa FA data from the white matter ROIs in WMParcStatsLUT.txt. or FreeSurferColorLUT.txt.

Hi Anastasia If I want to use Tracula DTI files instead, which file do I choose: Is it FA_ditifit.nii? Best Knut Jørgen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The i

[Freesurfer] obtain fa FA data from the white matter ROIs in WMParcStatsLUT.txt. or FreeSurferColorLUT.txt.

Hi, I would like to to obtain FA data from the white matter ROIs in WMParcStatsLUT.txt. or FreeSurferColorLUT.txt. So would it work to coregister a DWI file, either produced by dt_recon (or perhaps better - from Tracula) and an anatomy file in atlas space and then use WMParcStatsLUT.txt or F

Re: [Freesurfer] trouble with mailing list

atter but it appears to be more of an issue with the mail-archives.com<http://mail-archives.com> website (which is out of out hands) than the Freesurfer support list. Hopefully the issue will be resolved shortly. Thanks, -Zeke On 11/21/2016 11:24 AM, Knut J Bjuland wrote: Hi I have poste

[Freesurfer] trouble with mailing list

Hi I have posted two posts to the FreeSurfer mailing list that does not appear in the archive. Are there any trouble with the list or are there a trouble with my mailing client? Knut Jørgen Bjuland PhD ___ Freesurfer mailing list Freesurfer@nmr.mgh.

Re: [Freesurfer] trac-all -path Segmentation fault

Hei Er det id 2 og 3 du har problemer med? Det ser ut som at du ikke har kjørt bedpostx på disse to idene og jeg ser at du ikke har kjørt trac-all -prep utifra logfilen . [/work/projects/nn9208k/subjects/LMR/dtitracula/2]: ls dlabel dmri dpath scripts [/work/projects/nn9208k/subjects/LMR/dti

Re: [Freesurfer] Reproducibility of freesurfer analyses across different version of linux

On 08/28/2016 05:57 PM, R Edgar wrote: On 28 August 2016 at 06:59, Knut J Bjuland wrote: I found this paper about named “Reproducibility of neuroimaging analyses across operating systems” (Glatard et al., 2015). There were differences in cortical morphometry like cortical thicknes between

[Freesurfer] Reproducibility of freesurfer analyses across different version of linux

Dear FreeSurfer experts,I found this paper about named “Reproducibility of neuroimaging analyses across operating systems” (Glatard et al., 2015). There were differences in cortical morphometry like cortical thicknes between images proscced in the same version of freesurfer with different ver

Re: [Freesurfer] When I am run trac-all in Fedora 24 with the developmental version of FreeSurfer, it crashes when running flirt.fsl with this error message

Hi Anastasia Thanks. I am sending my entire trac-all.log Knut Jøgen On 07/12/2016 11:19 PM, Anastasia Yendiki wrote: Hi Knut Jørgen - Can you please send your entire trac-all.log? Thanks! a.y On Mon, 11 Jul 2016, Knut J Bjuland wrote: flirt.fsl -ref /home/knutjbj/subjects/023v4

[Freesurfer] When I am run trac-all in Fedora 24 with the developmental version of FreeSurfer, it crashes when running flirt.fsl with this error message

flirt.fsl -ref/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/refvol.fslregister.nii-in/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/movvol.fslregister.nii-bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90-searchrz -90 90 -verbose

[Freesurfer] How can I use mri_vol2surf to map the white matter volume cortical surface in order to generate a white matter map that is similar to the gray matter volume map produced by mris_preproc?

DearFreeSurferexperts, HowcanIusemri_vol2surftomapthewhitemattervolumecorticalsurfaceinordertogenerateawhitemattermapthatissimilartothegraymattervolumemapproducedbymris_preproc? ShouldIusebinarymaskcreatedinMatlabtoremovelabelsthatarenotwhitematter? Best regards KnutJørgenBjuland NTNU __

[Freesurfer] Freeview crash if started with argument from Matlab 2015a on Mac os 11.10.5

Dear FreeSurfer experts I have downloaded the FreeSurfer tutorials. When I try to load Freeview in Matlab with the argument that I found in the group tutorial Freeview will crash on Mac OS X 10.10.5, but it worked on Fedora 22. I am using Matlab because Freeview do not have FDR. Fdr is

Re: [Freesurfer] freesurfer-Linux-centos7_x86_64-dev-20150521 on ubuntu 14.04 crash with Illegal instruction (core dumped)

ithout it. Although that build is available via our dev > download page, it remains an unsupported build that exists primarily for > internal experimental purposes only. > > -Zeke > > On 05/22/2015 11:49 AM, Knut J Bjuland wrote: >> Hi >> >> I have tired the

[Freesurfer] freesurfer-Linux-centos7_x86_64-dev-20150521 on ubuntu 14.04 crash with Illegal instruction (core dumped)

Hi I have tired the freesurfer-Linux-centos7_x86_64-dev-20150521. When I start mri_convert on ubuntu 14.04.4 I get this results. knutjb@dmed4960:/usr/local/freesurfer60$ export FREESURFER_HOME= /usr/local/freesurfer60 knutjb@dmed4960:/usr/local/freesurfer60$ source /usr/local/freesurfer60/SetUpFr

[Freesurfer] mri_convert crash after updating with tracula add update 2014/05/26 on Ubuntu 14.04 lts

Dear Freesurfer experts,After I added the Tracula update at http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula, I have been unable to use mri_onvert. Since I have Ubuntu 14.04, I used the Centos 6 x86_64 version found at this link. However, when I tried to use mri_convert it segement fault. I

[Freesurfer] kvlQuantifyHippocampalSubfieldSegmentations.sh resultsDirectory 1, 10 gives error line 22: cd: left: No such file or directory

failed to do cd left I have issued this command both in tsch and in bash. However, when I run the command without any options in the same folder, it works but bails out as expected when it reaches fsaverage- Best regards, Knut J. Bjuland PhD candidate NTNU

[Freesurfer] ICV for adolescent and young adult in longitudinal stream

Dear FreeSurfer export, I have used the longitudinal stream in FreeSurfer. However, when I extracted the ICV for adolescents and young adult, I get the same number for those subjects that are present at two-time points. Will registration to a common space cause the change in ICV? Can this chan

[Freesurfer] Gyrification index vs cortical surface area

Dear FreeSurfer experts I have run analyses on gyrification index. I was wondering if anybody could tell me what exactly is the relationship between gyrification index and cortical area. My gyrification results and area results are to a large extent similar. Am I measuring approximately the sam

[Freesurfer] What is the best method to calculate cohenD or any other map of effective size with lme?

Dear FreeSurfer expert I have calculated the residuals as y-x*beta as described in (Bernal-Rusiel et al., 2012). What is the best method to calculate cohenD or any other map of effective size with lme? Can I calculate cohenD as R=y-desingmatrix*Bhat cohenD=gamma./(sqrt(sum(r.^2)/df2-1)) Ref

[Freesurfer] Dealing with missing clinical variables in lme analysis and test model fit between two models with the same number of random effects.

. Both models have one random effect. Your sincerely Knut J Bjuland ___ Freesurfer mailing list Freesurfer@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

Re: [Freesurfer] mri_convert WARNING: files are not found to be different and cannot be sorted and cannot fit in 256^3 mm^3 volume.

wrote: > Hi Knut > > is the FOV really 384mm?? That's awfully big and seems more likely to be > an error in the dicoms than real. > > cheers > Bruce > On Sat, 5 Jul 2014, Knut J Bjuland wrote: > >> Dear FreeSurfers, >> >> I have imported several dico

Re: [Freesurfer] mri_convert WARNING: files are not found to be different and cannot be sorted and cannot fit in 256^3 mm^3 volume.

07/05/2014 03:46 PM, Bruce Fischl wrote: > Hi Knut > > can you run mri_info on that dicom file? > > thanks > Bruce > On Sat, 5 Jul 2014, Knut J Bjuland > wrote: > >> Cut-and-paste the following info in

Re: [Freesurfer] mri_convert WARNING: files are not found to be different and cannot be sorted and cannot fit in 256^3 mm^3 volume.

cript/recon-all.log See also: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting recon-all -i dicom//1.dcm -s cd /mri/orig and mri_convert -ot mgz /pat/dicom//1.dcm 001.mgz with the same results knut j On 07/05/2014 12:36 PM, Knut J Bjuland wrote: > Dear FreeSurfers, &g

[Freesurfer] mri_convert WARNING: files are not found to be different and cannot be sorted and cannot fit in 256^3 mm^3 volume.

Dear FreeSurfers, I have imported several dicom files with recon-all -i -subjid id. All files were imported correctly, apart from one subjects. When I try to convert it direcelty with mri_convert -ot mgz dicom//1.dcm -s I get this error message. WARNING: files are not found to be diff

[Freesurfer] tksurfer bug report, input from keyboard is not accepted in ubuntu 14.04

workaround? Knut J Bjuland ___ Freesurfer mailing list Freesurfer@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

[Freesurfer] aberrantly high LGI value with localGI on longitudinal subjects, What is the best curse of action?

base before running the localGI again? Or is there any other options? regards Knut J Bjuland ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is

Re: [Freesurfer] Longitudinal recon-all –localGI after error on cross recon-all –localGI and optimal smoothing

that you want. I'd say that > with linear mixed model you want the same level of smoothing that you have in > equivalent cross-sectional analyses (i.e. most usually 10-15mm). > > Hope this helps, > > Marie > > > On May 29, 2014, at 1:29 PM, Knut J Bjuland >

Re: [Freesurfer] FDR correction in Matlab

Hi help lme_mass_FDR and help /lme_mass_FDR2/ For help with input and output? Knut J On 05/26/2014 11:24 AM, Nandita Vijayakumar wrote: Hi FS team, I was wondering if you could help me with FDR correction for linear mixed models within Matlab. I have run FDR2 correction using the follo

[Freesurfer] Longitudinal recon-all –localGI after error on cross recon-all –localGI and optimal smoothing

-randomness -autorecon3 , and should I rerun the longitudinal stream for these subjects before doing I use recon-all –long id base_id –localGI? What are the optimal smoothing when using the linear mixed models? Best regards Knut J Bjuland ___ Freesurfer

[Freesurfer] Tksurfer will not accept key input in Ubuntu 14.04

Bug report I am unable to enter number using the keyboard when using Tksurfer under Ubuntu 14.04. I have tried to enter a number in overlay configuration and smooth overlay. Is there any workaround? I have this bug on two different system with Ubuntu 14.04. Best regards Knut J Bjuland

Re: [Freesurfer] Reporting bhvat value from lme with contrast vector 0 1 0 1 0

present data from univariate lme? Knut Jørgen On 02/08/2014 04:10 AM, Knut J Bjuland wrote: Dear Freesurfers We are now finishing an article, where we have used linear mixed models included in FreeSurfer 5.3 for longitudinal changes between two-time points. We have used this model

[Freesurfer] reporting bhvat value from lme

Dear Freesurfers We are now finishing an article, where we have used linear mixed models included in FreeSurfer 5.3 for longitudinal changes between two-time points. We have used this model. Intercept(RF) + centered time+ group + group*centered time + sex(gender). Everything is clear except f

Re: [Freesurfer] Fwd: Problems with longitudinal analysis

o you know what is going on ? Best, Martin Original Message Subject:[Freesurfer] Problems with longitudinal analysis Date: Wed, 4 Dec 2013 22:04:07 +0100 From: Knut J Bjuland <mailto:knutjor...@outlook.com> To:

Re: [Freesurfer] TRACULA exists uncompleted

Hi You should do cat -n $RAW_DATA/Bled_Jean_Jacques/TENSEUR_50_directions_ASSET_10/20121113_141004COMA201210s010a1001.bvec and cat -n set bvalfile = $RAW_DATA/Bled_Jean_Jacques/TENSEUR_50_directions_ASSET_10/20121113_141004COMA201210s010a1001.bval to look for empty lines. Trac-all -prep -c ru

[Freesurfer] longitudinal 5.3 used with baseline fs 5.1 recon-all

Hi,we have finished cross sectional scanworkups in Freesurfer 5.1 and gone through qa. Can we use these scanworkups for further processing in the longitudinal stream in Freesurfer 5.3? Knut J___ Freesurfer mailing li

[Freesurfer] freesurfer map with low efftive size

How to detect group differences between groups with low group size like for instant n=8 vs n=50? Are there any statistics measures I could use like looking at interaction between group and gender, or should I use doss? Is it feasible to design a custom based design matrix? Knut J

Re: [Freesurfer] Resolved, crash during longitudinal process when it run mri_ca_register during CA reg.

Closed, not bug in Freesurfer. On 09/12/2013 10:31 PM, Knut J Bjuland wrote: When I run recon-all -base 1_template -tp 1_first -tp 1_secon -all -debug. It crash during CA Reg Thu Sep 12 19:59:01 CEST 2013. I can send the rest of the log. Knut J

Re: [Freesurfer] crash during longitudinal process when it run mri_ca_register during CA reg.

ete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 pass 1 of 1 setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... : dt=0.000, rms=0.932, neg=0, invalid=96777 On 09/12/2013 10:1

[Freesurfer] crash during longitudinal process when it run mri_ca_register

Hi, I have run recon-al longitudinal process on abel cluster with this command recon-all -base @filename@_template -tp @filename@ -tp @filename@v2 -all -debug. However, it crashed or is killed when it ran mri_ca_register. I have looked through the log, and I have not found a reason for it being

[Freesurfer] Crash in mri_register_ca during recon-all -base id -tp id1 -tp id2 -all

Hi, I have some trouble running recon-all longitudinal pipelines. When recon-all comes to mri_register_ca it crashes without giving a message, even tough 8g ram was available. I have run the program with -debug. Is there any other option I may use? The system is running Rocks 6.0 (Mamba), and i

Re: [Freesurfer] CUDA Error when runnign freesurfer

Hi can you send part of recon-all.log and do recon-all -i 242.nii.gz -s 242_FS -nuintensitycor-3T -nocanorm -openmp 8 -use-cuda -hippo-subfields -all -debug Knut J On 06/29/2013 06:06 PM, Salil Soman wrote: Hi, I am running freesurfer 5.3 on an ubuntu 13.04 with a nvidia card and the the

[Freesurfer] subj: Undefined variable.

Hi Strange error in tracula 5.1. When I use a dmric file that have worked before I now get subj: Undefined variable. I may have uppgrade tcsh. Is there any fix to get tracula-preproc to use the id from dmric files Knut J ___ Freesurfer mailing list F

Re: [Freesurfer] mri_info crashing (bits stored vs bits allocated?)

HI I have similar problem and filled a bug report at. Product: Fedorahttps://bugzilla.redhat.com/show_bug.cgi?id=905638 Patsy Franklin changed: What |Removed |Added Flags|needinfo?(pfrankli@redhat.c | |om) | Flags|ne

[Freesurfer] Updated info for freesurfer 5.2 on Fedora 18. update from Bugzilla. Freesurfer used unsupported, nonstandard salt to crypt()

HI I have copied the info from Bugzilla. Product: Fedora https://bugzilla.redhat.com/show_bug.cgi?id=905638 Patsy Franklin changed: What |Removed |Added Flags|needinfo?(pfrankli@redhat.c | |om) | Flags|needinfo?(p

[Freesurfer] surface area mesurment and qatools

Hi What would be the best way to measure cortical surface either the white surface area or pial surface? Is the total surface area calculated by mris_anatomical the same pial surface? When using QA tool which article should I cite? Knut J ___ Freesurf

[Freesurfer] read only cvs server is down

When I tries to download Freesurfer 5.2.0 beta source I get this error message. cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P dev cvs server: cannot find module `dev' - ignored cvs [checkout aborted]: cannot expand modules Knut J

[Freesurfer] cvs freesurfer cvs [checkout aborted]: cannot expand modules

Hi could you please add information about how to download from cvs? cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P -r dev Give this error message cvs [checkout aborted]: must specify at least one module or directory Knut J _

Re: [Freesurfer] bug repport mri_convert in freesurfer 5.1 segment fault on fedora 19

gt;> does the centos4_x86_64 v5.2 build work? >> no. >> >> >> I have filed a bug report on >> https://bugzilla.redhat.com/show_bug.cgi?id=905638 . It might be problem >> with mri_convert and glibc interaction. >> >> Knut J >>> n. >>&g

Re: [Freesurfer] bug repport mri_convert in freesurfer 5.1 segment fault on fedora 19

t; n. > > On Tue, 2013-01-29 at 20:33 +0100, Knut J Bjuland wrote: >> Hi Nick >> >> I reran dicom import from /usr/local/freesurfer/subject/sample*. I had >> 24254940 kB free memory but I still got a segmentation error.I used >> sample data from /usr/local/freesurf

Re: [Freesurfer] bug repport mri_convert in freesurfer 5.1 segment fault on fedora 19

rk on that? Nick On Tue, 2013-01-29 at 19:30 +0100, Knut J Bjuland wrote: When I run recon-all using freesurfer 5.2 latest beta it will segment crash. Linux mypc 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /home/knutjbj/freesurfer/ernie mri_convert

[Freesurfer] bug repport mri_convert in freesurfer 5.1 segment fault on fedora 19

When I run recon-all using freesurfer 5.2 latest beta it will segment crash. Linux mypc 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /home/knutjbj/freesurfer/ernie mri_convert /usr/local/freesurfer/subjects/sample-001.mgz /home/knutjbj/freesurfer/

[Freesurfer] None segmentation

Hi, How can I calculate the number of None segmentation in right or left hippocampus or another structure in Matlab or in Freesufer? Knut J ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https:/

Re: [Freesurfer] regarding use-mritotal

Hi, Talairach.xfm is a text file which contains a transformation matrix. Though there is small numerical difference between two transformation matrix made using mritotal and the default Talairach registration. The process of calculation the ICV may amplify this difference since it used the det

[Freesurfer] fixed version of mri_glmfit and mri_glmfit-sim

Hi I saw an updated version of mri_glmfit in ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/. Should I update this file in my freesurfer installation. What do this fix? Is is not in the release notes? Along with mri_glmfir-sim from Doug Greve ftp site. Knut J

Re: [Freesurfer] How can I get 300 dpi resolution or about when saving tiff files in tksurfer?

an change the dpi with convert (or photoshop), but it won't > change the # of pixels. > > cheers > Bruce > > > On Thu, 6 Dec 2012, Knut J Bjuland wrote: > >> >> How can I get 300 dpi resolution or about when saving tiff files in >> tksurfer? >>

[Freesurfer] How can I get 300 dpi resolution or about when saving tiff files in tksurfer?

How can I get 300 dpi resolution or about when saving tiff files in tksurfer? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only fo

[Freesurfer] update mri_glmfit

Hi I saw an updated version of mri_glmfit in ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/. Should I update this file in my freesurfer installation. What do this fix? Is is not in the release notes? Knut J ___ Fre

Re: [Freesurfer] error while compiling utils

Hi Kim You are missing some packages. https://help.ubuntu.com/community/CompilingEasyHowTo You should install teh essential package for compiling in ubuntu by sudo apt-get install build-essential and sudo apt-get install linux-libc-dev to get Linux headers in /usr/include/linux. When buildi

[Freesurfer] Cortical thickness percent difference surface maps script in matlab feedback wanted.

Dear Freesurfer expert I have produce a script to make percent difference in cortical thickens using information from the mailing list. Could you please take look if this script is correct, or if there is a better way to do it? function [ out ] = diff_map( difference, average ) %percent differ

[Freesurfer] calculate percent from two different mgh files

How can I dived a gamma.mgh with another gamma.mgh to get new mgh structure? Is there any Freesurfer Matlab function that I should use. I am able to use Matlab to calculate the difference for vol. n=size(gamm.vol(2)) for i=1:n; test=gamma.mgh.vol(i)/gamma.mgh(i) end I am trying to follo

  1   2   >