Freesurfer November 2016

freesurfer@nmr.mgh.harvard.edu

120 participants
214 discussions

problem of using freesurfer
by Hsin-Tsung Lee 15 Dec '16

15 Dec '16

Dear freesurfer community I have used the freesurfer v5.30 stable on linux, I want to fusion the CT image and the MRI T1 image. The CT image was signed form the epilepsy patient after the inserted depth electrode surgery. The MR image was sign before the operation. I tried to register them by the "bbregister" or "mri_robust_register" , but it didn't work good. And I had seen the website page " https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-June/046081.html" , does the "mri_coreg" is the better instruction to use in my case? And, I found that I can't find the download link of freesurfer v6.0 in your website, and the link " ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg.mac " is invalid to use. I really appreciate any help here HsinTsung Lee

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longHippoSubfields
by Christian Krog Tamnes 12 Dec '16

12 Dec '16

Dear Juan and FreeSurfer team, We are trying to test out the longitudinal hippocampus subfield segmentation pipeline, but can't seem to run/find the script (longHippoSubfieldsT1.sh). We have done the standard processing in v5.3 and have the following dev version: freesurfer-Linux-centos6_x86_64-dev-20160914-bdac8bc. Sorry for the basic question, but do we simply need a later dev build? Best regards, Christian

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TR : recon-all exited with ERRORS in Talairach
by jean-simon.boucher.1＠ens.etsmtl.ca 02 Dec '16

02 Dec '16

Hi Freesurfer Developpers, I'm trying to ''recon-all'' my MRI and I got an error in Talairach parts of the process. This is strange because I was able to complete the process entirely few weeks ago ... Here are the recon-all log files for the same subjects (the good one (few weeks ago) and the new one that I got now with ERROR). I've compared the 2 files and the only thing that is different is my platformversion (this is the linux version, right?). It has increased from 4.4.0.38 to 4.4.0.47. The only things that I have changed since the first time that I was able to perform the freesurfer process are: - Update on Linux - Installation of a new hard drive. Note here that I've tried to bypass (not using) the hard drive in my process. I've tried a lot of thing and one things that seem to be my problem is the Version of Perl (5.22.1) with my version of Freesurfer (5.3.0). (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-November/048807…) Strangely, I haven't upgraded any of theses since the first time that I was able to run Freesurfer. Moreover, I don't have the access to change the version of perl (yes I've tried to change it for version 5.16) Do you have any idea what I'm doing wrong? Thanks a lot! Jean-Simon Boucher B. Ing. Électrique (ÉTS)

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Demeaning variables
by Rodrigo Gonzalez Huerta 01 Dec '16

01 Dec '16

Hi Freesurfers, For obtaining my undergraduate degree I'm performing a study using Freesurfer. I'm stuck with the centering (de-meaning) issue. I have two discrete variables, gender, and patient-control, and a continuous variable which is age. The age population range goes from 20 to 55 years and is paired between patients and controls. Patient's disease affects cortical thickness over time and every patient has been presenting the disease for 6 years (no more, no less). I've runned QDEC and mri_glmfit using DODS obtaining the same results, the problem is that when I demean the age (I used the grandmean) the results are very differente. If I don't demean some clusters survive the monte-carlo multiple comparisons correction (p<0.05), but, when I demean no cluster survive. I have this questions: 1. Since most of my subjects are in the range of 20-35 years and only a few have more than 35 years, it is correct to use the mean? Wouldn't be better to use the median or some other value? 2. This is maybe a silly question, but why should I care about the intercept? I know that demeaning doesn't change the slope, just the intercept, but I don't understand why I should care, I read in some publications that demeaning is not always necessary. Other questions: 1. Most of my subjects are women (around 80%, N=18), Does it have an advantage to remove the males to get rid of the gender variable?, or should I continue as I've been doing, controlling for the effect of gender. 2. Since I don't know if this disease is more aggressive when is developed at some stage of life, I mean, if young patients are less affected than older patients after six years of presenting it, it is correct to control the effect of age? (Entering the variable as a nuisance factor), or should I search for an interaction between age and the condition variable? I only care about differences in cortical thickness. Any suggestion is very welcome, thanks in advance for your answer. Rodrigo

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DTI Multi band sequence?
by Martin Juneja 01 Dec '16

01 Dec '16

Hi, I was wondering if there is any way in FreeSurfer/FSL/MATLAB to determine whether the DTI data (in DICOM format) I have is multi-band sequence? I used dicominfo in MATLAB but couldn't find any information related to multi-band in the dicom header. Any help would be really appreciated.

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Re: [Freesurfer] obtain fa FA data from the white matter ROIs in WMParcStatsLUT.txt. or FreeSurferColorLUT.txt.
by Knut J Bjuland 01 Dec '16

01 Dec '16

Hi Anastasia If I want to use Tracula DTI files instead, which file do I choose: Is it FA_ditifit.nii? Best Knut Jørgen

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Re: [Freesurfer] Longitudinal TRACULA: mri_convert
by Vincent Koppelmans 30 Nov '16

30 Nov '16

Dear Anastasia, I emailed with Dr. Knut Jørgen Bjuland because he had a similar issue (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg39745.html) He mentioned that obtaining a new license could solve the issue. It did, so my problem is resolved. Best, Vincent ________________________________________ Dear Anastasia, I have checked the image and it looks good. I don't think the image is the problem, especially considering that my issue is also popping up with standard data. See for example the following code: $ echo $FREESURFER_HOME /home/mriuser/privatemodules/freesurfer $ cksum $(which mri_convert) 1305133180 29171478 /home/mriuser/privatemodules/freesurfer/bin/mri_convert $ echo $FSLDIR /home/mriuser/privatemodules/fsl $ mri_convert ${FSLDIR}/data/standard/MNI152_T1_1mm.nii.gz test.mgh mri_convert /home/mriuser/privatemodules/fsl/data/standard/MNI152_T1_1mm.nii.gz test.mgh $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ reading from /home/mriuser/privatemodules/fsl/data/standard/MNI152_T1_1mm.nii.gz... crypt_gkey = (null) Segmentation fault (core dumped) The reason I am posting this with 'Longitudinal TRACULA' in the title is because I only have this issue with the mri_convert that is bundled with the TRACULA update (see my first post). The original mri_convert bundled with the centOS6 64bit version of FS 5.3.0 (stable) does let me convert files. However, this version does not allow multiple frame numbers: Original frame options of mri_convert (FS v5.3.0 stable centos6 64) -f, --frame frameno keep only 0-based frame number Frame options of the updated mri_convert (tracula.update.centos6_x86_64.5.3.2014_05_26.tar.gz) -f, --frame frameno [...] keep only 0-based frame number(s) Longitudinal TRACULA pushes multiple files as arguments to 'mri_convert --frame', which is why I need the updated version. Do you have any suggestions for me? Thank you! best, Vincent ________________________________________ Hi Vincent - Looks like an mri_convert error, so not specific to TRACULA but probably something about the format of your input nifti volume. How did you create that volume? Can you open it in freeview and view it normally? a.y ________________________________________ From: freesurfer-boun...(a)nmr.mgh.harvard.edu [freesurfer-boun...(a)nmr.mgh.harvard.edu] on behalf of Vincent Koppelmans [vkop...(a)umich.edu] Sent: Wednesday, November 30, 2016 1:33 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Longitudinal TRACULA: mri_convert Hello Freesurfer experts, I am trying to run longitudinal TRACULA but I am getting an error early on in the process that seems to originate from mri_convert: #------------------------------------- /home/mriuser/privatemodules/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Wed Nov 30 09:10:55 EST 2016 mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz /datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz /datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz Segmentation fault (core dumped) Linux 3.10.0-327.4.4.el7.x86_64 #1 SMP Tue Jan 5 16:07:00 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Some information about my setup: -------------------------------- *Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 *Freesurfer TRACULA update installed: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-tracula-addons/t… *Linux version: CentOS Linux release 7.2.1511 (Core) centos-release-7-2.1511.el7.centos.2.10.x86_64 Is there a fix for this problem? Thanks! - Vincent

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Re: [Freesurfer] freesufer v6 beta - T2 pial refinement performance and nsigma_below setting
by Antonin Skoch 30 Nov '16

30 Nov '16

Dear experts, given sub-optimal results of my surfaces I referred to in my previous post, I have tested several different settings and input data preparation to obtain optimal pial surfaces in my modified HCP pipeline. I tested all variants in 5 representative subjects. My modified HCP pipeline uses FreeSurfer V6beta and full hires recon (-cm option) with 0.7mm3 data (including FreeSurferHiResWhite.sh and FreeSurferHiResPial.sh where effectively no up and downsampling is done since all steps are done in original 0.7 mm3 resolution). I have played with input data and parameters of 2nd pass mris_make_surfaces -T2pial in FreeSurferHiResPial.sh Since FreeSurferHiResPial.sh does not use aseg-informed and white surface-informed normalization and brain masking of T2 (which is default in recon-all), I also tested performance of this option (using commands borrowed from recon-all -T2pial). Since -nsigma_below 3 (default in FreeSurferHiResPial.sh) with combination of freeSurfer V6beta version of mris_make_surfaces cuts out some portions of gray matter in my data (in contrast to FreeSurfer 5.3 version where it seems that nsigma_below 3 suffices!), I increased -nsigma_below to 5 (which is default value used in recon-all -T2pial). My tested versions were following: For modified full hires HCP pipeline with FreeSurfer V6beta: 1. -nsigma_below 3 (original FreeSurferHiResPial.sh) 2. -nsigma_below 5 3. -nsigma_below 5 with additional masking of T2 by brainmask.mgz 4. -nsigma_below 5 with aseg-informed normalization of T2 (using mri_normalize) 5. -nsigma_below 5 with aseg-informed normalization of T2 (using mri_normalize) and masking of T2 by brainmask.mgz And, as Matt suggested, I also tried: 6. standard FreeSurfer V6 beta recon-all -pial and -T2pial (apart from standard recon-all I used as ?h.white input the output of FreeSurferHiResWhite.sh , but I think it should not matter in this context). My observations are following: It is definitely needed to increase -nsigma_below from 3 due to significant cut out of portions of gray matter in some regions, in some subjects these regions are very large. Increase nsigma_below to 5 prevents cutting out of gray matter, however it leads to leak of surfaces to cerebellum (as I showed in my previous post) for all my versions (to varying extent). I am not sure how much significant the extend of error is, looking subjective it seems significant, but accounting the fact that the data is of high resolution, the maximal error would be approx. 2 mm. -nsigma_below 5 with aseg-informed normalization does not work well in some areas and results in cutting out gray matter in some regions (but not to such great extend as in nsigma_below 3) FreeSurfer V6beta tends in some (not very large) areas to cut out gray matter. On the other hand, in some areas and in some subjects it produces largest leak of surfaces to dura and cerebellum from all my tested versions. mri_normalize of T2 has in some regions sub-optimal performance on pial surface estimation and actually performs worse than global (no aseg-informed and no white surface-informed) normalization ( especially at temporal poles, but also in some areas at convexity). I have indecisive results with masking. In some subjects it had almost no effect, in one subject it definitely improved the leak to dura, but in some subjects the results were quite opposite. I am not sure why the masking should matter since the mask is larger than the regions where the surfaces are extending, but I am not very familiar with internals of mris_make_surfaces (the masked T2 maybe after internal smoothing in mris_make_surfaces can propagate the voxel values even to regions relevant for surface estimation). Therefore I would tend to use the masking. Overall best results (better than with V6beta recon-all) I obtained with -nsigma_below 5 with global (no aseg-informed and white surface-informed) normalization of T2 as it is done in FreeSurferHiResPial.sh. My overall impresion: I was quite frustrated to observe, how much the results are dependent on particular setting of the parameters and input data. But maybe my expectations of accuracy of surfaces were unrealistically high.... Regards, Antonin

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Longitudinal TRACULA: mri_convert
by Vincent Koppelmans 30 Nov '16

30 Nov '16

Hello Freesurfer experts, I am trying to run longitudinal TRACULA but I am getting an error early on in the process that seems to originate from mri_convert: #------------------------------------- /home/mriuser/privatemodules/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Wed Nov 30 09:10:55 EST 2016 mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz /datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz /datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz Segmentation fault (core dumped) Linux 3.10.0-327.4.4.el7.x86_64 #1 SMP Tue Jan 5 16:07:00 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Some information about my setup: -------------------------------- *Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 *Freesurfer TRACULA update installed: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-tracula-addons/t… *Linux version: CentOS Linux release 7.2.1511 (Core) centos-release-7-2.1511.el7.centos.2.10.x86_64 Is there a fix for this problem? Thanks! - Vincent

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ERROR: cannot find RB_all_2008-03-26.gca
by Douglas Merkitch 30 Nov '16

30 Nov '16

Hello experts, I was attempting to test out the freesurfer v6 beta and encountered the following error during dicom conversion: "ERROR: cannot find /Applications/freesurfer_v6beta_16Nov2016/average/RB_all_2008-03-26.gca". I'm currently running freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae on a Mac Pro (3.33 GHz 6-Core Intel Xeon) with OS X 10.8.5. Any help would be greatly appreciated! Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853<tel:%28312%29%20563-3853> Fax: (312) 563-4660<tel:%28312%29%20563-4660> Email: Douglas_Merkitch(a)rush.edu<mailto:Douglas_Merkitch@rush.edu>

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Freesurfer November 2016