Freesurfer

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30076 discussions

Build problem
by Melvin Robinson 02 Dec '16

02 Dec '16

I'm having a small (?) build problem with freesurfer. My configure line merely points to the dependencies package and the--disable-Werror flag, but I get the following error. Grepping through the source I cannot find where the structure is defined. gcc -DHAVE_CONFIG_H -I. -I.. -I../include -pthread -DHAVE_OPENGL -g -O3 -msse2 -mfpmath=sse -Wall -DUSE_SSE_MATHFUN -m64 -DLinux -DANSI -fdata-sections -ffunction-sections -Wl,--gc-sections -I../dependencies/centos6-x86_64-packages/mni/current/include -MT oglutil.o -MD -MP -MF .deps/oglutil.Tpo -c -o oglutil.o oglutil.c In file included from ../include/transform.h:84:0, from ../include/mrisurf.h:209, from oglutil.c:43: ../include/mri.h:210:3: error: unknown type name 'General_transform' General_transform transform ; /* the next two are from this struct */ ^ ../include/mri.h:211:3: error: unknown type name 'Transform' Transform *linear_transform ; ^ ../include/mri.h:212:3: error: unknown type name 'Transform' Transform *inverse_linear_transform ; ^ ../include/mri.h:386:35: error: unknown type name 'General_transform' int MRIsetTransform(MRI *mri, General_transform *transform) ; ^ In file included from ../include/mrisurf.h:1793:0, from oglutil.c:43: ../include/label.h:54:3: error: unknown type name 'General_transform' General_transform transform ; /* the next two are from this struct */ ^ ../include/label.h:55:3: error: unknown type name 'Transform' Transform *linear_transform ; ^ ../include/label.h:56:3: error: unknown type name 'Transform' Transform *inverse_linear_transform ; ^ In file included from ../include/transform.h:84:0, from ../include/mrisurf.h:209, from oglutil.c:43:

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Surfaces without segmentation
by Hatton, Sean 02 Dec '16

02 Dec '16

Hello, We are just interested in generating the white and pial surfaces without segmentation. 1. Are there additional switches for running mris_make_surfaces without aseg (for -white section) or apar.annot (for -pial section)? 2. We would like to control intensity values - can we specify tissue class cutoffs in mri_normalize and mri_ca_normalize? Regards, Sean Hatton, PhD Postdoctoral Scholar, Department of Psychiatry UC San Diego

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'std: :bad_alloc'
by Allison Rainford 02 Dec '16

02 Dec '16

Hi FreeSurfer team, I'm trying to create a base for 5 time points in freesurfer version 5.1 and have run into issues with my job submission exiting in error. This is the command I originally tried using: runFreeSurferSinglePBS -N huey.sw -r "-all -base P040_2yr5tp -tp P040b_v0 -tp P040_v6 -tp P040_v12 -tp P040_v18 -tp P040c" -S /project/freesurfer/CNADC_FS/PPA_v5.1.0/ P040_2yr5tp This resulted in the following error while starting global iteration: 2: Resolution: 0 S( 256 256 256 ) T( 256 256 256 ) Iteration(f): 1 -- diff. to prev. transform: 0.127011 Iteration(f): 2terminate called after throwing an instance of 'std::bad_alloc' what(): St9bad_alloc Because this appears to be a memory issue, I tried running it with a new memory parameter, using the following flag per a colleague's recommendation: runFreeSurferSinglePBS -m 4GB -N huey.sw -r "-all -base P040_2yr5tp -tp P040b_v0 -tp P040_v6 -tp P040_v12 -tp P040_v18 -tp P040c" -S /project/freesurfer/CNADC_FS/PPA_v5.1.0/ P040_2yr5tp I've also opened each of the 5 time points for this subject and cannot see anything wrong with any of the individual time points. Any help is greatly appreciated! Thank you, Allison Rainford Research Study Assistant Cognitive Neurology and Alzheimer's Disease Center Northwestern University 320 East Superior Street Searle 11-579 Chicago, Illinois 60611 Email: allison.rainford(a)northwestern.edu

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Ubuntu or Centos?
by Brad Matushewski 02 Dec '16

02 Dec '16

I have had some issues with Ubuntu (installation stops before completing). I am currently trying to get a dual boot set up with Windows 10. Someone mentioned I should try Centos instead of Ubuntu? Thoughts? Pros vs Cons? -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Z K Sent: October 13, 2016 1:34 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all exited with ERRORS Yes, that would be a good option. Its a little work but here is a guide that I dug up which helps explain the process. For the version of linux to use... I would recommend Ubuntu 14.04.5 LTS (https://www.ubuntu.com/download/alternative-downloads) On 10/13/2016 01:25 PM, Brad Matushewski wrote: > Would a feasible approach be to set up a dual-boot on my PC so that I can boot directly into either a Windows or Linux environment? > > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Z K > Sent: Thursday, October 13, 2016 12:53 PM > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] recon-all exited with ERRORS > > I was afraid this was the case. Normally in this situation I would say set up a shared folder between the host and the virtual machines. But unfortunately there is a known bug in the the MNI tools shipped with freesurfer which makes this an incompatible arrangement. > > The disk space was assigned to allow perhaps a few subjects worth of data onto the virtual image, otherwise the download size would have been prohibitively large. If you want to process numerous subjects the VirtualBox version is insuffiecient, you will have to use the Mac or Linux version. > > > On 10/13/2016 12:39 PM, Brad Matushewski wrote: >> I would appear that the allotted hard drive space is fixed as a function of the Freesurfer installation. There does not appear to be an option to expand allotted space either at time of installation or after the fact. >> >> >> -----Original Message----- >> From: freesurfer-bounces(a)nmr.mgh.harvard.edu >> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Z K >> Sent: Thursday, October 13, 2016 11:03 AM >> To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu>; Brad >> Matushewski <bjmatush(a)uwo.ca> >> Subject: Re: [Freesurfer] recon-all exited with ERRORS >> >> >> I think its referring to the hard disk space in the virtual machine. You probably ran out which is not surprising, as the amount of free space provided with the disk image is fairly small. The fact the your host machine has 305Gb of HD on the host machine is unknown to the virtual machine. >> >> See if you can expand the hard disk space of the virtual machine (not sure if this is adjustable or not). Also, try setting up a shared folder between the two (this has other potential issues, but is worth trying). >> >> -Zeke >> >> >> On 10/13/2016 10:58 AM, Brad Matushewski wrote: >>> Thank you, Bruce for the rapid reply. I am running Freesurfer on a (Windows 10 based), virtual machine. I installed / set it up according to the directions posted here: >>> https://surfer.nmr.mgh.harvard.edu/fswiki/Installation/FreeSurferVir >>> t >>> u >>> alImage >>> >>> ...specifically referring to the recommended memory suggestions of 4MB. Otherwise, I saw no other options for specifying memory requirements. >>> >>> What is the nature of this memory error and how do I go about fixing it? I know that I have 305 Gb of HD. >>> >>> >>> >>> >>> >>> -----Original Message----- >>> From: freesurfer-bounces(a)nmr.mgh.harvard.edu >>> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce >>> Fischl >>> Sent: Thursday, October 13, 2016 9:43 AM >>> To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >>> Subject: Re: [Freesurfer] recon-all exited with ERRORS >>> >>> Hi Brad >>> >>> it looks like the recon failed as you ran out of disk space: >>> >>> cvarput: ncid 5: No space left on device >>> miicv_put: MINC package entry point >>> nu_evaluate: crashed while running mincmath (termination status=768) >>> nu_correct: crashed while running nu_evaluate (termination >>> status=768) >>> >>> >>> as for what would have been next, that of course depends on what you >>> want to study >>> >>> cheers >>> Bruce >>> >>> >>> On >>> Thu, >>> 13 Oct >>> 2016, Brad Matushewski wrote: >>> >>>> >>>> >>>> >>>> I just tried to run my first recon-all. >>>> >>>> >>>> >>>> What now? >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> Logo >>>> >>>> Brad J. Matushewski, M.Sc., R.Kin., CSEP-CEP. >>>> >>>> Laboratory for Brain & Heart Health School of Kinesiology Western >>>> University Room 402, Arthur & Sonia Labatt Health Sciences Building >>>> London, ON, Canada, N6A 5B9 >>>> Tel: (519) 661-2111 x 89066 >>>> Fax: (519) 850-2447 >>>> >>>> >>>> >>>> >>>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> _______________________________________________ >> 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. >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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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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Re: [Freesurfer] PCA on PET / Thickness in Freesurfer
by Foo Keat Mak 02 Dec '16

02 Dec '16

Thanks Doug. Does that mean that a one group design? With a contrast of 1 0 (adjusting for one variable)?

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PCA on PET / Thickness in Freesurfer
by Foo Keat Mak 01 Dec '16

01 Dec '16

Hi Freesurfer Team, For a given group, I want to look at the covariance patterns between thickness and PET. Within Freesurfer, what are some general workflow tips on how I could go about performing PCA (within modality) or joint ICA analyses looking at the covariance patterns across modalities? Is the -pca flag a good starting point? Any feedback is appreciated! Thanks a lot. Best Wishes, Elijah

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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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Freesurfer