Freesurfer December 2016

freesurfer@nmr.mgh.harvard.edu

95 participants
146 discussions

bbregister --init-reg not working (reg2subject --r returning empty string)
by Antonin Skoch 05 Dec '16

05 Dec '16

Dear experts, I am having trouble using --init-reg option in bbregister (FreeSurfer v6 beta version). It exits with error: must supply subject id. My command line is: bbregister --mov my_moveable.nii.gz --s my_subject_id --lta my_lta_out.lta --dti --init-reg my_initial_lta.lta I traced the problem to reg2subject --r my_initial_lta.lta which is executed inside bbregister. This script returns empty string. By examining reg2subject code, it in case of .lta searches for string "subject" in lta file. However there is no such string in my .lta. My .lta file was created by tkregister2 by conversion from fsl .mat file (without specification of subject) by command: tkregister2 --mov mov.nii.gz --targ targ.nii.gz --ltaout mov2targ.lta --fsl mov2targ.mat --reg /tmp/junk --noedit where mov2targ.mat is vox2vox fsl-style matrix encoding transformation from mov.nii.gz to targ.nii.gz. I checked validity of produced .lta file by tkregister2 and it looks OK. The straightforward remedy in my case possibly would be to remove reg2subject invocation from bbregister (since I am already providing the subject by --s option), or add subject id to .lta. General solution in bbregister code would possibly be to provide test whether subject id is specified and in case it is not, then read the subject id from registration file. Or read both and in case of non-empty return of reg2subject, then compare obtained subject id with subject id supplied by --s and in case of different strings, produce a warning and use one of them (--s would take precedence?). My second inquiry is following: My idea was to do the registration in 3 stages: provide rough alignment with .lta, then mri_coreg (or fsl-flirt) and then bb-registration. My experience is, that in some situations when the images are very differently aligned, the --init-fsl totally fails. Is it possible to realize it by supplying both --init-reg and --init-coreg (or even combination of --init-reg --init-best to try both mri_coreg and flirt)? Regards, Antonin Skoch

2 1

recon-all -use-gpu and cuda version
by Parzer, Peter 05 Dec '16

05 Dec '16

Hi, I just tried recon-all with the -use-gpu flag from the current development version of freesurfer (freesurfer-Linux-centos6_x86_64-dev-20161123-bb356e0), but it fail with the message that is cannot open libcudart.so.5.0. I have the current cuda version install (8.0). Does freesurfer only work with cuda 5.0? Is there a plan to link the forthcoming 6.0 version with the current version of cuda? Peter

2 3

Re: [Freesurfer] PCA on PET / Thickness in Freesurfer
by Elijah Mak 03 Dec '16

03 Dec '16

Hi Doug, Thanks. It works! What does each vertex represent in V.mgh? http://imgur.com/W1RZdKn Here are the results from the stats. Then, I would like to extract the 1st component and convert it into label for mri_segstats. How may I do that? 1 105131.57 105131.57 73.79 73.79 2 9130.61 114262.18 6.41 80.20 3 8052.58 122314.77 5.65 85.85 4 5480.79 127795.56 3.85 89.69 5 4398.33 132193.89 3.09 92.78 6 3504.02 135697.91 2.46 95.24 7 2386.62 138084.53 1.68 96.92 8 2055.74 140140.27 1.44 98.36 9 1603.79 141744.06 1.13 99.48 10 734.89 142478.95 0.52 100.00 11 0.00 142478.95 0.00 100.00 Thanks. Best Wishes, Elijah Re: [Freesurfer] PCA on PET / Thickness in Freesurfer <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50417.html> 2016-12-02 <http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=dat…> Thread <http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=sub…> Douglas N Greve <http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fro…> You can run it like that or with --osgm (instead of --fsgd and --C), osgm = one sample group mean. On 12/01/2016 07:13 PM, Foo Keat Mak wrote: > Hi Doug, > I have pasted the correspondences below. My question is, if I want to > identify the PCs in a group for a single modality (PET), how should I > run the mri_glmfit? A single group design with A contrast of 1 0 (for > a nuisance covariate)? > Thanks ! > Elijah > Doug: > For within modality, you can add --pca to mri_glmfit (run it with > --help to get more info). We do not have ICA tools in FS. > On 12/01/2016 02:04 PM, Foo Keat Mak wrote: > 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 > > > > ___ > Freesurfer mailing > list > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- > Douglas N. Greve, Ph.D. MGH-NMR Center gr...(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 Fax: > 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: > https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > ___ 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. > > > Sent from my iPad > > On 1 Dec 2016, at 23:30, Foo Keat Mak > wrote: > >> Thanks Doug. Does that mean that a one group design? With a contrast >> of 1 0 (adjusting for one variable)? >> >> > > > ___ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Centergr...(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2www.nmr.mgh.harvard.edu/facility/… Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Re: [Freesurfer] PCA on PET / Thickness in Freesurfer <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50407.html> 2016-12-01 <http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=dat…> Thread <http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=sub…> Foo Keat Mak <http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fro…> Hi Doug, I have pasted the correspondences below. My question is, if I want to identify the PCs in a group for a single modality (PET), how should I run the mri_glmfit? A single group design with A contrast of 1 0 (for a nuisance covariate)? Thanks ! Elijah Doug: For within modality, you can add --pca to mri_glmfit (run it with --help to get more info). We do not have ICA tools in FS. On 12/01/2016 02:04 PM, Foo Keat Mak wrote: > 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 > > > ___ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Centergr...(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2www.nmr.mgh.harvard.edu/facility/… Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://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. Sent from my iPad On 1 Dec 2016, at 23:30, Foo Keat Mak > wrote: Thanks Doug. Does that mean that a one group design? With a contrast of 1 0 (adjusting for one variable)? ___ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://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] PCA on PET / Thickness in Freesurfer <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50406.html> 2016-12-01 <http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=dat…> Thread <http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=sub…> Douglas N Greve <http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fro…> sorry, can you repost with previous correspondence? On 12/01/2016 06:30 PM, Foo Keat Mak wrote: > Thanks Doug. Does that mean that a one group design? With a contrast > of 1 0 (adjusting for one variable)? > > > > > ___ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Centergr...(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2www.nmr.mgh.harvard.edu/facility/… Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://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] PCA on PET / Thickness in Freesurfer <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50405.html> 2016-12-01 <http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=dat…> Thread <http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=sub…> Foo Keat Mak <http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fro…> Thanks Doug. Does that mean that a one group design? With a contrast of 1 0 (adjusting for one variable)? ___ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://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] PCA on PET / Thickness in Freesurfer <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50396.html> 2016-12-01 <http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=dat…> Thread <http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=sub…> Douglas N Greve <http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fro…> For within modality, you can add --pca to mri_glmfit (run it with --help to get more info). We do not have ICA tools in FS. On 12/01/2016 02:04 PM, Foo Keat Mak wrote: > 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 > > > ___ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Centergr...(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2www.nmr.mgh.harvard.edu/facility/… Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://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.

1 0

Open Neuroimaging Laboratory
by Satrajit Ghosh 03 Dec '16

03 Dec '16

Hi, The Open Neuroimaging Laboratory (http://openneu.ro) was one of the six finalists for the open science prize, and we presented our prototype platform at the NIH BD2K open science symposium on Dec 1. Check out our prototype for the #OpenSciencePrize and vote to help us advance in the finals! www.OpenSciencePrize.org <http://www.openscienceprize.org/> or https://goo.gl/o6dJRJ The platform is also the first one in the brain imaging arena that allows anyone to directly search for public data (some phenotypic and clinical info and T1 images) and then curate (mostly T1/T2 images currently) using an interactive, collaborative editor. We provide direct access to over 8k MRIs. And we would encourage you to use it to curate public data together. Every lab should not have to curate public data on their own, individually, separately, and redundantly. You can also upload your own images and freesurfer aseg or other annotations and fix them online collaboratively. More importantly, as these get fixed, we can use the cleaned data to start building better algorithms as well. To start, you can play with the thousands that are there (including an excellent collection of brains from other species: http://brainbox.pasteur.fr/project/braincatalogue/) and search for others here (http://openneu.ro/metasearch) any feedback is welcome. please post it here: https://neurostars.org/t/open-neuroimaging-laboratory/17/1 cheers, satra (on behalf of the Open Neuroimaging Laboratory)

1 0

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:

2 5

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

2 1

'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

1 0

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

2 4

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)

2 3

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)?

2 3

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer December 2016