Freesurfer

freesurfer@nmr.mgh.harvard.edu

2 participants
30134 discussions

Cortical thickness and FS-FAST on cerebellum
by stdp82＠virgilio.it 05 Dec '16

05 Dec '16

Hi list,I wonder whether is possible to:1) obtain cortical thickness from cerebellum and its subregions2) use cerebellum (or its subregions) as seed for FS-FAST analysis? Thanks in advance Kind regards Stefano

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

05 Dec '16

Dear Doug, yes, the point is, that my_initial_lta.lta does not have subject name in it. Your suggestion to rearrange parameters in bbregister indeed helped to get further, however, later ended with error in bbregister execution in call of mri_segreg, which does not pass the subject parameter and reads it from the .reg file: mri_segreg --mov /hydradb/hydra_io/vypocty/skoch/20160609_HCENAT_DWI/proc/HCE_C00573_20160524_1456_2/reg/tmp.bbregister.5112/template.nii --init-reg /hydradb/hydra_io/vypocty/skoch/20160609_HCENAT_DWI/proc/HCE_C00573_20160524_1456_2/reg/tmp.bbregister.5112/init.reg.5112.dat --out-reg /hydradb/hydra_io/vypocty/skoch/20160609_HCENAT_DWI/proc/HCE_C00573_20160524_1456_2/reg/tmp.bbregister.5112/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 The error is: mghRead(/hydradb/hydra_io/vypocty/skoch/20161008_HCENAT_struct/A_HCP_w_FS_dev_long/subject-unknown/mri/orig.mgz, -1): could not open file I solved the issue by additional appending subject id into my_initial_lta.lta file. It seems to work OK, bbregister finishes without error. Antonin ---------------------------------------------------------------------------------------------------- does my_initial_lta.lta have the subject name in it? If not, then put that argument before the --s On 12/05/2016 10:34 AM, Antonin Skoch wrote: > 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

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Odd Extremely High/Low Banding of Functional Values in Volume
by Dowling, Kevin Francis 05 Dec '16

05 Dec '16

Hello Freesurfer Experts, I’m attempting to look at activity in a working memory paradigm using blood folate levels as my covariate of interest while controlling for gender and age in 137 subjects. There were no errors (that I could find) in the concatenation or mri_glmfit commands, and subject registration looked ok for the functional data. When visualizing the right and left hemisphere surface sig.mgh files using tksurfer everything looks reasonable. However, when using tkmedit (tkmedit fsaverage1 orig.mgz –overlay sig.mgh –fminmax 1.3 3.3 –fmid 2.3) I am getting odd continuous bands of incredibly high and incredibly low activation spanning throughout most the volume (I’ve attached some screen grabs – the functional values in these bands are either 10000000000 or -10000000000 and look continuous from slice to slice). I’ve taken a look at the list and was not able to find a similar problem discussed. I would be most grateful for any guidance or trouble shooting suggestions you might have! I’ve also attached a text file copy of the glm and tkmedit results in case they would be of use. I'm using Freesurfer version 5.3 (nmr-stable53-env) on a Linux (Release 6.7 (Santiago), Kernel Linux 2.6.32-573.12.1.el6.x86_64 and GNOME 2.28.2) Thank you! Kevin Kevin Dowling Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street Charlestown, MA, 02129 (p) (617) 643 - 2479

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Edit to wm.seg.mgz.
by miracooloz＠gmail.com 05 Dec '16

05 Dec '16

3 3

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

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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.

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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:

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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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