Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

Freesurfer Question regarding infant brain reconstructions
by Katie Travis 22 Jul '08

22 Jul '08

Hello, I have some basic questions regarding some Freesurfer reconstructions that I've made on a set of infant brains (12-15month olds). Overall, the reconstructions have been successful. The exception being that the gray matter of the anterior temporal lobes are being underestimated, typically bilaterally. For example, when I look at an inflated surface, the temporal pole(s) appears pointed and has an almost triangular edge as opposed to a more "rounded" pole. To my eye, it appears that the the gray matter is being estimated very close to the border of the white matter in the anterior temporal lobe. I believe this to be happening since the wm in this age is not well- defined and it appears darker than most other wm in the cortex. I'm also finding in a few other areas (mostly motor and some anterior/ frontal cortex) that the white matter is also being overestimated (extending into gray matter areas). For my analyses, I'm hoping to estimate most accurately the wm/gm surfaces for source analyses I am doing with MEG data. The temporal lobes are of particular importance given the auditory nature of my task. I am new to the Freesurfer editing process, and was wondering if you have any suggestions about editing these surfaces. I would also be happy to try and send you data/screen shots of what I'm describing in terms of the surface segmentations if that would better assist you with my question. Thank you for your help, Katie Travis Neuroscience Doctoral Student Center for Research in Language and Multimodal Imaging Laboratory 9500 Gilman Drive, Mail Code 0562 La Jolla, CA 92093-0562 email: ktravis(a)ucsd.edu

2 1

Re: [Freesurfer] Preproc-sess: Spatial smoothing and brain masking
by Balaji Goparaju 22 Jul '08

22 Jul '08

Hi, I copied the new version of the programs mktemplate-sess surfsmooth-sess stc-sess mkbrainmask-sess mc-sess When i try to run preproc-sess -s LD-functional -fwhm 5 again, I get the following error, -------------------------------------------------------------- preproc-sess logfile is log/preproc-sess.log -------------------------------------------------------------- instem f mc 1 f fmc stc 0 fmc sm 1 fmc fmcsm5 mask 1 brain LD-functional MC ----------------------------- Tue Jul 22 09:25:08 EDT 2008 /Users/balajigoparaju/Desktop/subjectdata mc-sess -fstem f -fmcstem fmc -s LD-functional -d /Users/balajigoparaju/Desktop/subjectdata -fsd bold -new -update -no-inorm ---------------------------------------- /Applications/freesurfer/fsfast/bin/mc-sess: line 1: {rtf1macansicpg10000cocoartf824cocoasubrtf480: command not found /Applications/freesurfer/fsfast/bin/mc-sess: line 2: syntax error near unexpected token `}' /Applications/freesurfer/fsfast/bin/mc-sess: line 2: `{\fonttbl\f0\fswiss\fcharset77 Helvetica;}' ERROR: mc-sess failed And then i tried changing the mc-sess.backup file back to the mc-sess (Using the older version of mc-sess), and then the mc-sess and spatialsmooth-sess part of the preproc-sess program worked fine, but i get a similar error for the brainmask-sess program. Tue Jul 22 09:19:12 EDT 2008 /Users/balajigoparaju/Desktop/subjectdata mkbrainmask-sess -maskstem brain -fsd bold -s LD-functional -d /Users/balajigopa raju/Desktop/subjectdata -update ---------------------------------------- /Applications/freesurfer/fsfast/bin/mkbrainmask-sess: line 1: {rtf1macansicpg100 00cocoartf824cocoasubrtf480: command not found /Applications/freesurfer/fsfast/bin/mkbrainmask-sess: line 2: syntax error near unexpected token `}' /Applications/freesurfer/fsfast/bin/mkbrainmask-sess: line 2: `{\fonttbl\f0\fswi ss\fcharset77 Helvetica;}' ERROR: mkbrainmask-sess failed Thank you for any help.

2 1

Talairach Coordinates
by Steinmann, Iris 22 Jul '08

22 Jul '08

Dear FreeSurfers I use the command: <tkmedit-sess -s vpnXY -aparc+aseg -analysis ampmod -c AmvsSIN> and want to mark a point at special Talairach coordinates at this brain. When I type in the coordinates e.g. -46 -19 8 and press RETURN the the Numbers change to e.g. -46 -92 15. I dont found a possibility to mark the talairach coordinates I want. Can you help me? Thanks! Iris

1 0

Re: Freesurfer Digest, Vol 53, Issue 19
by Sebastian Moeller 22 Jul '08

22 Jul '08

Dear All, while being no exert, I assume the following: in spatialsmooth-sess from freesurfer 4.0.5, line 160, there is the following test: test $infunc -nt $outfunc This is used to skip processing if -update is specified, the test evaluates to 1 if $infunc exists and is older than $outfunc it evaluates to 0 if $infunc truely is newer than $outfunc; it ALSO evaluates to 1 if $outfunc does not exist (tested with macosx 10.5.4). So if $outfunc does not exist (and 'ls: 017/fmcsm5.nii: No such file or directory' is exactly pointing to ths configuration), then the processing is skipped. I would assume that running without the "- update" option should solve the problem... Or exchanging line 159 with something along the ines of: if ($UpdateOnly & !(-e $outfunc)) then So that the critical test is only run, if no $outfunc exists... Then again, I could be completely out to lunch, as I still use FS 3.0.5, and only looked at the 4.0.5 code... ahoi Sebastian On Jul 21, 2008, at 3:51 PM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 4 > Date: Mon, 21 Jul 2008 09:43:54 -0400 > From: "Balaji Goparaju" <balaji.goparaju(a)gmail.com> > Subject: [Freesurfer] Preproc-sess: Spatial smoothing and brain > masking > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <4002c9df0807210643q88b079blf1511f4eaf49e570(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > I used the command > > preproc-sess -s LD-functional -fwhm 5 > > However, the command does not seem create the fmcsm5.nii file. The > process > completes motion correction successfully, but it > does not complete the spatial smoothing and brain masking. I get a > "Motion > correction SUCCESSFULLY completed" message but > I only get a "Spatial smoothing done" message. I have already asked > this > question in the mailing list. and i was asked to check the > writing permissions of the directories. I have changed the "bold" > directory > and freesurfer directory to have read, write and execute > permisions using the "chmod -R 777" command. > > I get the following output: > > -------------------------------------------------------------- > preproc-sess logfile is log/preproc-sess.log > -------------------------------------------------------------- > instem f > mc 1 f fmc > stc 0 fmc > sm 1 fmc fmcsm5 > mask 1 brain > LD-functional MC ----------------------------- > Mon Jul 21 09:32:56 EDT 2008 > /Users/balajigoparaju/Desktop/subjectdata > mc-sess -fstem f -fmcstem fmc -s LD-functional -d > /Users/balajigoparaju/Desktop/subjectdata -fsd bold -new -update -no- > inorm > ---------------------------------------- > Logfile is > /Users/balajigoparaju/Desktop/subjectdata/log/mc-LD-functional- > bold.log > ------------------------------------------- > /Users/balajigoparaju/Desktop/subjectdata/LD-functional > RunList: 006 010 017 019 > Targ Stem is 006/f > Update not needed > -rwxrwxrwx 1 balajigo admin 41091424 Jul 11 10:15 006/fmc.nii > -rwxrwxrwx 1 balajigo admin 523 Jul 7 09:57 006/f.bhdr > Update not needed > -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 08:26 010/fmc.nii > -rwxrwxrwx 1 balajigo admin 523 Jul 7 09:57 010/f.bhdr > Update not needed > -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 17:03 017/fmc.nii > -rwxrwxrwx 1 balajigo admin 523 Jul 7 09:57 017/f.bhdr > Update not needed > -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 17:07 019/fmc.nii > -rwxrwxrwx 1 balajigo admin 523 Jul 7 09:57 019/f.bhdr > > > Mon Jul 21 09:32:57 EDT 2008 > mc-sess completed SUCCESSFULLY > LD-functional Smooth ------------------------ > Mon Jul 21 09:32:57 EDT 2008 > /Users/balajigoparaju/Desktop/subjectdata > spatialsmooth-sess -i fmc -o fmcsm5 -fwhm 5 -fsd bold -s LD- > functional -d > /Users/balajigoparaju/Desktop/subjectdata -update -noinorm > ---------------------------------------- > ------------------------------------------------ > ------------------------------------------------ > /Users/balajigoparaju/Desktop/subjectdata/LD-functional > Mon Jul 21 09:32:57 EDT 2008 > ~/Desktop/subjectdata/LD-functional/bold ~/Desktop/subjectdata > RunList 006 010 017 019 > /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold > ls: 006/fmcsm5.nii: No such file or directory > -rwxrwxrwx 1 balajigo admin 41091424 Jul 11 10:15 006/fmc.nii > Update not needed > /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold > ls: 010/fmcsm5.nii: No such file or directory > -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 08:26 010/fmc.nii > Update not needed > /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold > ls: 017/fmcsm5.nii: No such file or directory > -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 17:03 017/fmc.nii > Update not needed > /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold > ls: 019/fmcsm5.nii: No such file or directory > -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 17:07 019/fmc.nii > Update not needed > Started at Mon Jul 21 09:32:57 EDT 2008 > Ended at Mon Jul 21 09:32:59 EDT 2008 > spatiallysmooth-sess Done > LD-functional Inorm ------------------------ > Mon Jul 21 09:32:59 EDT 2008 > /Users/balajigoparaju/Desktop/subjectdata > mkbrainmask-sess -maskstem brain -fsd bold -s LD-functional -d > /Users/balajigoparaju/Desktop/subjectdata -update > ---------------------------------------- > ------------------------------------------------ > ------------------------------------------------ > /Users/balajigoparaju/Desktop/subjectdata/LD-functional > Mon Jul 21 09:32:59 EDT 2008 > /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold > ls: masks/brain.nii: No such file or directory > -rwxrwxrwx 1 balajigo admin 523 Jul 7 09:57 006/f.bhdr > Update not needed > Mon Jul 21 09:33:00 EDT 2008 > mkbrainmask-sess done > ---------------------------------------- > Started at Mon Jul 21 09:32:56 EDT 2008 > Ended at Mon Jul 21 09:33:00 EDT 2008 > preproc-sess done > > Any help is appreciated. > Thank you. -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 0 15 77 - 1 90 31 41 moeller(a)neuro.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

1 0

IO with freesurfer files (.mgh in particular) from Python
by Yaroslav Halchenko 21 Jul '08

21 Jul '08

Does anyone know any handy module to at least read in .mgh files from Python? Or should I simply try mri_convert them into .minc and use netcdf module within python? Thanks in advance for the ideas! -- Yaroslav Halchenko Research Assistant, Psychology Department, Rutgers-Newark Student Ph.D. @ CS Dept. NJIT Office: (973) 353-5440x263 | FWD: 82823 | Fax: (973) 353-1171 101 Warren Str, Smith Hall, Rm 4-105, Newark NJ 07102 WWW: http://www.linkedin.com/in/yarik

4 9

Preproc-sess: Spatial smoothing and brain masking
by Balaji Goparaju 21 Jul '08

21 Jul '08

Hi, I used the command preproc-sess -s LD-functional -fwhm 5 However, the command does not seem create the fmcsm5.nii file. The process completes motion correction successfully, but it does not complete the spatial smoothing and brain masking. I get a "Motion correction SUCCESSFULLY completed" message but I only get a "Spatial smoothing done" message. I have already asked this question in the mailing list. and i was asked to check the writing permissions of the directories. I have changed the "bold" directory and freesurfer directory to have read, write and execute permisions using the "chmod -R 777" command. I get the following output: -------------------------------------------------------------- preproc-sess logfile is log/preproc-sess.log -------------------------------------------------------------- instem f mc 1 f fmc stc 0 fmc sm 1 fmc fmcsm5 mask 1 brain LD-functional MC ----------------------------- Mon Jul 21 09:32:56 EDT 2008 /Users/balajigoparaju/Desktop/subjectdata mc-sess -fstem f -fmcstem fmc -s LD-functional -d /Users/balajigoparaju/Desktop/subjectdata -fsd bold -new -update -no-inorm ---------------------------------------- Logfile is /Users/balajigoparaju/Desktop/subjectdata/log/mc-LD-functional-bold.log ------------------------------------------- /Users/balajigoparaju/Desktop/subjectdata/LD-functional RunList: 006 010 017 019 Targ Stem is 006/f Update not needed -rwxrwxrwx 1 balajigo admin 41091424 Jul 11 10:15 006/fmc.nii -rwxrwxrwx 1 balajigo admin 523 Jul 7 09:57 006/f.bhdr Update not needed -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 08:26 010/fmc.nii -rwxrwxrwx 1 balajigo admin 523 Jul 7 09:57 010/f.bhdr Update not needed -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 17:03 017/fmc.nii -rwxrwxrwx 1 balajigo admin 523 Jul 7 09:57 017/f.bhdr Update not needed -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 17:07 019/fmc.nii -rwxrwxrwx 1 balajigo admin 523 Jul 7 09:57 019/f.bhdr Mon Jul 21 09:32:57 EDT 2008 mc-sess completed SUCCESSFULLY LD-functional Smooth ------------------------ Mon Jul 21 09:32:57 EDT 2008 /Users/balajigoparaju/Desktop/subjectdata spatialsmooth-sess -i fmc -o fmcsm5 -fwhm 5 -fsd bold -s LD-functional -d /Users/balajigoparaju/Desktop/subjectdata -update -noinorm ---------------------------------------- ------------------------------------------------ ------------------------------------------------ /Users/balajigoparaju/Desktop/subjectdata/LD-functional Mon Jul 21 09:32:57 EDT 2008 ~/Desktop/subjectdata/LD-functional/bold ~/Desktop/subjectdata RunList 006 010 017 019 /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold ls: 006/fmcsm5.nii: No such file or directory -rwxrwxrwx 1 balajigo admin 41091424 Jul 11 10:15 006/fmc.nii Update not needed /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold ls: 010/fmcsm5.nii: No such file or directory -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 08:26 010/fmc.nii Update not needed /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold ls: 017/fmcsm5.nii: No such file or directory -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 17:03 017/fmc.nii Update not needed /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold ls: 019/fmcsm5.nii: No such file or directory -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 17:07 019/fmc.nii Update not needed Started at Mon Jul 21 09:32:57 EDT 2008 Ended at Mon Jul 21 09:32:59 EDT 2008 spatiallysmooth-sess Done LD-functional Inorm ------------------------ Mon Jul 21 09:32:59 EDT 2008 /Users/balajigoparaju/Desktop/subjectdata mkbrainmask-sess -maskstem brain -fsd bold -s LD-functional -d /Users/balajigoparaju/Desktop/subjectdata -update ---------------------------------------- ------------------------------------------------ ------------------------------------------------ /Users/balajigoparaju/Desktop/subjectdata/LD-functional Mon Jul 21 09:32:59 EDT 2008 /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold ls: masks/brain.nii: No such file or directory -rwxrwxrwx 1 balajigo admin 523 Jul 7 09:57 006/f.bhdr Update not needed Mon Jul 21 09:33:00 EDT 2008 mkbrainmask-sess done ---------------------------------------- Started at Mon Jul 21 09:32:56 EDT 2008 Ended at Mon Jul 21 09:33:00 EDT 2008 preproc-sess done Any help is appreciated. Thank you.

2 5

preproc-sess : Problem with spatial smoothing and brain masking
by Balaji Goparaju 18 Jul '08

18 Jul '08

HI, I ran the preproc-sess command, but in the output for spatial smoothing, the fmcsm5 file is not created. It says [balaji-goparajus-computer:~/Desktop/subjectdata] balajigo% spatialsmooth-sess -i fmc -o fmcsm5 -fwhm 5 -fsd bold -s LD-functional -d /Users/balajigoparaju/Desktop/subjectdata -update -noinorm ------------------------------------------------ ------------------------------------------------ /Users/balajigoparaju/Desktop/subjectdata/LD-functional Thu Jul 17 16:03:47 EDT 2008 ~/Desktop/subjectdata/LD-functional/bold ~/Desktop/subjectdata RunList 006 010 017 019 /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold ls: 006/fmcsm5.nii: No such file or directory -rwxrwxrwx 1 balajigo admin 41091424 Jul 11 10:15 006/fmc.nii Update not needed /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold ls: 010/fmcsm5.nii: No such file or directory -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 08:26 010/fmc.nii Update not needed /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold ls: 017/fmcsm5.nii: No such file or directory -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 17:03 017/fmc.nii Update not needed /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold ls: 019/fmcsm5.nii: No such file or directory -rwxrwxrwx 1 balajigo admin 41091424 Jul 13 17:07 019/fmc.nii Update not needed Started at Thu Jul 17 16:03:47 EDT 2008 Ended at Thu Jul 17 16:03:48 EDT 2008 spatiallysmooth-sess Done Thank you for your help!

2 1

Bad Talairach
by Vina Goghari 17 Jul '08

17 Jul '08

Hi all, I get this error: Sat Jul 12 10:24:08 CDT 2008 talairach_avi done #-------------------------------------------- #@# Talairach Failure Detection Sat Jul 12 10:24:08 CDT 2008 /pkg/bliss_all_labs/tricam/FEP_Aro/cbx02/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0069, pval=0.0000 < threshold=0.0050) Linux bliss 2.6.9-67.0.15.ELsmp #1 SMP Tue Apr 22 13:58:43 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Sat Jul 12 10:24:08 CDT 2008 So I viewed the talairach transform using tkregister2 and this is what I see for target and moveable. How would I go about fixing something like this: See attached images. Thanks, Vina ------------------------------------------------------------------------

5 9

Re: [Freesurfer] FS processing of FTLD subjects
by Sky Raptentsetsang 16 Jul '08

16 Jul '08

Hi Bruce, Yes there is a major inhomogeneity issue that we deal with prior to running FS, along with an addition skull strip step. With all of our 4T data, because of the large bias field and hyper-intense Dura Matter, we perform a bias correction and skull-strip before the data is entered into FS. During these pre-processing steps we think that some orientation information is lost due to multiple format conversions. Forgive me but I am introducing other issues, but because of this loss of positional information I cannot reliably optimize the talairach transformation in tkregister2 (see attached picture). You will see that the reference point in the FOV of tkregister2 is in the wrong quadrant. Though from what I can see the talairach transforms seem to be good, but some appear to be slightly underestimated. So maybe this is probably a good target to try and fix the underestimation of our surfaces. This problem with viewing the talairach has never sat well with me, but the surfaces and segmentations in our other studies look good despite this issue. Is there a way to reset the FOV in tkregister so that I can reliably correct any slight errors in the talairach transform to see if this can fix what were seeing with this subject group? When I add control points in the area where wm should be, the segmentation that usually results includes anterior carotid artery or lots of the small pieces of dura that I was unable to threshold out. Our next option is to simply edit all non-brain tissue around these areas of atrophy, but if there is any other relatively less time consuming option then it would be much appreciated. Sky At 12:52 PM 7/16/2008, Bruce Fischl wrote: >Hi Sky, > >hard to tell from just the one slice. Is there a big bias field in the >data? Have you tried adding control points in the wm that you lose? > >cheers, >Bruce > >On Wed, 16 Jul 2008, Sky Raptentsetsang wrote: > >>Hello Surfers, >> >>I am trying to FreeSurfer process a group of subjects from our Frontal >>Temporal Lobar Dementia project that were scanned on our 4T Siemens MRI. >>So far this endeavor has only created long hours of edits due to the >>absence of any visible White Matter in the Frontal and/or Temporal Poles. >>I have included a couple pictures of FS surface estimate on two of our >>many problematic subjects. >>I am wondering if you have any solutions or input to help FS include >>these regions of great atrophy. >> >>Thanks in advance for any input on this tedious issue. >> >>Sky R.

1 0

Question about FreeSurfer citation
by Pedro Paulo de Magalhães Oliveira Junior 16 Jul '08

16 Jul '08

Hi, Some time ago I have asked a question similar to this and the answer was a page with a template: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation I would like to ask two questions: 1) Is this template a copy paste one? 2) Is there any concern regarding plagiarism using this template? I mean even if we make subtle changes, could the editor refuse the paper based on the fact we are using a material and methods based on a text model? Thanks, Pedro Paulo Oliveira Jr

2 1

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