Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30085 discussions

GLM model for cortical thickness!
by Dalwani, Manish 19 Nov '09

19 Nov '09

Hi All, If you don't have a linear trend in the Cortical thickness vs age correlation, is there a way to use a polynomial (quadratic, cubic) regression model to best fit the cortical thickness vs age using the GLM mechanism of freesurfer? Regards, Manish Dalwani Sr. PRA Univ. of CO

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Error in Recon-All nu_correct
by mmoayedi＠uhnres.utoronto.ca 19 Nov '09

19 Nov '09

Hi Everyone, We're having a problem in our preprocessing (see below). Any ideas what the problem may be? Many thanks, Massih #-------------------------------------------- #@# Nu Intensity Correction Thu Nov 19 13:40:47 EST 2009 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /usr/local/freesurfer/subjects/zeel3/skconF010304/F001/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.7.2.2 2009/05/04 16:16:27 nicks Exp $ Linux mpm-fmri.uhnres.utoronto.ca 2.6.9-55.ELsmp #1 SMP Fri Apr 20 16:36:54 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux Thu Nov 19 13:40:47 EST 2009 Can't do setuid (cannot exec sperl) tmpdir is ./tmp.mri_nu_correct.mni.21813 /usr/local/freesurfer/subjects/zeel3/skconF010304/F001/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.21813/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.21813/nu0.mnc $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from orig.mgz... TR=10.06, TE=4.20, TI=400.00, flip angle=20.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to ./tmp.mri_nu_correct.mni.21813/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Nov 19 13:40:50 EST 2009 nu_correct -clobber ./tmp.mri_nu_correct.mni.21813/nu0.mnc ./tmp.mri_nu_correct.mni.21813/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.21813/0/ Can't do setuid (cannot exec sperl) ERROR: nu_correct Linux mpm-fmri.uhnres.utoronto.ca 2.6.9-55.ELsmp #1 SMP Fri Apr 20 16:36:54 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Thu Nov 19 13:40:50 EST 2009

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Re: [Freesurfer] recon-all -all error with version 4.5
by Bruce Fischl 19 Nov '09

19 Nov '09

thanks. Did it also write the aseg.auto_noCCseg.mgz volume? That is, did mri_ca_label complete? On Thu, 19 Nov 2009, Xiangchuan Chen wrote: > Hi Bruce, > > I don't know if recon-all exactly stopped in the same place, but I think the > lines in the end of recon-all.log showed the same message. BTW, > aseg.auto_noCCseg.label_intensities.txt was written and saved on the hard > disk. I could open it and it looked similar to those in the non-error cases. > > Thanks, > Xiangchuan > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Wednesday, November 18, 2009 7:37 PM > To: Xiangchuan Chen > Cc: 'Freesurfer Mailing List'; 'Narly A Golestani' > Subject: Re: [Freesurfer] recon-all -all error with version 4.5 > > Hi Xiangchuan, > > so you found recon-all stopped in the same place (writing > aseg.auto_noCCseg.label_intensities.txt)? > > Bruce > On Wed, 18 Nov > 2009, Xiangchuan Chen wrote: > >> I had got the same error output with v4.50 but not v4.01 for one of my >> subjects. I guessed that something might be wrong with the skull-strip >> process. So, I ran this step with different wsthresh values (from 20 to > 30, >> increased by 1), and found that the brainmask looked very similar if the >> wsthresh value was set as 20-22 (if it was larger than 22, too much >> non-brain tissue was left in the brainmask). Then, I ran autorecon2. If > the >> wsthresh was 20, no luck; if it was 22, the autorecon2 went through > without >> error. >> >> There were other strange outputs from the skull-strip process for this >> specific subject (sorry, it is off-topic): when wsthresh=23~30, too much >> non-brain tissue was left in the brainmask, except for wsthresh=25 (part > of >> the cerebellum was removed). >> >> Hope that this information helps. >> >> Xiangchuan >> >> -----Original Message----- >> From: freesurfer-bounces(a)nmr.mgh.harvard.edu >> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Narly A >> Golestani >> Sent: Wednesday, November 18, 2009 8:15 AM >> To: Bruce Fischl >> Cc: Freesurfer Mailing List >> Subject: Re: [Freesurfer] recon-all -all error with version 4.5 >> >> >> Hi Bruce, >> >> There is plenty of disk space, and the >> 'aseg.auto_noCCseg.label_intensities.txt' file *has* successfully been >> written to the subject's 'mri' directory. >> >> best, >> Narly. >> >> On Wed, 18 Nov 2009, Bruce Fischl wrote: >> >>> did you run out of disk space? Is the file >>> aseg.auto_noCCseg.label_intensities.txt writeable in the subject's dir? >>> On >>> Wed, 18 Nov 2009, Narly A Golestani wrote: >>> >>>> >>>> >>>> Dear all, >>>> >>>> I am encountering a problem with 'recon-all -all' with one subject using >>>> freesurfer version 4.5 which I did not encounter when using version 4.4. >>>> With the older version, the stream ran without error, whereas the >>>> processing produces the following error with version 4.5: >>>> >>>> >>>> ######################## >>>> >>>> ..... >>>> >>>> gca peak WM_hypointensities = 0.15609 (88) >>>> gca peak non_WM_hypointensities = 0.10304 (57) >>>> gca peak Optic_Chiasm = 0.34849 (76) >>>> mri_ca_label GCA sequential renormalization: label 28 not consistently >>>> computed. >>>> >>>> not using caudate to estimate GM means >>>> setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 >>>> estimating mean gm scale to be 1.00 x + 0.0 >>>> estimating mean wm scale to be 1.00 x + 0.0 >>>> estimating mean csf scale to be 0.97 x + 0.0 >>>> Left_Pallidum too bright - rescaling by 0.998 (from 1.000) to 107.8 (was >>>> 108.0) >>>> Right_Pallidum too bright - rescaling by 0.998 (from 1.000) to 107.8 >> (was >>>> 108.0) >>>> saving intensity scales to aseg.auto_noCCseg.label_intensities.txt >>>> Linux aria 2.6.16.60-0.39.3-smp #1 SMP Mon May 11 11:46:34 UTC 2009 >> x86_64 >>>> x86_64 x86_64 GNU/Linux >>>> >>>> recon-all exited with ERRORS at Wed Nov 18 04:02:23 CET 2009 >>>> >>>> ######################## >>>> >>>> I have tried simply rerunning the recon-all -all stream but the error is >>>> reproduced consistently. This seems strange since there was no such >>>> error with the very same data using version 4.4. >>>> >>>> Is there any way to correct for this problem so that the stream can run >>>> successfully? >>>> >>>> >>>> Thanks in advance and best wishes, >>>> Narly. >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> >> >> ==================================== >> Narly Golestani >> Institute of Cognitive Neuroscience >> 17 Queen Square >> London WC1N 3AR >> United Kingdom >> Tel: +44 (0)20 7679 7529 >> ==================================== >> >> _______________________________________________ >> 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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Re: [Freesurfer] recon-all -all error with version 4.5
by Bruce Fischl 19 Nov '09

19 Nov '09

Hi Xiangchuan, so you found recon-all stopped in the same place (writing aseg.auto_noCCseg.label_intensities.txt)? Bruce On Wed, 18 Nov 2009, Xiangchuan Chen wrote: > I had got the same error output with v4.50 but not v4.01 for one of my > subjects. I guessed that something might be wrong with the skull-strip > process. So, I ran this step with different wsthresh values (from 20 to 30, > increased by 1), and found that the brainmask looked very similar if the > wsthresh value was set as 20-22 (if it was larger than 22, too much > non-brain tissue was left in the brainmask). Then, I ran autorecon2. If the > wsthresh was 20, no luck; if it was 22, the autorecon2 went through without > error. > > There were other strange outputs from the skull-strip process for this > specific subject (sorry, it is off-topic): when wsthresh=23~30, too much > non-brain tissue was left in the brainmask, except for wsthresh=25 (part of > the cerebellum was removed). > > Hope that this information helps. > > Xiangchuan > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Narly A > Golestani > Sent: Wednesday, November 18, 2009 8:15 AM > To: Bruce Fischl > Cc: Freesurfer Mailing List > Subject: Re: [Freesurfer] recon-all -all error with version 4.5 > > > Hi Bruce, > > There is plenty of disk space, and the > 'aseg.auto_noCCseg.label_intensities.txt' file *has* successfully been > written to the subject's 'mri' directory. > > best, > Narly. > > On Wed, 18 Nov 2009, Bruce Fischl wrote: > >> did you run out of disk space? Is the file >> aseg.auto_noCCseg.label_intensities.txt writeable in the subject's dir? >> On >> Wed, 18 Nov 2009, Narly A Golestani wrote: >> >>> >>> >>> Dear all, >>> >>> I am encountering a problem with 'recon-all -all' with one subject using >>> freesurfer version 4.5 which I did not encounter when using version 4.4. >>> With the older version, the stream ran without error, whereas the >>> processing produces the following error with version 4.5: >>> >>> >>> ######################## >>> >>> ..... >>> >>> gca peak WM_hypointensities = 0.15609 (88) >>> gca peak non_WM_hypointensities = 0.10304 (57) >>> gca peak Optic_Chiasm = 0.34849 (76) >>> mri_ca_label GCA sequential renormalization: label 28 not consistently >>> computed. >>> >>> not using caudate to estimate GM means >>> setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 >>> estimating mean gm scale to be 1.00 x + 0.0 >>> estimating mean wm scale to be 1.00 x + 0.0 >>> estimating mean csf scale to be 0.97 x + 0.0 >>> Left_Pallidum too bright - rescaling by 0.998 (from 1.000) to 107.8 (was >>> 108.0) >>> Right_Pallidum too bright - rescaling by 0.998 (from 1.000) to 107.8 > (was >>> 108.0) >>> saving intensity scales to aseg.auto_noCCseg.label_intensities.txt >>> Linux aria 2.6.16.60-0.39.3-smp #1 SMP Mon May 11 11:46:34 UTC 2009 > x86_64 >>> x86_64 x86_64 GNU/Linux >>> >>> recon-all exited with ERRORS at Wed Nov 18 04:02:23 CET 2009 >>> >>> ######################## >>> >>> I have tried simply rerunning the recon-all -all stream but the error is >>> reproduced consistently. This seems strange since there was no such >>> error with the very same data using version 4.4. >>> >>> Is there any way to correct for this problem so that the stream can run >>> successfully? >>> >>> >>> Thanks in advance and best wishes, >>> Narly. >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> > > ==================================== > Narly Golestani > Institute of Cognitive Neuroscience > 17 Queen Square > London WC1N 3AR > United Kingdom > Tel: +44 (0)20 7679 7529 > ==================================== > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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Source request for PPC Linux build
by Andre Gouws 19 Nov '09

19 Nov '09

Hi .. I recently spent a significant amount of time getting an automated processing stream for Freesurfer running on our OSX PPC cluster .. .. and then our IT manager upgraded all 100 nodes to Linux .. As far as I can see, there is no PPC Linux build available .. thus would it be possible for us to get hold of a previous version / the current source to compile for PPC Linux? .. or am I just not looking in the right place :) Thanks Andre' ************************************************************************ Andre Gouws York Neuroimaging Centre The Biocentre York Science Park Heslington YO10 5DG Tel: +44 (0) 1904 435328 Fax: +44 (0) 1904 435356

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recon without normalization
by africa millan 18 Nov '09

18 Nov '09

Hello all, When I run the function recon-all -subjid s00x -autorecon1 -autorecon2 -nonormalization I've got an ERROR message: Skull Stripping /root/trabajo/freesurfer/subjects/c1prueba/mri mri_watershed -T1 -brain_atlas /root/trabajo/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz If this is incorrect, please exit with CTL-C ERROR: cannot find /root/trabajo/freesurfer/subjects/c1prueba/mri/T1.mgz mri_watershed Error: read failed Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Nov 18 11:05:17 CET 2009 So, when I run the recon-all -subjid s00x -autorecon1 -autorecon2 -nonormalization,as the error message says, a T1.mgz is needed.How can I obtain the T1.mgz to be able to run this recon-all. In fact, the only file that is needed to run the recon-all -autorecon1 -autorecon 2 is the 001.mgz,isn't it? Thanks for your help. Africa From: africa_millan(a)hotmail.es To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] recon without normalization Date: Wed, 18 Nov 2009 11:32:05 +0100 Hello, When I run the function recon-all -subjid s00x -autorecon1 -autorecon2 -nonormalization I've got an ERROR message: Skull Stripping /root/trabajo/freesurfer/subjects/c1prueba/mri mri_watershed -T1 -brain_atlas /root/trabajo/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz If this is incorrect, please exit with CTL-C ERROR: cannot find /root/trabajo/freesurfer/subjects/c1prueba/mri/T1.mgz mri_watershed Error: read failed Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Nov 18 11:05:17 CET 2009 When I open de mri file of the subject, I realize that there is not any T1.mgz file, because freesurfer did not generate it. So the question is, when I run the function recon-all with the -nonormalization flag added, does freesurfer skip the generation of the T1.mgz file? Thanks for your help, Africa. > Date: Tue, 17 Nov 2009 13:25:56 -0500 > From: sita(a)nmr.mgh.harvard.edu > To: africa_millan(a)hotmail.es > Subject: RE: [Freesurfer] recon without normalization > > > > Yes, that looks okay. You can also add -autorecon3 flag if you want the > dataset to go through the whole recon-all stream. > > Thanks, > Sita. > > > > On Tue, 17 Nov 2009, africa millan wrote: > > > > > Hello Sita, > > > > > > > > Is this the right way to add the -nonormalization flag to the recon-all function to skip the normalization step during the first recon-all??: > > > > > > > > "recon-all -subjid s00x -autorecon1 -autorecon2 -nonormalization " > > > > > > > > > > > > Thanks for your help! > > > > > > > > Africa. > > > > > > > > > > > > > > > >> Date: Thu, 12 Nov 2009 13:24:54 -0500 > >> From: sita(a)nmr.mgh.harvard.edu > >> To: africa_millan(a)hotmail.es > >> CC: freesurfer(a)nmr.mgh.harvard.edu > >> Subject: Re: [Freesurfer] recon without normalization > >> > >> > >> > >> You can run recon-all with -nonormalization flag, which will skip that > >> step. > >> > >> Sita. > >> > >> > >> > >> On Thu, 12 Nov 2009, africa millan wrote: > >> > >>> > >>> Hello, > >>> > >>> > >>> > >>> Another question:If during the first recon-all, freesurfer makes skullstripping and normalization automatically... Is there any way to run the first recon-all without automatic normalization? > >>> > >>> > >>> > >>> Is it possible? > >>> > >>> > >>> > >>> Thanks > >>> > >>> Af. > >>> > >>> _________________________________________________________________ > >>> Descubre todas las formas en que puedes estar en contacto con amigos y familiares. > >>> http://www.microsoft.com/windows/windowslive/default.aspx > > > > _________________________________________________________________ > > Sólo hay un loro experto en Windows 7 en todo el mundo. Y vive en Sietes ¡Cónocelo! > > http://www.sietesunpueblodeexpertos.com/ 49 habitantes, 49 expertos en Windows 7. Así es Sietes, ¡Visítalo! 49 habitantes, 49 expertos en Windows 7. Así es Sietes, ¡Visítalo! _________________________________________________________________ Date una vuelta por Sietes y conoce el pueblo de los expertos en Windows 7 http://www.sietesunpueblodeexpertos.com/

3 2

registration to a template
by Jared Price 18 Nov '09

18 Nov '09

Hi all, Does anyone have any recommendations for testing anatomical similarity between 2 different subjects? Jared

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research position in San Francisco, CA
by Brian Roach 18 Nov '09

18 Nov '09

Freesurfer users, We are looking for new and experienced brain imagers with a background in signal processing to work in our UCSF-affiliated research lab. Please apply at the following link if interested: http://jobs-ncire.icims.com/jobs/1448/job thank you, Brian

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recon-all -all error with version 4.5
by Narly A Golestani 18 Nov '09

18 Nov '09

Dear all, I am encountering a problem with 'recon-all -all' with one subject using freesurfer version 4.5 which I did not encounter when using version 4.4. With the older version, the stream ran without error, whereas the processing produces the following error with version 4.5: ######################## ..... gca peak WM_hypointensities = 0.15609 (88) gca peak non_WM_hypointensities = 0.10304 (57) gca peak Optic_Chiasm = 0.34849 (76) mri_ca_label GCA sequential renormalization: label 28 not consistently computed. not using caudate to estimate GM means setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.97 x + 0.0 Left_Pallidum too bright - rescaling by 0.998 (from 1.000) to 107.8 (was 108.0) Right_Pallidum too bright - rescaling by 0.998 (from 1.000) to 107.8 (was 108.0) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux aria 2.6.16.60-0.39.3-smp #1 SMP Mon May 11 11:46:34 UTC 2009 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Nov 18 04:02:23 CET 2009 ######################## I have tried simply rerunning the recon-all -all stream but the error is reproduced consistently. This seems strange since there was no such error with the very same data using version 4.4. Is there any way to correct for this problem so that the stream can run successfully? Thanks in advance and best wishes, Narly.

3 4

White matter edits - when to do manual corrections?
by Lena Palaniyappan 18 Nov '09

18 Nov '09

Dear group 1. Do we have to correct minor problems that are visible on visual inspection of white matter surface even if the surface image appears smooth with no potholes/handles? Is there any way of knowing when to start or stop manual corrections for wm/pial surfaces? 2. In the attached slice 117, you can see that the main surface is not continuous along the medial aspect of both hemispheres do we have to correct this? If yes, what is the best way of correcting this defect? 3. In the attached slice 114, the wm surface is seen outside the pial surface but tksurfer inspection does not reveal any immediately obvious defects what should I do? Many thanks in advance _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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