Freesurfer December 2011

freesurfer@nmr.mgh.harvard.edu

98 participants
157 discussions

tracula failed to find header file for -t
by Scott Hayes 12 Dec '11

12 Dec '11

Hi, I have received the following error message (copied from trac-all.log file). fslstats -t /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi.nii.gz -k /Volumes/RAID_4TB/futhink/nc331_recon/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi_snr.txt ** ERROR (nifti_image_read): failed to find header file for '-t' ** ERROR: nifti_image_open(-t): bad header info Error: failed to open file -t ERROR: Could not open image -t Image Exception : #22 :: Failed to read volume -t terminate called after throwing an instance of 'RBD_COMMON::BaseException' The file (dwi.nii.gz) exists in the correct location, and appears to have the correct number of frames (60 directions + 10 b0). We scan on a Siemens 3T tim trio. I unpack the data using unpacksdcmdir and I specify the resulting .mgz file in the tracula config file. Running locally on mac os 10.6.8. Any suggestions would be appreciated. Thanks, Scott

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Re: [Freesurfer] tracula and snow leopard: can't allocate region / memory error
by Anastasia Yendiki 12 Dec '11

12 Dec '11

Hi Scott - Sending to the list is always good so that others can find it in the archives when they have similar problems. Do you specify the .dcm or .mgz file in your dmrirc? Does dwi.nii.gz have the right dimensions/frames? a.y On Mon, 12 Dec 2011, Scott Hayes wrote: > Thanks for the prompt response Anastasia--I ran it over the weekend > and it worked. > > I've subsequently encountered a new issue (copied below from the > trac-all.log). The file (dwi.nii.gz) exists in the correct location > (it was written there by tracula). I use unpacksdcmdir for unpacking > the dicoms, and then point the config file to the appropriate .mgz > file, so I'm not doing anything particularly unusual in terms of > unpacking or messing w/ the headers (We scan on a Siemens 3T tim > trio.) I can send this to the listserv if you prefer. > Best, > Scott > > fslstats -t /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi.nii.gz -k > /Volumes/RAID_4TB/futhink/nc331_recon/dlabel/diff/White-Matter++.bbr.nii.gz > -m -s | awk '{print $1/$2}' > > /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi_snr.txt > ** ERROR (nifti_image_read): failed to find header file for '-t' > ** ERROR: nifti_image_open(-t): bad header info > Error: failed to open file -t > ERROR: Could not open image -t > Image Exception : #22 :: Failed to read volume -t > terminate called after throwing an instance of 'RBD_COMMON::BaseException' > > > > On Fri, Dec 9, 2011 at 12:44 PM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: >> >> Hi Scott - Here are the tracula executables for snow leopard that we posted >> in response to that thread: >> >> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopar… >> >> Let me know if this solves the memory errors. >> >> a.y >> >> >> On Fri, 9 Dec 2011, Scott Hayes wrote: >> >>> Hi Anastasia, >>> I've encountered an error using tracula w/ snow leopard OS that was >>> previously reported on the FS listserv: >>> >>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18829.html >>> >>> I'm wondering if there is a documented solution available? >>> Recompiling from source code would be beyond my expertise. >>> >>> David: I'm cc'ing you just as a heads up--all of the workstations in >>> the imaging center run snow leopard OS. >>> >>> Best, >>> Scott >>> >> >> >> 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. >> > > > >

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mri_ca_register from virtual box
by Lorenzo Busti 12 Dec '11

12 Dec '11

*Hi everyone * *I got this error while running one of my subjects* * * mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed ERROR: mri_ca_register with non-zero status 252 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Thu Nov 24 05:15:42 EST 2011 /home/virtualuser/freesurfer/subjects/Petrollini2/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s Petrollini2 exited with ERRORS at Thu Nov 24 05:15:43 EST 2011 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting *I'm working with a virtual machine on a 32 bit computer with 4GB of RAM(2-core Intel processor 2.00 GHz). I raised the ram dedicated to the virtual machine to 1,5 GB: this is the max value permitted before the selecting bar of the virtual box changes from green to red (is it sufficent?)* *I have free space for data. * *Can you help me in solving this problem?* *Thanks* *Lorenzo Busti* * *

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References/materials for interaction analysis in freesurfer
by Bhavani Shankara Bagepally 12 Dec '11

12 Dec '11

Dear Sir/Freesurfer experts, We are working of genes and gene- gene interaction on cortical thickness using freesurfer. Please let me know if there any material/publications for validation of free surfer based analysis mainly on gene-gene interaction or any of the Interaction statistics using freesurfer. Many thanks in advance -- Dr. BHAVANI SHANKARA BAGEPALLY MBBS, (PhD in Clinical Neuroscience) NIMHANS, Bangalore, INDIA-560029 email: bshankara(a)gmail.com

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preprocessing error
by Maryam Vaziri Pashkam 11 Dec '11

11 Dec '11

Hi, I am running preprocessing on my data using freesurfer 5.1, fsl 4.1.7, and matlab R2009a (I also tried it with matlab 2007a) on Harvard cluster and I am receiving an error. I connect to the cluster using terminal and SSH connection in mac. the preprocessing is stalled in the middle with this error: ++ Max displacement in automask = 0.79 (mm) at sub-brick 3 Can't connect? tcp_connect[connect]: Connection timed out ++ Wrote dataset to disk in 004/tmp.mc-afni2.20850/outvol.nii.gz ** Warning: overwriting file 004/fmcpr.mcdat Can't connect? tcp_connect[connect]: Connection timed out Can't connect? tcp_connect[connect]: Connection timed out Can't connect? tcp_connect[connect]: Connection timed out It does not stop running and output an error. But rather keeps printing the last line and does not move forward. Any idea where the problem might be? Thanks, Maryam

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problem with visualizing hippo-subfields
by Tetiana Dadakova 10 Dec '11

10 Dec '11

Dear FreeSurfer list, I ran recon-all -bert -hippo-subfields, which finished without error. Now I try to open it with freeview using: cd $SUBJECTS_DIR/bert/mri freeview nu.mgz \ -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt But get the following error: "Failed to load posterior_left_CA1.mgz". (posterior_left_CA1.mgz exists in bert/mri) Do you have an idea why it goes wrong? Thank you, Tanja.

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extracting time courses from fMRI
by Hellyer, Peter 09 Dec '11

09 Dec '11

Hi All, I'm trying to extract time courses from functional data I started by registering my motion corrected functional data to my segmentation using bbregister, then I used: mri_vol2surf --src Motioncorrectedfunctional.nii.gz --srcreg register.dat --out suface.mgz —hemi rh & mri_segstats --in surface.mgz --annot subject rh aparc --sum sum_output --avgwf Timecourse_output Is this a sensible thing to do? I'm not particually sure about the mri_vol2surf step.. Thanks in advance. Pete

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Re: [Freesurfer] tcl script question: labl_set_color
by Justin Baker 09 Dec '11

09 Dec '11

OK, right-clicking on the surface did in fact de-select the label (turning it all to a uniform color). Way to script a right-click? (I see left click...) Now that this is more or less working, I am looking to do something slightly different: i.e., combine the boundaries of one set of regions, one highlighed region, and an activation map. Is there a way to fill just one label and leave outlines for a different set of labels in the same image? Or alternatively set a different outline color for one label? As in my previous post, I am looking to do this via tcl script if possible. Thanks. On Mon, Dec 5, 2011 at 3:07 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > yes, just use the -tcl <script name> option, but don't but an "exit" > command at the end of the tcl script > > cheers > Bruce > > On Mon, 5 Dec 2011, Justin Baker wrote: > > Ah - in that case I have a total newbie question, since I primarily use >> tksurfer via command line: >> >> Is there a way to load up a case using the tcl script, but then leave it >> open rather than quit? >> This way I could try de-selecting with right-click. >> >> Thanks. >> >> On Mon, Dec 5, 2011 at 9:05 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> I think so, but I want to see if it fixes your problem before I go >> digging through the >> tcl code to see what it is >> On Mon, 5 Dec 2011, Justin Baker wrote: >> >> Is there a command to do this via tcl script? >> >> Justin >> >> On Sun, Dec 4, 2011 at 8:49 PM, Bruce Fischl < >> fischl(a)nmr.mgh.harvard.edu> >> wrote: >> What happens if you right click on the surface then? >> >> >> >> On Dec 4, 2011, at 8:17 PM, Justin Baker < >> justintbaker(a)gmail.com> >> wrote: >> >> Hi Bruce, >> >> Thanks. Some progress! That resulted in the label border >> turning red, but the fill is still white. Any other >> thoughts? >> >> Cheers, >> Justin >> >> On Wed, Nov 30, 2011 at 2:54 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> wrote: >> Hi Justin >> >> try unselecting the label with: >> >> labl_select -1 >> >> cheers >> Bruce >> On Wed, 30 Nov 2011, Justin Baker wrote: >> >> >> I am trying to use tksurfer to >> script overlay of a label + >> functional map >> onto an fsaverage5 surface. >> >> In particular, I want to set the >> label to "fill" and color it red. >> >> I have: >> >> set labelstyle 0 >> labl_set_color 0 255 0 0 >> >> As you can see below, the output >> of label_print_list shows that the >> color of >> the label should be "255 0 0 " but >> it looks white in the output >> image. >> >> Am I missing something? Thanks >> >> ------------ >> subject is fsaverage5 >> hemi is lh >> surface is inflated >> >> Label 0 >> Name: >> lh.17Networks_LH_ContB_PFClv.**label, >> 109 vertices >> Structure: -1 Color: 255 0 >> 0 Visible: 1 >> Bounds: x -20.879234 >> 12.792567 y -4.000000 109.853737 z >> -4.033233 >> 4.040778 >> >> >> >> >> >> >> >> 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<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. >> >> >> >> >> >> >>

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[FreeSurfer]: mkanalysis-sess
by tapsya＠nmr.mgh.harvard.edu 09 Dec '11

09 Dec '11

Hi Doug, It seems that there are still problems related to using -per-session. Preproc-sess now finishes apparently fine (correct file names are generated, i.e., fmc.*) but the analyses again defaults to using -per-run at mkanalysis-sess. Specifically, mkanalysis-sess creates an analysis.info file (attached) where the parameters mcstem and nuisreg still point to -per-run (mcstem fmcpr and nuisreg mcprextreg 3). Consequently the rest of the analysis fails. I have attached the analysis.info file in the email Thank you for your help again! -Tapsya Details: Machine: adapt nmr-dev-env (vs 5.1) preproc-sess -s avml07 -surface faverage lhrh -mni305 -per-session -so siemens -fsd bold -fwhm 5 set ana_BASIC_lh = ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat_lh mkanalysis-sess -analysis $ana_BASIC_lh -surface fsaverage lh -fwhm 5 -TR 1.15 -paradigm AVML_BRERT_ISIXTR_001_18cat.par -event-related -nconditions 18 -fir 2.3 18.4 -mcextreg -polyfit 5 -runlistfile rlf_ISIXTR_BERT.txt -stc siemens -force -fsd bold -tpef tpef.txt --------------------------------------------------------------------------- > >> I just ran this co > mmand and it completed successfully >> preproc-sess -s avml07 -mni305 -per-session -so siemens -fsd bold -fwhm > 5 >> Is this what you ran? I'm also running it to generate the surfaces now, > but it does not seem to be complaining. >> doug >> >> Douglas N Greve wrote: >>> I'm currently running >>> preproc-sess -s avml07 -mni305 -per-session -so siemens -fsd bold -fwhm >>> 5 >>> and it seems to be going ok, I won't know until tomorrow whether this > is really working or not >>> doug >>> raij(a)nmr.mgh.harvard.edu wrote: >>>> Still no luck. mc-sess is stubbornly using -per-run despite that the > preproc-sess requests per-sess. This may be where things get on the > wrong >>>> track. -Tommi >>>>> Sorry, what I meant was for you to change the name and then run the > stream as usual. >>>>> doug >>>>> raij(a)nmr.mgh.harvard.edu wrote: >>>>>> Done. I also made a backup of the registration. The entire >>>>>> directory at >>>>>> /space/adapt/1/users/raij/AVISI_FSFAST5.1/ >>>>>> is a copy of the actual data residing elsewhere (apart from the > Freesurfer >>>>>> recons) so feel free to change anything you need. -Tommi >>>>>>> I think I've found the problem, but it's going to be a bit >>>>>>> difficult to >>>>>>> fix. Can you change the name of your registration file to >>>>>>> register.dof6.dat and remove write permissions so that it does not >>>>>>> get >>>>>>> overwritten? >>>>>>> doug >>>>>>> raij(a)nmr.mgh.harvard.edu wrote: >>>>>>>> Yes we have. It exits with the same error as below. -Tommi >>>>>>>>> Have you tried specifying your regfile with -regfile? >>>>>>>>> doug >>>>>>>>> raij(a)nmr.mgh.harvard.edu wrote: >>>>>>>>>> Hi Doug, >>>>>>>>>> Thank you for your help today! I tried running preproc-sess > again >>>>>>>>>> but >>>>>>>>>> it >>>>>>>>>> again exits with per-session related errors. However, the errors > are >>>>>>>>>> different than before so I think the changes you made were a > step to >>>>>>>>>> the >>>>>>>>>> right direction. This time >>>>>>>>>> preproc-sess \ >>>>>>>>>> -sf subjectname \ >>>>>>>>>> -df sessdir \ >>>>>>>>>> -mni305 \ >>>>>>>>>> -per-session \ >>>>>>>>>> -sliceorder siemens \ >>>>>>>>>> -fsd bold \ >>>>>>>>>> -fwhm 5 \ >>>>>>>>>> -surface $SUBJECT lhrh \ >>>>>>>>>> -noreg \ # I want to use my manually adjusted >>>>>>>>>> bold/register.dof6.dat >>>>>>>>>> file >>>>>>>>>> (1) mc-sess output is still saved with the per-run stem (pr) > despite >>>>>>>>>> that >>>>>>>>>> we defined -per-session. >>>>>>>>>> (2) stc-sess output is still saved with the per-run stem (pr) > despite >>>>>>>>>> that >>>>>>>>>> we defined -per-session. >>>>>>>>>> (3) rawfunc2surf-sess defaults to -per-run and then expects to >>>>>>>>>> find >>>>>>>>>> instem >>>>>>>>>> fmcpr.siemens >>>>>>>>>> (4) ERROR: cannot find >>>>>>>>>> /autofs/space/adapt_001/users/raij/AVISI_FSFAST5.1/avml07/bold/002/register.dof6.dat. > Apparently the script looks for the registration file inside the > run >>>>>>>>>> directory (as it should for per-run analysis) instead of the fsd > <bold> >>>>>>>>>> where it should reside for a -per-session analysis. This forces >>>>>>>>>> the >>>>>>>>>> script >>>>>>>>>> to exit. >>>>>>>>>> I changed permissions so that you can write in the study >>>>>>>>>> directory. >>>>>>>>>> For details please see below. >>>>>>>>>> Thanks! >>>>>>>>>> -Tommi & Tapsya >>>>>>>>>> on machine avml >>>>>>>>>> nmr-dev-env (vs 5.1) >>>>>>>>>> cd /space/adapt/1/users/raij/AVISI_FSFAST5.1/avml07 >>>>>>>>>> setenv SUBJECTS_DIR /space/adapt/1/users/tapsya/subject_MRIs > setenv SUBJECT avml07 >>>>>>>>>> logs in /space/adapt/1/users/raij/AVISI_FSFAST5.1/avml07/log > preproc-sess log file >>>>>>>>>> $Id: preproc-sess,v 1.48 2011/11/14 17:41:35 greve Exp $ raij >>>>>>>>>> setenv FREESURFER_HOME /usr/local/freesurfer/dev >>>>>>>>>> setenv SUBJECTS_DIR /space/adapt/1/users/tapsya/subject_MRIs > Linux avml 2.6.32-131.12.1.el6.x86_64 #1 SMP Mon Sep 26 >>>>>>>>>> 10:13:43 BST >>>>>>>>>> 2011 >>>>>>>>>> x86_64 x86_64 x86_64 GNU/Linux >>>>>>>>>> /autofs/space/adapt_001/users/raij/AVISI_FSFAST5.1/avml07 > /usr/local/freesurfer/dev/fsfast/bin/preproc-sess >>>>>>>>>> -sf subjectname -df sessdir -mni305 -per-session -sliceorder > siemens >>>>>>>>>> -fsd >>>>>>>>>> bold -fwhm 5 -surface avml07 lhrh -noreg >>>>>>>>>> Mon Nov 14 20:07:57 EST 2011 >>>>>>>>>> instem f >>>>>>>>>> mc 1 f fmcpr >>>>>>>>>> stc 1 fmcpr fmcpr.siemens >>>>>>>>>> sm 0 >>>>>>>>>> mask 1 brain >>>>>>>>>> ---------------------------- Original Message >>>>>>>>>> ---------------------------- >>>>>>>>>> Subject: [FreeSurfer]: preproc-sess error >>>>>>>>>> From: tapsya(a)nmr.mgh.harvard.edu >>>>>>>>>> Date: Thu, November 10, 2011 1:41 pm >>>>>>>>>> To: freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>> Cc: raij(a)nmr.mgh.harvard.edu >>>>>>>>>> -------------------------------------------------------------------------- > Dear Doug, >>>>>>>>>> We have encountered errors running preproc-sess (FSFAST v5.1) > command >>>>>>>>>> with >>>>>>>>>> the flag "-per-session". The command line is >>>>>>>>>> on machine adapt (same result on machine avml) >>>>>>>>>> cd /space/adapt/1/users/raij/AVISI_FSFAST5.1/avml07 >>>>>>>>>> setenv SUBJECTS_DIR /space/adapt/1/users/tapsya/subject_MRIs > setenv SUBJECT avml07 >>>>>>>>>> nmr-std-env (=FS 5.1) >>>>>>>>>> preproc-sess \ >>>>>>>>>> -sf subjectname >>>>>>>>>> -df sessdir \ >>>>>>>>>> -mni305 \ >>>>>>>>>> -per-session \ >>>>>>>>>> -sliceorder siemens \ >>>>>>>>>> -fsd bold \ >>>>>>>>>> -fwhm 5 \ >>>>>>>>>> The error message: >>>>>>>>>> ... >>>>>>>>>> stc-sess Done >>>>>>>>>> avml07 To MNI305 ---------------- >>>>>>>>>> rawfunc2tal-sess -fwhm 5 -s avml07 -d >>>>>>>>>> /autofs/space/adapt_001/users/raij/AVISI_FSFAST5.1 -fsd bold > -stc >>>>>>>>>> siemens -update -subcort-mask >>>>>>>>>> ---------------- >>>>>>>>>> 1/1 avml07 >>>>>>>>>> 1/1 avml07 002 ---------------- >>>>>>>>>> "ERROR: could not determine file for >>>>>>>>>> /autofs/space/adapt_001/users/raij/AVISI_FSFAST5.1/avml07/bold/002/fmcpr.siemens" > Hence it looks like rawfunc2tal-sess is searching for -per-run > files (stem fmcpr*) rather than -per-session files (stem fmc*). > We tried to take control over the stems and added the following > lines: >>>>>>>>>> -mcin f \ >>>>>>>>>> -mcout fmc \ >>>>>>>>>> -stcin fmc \ >>>>>>>>>> -stcout fmcstc \ >>>>>>>>>> -smin fmcstc \ >>>>>>>>>> -smout fmcstcsm5 \ >>>>>>>>>> OR (modern naming conventions): >>>>>>>>>> -mcin f >>>>>>>>>> -mcout fmc >>>>>>>>>> -stcin fmc >>>>>>>>>> -stcout fmc.siemens \ >>>>>>>>>> -smin fmc.siemens \ >>>>>>>>>> -smout fmc.siemens.sm5.mni305.2mm \ >>>>>>>>>> However, these resulted in the same error. >>>>>>>>>> We also tried this on a more recent data set and received the >>>>>>>>>> same >>>>>>>>>> error. >>>>>>>>>> In summary, it appears that rawfunc2tal-sess (and in fact also > rawfunc2surf-sess) expect the stem fmcpr even when we use > per-session >>>>>>>>>> (where they should expect the stem fmc). >>>>>>>>>> Any help would be greatly appreciated! >>>>>>>>>> Best regards, >>>>>>>>>> Tapsya >>>>>>>>> -- >>>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>>> MGH-NMR Center >>>>>>>>> greve(a)nmr.mgh.harvard.edu >>>>>>>>> Phone Number: 617-724-2358 >>>>>>>>> Fax: 617-726-7422 >>>>>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>> -- >>>>>>> Douglas N. Greve, Ph.D. >>>>>>> MGH-NMR Center >>>>>>> greve(a)nmr.mgh.harvard.edu >>>>>>> Phone Number: 617-724-2358 >>>>>>> Fax: 617-726-7422 >>>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> -- >>>>> Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> greve(a)nmr.mgh.harvard.edu >>>>> Phone Number: 617-724-2358 >>>>> Fax: 617-726-7422 >>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> >> > >

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mri_surf2surf error - Return code 254
by John Griffiths 09 Dec '11

09 Dec '11

Dear list, I am having the following memory allocation problem when running mri_surf2surf. Can't find any mention of this error on the list or the internet - sorry if I've missed anything. mri_surf2surf --cortex --fwhm 5.0000 --hemi lh --sval /home/jdg45/lh.pial_converted.mgz --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: srcsubject = CBU070282 srcval = /home/jdg45/lh.pial_converted.mgz srctype = trgsubject = CBU070282 trgval = /home/jdg45/CBU070282_smoother_surf.mgz trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /work/imaging5/Freesurfer/CBU070282/surf/lh.sphere.reg Loading source data Standard error: MRIalloc: could not allocate 2032167524 slices Cannot allocate memory Return code: 254 Any suggestions? Thanks, john

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Freesurfer December 2011