Re: [Freesurfer] problem when convert dcm to mgz
Hi Bruce, The dcm files are from SIMENS MAGNETOM VISION plus. The file does exist. Myriam Siefert met same problem. She suggested me to convert the dcm to nii file. Because Freesurfer cannot read header of the some dcm files. After converting to nii, it seems working now. The analysis is running now. Regards, Yawu -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: 27. heinäkuuta 2012 16:47 To: Liu Yawu Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] problem when convert dcm to mgz Hi Yawu where did you get that dicom from? Does the file you are pointing to exist? cheers Bruce On Fri, 27 Jul 2012, Liu Yawu wrote: Hi, I recently install Freesurfer under ubuntu. I tested two own data. It works in one our own case, but did not work for other cases. The problem is the Freesurfer not found or unknown file type for file /home/d4201z/Desktop/im_4/2000110815073505086.dcm when convert convert dcm to mgz. Any helps are appreciated! Here are detailed inf: FREESURFER_HOME: /usr/local/src/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Debian version: wheezy/sid Kernel info: Linux 3.2.0-27-generic x86_64 1. the entire command-line executed recon-all -s APauli \ -i /home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.282911170905084.dcm 2. the error message generated file not found or unknown file type for file /home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.282911170905084.dcm 3. the subject's /script/recon-all.log Fri Jul 27 12:20:31 EEST 2012 /usr/local/src/freesurfer/subjects/APauli /usr/local/src/freesurfer/bin/recon-all -s APauli -i /home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.282911170905084.dcm subjid APauli setenv SUBJECTS_DIR /usr/local/src/freesurfer/subjects FREESURFER_HOME /usr/local/src/freesurfer Actual FREESURFER_HOME /usr/local/src/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux d4201z-CELSIUS-M470-2 3.2.0-27-generic #43-Ubuntu SMP Fri Jul 6 14:25:57 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 95900 maxlocks unlimited maxsignal95900 maxmessage 819200 maxnice 0 maxrtprio0 maxrttimeunlimited total used free sharedbuffers cached Mem: 1229825228804849417768 0 127152 973356 -/+ buffers/cache:1779976 10518276 Swap: 19529724 0 19529724 program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:31-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:31-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:31-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:31-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:31-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: d4201z Machine:
Re: [Freesurfer] Issues with Tracula
Nope, I have the same files as before :( 2012/7/27 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu The monitoring script that bedpostx runs and tells you if things have or haven't finished properly can't always be trusted. So if that's the only error message you see, I wouldn't worry about it. Have the *ph1* and *th1* files appeared this time? On Fri, 27 Jul 2012, Sergio Medina wrote: What a coincide! Our teams have both chosen the same release cycle strategy :P I ran bedpostx_postproc and I've got so many errors that makes me think the problem is before this step (see output in attached n1-bedpostx-postproc.txt). So, I ran again bedpostx on the dmri directory, which the first run *seemed* to finish and didn't throw any error (I attached the output in the first email). This run did finish, and it did throw errors (full output in n2-bedpostx-dmri.txt): [...] slice 63 has already been processed wc: /volatile/tracula/results/**Diff001/dmri.bedpostX/**commands.txt: No such file or directory Queuing post processing stage 64 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. kill: 276: No such process Then I started wondering whether I do have the right data to actually run bedpostx, so I run the script that checks that: bedpostx_datacheck, the output (n3-bedpostx-datacheck.txt) doesn't show any signs of errors so I would like to assume everything is ok with the input data... Any idea? Thanks, once again. Sergio. 2012/7/27 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Hi Sergio - As with any imminent new version release, it's happening soon. I'd say in a month, I'm just not sure a month from when :P The fact that the temporary files (everything with *slice* in the name) are still in your bedpostx directory means that bedpostx didn't finish running properly. You can try running the last step of bedpostx and see if you get any error messages that give you any clues: bedpostx_postproc.sh /volatile/tracula/results/**Diff001/dmri Normally this step merges the individual slices into volumes and deletes the temporary files. If all else fails, I'd ask the FSL gurus. Hope this helps, a.y On Fri, 27 Jul 2012, Sergio Medina wrote: Anastasia, Thanks for such a quick reply! Please find my answers inline... 2012/7/26 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Hi Sergio - Thank you for your kind words, and also thank you for taking the time to search the archives for answers! The first problems you had with running bedpostx through trac-all have to do with trac-all assuming an older version of FSL than the current one, and this'll be fixed in the upcoming release of trac-all. Indeed the thing to do in the meantime is to run bedpostx by itself, as you did. I apologize for the inconvenience. Great! By any chance, do you know when that release will happen? About the problem you had when you ran bedpostx directly: do you get the other outputs of bedpostx, listed here? Are there any other, temporary files left over as well? http://www.fmrib.ox.ac.uk/fsl/**fdt/fdt_bedpostx.htmlhttp://www.fmrib.ox.ac.uk/fsl/fdt/fdt_bedpostx.html I have all of them, except for nodif_brain. And I only have the ones with i=2 while I should have the ones with i=1 too. Attached you can find two files, the output of ls -Rah on both dmri and dmri.bedpostX directories. The merged_ph?samples are the orientation angles of the each of the two anisotropic compartments (sticks, fibers, whatever you want to call them) that bedpostx fit in each voxel. So 1 is the orientation angle of the largest stick/fiber, and 2 the one of the 2nd largest. If there's a 2, there should be a 1! But there are not :( Also, I looked at your dmrirc file and noticed that you decreased the # of control points b/c you hate waiting :) I just wanted to warn you that decreasing that # might make you wait longer b/c make fitting a spline with fewer control points to initialize the
Re: [Freesurfer] Recon-all -qcache curvature error recon-all make -all
Hello, I emailed last week to ask about an error I was getting. Has anyone had a chance to look into it? Thank you very much. Best wishes, Clare From: Gibbard, Clare Sent: 25 July 2012 16:45 To: Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Recon-all -qcache curvature error recon-all make -all Hi Bruce, Thanks, I've attached the end of the recon-all.log file for one of the subjects (the whole thing was too large). This is what I get when I run recon-all -version: $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ When I try to run recon-all -s subject_no -make all I don't think anything comes up in the log. I get this in the terminal window: clare@clare-OptiPlex-990:~/subjects$ recon-all -s subject_20 -make all Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Subject 'subject_20': make all make: Nothing to be done for `all'. clare@clare-OptiPlex-990:~/subjects$ Let me know if you need anything else. Thank you. Best wishes, Clare From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: 25 July 2012 14:44 To: Gibbard, Clare Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all -qcache curvature error recon-all make -all Hi Clare can you send us the screen output and also what version you are running? thanks Bruce On Wed, 25 Jul 2012, Gibbard, Clare wrote: Hello, I have run several scans using recon-all -all -subjid subject_no -expert expert.opts where my expert.opts file changes the parameters for the mri_normalize step (this works well in my scans). I then had to edit a few of the scans by adding in more white matter and a few control points. I re-ran them to incorporate the edits using recon-all -s subject_no -make all -xopts-use. This worked well. I then ran recon-all -s subject_no -qcache ready for doing a group analysis. I got an error reading the curvature file in those subjects I had edited. I can see from the mailing list that others have had this error previously and ran recon-all -s subject_no -make all to fix it. I tried this, but I got a message saying that there was nothing to be done for all. Are you able to advise me on what I can try now? Do I need to go back a step? Thank you very much, Clare 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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tcsh: tailarach_avi: Command not found
Try re-installing. Make sure you have enough disk space. doug On 07/30/2012 12:43 AM, Fidel Vila wrote: Hi Doug. The missing files are NOT in $FREESURFER_HOME/bin; So, I guess that's why they are not found even though the path is set up in the system PATH variable. Suggestions? Fidel Are the missing files in $FREESURFER_HOME/bin and is that path in your system PATH variable? On 07/26/2012 01:29 PM, Fidel Vila wrote: Thanks for your prompt reply, Doug. I've been checking and following the wiki instructions with regards to setting up proper paths, and I could not find an obvious (to me) problem there. I attach a file with things I have tried and issues I have found. Further advice will be greatly appreciate it. Many thanks, Fidel On 25-Jul-12, at 8:22 PM, Douglas Greve wrote: did you set up your environment so that your path environment variable has all the proper paths in it? Look at the wiki for instructions. doug On 7/25/12 7:57 PM, Fidel Vila wrote: Hi Freesurfer experts, I recently installed FS (PowerPC architecture version available on FS website) on a Mac OS X 10.4.11 and I get the attached output error when running recon-all. Advice on how to troubleshoot this would be appreciate. Thanks, Fidel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@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@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Fidel Vila-Rodriguez, MD, FRCPC Clinical Assistant Professor, Faculty of Medicine, Dpt. of Psychiatry, University of British Columbia UBC Clinician Investigator Fellow UBC Graduate Program in Neuroscience Ph.D Candidate BC Mental Health and Addiction Research Institute A3-128-4, 938 West 28th Ave Vancouver, BC V5Z 4H4 Tel: 604-875-2000 Ext. 4732 Fax: 604-875-3871 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Smoothing in -qcache and the -fwhm option in mri_glmfit
Hi Jeni, you should not smooth with both. If you want to smooth within a given label with surf2surf, pass that label to surf2surf then don't smooth with glmfit. doug On 07/30/2012 12:46 AM, Jeni Chen wrote: Hi Doug, When you say If you smooth using surf2surf, then do not smooth using glmfit... are you referring to smoothing the whole hemisphere, or with a label? In other words, if I had asked surf2surf to smooth only inside a label, then no need to smooth again in glmfit. But if I did a smoothing of 10mm in surf2surf on the entire hemisphere instead (i.e. without --label option in surf2surf), then I will need to do smoothing in glmfit. Did I get it right? By the way, thank you for replying- on midnight Sunday! (unless you are in a different time zone...) Jeni On 2012-07-30, at 12:04 AM, Douglas Greve wrote: Hi Jeni, usually you smooth with surf2surf and include a mask or label to indicate that it should only be smoothed inside the mask/label. mri_glmfit will create a mask from non-zero voxels; if you ask glmfit to smooth, then it will only smooth inside of the mask. If you smooth using surf2surf, then do not smooth using glmfit. doug On 7/29/12 11:49 PM, Jeni Chen wrote: Now I'm confused... So if I included a mask in my GLM analysis (which I did), then I should add the -fwhm option in mri_glmfit? If that's the case, does that mean my -y input file should be unsmoothed to avoid double-smoothing? Jeni On 2012-07-29, at 11:31 PM, Douglas Greve wrote: Mostly yes. The one in mri_glmfit will also do smoothing within a given mask by default, but basically they do the same thing. doug On 7/29/12 11:15 PM, Jeni Chen wrote: So essentially the -fwhm option in mri_glmfit does the same thing as mri_surf2surf --fwhm ? Just want to make sure... Thanks again! Jeni 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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all
Hi Susan, if you are not doing a thickness study, then I don't think it will matter much if you have 1 or 2 or 3 T1s. There's not an easy way to compare the recons. You can do a paired difference using 1 T1 vs mult T1s. That will mostly give you bias information, not accuracy or repeatability. doug On 07/30/2012 01:18 AM, Susan Alice McLaughlin wrote: Hi Freesurfer experts, We’ve been collecting structural (1mm isotropic) and functional (2.75x2.75x3mm) data on a Philips 3T scanner using an 8-channel head coil. We are reconstructing each subject’s surface and mapping functional data processed in FSL’s FEAT to the surface. For some subjects, we have only 1 MPRAGE, but for others, we have multiple (2 or 3) MPRAGEs, acquired in separate scanning sessions. Looking back at the list serve and FSLwiki (http://surfer.nmr.mgh.harvard.edu/fswiki/FsQuizAnswers), it appears that our SNR should be good enough that we do not need -- and perhaps SHOULD NOT use --multiple MPRAGEs when using recon-all. Is there general agreement on this? How does one go about quantitatively comparing one surface reconstruction derived from 1 MPRAGE to another derived from 2 MPRAGEs? Thank you, Susan McLaughlin Doctoral Candidate SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) Dept. of Speech and Hearing Sciences University of Washington ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] problem when convert dcm to mgz
where did this file come from? Can you upload it to our file drop (URL at the end of this email)? doug On 07/30/2012 01:51 AM, Liu Yawu wrote: Hi Doug, Thanks for your reply. Here are the message: ERROR: /home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.282911170905084.dcm is not a dicom file or some other problem Entering IsDICOM (/home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.282911170905084.dcm) Opening /home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.282911170905084.dcm as part10 DCM_FILEOPENFAILED 280092 DCM Unrecognized VR code ( ) in readVRLength 20092 DCM failed to open file: /home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.282911170905084.dcm in DCM_OpenFile Opening as littleendian DCM_FILEOPENFAILED Opening as bigendian DCM_FILEOPENFAILED Opening as format conversion DCM_ILLEGALOPTION Leaving IsDICOM (/home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.282911170905084.dcm) ERROR: /home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.282911170905084.dcm is not a dicom file or some other problem Yawu From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, July 27, 2012 7:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] problem when convert dcm to mgz Can you send the result of mri_probedicom --i /home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.282911170905084.dcm doug On 07/27/2012 05:38 AM, Liu Yawu wrote: Hi, I recently install Freesurfer under ubuntu. I tested two own data. It works in one our own case, but did not work for other cases. The problem is the Freesurfer not found or unknown file type for file /home/d4201z/Desktop/im_4/2000110815073505086.dcm when convert convert dcm to mgz. Any helps are appreciated! Here are detailed inf: FREESURFER_HOME: /usr/local/src/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Debian version: wheezy/sid Kernel info: Linux 3.2.0-27-generic x86_64 1. the entire command-line executed recon-all -s APauli \ -i /home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.282911170905084.dcm 2. the error message generated file not found or unknown file type for file /home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.282911170905084.dcm 3. the subject's /script/recon-all.log Fri Jul 27 12:20:31 EEST 2012 /usr/local/src/freesurfer/subjects/APauli /usr/local/src/freesurfer/bin/recon-all -s APauli -i /home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.282911170905084.dcm subjid APauli setenv SUBJECTS_DIR /usr/local/src/freesurfer/subjects FREESURFER_HOME /usr/local/src/freesurfer Actual FREESURFER_HOME /usr/local/src/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux d4201z-CELSIUS-M470-2 3.2.0-27-generic #43-Ubuntu SMP Fri Jul 6 14:25:57 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 95900 maxlocks unlimited maxsignal95900 maxmessage 819200 maxnice 0 maxrtprio0 maxrttimeunlimited total used free sharedbuffers cached Mem: 1229825228804849417768 0 127152 973356 -/+ buffers/cache:1779976 10518276 Swap: 19529724 0 19529724 program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:31-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:31-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion:
Re: [Freesurfer] Recon-all -qcache curvature error recon-all make -all
Hi Clare, what kind of edits did you make? Can you send the terminal output when you ran qcache? doug On 07/30/2012 05:50 AM, Gibbard, Clare wrote: Hello, I emailed last week to ask about an error I was getting. Has anyone had a chance to look into it? Thank you very much. Best wishes, Clare From: Gibbard, Clare Sent: 25 July 2012 16:45 To: Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Recon-all -qcache curvature error recon-all make -all Hi Bruce, Thanks, I've attached the end of the recon-all.log file for one of the subjects (the whole thing was too large). This is what I get when I run recon-all -version: $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ When I try to run recon-all -s subject_no -make all I don't think anything comes up in the log. I get this in the terminal window: clare@clare-OptiPlex-990:~/subjects$ recon-all -s subject_20 -make all Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Subject 'subject_20': make all make: Nothing to be done for `all'. clare@clare-OptiPlex-990:~/subjects$ Let me know if you need anything else. Thank you. Best wishes, Clare From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: 25 July 2012 14:44 To: Gibbard, Clare Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all -qcache curvature error recon-all make -all Hi Clare can you send us the screen output and also what version you are running? thanks Bruce On Wed, 25 Jul 2012, Gibbard, Clare wrote: Hello, I have run several scans using recon-all -all -subjid subject_no -expert expert.opts where my expert.opts file changes the parameters for the mri_normalize step (this works well in my scans). I then had to edit a few of the scans by adding in more white matter and a few control points. I re-ran them to incorporate the edits using recon-all -s subject_no -make all -xopts-use. This worked well. I then ran recon-all -s subject_no -qcache ready for doing a group analysis. I got an error reading the curvature file in those subjects I had edited. I can see from the mailing list that others have had this error previously and ran recon-all -s subject_no -make all to fix it. I tried this, but I got a message saying that there was nothing to be done for all. Are you able to advise me on what I can try now? Do I need to go back a step? Thank you very much, Clare 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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] problem when convert dcm to mgz
glad to hear it, but I'm surprised that there are dicoms that we can't read. Maybe it's just an old variant of the format? good luck Bruce On Mon, 30 Jul 2012, Liu Yawu wrote: Hi Bruce, The dcm files are from SIMENS MAGNETOM VISION plus. The file does exist. Myriam Siefert met same problem. She suggested me to convert the dcm to nii file. Because Freesurfer cannot read header of the some dcm files. After converting to nii, it seems working now. The analysis is running now. Regards, Yawu -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: 27. heinäkuuta 2012 16:47 To: Liu Yawu Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] problem when convert dcm to mgz Hi Yawu where did you get that dicom from? Does the file you are pointing to exist? cheers Bruce On Fri, 27 Jul 2012, Liu Yawu wrote: Hi, I recently install Freesurfer under ubuntu. I tested two own data. It works in one our own case, but did not work for other cases. The problem is the Freesurfer not found or unknown file type for file /home/d4201z/Desktop/im_4/2000110815073505086.dcm when convert convert dcm to mgz. Any helps are appreciated! Here are detailed inf: FREESURFER_HOME: /usr/local/src/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Debian version: wheezy/sid Kernel info: Linux 3.2.0-27-generic x86_64 1. the entire command-line executed recon-all -s APauli \ -i /home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.282911170905084.dcm 2. the error message generated file not found or unknown file type for file /home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.282911170905084.dcm 3. the subject's /script/recon-all.log Fri Jul 27 12:20:31 EEST 2012 /usr/local/src/freesurfer/subjects/APauli /usr/local/src/freesurfer/bin/recon-all -s APauli -i /home/d4201z/Desktop/im_3/1.3.12.2.1107.5.2.4.7668.282911170905084.dcm subjid APauli setenv SUBJECTS_DIR /usr/local/src/freesurfer/subjects FREESURFER_HOME /usr/local/src/freesurfer Actual FREESURFER_HOME /usr/local/src/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux d4201z-CELSIUS-M470-2 3.2.0-27-generic #43-Ubuntu SMP Fri Jul 6 14:25:57 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 95900 maxlocks unlimited maxsignal95900 maxmessage 819200 maxnice 0 maxrtprio0 maxrttimeunlimited total used free sharedbuffers cached Mem: 1229825228804849417768 0 127152 973356 -/+ buffers/cache:1779976 10518276 Swap: 19529724 0 19529724 program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:31-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:31-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:31-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:31-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: d4201z Machine: d4201z-CELSIUS-M470-2 Platform: Linux PlatformVersion: 3.2.0-27-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/27-09:20:31-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS:
[Freesurfer] Non rigid registration
Hi, In our functional MRI studies, we co-registration the functional images to anatomical scans (a part of preproc-sess routine in version 5) before measuring the contrasts. But for one of our studies, a reviewer has asked if a “non-rigid image registration” would change results when we are assessing activity within artifact-prone brain areas (e.g. anterior temporal areas). As far as I know, freesurfer registration works fine and even in this study, we have found very strong activity/contrast within anterior tempotal lobe. But I was wondering whether you have tested this possibility or not. If yes, then I appreciate if you can introduce me a reference (published article) to support our answer. Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Non rigid registration
It depends on what the reviewer is concerned about. You don't want to use a fully non-rigid registration because the drop out will look like the edge of the brain, and the non-rigid will warp it incorrectly. If he/she is talking about using something more constrained like B0 correction, then it is possible that some things could change. In general, where you have B0 distortion you also have dropout, so correcting for B0 distortion often has a very small effect (no ref on that unfortunately). doug On 07/30/2012 11:01 AM, SHAHIN NASR wrote: Hi, In our functional MRI studies, we co-registration the functional images to anatomical scans (a part of preproc-sess routine in version 5) before measuring the contrasts. But for one of our studies, a reviewer has asked if a “non-rigid image registration” would change results when we are assessing activity within artifact-prone brain areas (e.g. anterior temporal areas). As far as I know, freesurfer registration works fine and even in this study, we have found very strong activity/contrast within anterior tempotal lobe. But I was wondering whether you have tested this possibility or not. If yes, then I appreciate if you can introduce me a reference (published article) to support our answer. Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 ___ Freesurfer mailing list Freesurfer@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] Label to ROI volume
Dear FS Experts, I have run recon-all on my subjects. I'm looking to convert the V1 and various BA labels to ROIs in 3D anatomical space (orig.mgz). How would I convert my freesufer label files to ROIs. Thank you! Massieh Moayedi ___ Freesurfer mailing list Freesurfer@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] Error with recon-all import step. ERROR: the pixel data cannot be loaded as it is JPEG compressed.
I am trying to import an MPRAGE structural sequence of 160 images acquired from a Siemens Allegro. Only one of my subjects displays the following error message when I try to import him using the recon-all -s Subject -i function. Below is the brief error message and full log. Thanks in advance for any assistance. *ERROR: the pixel data cannot be loaded as it is JPEG compressed.* Full Log Below: [Jill:freesurfer/subjects/RawDicoms] lab% recon-all -s SZ0069TS -i SZ0069TS/IM-0001-441581576-0001.dcm Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin Jill.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 /Applications/freesurfer/subjects/SZ0069TS \n mri_convert /Applications/freesurfer/subjects/RawDicoms/SZ0069TS/IM-0001-441581576-0001.dcm /Applications/freesurfer/subjects/SZ0069TS/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/subjects/RawDicoms/SZ0069TS/IM-0001-441581576-0001.dcm /Applications/freesurfer/subjects/SZ0069TS/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Applications/freesurfer/subjects/RawDicoms/SZ0069TS/IM-0001-441581576-0001.dcm... Getting Series No INFO: Found 163 files in /Applications/freesurfer/subjects/RawDicoms/SZ0069TS INFO: Scanning for Series Number 20 Scanning Directory INFO: found 160 files in series INFO: loading series header info. RunNo = 19 INFO: sorting. INFO: (256 256 160), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix - 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; *ERROR: the pixel data cannot be loaded as it is JPEG compressed.* (Transfer Syntax UID: 1.2.840.10008.1.2.4.70) Darwin Jill.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 recon-all -s SZ0069TS exited with ERRORS at Mon Jul 30 11:38:40 CDT 2012 For more details, see the log file /Applications/freesurfer/subjects/SZ0069TS/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Take care, Nathan Hutcheson Graduate Research Assistant 501 Sparks Center 1748 7th Ave South Birmingham, AL 35233 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Label to ROI volume
try mri_label2vol (assuming by 'ROI' you mean a 3D volume) On Mon, 30 Jul 2012, mmoay...@uhnres.utoronto.ca wrote: Dear FS Experts, I have run recon-all on my subjects. I'm looking to convert the V1 and various BA labels to ROIs in 3D anatomical space (orig.mgz). How would I convert my freesufer label files to ROIs. Thank you! Massieh Moayedi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Error with recon-all import step. ERROR: the pixel data cannot be loaded as it is JPEG compressed.
it looks like someone accidentally turn on jpeg compression on the console. Our converter does not read jpeg. You can use dcmdjpeg from the dcmtk toolkit to create new dicoms that are uncompressed, something like dcmdjpeg +te old.dcm new.dcm doug On 07/30/2012 01:00 PM, Nathan Hutcheson wrote: I am trying to import an MPRAGE structural sequence of 160 images acquired from a Siemens Allegro. Only one of my subjects displays the following error message when I try to import him using the recon-all -s Subject -i function. Below is the brief error message and full log. Thanks in advance for any assistance. *ERROR: the pixel data cannot be loaded as it is JPEG compressed.* Full Log Below: [Jill:freesurfer/subjects/RawDicoms] lab% recon-all -s SZ0069TS -i SZ0069TS/IM-0001-441581576-0001.dcm Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin Jill.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 /Applications/freesurfer/subjects/SZ0069TS \n mri_convert /Applications/freesurfer/subjects/RawDicoms/SZ0069TS/IM-0001-441581576-0001.dcm /Applications/freesurfer/subjects/SZ0069TS/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/subjects/RawDicoms/SZ0069TS/IM-0001-441581576-0001.dcm /Applications/freesurfer/subjects/SZ0069TS/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Applications/freesurfer/subjects/RawDicoms/SZ0069TS/IM-0001-441581576-0001.dcm... Getting Series No INFO: Found 163 files in /Applications/freesurfer/subjects/RawDicoms/SZ0069TS INFO: Scanning for Series Number 20 Scanning Directory INFO: found 160 files in series INFO: loading series header info. RunNo = 19 INFO: sorting. INFO: (256 256 160), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix - 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; *ERROR: the pixel data cannot be loaded as it is JPEG compressed.* (Transfer Syntax UID: 1.2.840.10008.1.2.4.70) Darwin Jill.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 recon-all -s SZ0069TS exited with ERRORS at Mon Jul 30 11:38:40 CDT 2012 For more details, see the log file /Applications/freesurfer/subjects/SZ0069TS/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Take care, Nathan Hutcheson Graduate Research Assistant 501 Sparks Center 1748 7th Ave South Birmingham, AL 35233 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 ___ Freesurfer mailing list Freesurfer@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] tracula error...
Hi: I ran trac-all -prep -c dmrirc and it finished ok... Then, when I tried to run the command trac-all -bedp -c dmrirc, I got the error: ln -sf /usr/local/freesurfer/subjects/bmvf_23_7_2012/dlabel/diff/anat_brain_mask.bbr.nii.gz /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri/nodif_brain_mask.nii.gz ln -sf /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri/dwi.nii.gz /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri/data.nii.gz WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_seychelles /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri subjectdir is /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri Making bedpostx directory structure Queuing preprocessing stages [: 223: NONE: unexpected operator [: 314: NONE: unexpected operator [: 327: xbedpostx_pre: unexpected operator [: 486: x: unexpected operator [: 486: -le: argument expected Queuing parallel processing stage [: 223: NONE: unexpected operator [: 327: xbedpostx: unexpected operator [: 486: x27: unexpected operator 0 slices processed Queuing post processing stage [: 223: NONE: unexpected operator [: 314: NONE: unexpected operator [: 327: xbedpostx_post: unexpected operator [: 486: x: unexpected operator [: 486: -le: argument expected That problem occurr because my PC is not a parallelized environment?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Issues with Tracula
Hi Sergio - Sorry, if this occurs independently of trac-all, whenever you run bedpostx directly, you're better off asking for help on the FSL list. We've never run into this problem with bedpostx up till now. a.y On Mon, 30 Jul 2012, Sergio Medina wrote: Nope, I have the same files as before :( 2012/7/27 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu The monitoring script that bedpostx runs and tells you if things have or haven't finished properly can't always be trusted. So if that's the only error message you see, I wouldn't worry about it. Have the *ph1* and *th1* files appeared this time? On Fri, 27 Jul 2012, Sergio Medina wrote: What a coincide! Our teams have both chosen the same release cycle strategy :P I ran bedpostx_postproc and I've got so many errors that makes me think the problem is before this step (see output in attached n1-bedpostx-postproc.txt). So, I ran again bedpostx on the dmri directory, which the first run *seemed* to finish and didn't throw any error (I attached the output in the first email). This run did finish, and it did throw errors (full output in n2-bedpostx-dmri.txt): [...] slice 63 has already been processed wc: /volatile/tracula/results/Diff001/dmri.bedpostX/commands.txt: No such file or directory Queuing post processing stage 64 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. kill: 276: No such process Then I started wondering whether I do have the right data to actually run bedpostx, so I run the script that checks that: bedpostx_datacheck, the output (n3-bedpostx-datacheck.txt) doesn't show any signs of errors so I would like to assume everything is ok with the input data... Any idea? Thanks, once again. Sergio. 2012/7/27 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Hi Sergio - As with any imminent new version release, it's happening soon. I'd say in a month, I'm just not sure a month from when :P The fact that the temporary files (everything with *slice* in the name) are still in your bedpostx directory means that bedpostx didn't finish running properly. You can try running the last step of bedpostx and see if you get any error messages that give you any clues: bedpostx_postproc.sh /volatile/tracula/results/Diff001/dmri Normally this step merges the individual slices into volumes and deletes the temporary files. If all else fails, I'd ask the FSL gurus. Hope this helps, a.y On Fri, 27 Jul 2012, Sergio Medina wrote: Anastasia, Thanks for such a quick reply! Please find my answers inline... 2012/7/26 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Hi Sergio - Thank you for your kind words, and also thank you for taking the time to search the archives for answers! The first problems you had with running bedpostx through trac-all have to do with trac-all assuming an older version of FSL than the current one, and this'll be fixed in the upcoming release of trac-all. Indeed the thing to do in the meantime is to run bedpostx by itself, as you did. I apologize for the inconvenience. Great! By any chance, do you know when that release will happen? About the problem you had when you ran bedpostx directly: do you get the other outputs of bedpostx, listed
Re: [Freesurfer] tracula error...
Hi Gonzalo - This has come up a few times recently. Please see here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23064.html Hope this helps, a.y On Mon, 30 Jul 2012, Gonzalo Rojas Costa wrote: Hi: I ran trac-all -prep -c dmrirc and it finished ok... Then, when I tried to run the command trac-all -bedp -c dmrirc, I got the error: ln -sf /usr/local/freesurfer/subjects/bmvf_23_7_2012/dlabel/diff/anat_brain_mask.bbr.nii.gz /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri/nodif_brain_mask.nii.gz ln -sf /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri/dwi.nii.gz /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri/data.nii.gz WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_seychelles /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri subjectdir is /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri Making bedpostx directory structure Queuing preprocessing stages [: 223: NONE: unexpected operator [: 314: NONE: unexpected operator [: 327: xbedpostx_pre: unexpected operator [: 486: x: unexpected operator [: 486: -le: argument expected Queuing parallel processing stage [: 223: NONE: unexpected operator [: 327: xbedpostx: unexpected operator [: 486: x27: unexpected operator 0 slices processed Queuing post processing stage [: 223: NONE: unexpected operator [: 314: NONE: unexpected operator [: 327: xbedpostx_post: unexpected operator [: 486: x: unexpected operator [: 486: -le: argument expected That problem occurr because my PC is not a parallelized environment?... Sincerely, ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] More than two time-points in longitudinal base = Memory allocation error?
Hi Liz, you need more memory (see the error message: cannot allocate memory). Best, Martin On Mon, 2012-07-23 at 10:21 +1000, Liz Bowman wrote: Hello, I have several patients scans taken over multiple time points (up to nine time points in some patients). I thought I might be able to use these to create a base template for longitudinal processing, however the process fails and exits with errors if I try to create a base with more than two time points from a patient. This is a sample of the error log of the most recent attempt, with three timepoints: Resolution: 1 S( 128 128 128 ) T( 128 128 128 ) Iteration(f): 1 -- diff. to prev. transform: 0.876663 Iteration(f): 2 -- diff. to prev. transform: 0.0148738 Iteration(f): 3 -- diff. to prev. transform: 0.00156813 0.01 :-) Resolution: 0 S( 256 256 256 ) T( 256 256 256 ) Iteration(f): 1 -- diff. to prev. transform: 0.263086 Iteration(f): 2mri_robust_template(1035) malloc: *** mmap(size=262144) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(256, 256, 256): could not allocate 262144 bytes for 68th slice Cannot allocate memory Darwin 550D-UOM88670.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 recon-all -s KSx3 exited with ERRORS at Mon Jul 23 10:15:13 EST 2012 For more details, see the log file /Applications/freesurfer/subjects/KSx3/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I would be grateful for any advice. Regards, EA Bowman ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] SUBJECTS_DIR not defined in environment
Hi Matthew what shell are you using? If you type printenv SUBJECTS_DIR right before calling mri_segstats, what does it return? And when do you get that output? Are you sourcing the FreeSurferEnv.csh file? Don't execute it as otherwise it pushes a new shell, sets all that stuff, then pops out of it erasing all the stuff it set cheers Bruce On Mon, 30 Jul 2012, Matthew Goldfinger wrote: Dear Freesurfers, Forgive me for asking about what appears to be a very simple issue but I am stumped. I have defined my SUBJECTS_DIR as evidenced by this output. - freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni But upon trying to execute the following: mri_segstats --seg /Applications/freesurfer/subjects/bert/mri/aseg.mgz --sum /Applications/freesurfer/subjects/bert/stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --subject bert --brainmask mri/brainmask.mgz --brain-vol-from-seg I get the error that SUBJECTS_DIR not defined in environment. My code has been edited to not even use this variable and yet the issue stills stands. Please advise on how to circumvent this error. Ever thankful, Matthew Goldfinger ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] SUBJECTS_DIR not defined in environment
Ok the main email is CC'd. Below is what I did and the output I received. The goal is to get a brain volume, Subdural space and/or a CSF volume to estimate how much room for displacement/deformation the brain has. Thanks in advance for your help. Matthews-MacBook-Pro-2:~] matthew% printenv SUBJECTS_DIR /Applications/freesurfer/subjects [Matthews-MacBook-Pro-2:~] matthew% sudo mri_segstats --seg /Applications/freesurfer/subjects/bert/mri/aseg.mgz --sum /Applications/freesurfer/subjects/bert/stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --subject bert --brainmask mri/brainmask.mgz --brain-vol-from-seg $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg /Applications/freesurfer/subjects/bert/mri/aseg.mgz --sum /Applications/freesurfer/subjects/bert/stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /Applications/freesurfer/FreeSurferColorLUT.txt --subject bert --brainmask mri/brainmask.mgz --brain-vol-from-seg sysname Darwin hostname Matthews-MacBook-Pro-2.local machine x86_64 user root ERROR: SUBJECTS_DIR not defined in environment On Mon, Jul 30, 2012 at 10:38 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Matthew Could you cc the list so others can answer? Can you also send us the screen output showing exactly what you did? Thanks Bruce On Jul 30, 2012, at 8:19 PM, Matthew Goldfinger mattgoldfin...@gmail.com wrote: Bruce, When I execute printenv it gives me the correct path name (/Applications/freesurfer/subjects). Upon original set up I automatically sourced to freesurfersetup.csh as was described in the setup instructions. How should I source to have Freesurfer commands available without running into this problem? Matthew S. Goldfinger On Mon, Jul 30, 2012 at 8:02 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Matthew what shell are you using? If you type printenv SUBJECTS_DIR right before calling mri_segstats, what does it return? And when do you get that output? Are you sourcing the FreeSurferEnv.csh file? Don't execute it as otherwise it pushes a new shell, sets all that stuff, then pops out of it erasing all the stuff it set cheers Bruce On Mon, 30 Jul 2012, Matthew Goldfinger wrote: Dear Freesurfers, Forgive me for asking about what appears to be a very simple issue but I am stumped. I have defined my SUBJECTS_DIR as evidenced by this output. - freesurfer-Darwin-leopard-**i686-stable-pub-v5.1.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/**fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/**subjects MNI_DIR /Applications/freesurfer/mni But upon trying to execute the following: mri_segstats --seg /Applications/freesurfer/**subjects/bert/mri/aseg.mgz --sum /Applications/freesurfer/**subjects/bert/stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab $FREESURFER_HOME/**FreeSurferColorLUT.txt --subject bert --brainmask mri/brainmask.mgz --brain-vol-from-seg I get the error that SUBJECTS_DIR not defined in environment. My code has been edited to not even use this variable and yet the issue stills stands. Please advise on how to circumvent this error. Ever thankful, Matthew Goldfinger 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/**compliancelinehttp://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@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.
