[Freesurfer] recon-all exits with errors
Hello All, I have a library problem when I run recon-all. Recon-all exits with ERROR during the cortribbon step. I am using FC8 x86_64 OS on an Intel Xeon 64 bit machine. I have installed CentOS4-x86_64-v4.0.2 version of freesurfer. The library in question libexpat.so.0 has been installed and is located in /usr/lib however, the problem persists. The command and error is: recon-all -s 24560 -cortribbon INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-r--r-- 1 giang users 698777 Apr 1 11:29 /usr/local/freesurfer/subjects/24560/scripts/recon-all.log Linux snood.wpic.upmc.edu 2.6.24.3-12.fc8 #1 SMP Tue Feb 26 14:21:30 EST 2008 x86_64 x86_64 x86_64 GNU/Linux INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer Previous: /Applications/freesurfer # [EMAIL PROTECTED] Cortical ribbon mask Tue Apr 1 14:24:12 EDT 2008 /usr/local/freesurfer/subjects/24560/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance 24560 mris_volmask.bin: error while loading shared libraries: libexpat.so.0: cannot open shared object file: No such file or directory Linux snood.wpic.upmc.edu 2.6.24.3-12.fc8 #1 SMP Tue Feb 26 14:21:30 EST 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Tue Apr 1 14:24:12 EDT 2008 Any help is greatly appreciated. Thank you, Dhruman ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] recon-all exits with error
Hello All, I have a library problem when I run recon-all. Recon-all exits with ERROR during the cortribbon step. I am using FC8 x86_64 OS on an Intel Xeon 64 bit machine. I have installed CentOS4-x86_64-v4.0.2 version of freesurfer. The library in question libexpat.so.0 has been installed and is located in /usr/lib however, the problem persists. The command and error is: recon-all -s 24560 -cortribbon INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-r--r-- 1 giang users 698777 Apr 1 11:29 /usr/local/freesurfer/subjects/24560/scripts/recon-all.log Linux snood.wpic.upmc.edu 2.6.24.3-12.fc8 #1 SMP Tue Feb 26 14:21:30 EST 2008 x86_64 x86_64 x86_64 GNU/Linux INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer Previous: /Applications/freesurfer # [EMAIL PROTECTED] Cortical ribbon mask Tue Apr 1 14:24:12 EDT 2008 /usr/local/freesurfer/subjects/24560/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance 24560 mris_volmask.bin: error while loading shared libraries: libexpat.so.0: cannot open shared object file: No such file or directory Linux snood.wpic.upmc.edu 2.6.24.3-12.fc8 #1 SMP Tue Feb 26 14:21:30 EST 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Tue Apr 1 14:24:12 EDT 2008 Any help is greatly appreciated. Thank you, Dhruman PS: Sorry if you received the email twice. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] CentOS 5.1 and freesurfer and tksurfer
Hi all, I am facing the same problem with CentOS 5 and tksurfer.Is there any fix for this problem? Thank you, -Dhruman -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Nick Schmansky Sent: Tuesday, February 19, 2008 10:03 AM To: [EMAIL PROTECTED] Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] CentOS 5.1 and freesurfer and tksurfer Does glxgears work? That is an app that comes with Linux that exercises the GLX (OpenGL X extension) code. On Tue, 2008-02-19 at 20:41 +0800, [EMAIL PROTECTED] wrote: Dear FS experts, I install CentOS 5.1 and latest version of ATI driver and FS4.0.2, when I start tkmedit, it looks fine. In tksurfer, it just appear a sliver of surface without error message. In console, it stock on reading vertex. Is there anyway to correct it ? Thanks replay Kl chen ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] System requirements.
Hello All, I have a P4 1.5 GHZ, 1GB ram, 65GB hard disk running redhat fedora core release 5. I am planning to install the latest version of freesurfer on it. It will be a dedicated system for a small study with the only task of processing the data on freesurfer. Will this work? I understand that it will be slow, but are there any chances of installation not working just because of hardware qualifications? Thank you, Dhruman D. Goradia (M.S.) Research Specialist. Western Psychiatric Institute and Clinic. 3811 O'Hara St. Suite 431 Pittsburgh, PA 15213 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Edit label
Hi all, I am interested in lobe wise surface measurement. I read Desikan et al. paper to understand that their atlas divides the lobes into different region and freesurfer uses that atlas to gets measurement for each region. Is it possible to load the Desikan label and edit it to fuse all the region belonging to each lobe and create a new label, which I could use to get surface measurement? Thanks in advance. Dhruman ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Edit label
Hello Rahul, Thank you for your reply. I tried to combine the different regions to create one label for each lobe but could not figure it out. Can you suggest how I can combine different regions using tksurfer? Is there a wiki page where the steps are explained? Thank you -Dhruman -Original Message- From: Rahul Desikan [mailto:[EMAIL PROTECTED] Sent: Thursday 27 July 2006 15:15 To: Goradia, Dhruman D Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edit label Hi Dhruman, If you are interested in lobe-wise comparisons, you can indeed add up the individual regions of a specific lobe, create one massive label for that lobe, and get statistics on those. For example, if you were interested in the temporal lobe, you could combine: lateral occipital cuneus lingual pericalcarine and generate an *h.occiptal.label (you can use tksurfer to combine the regions). You could do the same for the other labels and thus create a 'lobe based' parcellation. Once you are done, you can use mris_anatomical_stats to generate stats on the new labels you have generated. best, Rahul On Thu, 27 Jul 2006, Goradia, Dhruman D wrote: Hi all, I am interested in lobe wise surface measurement. I read Desikan et al. paper to understand that their atlas divides the lobes into different region and freesurfer uses that atlas to gets measurement for each region. Is it possible to load the Desikan label and edit it to fuse all the region belonging to each lobe and create a new label, which I could use to get surface measurement? Thanks in advance. Dhruman -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Aseg.stats measurements
Hi all, Can anyone tell me how freesurfer defines Intracranial volume, Brain segmentation volume and Brain mask volume? What is the difference between the 3 measures? -Dhruman ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Exporting Anatomical Stats
I have a freesurfer version that was released in Feb. (I think the version is 3.0 dev). I looked in the bin and could not find asegstat2table and aparcstat2table function files. Is it possible for anyone to send those files? Also, will those file be compatible with the version of freesurfer I am using. Thank you -Dhruman -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Thursday 15 June 2006 13:18 To: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Exporting Anatomical Stats How do I go about finding/getting these tables? Sorry, I am fairly new to the program. Quoting Jenni Pacheco [EMAIL PROTECTED]: In the latest version there is asegstats2table and aparcstats2table which will do what you want. Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Thursday, June 15, 2006 9:42 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Exporting Anatomical Stats I ran all three -autorecons and also was able to get my volumetric statistics. I was wondering if there is a way (make my life easier) to export all the information given in the anatomical stats directly to a spreadsheet format without having to copy and paste eveything. I have OpenOffice.org Calc on this computer, although I've never used it before. ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Question regarding Outputs
Hello all, The output of mris_anatomical_stats has a measurement called TotalWhiteMatterVolume for each hemisphere. From aseg.stat the measures for cerebellum-white volume and cerebral-white volume for each hemisphere can be obtain, but the sum of both the measures obtained from aseg is less than the total white matter volume obtained from the surface measures. Should they be different? If so what is the difference in measurement criteria? Thank you -Dhruman ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Volume measurements.
Hi all, In the aseg.stats file there is a measurement called Brain segmentation volume. Can someone tell me what it is? Is this same as whole brain GM volume? If not is there a way to compute that? -Dhruman ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] want to view one segmented subcortical object at a time...
Hello Bruce and all, Is it possible to perform group analysis based only on a particular subcortical region of interest and visualize it? -Dhruman -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bruce Fischl Sent: Monday 20 March 2006 16:20 To: Shahabuddin Ansari Cc: freesurfer@nmr.mgh.harvard.edu; Steve Pieper Subject: Re: [Freesurfer] want to view one segmented subcortical object ata time... Hi Shahab, we don't have anything to do that, although I think slicer probably can do it with our data. Bruce On Mon, 20 Mar 2006, Shahabuddin Ansari wrote: Hello, I have segmented subcortical regions of the whole brain from Freesurfer. Can somebody help me how to view one object (say right hippocampus) at a time. Thanks Shahab __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Faster and Parallel recon-all
Hi Daniel, I was having a second look at the script and apparently the script is fine with a small spelling error. The STAT variable which is set at 3 different instances has spelling error in scripts where t is missing. Once this was corrected the script is fine but it's still not working. It initiates all the processes and then just sits idle. After waiting for half an hour it still does not make step1-00.done (I start directly with motion cor) keeping all the other processes waiting. I am still probing into this. If you can think of something that might be of help then let me know. -Dhruman -Original Message- From: Daniel Goldenholz [mailto:[EMAIL PROTECTED] Sent: Tuesday 21 March 2006 11:25 To: Goradia, Dhruman D Subject: Re: [Freesurfer] Faster and Parallel recon-all Dhruman That's confusing. I think you should take one line of executable code from your script that produces that behavior and then email it to the freesurfer list. It sounds to me like the recon-all script ASSUMES that the log file exists if you specify a name. I thought it actually creates one first, but I could have been mistaken there, and if so I will need to add a few extra lines of code. PLEASE follow up on this. It will help others. The other thing to try is to create a text file first, such as like this: echo #Starting recon-all manually... /Applications/freesurfer/subjects/ddg6/scripts/recon-all-status.log and then see if my script is ok. Keep me posted. D Goradia, Dhruman D wrote: Hi Daniel, I tried to use the script super-recon on mac OX S using bash shell. I made the necessary changes to make it operable in bash. However when I run the script its gives me the following error: Tcsh:/Applications/freesurfer/subjects/ddg6/scripts/recon-all-status.lo g :not a file or directory. I tried to run the first 3 steps of the script (motioncor, nuintensitycor, talairach) and it gives the above error. However if I remove the log and status flags, the first 3 steps executes properly. Do you have any idea why? Do you see any problem if I delete the log and status flags from the whole script and use it? -Dhruman -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Daniel Goldenholz Sent: Thursday 16 March 2006 15:17 Cc: Freesurfer Mailing List; Nick Schmansky Subject: Re: [Freesurfer] Faster and Parallel recon-all Ah. Silly me, I didn't notice the -log and -status options. Thanks Nick. I have now included those into my super-recon script as well. Problem solved. (if you have seen my script already, you may need to hit RELOAD on your browser to see the new version) Daniel Nick Schmansky wrote: The script looks good. The one thing it needs though is for the right and left hemi steps to log to separate files, otherwise output to recon- all.log will be interleaved, making debugging impossible. On Thu, 2006-03-16 at 12:15 -0500, Daniel Goldenholz wrote: Ooops. I sent the below with the wrong subject tag. Here it is again: Daniel Goldenholz wrote: Freesurfers I was hoping someone else would do this, but well, it seems that no one did. So I went ahead and made this myself. Amusingly, I don't NEED to reconstruct any brains right now, so I don't have anything to test this out with. Please someone try it, and let me know if it is helpful. What I did was write a script that runs each and every part of the recon-all -all stream, one command at a time. (based on the NEW version 3 stream). Each one is loaded with -waitfor and -notify so that the dependency structure is intact. However, ALL of the commands start running in the background! If you have a 2 more processor system, then recon-all should complete in about HALF the time as it usually does, since all the hemisphere specific stuff can be done in parallel. At the completion of each hemipshere, it will email you. I included a command for each minute step so that people can easily fiddle with options and commands and so forth. Obviously, if you run recon-all -autoreon1, then you can then run my script (after deleting the step1-??.done lines). If you run recon-all -autorecon2, then you can run my script (after deleting the step1-??.done and step2-??.done lines) And so forth. To see the script, go here: http://www.nmr.mgh.harvard.edu/~daniel click on fMRI scripts click on super-recon Enjoy, and PLEASE email me if you use this. If there are corrections I can easily post them. Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Output of mris_anatomical_stats
Hi, The output of function mris_anatomical_stats contains the following measurements: integrated rectified mean curvature, integrated rectified Gaussian curvature, folding index and intrinsic curvature index. Can someone please give me a brief explanation of what these measurements are or suggest some reading material. -Dhruman Dhruman D. Goradia (M.S.) Research Specialist. Western Psychiatric Institute and Clinic. 3811 O'Hara St. Suite 431 Pittsburgh, PA 15213 Phone: 412-586-9017 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Problem with setting segmentation threshold values
Hi, I am interested in changing the white matter low limit for the segmentation step. For this I typed the following in the command prompt: recon-all subjid subjectname -autorecon2 seg-wlo low limit value this gave me an error stating that it could not recognize seg-wlo flag. I was wondering if there is a mistake in writing the command? I would also like to know if there is any default lower limit for gray matter threshold used my mri_segment? If so what is it and can it be changed? Thank you. Dhruman Dhruman D. Goradia Research Specialist Western Psychiatric Institute and Clinic 3811 OHara St Suit 431 Pittsburgh PA 15213. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
