Re: [Freesurfer] Total cerebral volume.
Hi Doug, I sum all structures except ventricle, CSF, cerebellum and brainstem in order to compare with SubCortGrayVol. Even the former includes some white matter structures and all subcortical structures, it is smaller compared to SubCortGrayVol.My original question is about calculating the total cerebral volumes, when I foundCortexVol CorticalWhiteMatterVol SubCortGrayVol is much bigger thanCortexVol CorticalWhiteMatterVol Sum(all structures (after ICV inthe list) except ventricle, CSF, cerebellum and brainstem).Hope I explained it better this time.Cheers,Zheng HuiOn 11/6/12 2:14 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:Hi Zheng, there is something wrong with your math. When I sum up all the columns in your table from Left-Lateral-Ventricle to CC_Anterior, I get 215952 for the first row (you get only 67548). Can you double check your calculations?dougOn 10/28/2012 11:53 PM, Zheng Hui wrote: Forgot to attach the excel file. Sorry for that. From: zhenghui zheng@duke-nus.edu.sg mailto:zheng@duke-nus.edu.sg Date: Monday, October 29, 2012 11:52 AM To: Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Subject: [Freesurfer] Total cerebral volume. Hi Doug, Thanks for replying. But our datasets do showed that Sum(all structures (after ICV in the list) except ventricle, CSF, cerebellum and brainstem) is much smaller SubCortGrayVol. The former is only about 30-40% of the later. We are using FS 5.1.0 without the SupraTentorialVol fix.I attached the aseg file for your reference (the last three columns in the sheet). Thanks, Zheng Hui On 10/24/2012 09:01 AM, Zheng Hui wrote: Hi freesurfer, We are trying to calculate the total cerebral volume which excludes cerebellum, brainstem, ventricle and CSF from the aseg.txt. Do we use CortexVol CorticalWhiteMatterVol SubCortGrayVol Or CortexVol CorticalWhiteMatterVol Sum(all structures (after ICV in the list) except ventricle, CSF, cerebellum and brainstem) This should give very close to the same value. I don't think it makes a difference.Also, I saw Doug's post about the bug fixing for SupraTentorialVol. To re-run the segstats for longitudinal subjects, any extra step other than recon-all –long tpN baseID –segstats and does it affect any other structure or just SupraTentorialVol? It should not affect other structures. doug-- Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.eduPhone Number: 617-724-2358Fax: 617-726-7422Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportingFileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose 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.
Re: [Freesurfer] Feature request (adding origin info to surface files)
Thanks for the reply Nick, Yes mris_info does return information I would need. volume geometry: extent : (256, 256, 256) voxel : ( 1., 1., 1.) x_(ras) : (-1., 0., 0.) y_(ras) : ( 0., 0., -1.) z_(ras) : ( 0., 1., 0.) c_(ras) : ( 5.8612, -8.9756, -36.8004) file: ../mri/filled-pretess255.mgz interestingly even if I move the surface file out of the subject's surf directory it still returns this info, making me think that it is in the file somewhere. I was looking at read_surf.m last night and it doesnt seem to do anything with this info, and http://wideman-one.com/gw/brain/fs/surfacefileformats.htm doesn't mention any of this info being in the file. is there an updated spec file on the file formats? Thanks. -Luke On Wed, Nov 7, 2012 at 3:26 PM, Nick Schmansky ni...@nmr.mgh.harvard.eduwrote: Luke, A quick answer (w/o looking into it too much): does: mris_info rh.pial give you the info you need? what i'm not sure of is whether everything you see in that output is available in the structure that the matlab surface reader loads. Nick On Wed, 2012-11-07 at 09:17 -0500, Luke Bloy wrote: Hi all, I’m not sure where the best place to make this request is… so I thought I’ll put this here. I often use freesurfer generated surfaces and images in other software packages (Slicer, Matlab etc) for various things. The MGZ files include the origin in the file headers, meaning that software can correctly interpret the world spaces of these images, allowing correct overlays with other results computed from the same scans. The problem is that the surface files treat the 128,128,128 voxel ( of the T1.mgz and other images) as the origin. But the world coordinates of this origin are, to my knowledge not in the surface files. This creates the situation that to correctly interpret these surfaces in relation to other coordinates systems, basically I either need to ignore the world coordinates and do some registration, or I need to load both an mgz file (to get the origin) and surface files to learn correct world coordinates of the surfaces. Ideally it seems like this information should be included in the surface files themselves. Hopefully my description of the problem makes some sense. Thanks. Luke ___ 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 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] process exited abnormally
Dear all, I am trying to run recon all and FS will either exists with this * child process exited abnormally*...or just a blank window appears with leaving the system to freeze.So i have to power off the VM and start all over again. Does it have to do with the system requirements.I am using VM,. Thanks a lot, chikku ___ 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] process exited abnormally
how much RAM does the VM have? On Thu, 8 Nov 2012, Varghese Chikku wrote: Dear all, I am trying to run recon all and FS will either exists with this child process exited abnormally...or just a blank window appears with leaving the system to freeze.So i have to power off the VM and start all over again. Does it have to do with the system requirements.I am using VM,. Thanks a lot, chikku ___ 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] process exited abnormally
Thanks Bruce,I am currently using 4GB ram and i5 intel processor. On 8 November 2012 15:08, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: how much RAM does the VM have? On Thu, 8 Nov 2012, Varghese Chikku wrote: Dear all, I am trying to run recon all and FS will either exists with this child process exited abnormally...or just a blank window appears with leaving the system to freeze.So i have to power off the VM and start all over again. Does it have to do with the system requirements.I am using VM,. Thanks a lot, chikku 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.
Re: [Freesurfer] checking talairach.lta
This could be a number of things. Did you restore the tkregister2 to the original? The tkregister2.bin command was compiled under Redhat OS5. What OS are you using? doug On 11/07/2012 06:15 PM, Eric Cunningham wrote: i tried replacing this file in tktools with the new tkregister2.bin, and i get a new error: /lib64/tls/libc.so.6: version GLIBC_2.4 not found On Mon, Nov 5, 2012 at 6:06 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: OK, I see the problem. I should have told you to put tkregsiter2.bin into /apps/fs510/tktools/ (after making a copy of the one there). doug On 11/5/12 5:00 PM, Eric Cunningham wrote: [e4fs@cluster bin]$ ls -l `which tkregister2.bin` -rwxr-xr-- 1 jsadinol fs 21663433 May 22 2011 /apps/fs510/tktools/ tkregister2.bin [e4fs@cluster bin]$ tkregister2 --all-info ProgramName: tkregister2.in http://tkregister2.in/ ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/11/05-21:43:36-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: e4fs Machine: cluster.mrilab.net http://cluster.mrilab.net/ Playform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 fyi: /apps/fs510/ = $FREESURFER_HOME i tried replacing this file in tktools with the new tkregister2.bin, and i get a new error: /lib64/tls/libc.so.6: version GLIBC_2.4 not found On Mon, Nov 5, 2012 at 11:34 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Can you send me the result of ls -l `which tkregister2.bin` and tkregister2 --all-info doug On 11/05/2012 03:54 PM, Eric Cunningham wrote: retried it, same error new file is .bin, old file is tkregister2, no old tkregister2.bin file appeared to be in the folder $FREESURFER_HOME/bin On Mon, Nov 5, 2012 at 10:49 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: I'm not sure that was the right thing to do. There should be two files: tkregister2 and tkregister2.bin. tkregister2 is just a script that calls tkregister2.bin after setting up some environment variables. Try keeping the original file name. doug On 11/05/2012 03:43 PM, Eric Cunningham wrote: i am sure there is one irregularity, namely that the '.bin' extension is absent from our old file, so i renamed the new file without it (as tkregister2) and moved the other one to tkregister2_backup the command i listed from previous threads was given to someone else from our lab (and probably worked), so it is likely that the problem is somewhere on our side, i was just hoping that it was known and recognizable from the error On Mon, Nov 5, 2012 at 10:15 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: are you sure you are using the new version? On 11/05/2012 02:38 PM, Eric Cunningham wrote: tried the new version, and it errored out at the same step ERROR: Option --lta-inv unknown thanks again for your help! On Mon, Nov 5, 2012 at 8:16 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
Re: [Freesurfer] fs-fast preprocessing resting state
Hi Chris, the problem is that you do not have FSLDIR defined. Assuming you have FSL installed, then setenv FSLDIR /place/where/fsl/is/installed doug On 11/06/2012 09:09 PM, Chris McNorgan wrote: Hi Doug, Attached are two plain-text files: fslog2.txt contains the redirected terminal output after executing: preproc-sess -s sub00294 -fsd rest -per-run -surface self lhrh -mni305 -fwhm 0 ~/fslog2.txt 294files.txt contains the output of `find` for all files in the project directory related to this participant *after* executing preproc-sess, in case any clue can be found in this information (I omitted files in the log/ directory). Thanks, Chris -- 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] Surface-based normalization, smoothing and averaging
On 10/25/2012 04:25 PM, Shigetoshi Takaya wrote: Dear Freesurfer experts, I would like to have your help. I have a volume data of a certain parameter on white/grey matter boundary (X.nii). What I want to do are as follows: Step 1: I want to register it onto a standard space using surface-based alignment and smooth it. Step 2: I want to generate the averaged images of several subjects on the standard inflated surface. My questions are follows: Q1) For Step 1, I guess I need to convert the image using mri_vol2surf (X.nii -- X.mgh), then use mri_surf2surf and mris_smooth. If it is the case what should I use fortarget subject name for mri_sur2surf? You should register X.nii to the anatomical with bbregister. This creates a registration file. Then use mri_vol2surf with this registration file to map to the surface. If you want the result to be on the individual subject's anatomy, then no need to specify a target subject. If you want it to be map from the individual's surface to the average surface, then specify fsaverage as the target. Q2) How to do Step 2? Do step 1 and specify fsaverage as the target (this puts them all in the same space). You can then put all of your subjects into one file with mri_concat. From there you can take the mean across all subjects to create a single map, or you can do something more sophisticated like fitting a GLM (mri_glmfit). doug Thanks in advance, Shige ___ 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] Total cerebral volume.
Can you send me the aseg.stats file for a single subject where you are seeing this effect? doug On 11/08/2012 03:45 AM, Zheng Hui wrote: Hi Doug, I sum all structures except ventricle, CSF, cerebellum and brainstem in order to compare with SubCortGrayVol. Even the former includes some white matter structures and all subcortical structures, it is smaller compared to SubCortGrayVol. My original question is about calculating the total cerebral volumes, when I found *CortexVol + CorticalWhiteMatterVol + SubCortGrayVol* is much bigger than *CortexVol + CorticalWhiteMatterVol + Sum(all structures (after ICV in the list) except ventricle, CSF, cerebellum and brainstem)*. Hope I explained it better this time. Cheers, Zheng Hui On 11/6/12 2:14 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Zheng, there is something wrong with your math. When I sum up all the columns in your table from Left-Lateral-Ventricle to CC_Anterior, I get 215952 for the first row (you get only 67548). Can you double check your calculations? doug On 10/28/2012 11:53 PM, Zheng Hui wrote: Forgot to attach the excel file. Sorry for that. From: zhenghui zheng@duke-nus.edu.sg mailto:zheng@duke-nus.edu.sg mailto:zheng@duke-nus.edu.sg mailto:zheng@duke-nus.edu.sg%3E Date: Monday, October 29, 2012 11:52 AM To: Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu%3E Subject: [Freesurfer] Total cerebral volume. Hi Doug, Thanks for replying. But our datasets do showed that Sum(all structures (after ICV in the list) except ventricle, CSF, cerebellum and brainstem) is much smaller SubCortGrayVol. The former is only about 30-40% of the later. We are using FS 5.1.0 without the SupraTentorialVol fix.I attached the aseg file for your reference (the last three columns in the sheet). Thanks, Zheng Hui On 10/24/2012 09:01 AM, Zheng Hui wrote: Hi freesurfer, We are trying to calculate the total cerebral volume which excludes cerebellum, brainstem, ventricle and CSF from the aseg.txt. Do we use CortexVol + CorticalWhiteMatterVol + SubCortGrayVol Or CortexVol + CorticalWhiteMatterVol + Sum(all structures (after ICV in the list) except ventricle, CSF, cerebellum and brainstem) This should give very close to the same value. I don't think it makes a difference. Also, I saw Doug's post about the bug fixing for SupraTentorialVol. To re-run the segstats for longitudinal subjects, any extra step other than recon-all –long tpN baseID –segstats and does it affect any other structure or just SupraTentorialVol? It should not affect other structures. doug -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto: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 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
[Freesurfer] pre-processing error?
Hello, I am having trouble with the pre-processing step. When I enter the recon-all subject-id command I get an error: [Lisa-Koskis-iMac:/Applications/freesurfer/subjects] root# recon-all -s ms_018 ERROR: nothing to do When I enter 'recon-all -s ms_018 -qcache' I get a long list of output but I don't think it worked correctly: [Lisa-Koskis-iMac:/Applications/freesurfer/subjects] root# recon-all -s ms_018 -qcache 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 -rw-rw-r-- 1 root wheel 87913 Nov 8 10:52 /Applications/freesurfer/subjects/ms_018/scripts/recon-all.log Darwin Lisa-Koskis-iMac.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 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/freesurfer/ Previous: /Applications/freesurfer /Applications/freesurfer/subjects/ms_018/surf # #@# Qdec Cache lh thickness fsaverage Thu Nov 8 11:46:43 EST 2012 INFO: File lh.thickness does not exist! Skipping creation of smoothed data for lh.thickness # #@# Qdec Cache lh area fsaverage Thu Nov 8 11:46:43 EST 2012 INFO: File lh.area does not exist! Skipping creation of smoothed data for lh.area # #@# Qdec Cache lh area.pial fsaverage Thu Nov 8 11:46:43 EST 2012 INFO: File lh.area.pial does not exist! Skipping creation of smoothed data for lh.area.pial # etc recon-all -s ms_018 finished without error at Thu Nov 8 11:46:43 EST 2012 done My goal is to eventually be able to bring up my T1 images with the qdec application and segment the motor cortex. When I use the tkmedit command it works correctly (I have converted my files to .mgz already). Do you know if it is a pre-processing error that is preventing me from getting the qdec application to work with my own brain images? I cannot open files in qdec currently. Many thanks, Julia ___ 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] FW: FreeSurfer remote access question
Hello, We recently installed freesurfer on an Ubuntu 12.04 workstation for doctors in Emergency room which will be used for CT scan analysis. In such case, remote access is required for multiple users. No difficulty was encountered when we tested tkmedit bert orig.mgz locally. However, it shows error message GLUT: Fatal Error in tkmedit.bin: visual with necessary capabilities not found. When it was tried remotely. Is there any way that this can be resolved? Thank you. Best, Hua Li System Administrator 3D Imaging Service Massachusetts General Hospital Tel: 1-(617)-726-9465 ___ 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] FW: FreeSurfer remote access question
Did you already try the suggestions on?: http://surfer.nmr.mgh.harvard.edu/fswiki/RemoteAccess Dan On Thu, Nov 8, 2012 at 3:04 PM, Li, Hua hl...@partners.org wrote: Hello, We recently installed freesurfer on an Ubuntu 12.04 workstation for doctors in Emergency room which will be used for CT scan analysis. In such case, remote access is required for multiple users. No difficulty was encountered when we tested tkmedit bert orig.mgz locally. However, it shows error message “GLUT: Fatal Error in tkmedit.bin: visual with necessary capabilities not found.” When it was tried remotely. Is there any way that this can be resolved? Thank you. Best, Hua Li System Administrator 3D Imaging Service Massachusetts General Hospital Tel: 1-(617)-726-9465 ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FW: FreeSurfer remote access question
What kind of remote access are you using? Bruce On Nov 8, 2012, at 3:04 PM, Li, Hua hl...@partners.org wrote: Hello, We recently installed freesurfer on an Ubuntu 12.04 workstation for doctors in Emergency room which will be used for CT scan analysis. In such case, remote access is required for multiple users. No difficulty was encountered when we tested tkmedit bert orig.mgz locally. However, it shows error message “GLUT: Fatal Error in tkmedit.bin: visual with necessary capabilities not found.” When it was tried remotely. Is there any way that this can be resolved? Thank you. Best, Hua Li System Administrator 3D Imaging Service Massachusetts General Hospital Tel: 1-(617)-726-9465 ___ 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] pre-processing error?
In the first command, you need to tell recon-all to do something. Eg, if you add -all, it tells it to analyze everything (keeping any manual edits you might have made). You can also try -make all and it will attempt to update the results (so it will not re-run any steps if it thinks that re-running it would not make a difference). doug On 11/08/2012 11:52 AM, Julia Nantes wrote: Hello, I am having trouble with the pre-processing step. When I enter the recon-all subject-id command I get an error: [Lisa-Koskis-iMac:/Applications/freesurfer/subjects] root# recon-all -s ms_018 ERROR: nothing to do When I enter 'recon-all -s ms_018 -qcache' I get a long list of output but I don't think it worked correctly: [Lisa-Koskis-iMac:/Applications/freesurfer/subjects] root# recon-all -s ms_018 -qcache 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 -rw-rw-r-- 1 root wheel 87913 Nov 8 10:52 /Applications/freesurfer/subjects/ms_018/scripts/recon-all.log Darwin Lisa-Koskis-iMac.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 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/freesurfer/ Previous: /Applications/freesurfer /Applications/freesurfer/subjects/ms_018/surf # #@# Qdec Cache lh thickness fsaverage Thu Nov 8 11:46:43 EST 2012 INFO: File lh.thickness does not exist! Skipping creation of smoothed data for lh.thickness # #@# Qdec Cache lh area fsaverage Thu Nov 8 11:46:43 EST 2012 INFO: File lh.area does not exist! Skipping creation of smoothed data for lh.area # #@# Qdec Cache lh area.pial fsaverage Thu Nov 8 11:46:43 EST 2012 INFO: File lh.area.pial does not exist! Skipping creation of smoothed data for lh.area.pial # etc recon-all -s ms_018 finished without error at Thu Nov 8 11:46:43 EST 2012 done My goal is to eventually be able to bring up my T1 images with the qdec application and segment the motor cortex. When I use the tkmedit command it works correctly (I have converted my files to .mgz already). Do you know if it is a pre-processing error that is preventing me from getting the qdec application to work with my own brain images? I cannot open files in qdec currently. Many thanks, Julia ___ 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.
