Re: [Freesurfer] How to switch order of Talairach and nu-correction stages in recon-all
glad to hear it worked. it can be tricky getting the stream to work in a 'one size fits all' kind of way. n. On Thu, 2012-04-19 at 16:45 -0700, Joshua Lee wrote: Nick, Thank you. This recon-all script resolved my problems. I really appreciate this post. - Josh - Joshua Lee UC Davis On Tue, Apr 17, 2012 at 7:51 AM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Ed, email probably trounced it. recon-all is a text file. attached is a gzipped version. use gunzip to unpack it. N. On Tue, 2012-04-17 at 16:45 +0200, Ed Gronenschild wrote: Hi Nick, It does not work properly, it only produces an error message, even with no option at all: 'nknown option: '- Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ...]. Ed On 17 Apr 2012, at 16:28, Nick Schmansky wrote: a modified recon-all is attached. it will run nu_correct prior to the talairach stage, as will be the case with v5.2. so you can just run: recon-all -s subjid -all -clean-tal n. On Tue, 2012-04-17 at 08:58 +0200, Ed Gronenschild wrote: Hi Nick, The option -talairach-nu is not recognized in version v5.1.0. How can I proceed now? Ed On 16 Apr 2012, at 17:32, Nick Schmansky wrote: Ed, Hi, no there is not an option to switch them. The nu correct stage in 5.1 needs the talairach to run. However, if your intent is to get a better talairach result by using the nu corrected input (as it did prior to v5.1), then you can do the following: recon-all -s subjid -motioncor -talairach -nuintensitycor then run: recon-all -s subjid -all -talairach-nu -clean-tal on the second run, it will use the nu.mgz in the talairach stage. Note that in the next version, v5.2, one iteration of nu_correct will be run prior to the talairach stage to use as input to the talairach stage, in order to get the better talairach results that people were seeing prior to v5.1. it will still run the current nu_correct stage to create nu.mgz (the nu used in talairach gets discarded). Nick On Mon, 2012-04-16 at 09:10 +0200, Ed Gronenschild wrote: Hi, As of version 5.1 the Talairach stage precedes the nu-correction stage. Is there an option or possibility to switch this order? Cheers, Ed ___ 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. recon-all ___ 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] WM modification
I'm running the FS v5.1 under centOS 4.3 and after changing the mri_segstats you send me, i always get the following error message:mri_segstats: /lib64/tls/lib.so.6: version 'GLIBC_2.4' not found (required for mri_segstats).Does this is normal, since the same FS version was running perfectly just before changing the mri_segstats file.I have search the lib.so.6 and I have it, but not sure about the GLIBC_2.4 do you know how can i check it? or where can I find it for my centOS distribution?Bests,GabrielEl 17/04/12, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:It should not have changed the WM volume. Did you happen to see the thread about a bug in mri_segstats? It could be causing this. You can get a new version here:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linuxThe only thing that we have that comes close to quantifying lesions is the volume of WM hypointensities. This will likely underestimate the lesion volume by a lot.dougOn 04/16/2012 04:58 AM, Gabriel Gonzalez Escamilla wrote: Dear freesurfers, May be a silly question: I'd modified the wm.mgz using the lastest current version of FS as suggested in http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits?highlight=%28matter%29%7C%28White%29 Is there any output on FS that quantifies the lesions as volume or something like? When I'd checked the aseg.stats the cortical wm for both hemispheres has changed, as a matter of fact it has been increased when I filled the lesions, which I'm guessing would be a normal behavior, but I'm wondering how to know how much of this wm is lesioned ? Could you guide me on this? Many thanks in advanced , Gabriel. -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- 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.html___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe 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.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ 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] long_qdec_table error
Martin, I'm getting the following error when running long_qdec_table: = [derin@otis ccnm_mprage_v4.5_long]$ long_qdec_table --qdec qdec/ccnm_prog_30_long_Th.qdec.table.dat --cross --out qdec/ccnm_prog_30_long_Th.cross.qdec.table.dat Parsing the qdec table: qdec/ccnm_prog_30_long_Th.qdec.table.dat Traceback (most recent call last): File /pkg/brainmap/freesurfer-v5.1.0/bin/long_qdec_table, line 142, in ? longqdec = LongQdecTable(options.qdec) File /pkg/brainmap/freesurfer-v5.1.0/bin/LongQdecTable.py, line 30, in __init__ self.parse(stpmap) File /pkg/brainmap/freesurfer-v5.1.0/bin/LongQdecTable.py, line 58, in parse if strlst[0].upper() == 'SUBJECTS_DIR': IndexError: list index out of range = I haven't had much luck troubleshooting it, maybe I have too many numerical variables in the table? I guess I could always reconstruct it by hand, but wondering if you had any thoughts, thanks. FS v5.1.0 CentOS 4 -Derin ___ 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] Another -use-gpu experiment
Freesurfers,
I'd like to add my two about a recent experiment I ran with recon-all -use-gpu.
(I'm using v5.1)
I took 6 T1 scans, imported them into two subjects a piece (gpu_SUBJID,
cpu_SUBJID) and ran 'recon-all -all -use-gpu' on the gpu_ subject and the
normal 'recon-all -all' on the cpu subjects. All gpu subjects ran on a single
GTX 480.
On average, I saw about a 16% speedup using GPU hardware, which translates to
about 4 hours on the hardware I'm using.
Qualitatively, the final inflated surfaces and {w,g}m boundaries are very
similar.
Two questions:
1) Would you recommend -use-gpu for production analyses using FS v5.1?
2) Separately from the above experiment, I ran one gpu subject using 4 GTX 480s
and saw no significant time difference. Is this to be expected, ie your CUDA
code doesn't scale across multiple GPUs? Just curious, certainly not a
deal-breaker if it doesn't.
Thanks for your input.
Scott Burns
Neuroimaging Analyst
Education and Brain Science Lab
Kennedy Center
Vanderbilt University
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[Freesurfer] Brainmask.nii Reading
Dear FS friends I need to do skull stripping of MRI images, and for this purpose I have used FS. For reading the data from brainmask.mgz, I converted it to brainmask.nii. Can you please tell me how can I read the data from brainmask.nii is MATLAB? Do you know other way of reading the data from brainmask.mgz? I am looking forward to hear from you. Thanks in advance -- Best Regards --- Nooshin N. Zadeh Graduate Assistant Departments of Electrical Engineering and Neurology University of Miami ** * * * * ___ 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] Brainmask.nii Reading
Hi Nooshin the function MRIread should load either the .nii or the .mgz in matlab. cheers Bruce On Fri, 20 Apr 2012, Nooshin Zadeh wrote: Dear FS friends I need to do skull stripping of MRI images, and for this purpose I have used FS. For reading the data from brainmask.mgz, I converted it to brainmask.nii. Can you please tell me how can I read the data from brainmask.nii is MATLAB? Do you know other way of reading the data from brainmask.mgz? I am looking forward to hear from you. Thanks in advance -- Best Regards --- Nooshin N. Zadeh Graduate Assistant Departments of Electrical Engineering and Neurology University of Miami ___ 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] Failure to download
Hi freesurfers, I tried to download the tutorial dataset for inspection of fs output, but receive this error message repeatedly, even with the -c flag: glia:shantanu[30] wget -c ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tar.gz --2012-04-20 15:27:05-- ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tar.gz = buckner_data-tutorial_subjs.tar.gz Resolving surfer.nmr.mgh.harvard.edu... 132.183.202.158 Connecting to surfer.nmr.mgh.harvard.edu|132.183.202.158|:21... connected. Logging in as anonymous ... Logged in! == SYST ... done.== PWD ... done. == TYPE I ... done. == CWD (1) /pub/data ... done. == SIZE buckner_data-tutorial_subjs.tar.gz ... 11245151143 == PASV ... done.== REST 4704874496 ... done. == RETR buckner_data-tutorial_subjs.tar.gz ... done. Length: 11245151143 (10G), 6540276647 (6.1G) remaining (unauthoritative) 43% [+++ ] 4,852,605,832 6.82M/s in 22s buckner_data-tutorial_subjs.tar.gz: Input/output error, closing control connection. Thanks in advance for any help. -shantanu ___ 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] mris_expand not working since upgrading to v.5.1.0
Hello, I have recently upgraded from running version 4.0.2 of Freesurfer to the most current version (v.5.1.0), and have encountered a problem. I used to be able to expand the recon-all generated white matter volume by a percentage of the grey matter thickness using mris_expand, but ever since changing to the most current version, the mris_expand command is not returning correct results. The command I use is: mris_expand -thickness ./lh.white $1 lh.white.expanded where $1 is a variable indicating the percentage I wish to expand by. Since the version change, mris_expand does not seem to actually change the volume of lh.white, with the output file lh.white.expanded looking identical to lh.white after running the command. This occurs regardless of the value I enter for $1 (be it very large, very small, or even negative) The command appears to run normally as it did in v.4.0.2 and does not give any error message, but the output volume appears unchanged from the input volume. Have the parameters or flags for this command changed between the versions, or has mris_expand been deprecated? If so, what flags or command should I use instead? Thanks, - Andrew ___ 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] -clean
If I were to want to re-run a recon-all completely fresh on a subject, what do I need to do aside from creating a new subject directory? I had previously thought that by adding the -all flag, all old files would be over written (i.e. overwrite with a new brainmask.mgz). I want everything fresh. Does the -clean flag do it all? Thanks Josh ___ 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] mri_cvs_register error in step 2
Hi Jackie, What is the size of the *resample* files? The only thing I can think about is that the files are corrupted and the code cannot read those files in. You could try to read the resampled files into Freeview, to test whether they can be opened or you could delete the files and then they will be regenerated. --Lilla On Thu, 19 Apr 2012, Jackie Leung wrote: ok... please see attached. note: The directory name is different in this log file, but the error is the same. I've been testing this problem with many different directories. thanks, jackie On Thu, Apr 19, 2012 at 5:37 PM, Lilla Zollei lzol...@nmr.mgh.harvard.edu wrote: Hi Jackie, Could you attach the log file? Thanks, Lilla On Thu, 19 Apr 2012, Jackie Leung wrote: hi, I'm trying to run mri_cvs_register and I'm getting a strange error message. MRISread(CVS_test_26to47_1/lh.resample.white): could not open file No such file or directory Error reading surface CVS_test_26to47_1/lh.resample.white I've checked the directory and the file definitely exists. It seems to be popping up in step 2 of the script, where it calls the surf2vol function. I've tried running this function on its own and didn't get this error, so I'm really confused as to what the problem may be. Any help will be greatly appreciated! thanks, jackie 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. -- Jackie Leung Lab Research Project Coordinator Dept of Physiology Experimental Medicine Hospital for Sick Children Tel: (416) 813-7654 x2396 ___ 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] -clean
Hi Josh if you specify a new directory that will certainly work. We try very hard to preserve any manual interventions you have taken so that is why -all doesn't start fresh - we don't want it to. cheers Bruce On Fri, 20 Apr 2012, Joshua Lee wrote: If I were to want to re-run a recon-all completely fresh on a subject, what do I need to do aside from creating a new subject directory? I had previously thought that by adding the -all flag, all old files would be over written (i.e. overwrite with a new brainmask.mgz). I want everything fresh. Does the -clean flag do it all? Thanks Josh ___ 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] improving automated cerebellar parcellation
HI Anthony I would make sure to include an entire brain labeling in the training set. You can do this by pasting your manual labels into our aseg of the subjects in question. cheers Bruce On Fri, 20 Apr 2012, Anthony Dick wrote: Hello, I developed a new atlas for parcellating the cerebellum, based on 20 brains manually segmented by Jörn Diedrichsen, which he was kind enough to share (note these also formed the basis for his 2009 paper in Neuroimage (46; 39-46). I got the segmentation to work, but I would not say it works well. As you can see from the attached image, it is not ready for prime-time. On the left is the brain of subject 1, manually segmented. On the right is the brain of the same subject with the automated sementation, based on the developed atlas. My question is, how can I improve it? I realize this is an open question and potentially difficult to answer without some probing, but this is a resource I think a lot of users would like to have access to, so perhaps it is worth the effort. Anthony ___ 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] improving automated cerebellar parcellation
Thanks Bruce. What's the easiest way to paste those labels. Manually through tkmedit, or through the command line? Anthony On 4/20/12 3:53 PM, Bruce Fischl wrote: HI Anthony I would make sure to include an entire brain labeling in the training set. You can do this by pasting your manual labels into our aseg of the subjects in question. cheers Bruce On Fri, 20 Apr 2012, Anthony Dick wrote: Hello, I developed a new atlas for parcellating the cerebellum, based on 20 brains manually segmented by Jörn Diedrichsen, which he was kind enough to share (note these also formed the basis for his 2009 paper in Neuroimage (46; 39-46). I got the segmentation to work, but I would not say it works well. As you can see from the attached image, it is not ready for prime-time. On the left is the brain of subject 1, manually segmented. On the right is the brain of the same subject with the automated sementation, based on the developed atlas. My question is, how can I improve it? I realize this is an open question and potentially difficult to answer without some probing, but this is a resource I think a lot of users would like to have access to, so perhaps it is worth the effort. Anthony 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. -- Anthony Steven Dick, Ph.D. Assistant Professor Department of Psychology Florida International University Modesto A. Maidique Campus DM 296B 11200 S.W. 8th Street Miami, FL 33199 Phone: 305-348-4202 (try this first) Lab Phone: 305-348-9057 or 305-348-9055 Fax: 305-348-3879 Email: ad...@fiu.edu Webpage: http://www.fiu.edu/~adick Lab Webpage: http://dcn.fiu.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] improving automated cerebellar parcellation
probably in matlab On Fri, 20 Apr 2012, Anthony Dick wrote: Thanks Bruce. What's the easiest way to paste those labels. Manually through tkmedit, or through the command line? Anthony On 4/20/12 3:53 PM, Bruce Fischl wrote: HI Anthony I would make sure to include an entire brain labeling in the training set. You can do this by pasting your manual labels into our aseg of the subjects in question. cheers Bruce On Fri, 20 Apr 2012, Anthony Dick wrote: Hello, I developed a new atlas for parcellating the cerebellum, based on 20 brains manually segmented by Jörn Diedrichsen, which he was kind enough to share (note these also formed the basis for his 2009 paper in Neuroimage (46; 39-46). I got the segmentation to work, but I would not say it works well. As you can see from the attached image, it is not ready for prime-time. On the left is the brain of subject 1, manually segmented. On the right is the brain of the same subject with the automated sementation, based on the developed atlas. My question is, how can I improve it? I realize this is an open question and potentially difficult to answer without some probing, but this is a resource I think a lot of users would like to have access to, so perhaps it is worth the effort. Anthony 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.
Re: [Freesurfer] -clean
I have not done any manual interventions. I would like to re-run recon-all with different expert options in mri_normalize, and -skullstrip, and -mprage, and wanted be sure that my changes would be reflected in the downstream output. - On Fri, Apr 20, 2012 at 12:52 PM, Joshua Lee jki...@ucdavis.edu wrote: If I were to want to re-run a recon-all completely fresh on a subject, what do I need to do aside from creating a new subject directory? I had previously thought that by adding the -all flag, all old files would be over written (i.e. overwrite with a new brainmask.mgz). I want everything fresh. Does the -clean flag do it all? Thanks Josh ___ 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] Another -use-gpu experiment
On Fri, Apr 20, 2012 at 12:52 PM, Burns, Scott S scott.s.bu...@vanderbilt.edu wrote: 2) Separately from the above experiment, I ran one gpu subject using 4 GTX 480s and saw no significant time difference. Is this to be expected, ie your CUDA code doesn't scale across multiple GPUs? Just curious, certainly not a deal-breaker if it doesn't. Nothing I added (primarily mri_ca_register and mri_em_register) makes use of multiple GPUs, any more than Freesurfer makes use of multiple cores. I don't know about any additions since. If you have more than one GPU, you can run more than one subject at once (if you point each run to a different GPU). Also, make sure you're using the Fermi binaries on that GTX 480. Richard ___ 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] mri_cvs_register error in step 2
The files in the folder are around 4.7MB... and 2 .annot files that are around 1Mb. I am able to open these surface files using Freeview. Like I said before, I tried copying and surf2vol command line and running it separately, and this error won't appear. In contrast, if i run mri_cvs_register --mov sub26 --template sub47 --outdir CVS_test_26to47_1 --step2 --nocleanup The same error pops up. very puzzling. i will rerun everything overnight to see if i get the same problem. thanks, jackie On Fri, Apr 20, 2012 at 3:56 PM, Lilla Zollei lzol...@nmr.mgh.harvard.eduwrote: Hi Jackie, What is the size of the *resample* files? The only thing I can think about is that the files are corrupted and the code cannot read those files in. You could try to read the resampled files into Freeview, to test whether they can be opened or you could delete the files and then they will be regenerated. --Lilla On Thu, 19 Apr 2012, Jackie Leung wrote: ok... please see attached. note: The directory name is different in this log file, but the error is the same. I've been testing this problem with many different directories. thanks, jackie On Thu, Apr 19, 2012 at 5:37 PM, Lilla Zollei lzol...@nmr.mgh.harvard.edu wrote: Hi Jackie, Could you attach the log file? Thanks, Lilla On Thu, 19 Apr 2012, Jackie Leung wrote: hi, I'm trying to run mri_cvs_register and I'm getting a strange error message. MRISread(CVS_test_26to47_1/lh.**resample.white): could not open file No such file or directory Error reading surface CVS_test_26to47_1/lh.resample.**white I've checked the directory and the file definitely exists. It seems to be popping up in step 2 of the script, where it calls the surf2vol function. I've tried running this function on its own and didn't get this error, so I'm really confused as to what the problem may be. Any help will be greatly appreciated! thanks, jackie 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. -- Jackie Leung Lab Research Project Coordinator Dept of Physiology Experimental Medicine Hospital for Sick Children Tel: (416) 813-7654 x2396 -- Jackie Leung Lab Research Project Coordinator Dept of Physiology Experimental Medicine Hospital for Sick Children Tel: (416) 813-7654 x2396 ___ 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.
