Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30088 discussions

Re: [Freesurfer] Freeview
by Ruopeng Wang 28 Oct '13

28 Oct '13

Was that from freeview or tksurfer? On 10/28/2013 02:06 PM, Lindsay Squeglia wrote: > Hi Ruopeng, > > Thanks for your response! I used to do it all the time in the previous > versions of FreeSurfer (see attached). I am not sure why the new > version is different. > > Thanks! > Lindsay > > > > > On Mon, Oct 28, 2013 at 11:01 AM, Ruopeng Wang > <rpwang(a)nmr.mgh.harvard.edu <mailto:rpwang@nmr.mgh.harvard.edu>> wrote: > > Hi Lindsay, > > I think there was no such option to display multiple surface > labels at once even in the old version. However, we will add it in > the future. > > Best, > Ruopeng > > > On 10/28/2013 01:48 PM, Lindsay Squeglia wrote: >> Hi all, >> >> I recently updated to FreeSurfer version 5.3.0, and I am now >> having problems with freeview that I didn't have on the older >> versions. When I go to "Surfaces" and "Load Labels", it only >> shows one label at a time. Previously, I could add several labels >> and all would appear on the Figure. Does anyone know a fix for this? >> >> Thanks! >> Lindsay >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)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. > > > > > -- > Lindsay M. Squeglia, Ph.D. > Postdoctoral Fellow > University of California San Diego > office phone: 858-822-2306 > email: lsquegli(a)ucsd.edu <mailto:lsquegli@ucsd.edu>

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Issue with 5.3.0 nu_correction?
by Natalie Garcia 28 Oct '13

28 Oct '13

Hi all, I've tried running auto-recon with version 5.3.0 (on Mac OSX v10.8.2) and the processing stream seems to fail at the intensity correction point. Not sure if it helps, but when I look at the output from the PBS script, I see "nu_correct: Command not found." Any suggestions on what I might be able to do to fix this? Any help would be greatly appreciated. Natalie -- Natalie V. Garcia Graduate Student, Cognitive Psychology Psychology Department The Pennsylvania State University 423 Moore Building nvg109(a)psu.edu

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Freeview
by Lindsay Squeglia 28 Oct '13

28 Oct '13

Hi all, I recently updated to FreeSurfer version 5.3.0, and I am now having problems with freeview that I didn't have on the older versions. When I go to "Surfaces" and "Load Labels", it only shows one label at a time. Previously, I could add several labels and all would appear on the Figure. Does anyone know a fix for this? Thanks! Lindsay

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Problem generating volume stats with hippocampal segmentation script
by Erin Walsh 28 Oct '13

28 Oct '13

Hi, I'm experiencing a problem when running the automated hippocampal subfield segmentation script. Unfortunately, I have been unable to determine the cause of the error. After reconstructing all participant data with the -hippo-subfields flag, I ran the "kvlQuantifyHippocampalSubfieldSegmentations.sh" script. The script seems to be working fine, generating subfield values for all participants until the very end when it attempts to generate the stat tables (I think). At this point, I receive the following error: /Applications/freesurfer/bin/kvlQuantifyHippocampalSubfieldSegmentations.sh: line 22: volumeStats_left.txt: Permission denied failed to do kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt I've copied some output and the error message below, including the last participant in our folder it runs through before attempting to generate volume stats. Thanks for any help you can offer! Best Erin -- Erin Walsh, Ph.D. Postdoctoral Research Associate University of Wisconsin-Madison Department of Psychiatry: Abercrombie Lab<http://www.psychiatry.wisc.edu/abercrombie/> 6001 Research Park Blvd. Madison, WI 53719 edubwalsh(a)gmail.com Relevant information: FREESURFER_HOME: /Applications/freesurfer Current working dir ran command: /Applications/freesurfer/subjects/CORTMR/recon Build stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 Kernel info: Darwin 12.4.0 x86_64 Command line ran: kvlQuantifyHippocampalSubfieldSegmentations.sh Output/Error (after seemingly generating hippocampal subfield values for all participants): ... cd 228/ Quantifying subject 228/ left Doing left side cd mri kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2_3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4_DG.mgz posterior_left_hippocampal_fissure.mgz > volumeStats_left.txt cd .. Quantifying subject 228/ right Doing right side cd mri kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable.txt posterior_Right-Hippocampus.mgz posterior_right_presubiculum.mgz posterior_right_CA1.mgz posterior_right_CA2_3.mgz posterior_right_fimbria.mgz posterior_right_subiculum.mgz posterior_right_CA4_DG.mgz posterior_right_hippocampal_fissure.mgz > volumeStats_right.txt cd .. cd .. cd fsaverage/ Quantifying subject fsaverage/ left Doing left side cd mri kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2_3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4_DG.mgz posterior_left_hippocampal_fissure.mgz > volumeStats_left.txt /Applications/freesurfer/bin/kvlQuantifyHippocampalSubfieldSegmentations.sh: line 22: volumeStats_left.txt: Permission denied failed to do kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2_3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4_DG.mgz posterior_left_hippocampal_fissure.mgz > volumeStats_left.txt

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CVS registration questions
by raij＠nmr.mgh.harvard.edu 28 Oct '13

28 Oct '13

Hi Lilla et al, I am preparing to CVS register 30+ subjects to improve FSL probabilistic tractography alignment across subjects. First, thanks for a really cool tool! Then, I have some questions: 1. mri_cvs_register step1 is spherical registration. However, I have already run FS5.3 recon-all -all for all subjects, which includes spherical registration. Are the recon-all and mri_cvs_register spherical registrations identical? If so, will mri_cvs_register be able to use the previously computed spherical registration (with flags --step2 --step3), or will it need to compute a new spherical registration? Will mri_cvs_register overwrite any of my earlier recon-all results? 2. What are the pros and cons for using one of the following as templates, and which one would you recommend: -Randomly selected individual subject -CVS35 -CVS35_inMNI152 3. When using MNI152_1mm as template, I guess this is a 1 mm resolution image (as $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri/T1.mgz seems to be in 1 mm resolution)? Technically, is this the cvs_avg35 image that has been CVS-registered with the MNI152_1mm image? Or is this a FLIRT-type 3D registration from cvs_avg35 to MNI152_1mm without surface information (I guess extracting the surface from MNI152 would be difficult)? 4. I run into the following error in FS stable 5.3 (source /usr/local/freesurfer/nmr-stable53-env): mri_cvs_check --mov $SUBJECT Using the CVS template as registration target. The following files are missing: /usr/local/freesurfer/stable5_3_0/bin/mri_cvs_register.settings.txt You need to find these files or run reconall on the data in order to run mri_cvs_register. Is this file required, or is this a bogus error? 5. Are there parallel processing versions that could be run on the cluster? Thanks! Tommi --- Tommi Raij, MD, PhD TM Core Director MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz doesnot have mri_strip_skull codes
by Rujing Zha 28 Oct '13

28 Oct '13

Dear FreeSurfer Users, I downloaded FreeSurfer latest version in this website:ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurf…. I want to strip 3d structure skull by mri_strp_skull,but this package does not have this codes.Why? What else can I do? Thanks! Any reply and advice will be appreciated! Best. 2013-10-28 Rujing Zha

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Re: [Freesurfer] installation trouble - error message subjects directory not recognised
by Z K 28 Oct '13

28 Oct '13

Sven, Well that certainly is odd that. My guess is that there is some sort of extension that Mac is hiding in the finder window (along the lines of what you were talking about with the text editor). Im also a little concerned about the double '//' that is part of your FREESURFER_HOME environment variable. That should not be there, although I don't think its necessarily a problem. Please open a terminal and type the following command: 'touch /Applications/freesurfer/.license' That should fix your problem. Let me know if not. Also, please CC the list on these responses so that they can be stored for others to view. -Zeke On 10/24/2013 02:29 PM, muellersvenc wrote: > Hi Zeke, > > the output in both cases is: "no such file or directory". I have attached a screenshot to this email and you can see my freesurfer directory and the .license file at the very top. Is this maybe a problem with creating such a file with the text editor? There is also a file called LICENSE in the directory but this just contains the license agreement. > > I really appreciate you helping me as I am keen on getting freesurfer to work. So, thank you so much for your time and effort in helping me through this! Much appreciated! > > Sven > > > > > > On 24-okt-2013, at 17:35, Z K wrote: > >> If there really is a .license in the FREESURFER_HOME directory then everything should be working fine. What is the output when you type: >> >> 'ls -l /Applications/freesurfer/.license' >> >> at the command line? And what is the output when you type: >> >> 'ls -l $FREESURFER_HOME/.license' >> >> >> On 10/24/2013 11:25 AM, muellersvenc wrote: >>> Hi Zeke, >>> >>> that seems to have worked (strangely because I didn't really do anything different before other than a fresh reinstall). >>> >>> However, now I have problems with the license file when trying to test the installation as suggested on the "Testing your freesurfer installation" webpage. >>> >>> I did a fresh installation, then created a ".license" file using the text editor containing the three lines that were sent to me by email and placed this file into the freesurfer folder which is my FREESURFER_HOME (/Applications/freesurfer). Then I did the sourcing. And then when I type for instance >>> >>> [pp05c332:/Applications] switch% tkmedit bert orig.mgz >>> -------------------------------------------------------------------------- >>> ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. >>> If you are outside the NMR-Martinos Center, >>> go to http://surfer.nmr.mgh.harvard.edu to >>> get a valid license file (it's free). >>> If you are inside the NMR-Martinos Center, >>> make sure to source the standard environment. >>> -------------------------------------------------------------------------- >>> [pp05c332:/Applications] switch% >>> >>> >>> Any ideas what I am doing wrong? I changed the settings on my computer a while ago and I can see the hidden files so can also see that there is a file called ".license" in the freesurfer folder but am not sure why freesurfer is not recognising it. >>> >>> Many thanks in advance for your help! >>> >>> sven >>> >>> >>> >>> On 24-okt-2013, at 16:39, Z K wrote: >>> >>>> Hi Sven, >>>> >>>> Whats most likely happening is that you are defining SUBJECTS_DIR prior to sourcing SetUpFreeSurfer.csh. Freesurfer will not overwrite the SUBJECTS_DIR environment variable if it already exists at the time of sourcing the SetUpFreeSurfer.csh. This is most likely occuring in your .cshrc file. >>>> >>>> To verify, type 'echo $SUBJECTS_DIR' before sourcing and see what the output says. >>>> >>>> -Zeke >>>> >>>> On 10/24/2013 09:10 AM, muellersvenc wrote: >>>>> Hi all, >>>>> >>>>> I am running into trouble testing my freesurfer installation on a Mac (10.6.8). I followed all steps in the guide but there is something funny that freesurfer does not seem to recognise its own "subjects" directory (see attached screenshot). If screenshot is not visible, it says: >>>>> >>>>> -------- freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 -------- >>>>> Setting up environment for FreeSurfer/FS-FAST (and FSL) >>>>> WARNING: Applications/freesurfer/subjects does not exist >>>>> FREESURFER_HOME /Applications/freesurfer >>>>> FSFAST_HOME /Applications/freesurfer/fsfast >>>>> FSF_OUTPUT_FORMAT nii.gz >>>>> SUBJECTS_DIR Applications/freesurfer/subjects >>>>> MNI_DIR /Applications/freesurfer/mni >>>>> FSL_DIR /usr/local/fsl >>>>> >>>>> I think it might have to do with the fact that there is a "/" missing in front of the "Applications" but I don't know where/how to change this. I checked my StartUp.csh file and there everything seems fine. However, the subjects directory was definitely created by freesurfer (also screenshot) so there is a mismatch somewhere. >>>>> >>>>> I am sure it is a simple thing but can someone please let me know what I should do so I can start to enjoy freesurfer? >>>>> >>>>> Many thanks in advance, >>>>> >>>>> sven >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)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. >>>> >>> >>> >>> >

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Power of MRI machine
by Muhammad Naveed Iqbal Qureshi 28 Oct '13

28 Oct '13

Dear Community, Is it possible to detect the scanning power (either 1.5 or 3 tesla) of MRI acquisition machine from the dicom images, if we do not know about the scanner properties? Best Regards, Muhammad Naveed Iqbal Qureshi

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Re: [Freesurfer] Incorrect orientations from MRI convert
by Chiu, Bryan (PHTH) 27 Oct '13

27 Oct '13

Hi Douglas, I've looked at the original images in freeview and they follow the correct talairach coordinates. I've run mri_convert again and the files follow the correct talairach coordinates. It appears this may have been a 'one-off' issue. Will update after I autorecon everything. - Bryan

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R: Re: R: Re: analysis on 4-6yrs pat
by crailo＠inwind.it 25 Oct '13

25 Oct '13

Hi Bruce, I guess running from scratch is the easiest way. I tried to upload the whole dir but it seems I cannot have access to it. Thanks Regards Antonio >----Messaggio originale---- >Da: fischl(a)nmr.mgh.harvard.edu >Data: 25/10/2013 15.33 >A: "crailo(a)inwind.it"<crailo(a)inwind.it> >Cc: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: analysis on 4-6yrs pat > >Hi Antonio > >I need the whole subject directory to diagnose what happened with the FS >analysis. Or I can try rerunning it from scratch here instead if you >prefer >Bruce >On Fri, 25 Oct 2013, crailo(a)inwind.it wrote: > >> Hi Bruce, >> thanks for the reply. I have uploaded two images, the original one and the one >> preprocessed via 3D slicer N3. >> Thanks >> Regards >> Antonio >> >>> ----Messaggio originale---- >>> Da: fischl(a)nmr.mgh.harvard.edu >>> Data: 25/10/2013 14.07 >>> A: "crailo(a)inwind.it"<crailo(a)inwind.it> >>> Cc: <freesurfer(a)nmr.mgh.harvard.edu> >>> Ogg: Re: [Freesurfer] analysis on 4-6yrs pat >>> >>> Hi Antonio >>> >>> it's tough to diagnose from one slice. Is the top of the head in general >>> darker than the bottom? It looks like it, but that might also be lower >>> myelin content. If you upload the subject we'll take a look. >>> >>> cheers >>> Bruce >>> On Fri, 25 Oct >>> 2013, crailo(a)inwind.it wrote: >>> >>>> >>>> Dear Freesurfer experts, >>>> >>>> I am trying to run cortical thickness analysis on 4-6 yrs old patients but >> I >>>> have some problem to get nice cortical gray matter. I have tried to run >>>> several N3 but with no success so I would need to ask whether you could >> give >>>> me hints to improve that. Please find attached a screenshot of what I do >>>> get. >>>> >>>> >>>> Many thanks for any help. >>>> >>>> >>>> Best Wishes >>>> >>>> Antonio >>>> >>>> >>>> >>> >>> >>> 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(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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